Starting phenix.real_space_refine on Mon Nov 18 04:53:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f56_28861/11_2024/8f56_28861.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f56_28861/11_2024/8f56_28861.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f56_28861/11_2024/8f56_28861.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f56_28861/11_2024/8f56_28861.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f56_28861/11_2024/8f56_28861.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f56_28861/11_2024/8f56_28861.cif" } resolution = 2.98 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.072 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 88 5.16 5 C 9992 2.51 5 N 2634 2.21 5 O 2917 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 15631 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 7730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1007, 7730 Classifications: {'peptide': 1007} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 40, 'TRANS': 966} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 7901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1032, 7901 Classifications: {'peptide': 1032} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 41, 'TRANS': 990} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Time building chain proxies: 9.74, per 1000 atoms: 0.62 Number of scatterers: 15631 At special positions: 0 Unit cell: (79.18, 123.05, 144.45, 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 88 16.00 O 2917 8.00 N 2634 7.00 C 9992 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: 4.15 Conformation dependent library (CDL) restraints added in 2.2 seconds 4066 Ramachandran restraints generated. 2033 Oldfield, 0 Emsley, 2033 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3760 Finding SS restraints... Secondary structure from input PDB file: 73 helices and 15 sheets defined 61.2% alpha, 17.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.73 Creating SS restraints... Processing helix chain 'A' and resid 1 through 8 removed outlier: 3.593A pdb=" N PHE A 5 " --> pdb=" O MET A 1 " (cutoff:3.500A) Processing helix chain 'A' and resid 8 through 29 removed outlier: 3.828A pdb=" N ALA A 12 " --> pdb=" O ARG A 8 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 61 Processing helix chain 'A' and resid 61 through 70 Processing helix chain 'A' and resid 99 through 118 removed outlier: 3.766A pdb=" N SER A 113 " --> pdb=" O ASN A 109 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N ARG A 116 " --> pdb=" O GLN A 112 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N LYS A 117 " --> pdb=" O SER A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 126 Processing helix chain 'A' and resid 150 through 162 Processing helix chain 'A' and resid 162 through 168 Processing helix chain 'A' and resid 189 through 196 Processing helix chain 'A' and resid 199 through 211 removed outlier: 3.765A pdb=" N ASN A 211 " --> pdb=" O ILE A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 248 removed outlier: 3.668A pdb=" N PHE A 246 " --> pdb=" O THR A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 265 No H-bonds generated for 'chain 'A' and resid 262 through 265' Processing helix chain 'A' and resid 298 through 315 Processing helix chain 'A' and resid 329 through 359 Processing helix chain 'A' and resid 361 through 387 Proline residue: A 368 - end of helix removed outlier: 3.724A pdb=" N ALA A 371 " --> pdb=" O ILE A 367 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL A 372 " --> pdb=" O PRO A 368 " (cutoff:3.500A) Proline residue: A 373 - end of helix Processing helix chain 'A' and resid 391 through 423 removed outlier: 3.785A pdb=" N GLY A 403 " --> pdb=" O VAL A 399 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N VAL A 406 " --> pdb=" O ILE A 402 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N ASP A 407 " --> pdb=" O GLY A 403 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N ASP A 408 " --> pdb=" O LEU A 404 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N ALA A 409 " --> pdb=" O LEU A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 452 removed outlier: 5.589A pdb=" N GLY A 440 " --> pdb=" O GLY A 436 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N ALA A 441 " --> pdb=" O GLN A 437 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL A 452 " --> pdb=" O VAL A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 458 removed outlier: 4.419A pdb=" N MET A 456 " --> pdb=" O VAL A 452 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ALA A 457 " --> pdb=" O PHE A 453 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N PHE A 458 " --> pdb=" O VAL A 454 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 452 through 458' Processing helix chain 'A' and resid 460 through 486 Processing helix chain 'A' and resid 487 through 496 removed outlier: 3.820A pdb=" N ALA A 491 " --> pdb=" O ILE A 487 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 502 removed outlier: 3.974A pdb=" N LYS A 501 " --> pdb=" O LYS A 498 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYS A 502 " --> pdb=" O PRO A 499 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 498 through 502' Processing helix chain 'A' and resid 510 through 536 Processing helix chain 'A' and resid 536 through 558 removed outlier: 4.019A pdb=" N TRP A 540 " --> pdb=" O ARG A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 582 through 600 Processing helix chain 'A' and resid 642 through 655 Processing helix chain 'A' and resid 690 through 708 Processing helix chain 'A' and resid 730 through 737 Processing helix chain 'A' and resid 740 through 752 Processing helix chain 'A' and resid 775 through 778 Processing helix chain 'A' and resid 780 through 786 Processing helix chain 'A' and resid 834 through 848 removed outlier: 3.720A pdb=" N GLN A 848 " --> pdb=" O SER A 844 " (cutoff:3.500A) Processing helix chain 'A' and resid 858 through 891 removed outlier: 3.521A pdb=" N GLN A 863 " --> pdb=" O ALA A 859 " (cutoff:3.500A) Proline residue: A 872 - end of helix Processing helix chain 'A' and resid 893 through 901 removed outlier: 3.517A pdb=" N LEU A 901 " --> pdb=" O PHE A 897 " (cutoff:3.500A) Processing helix chain 'A' and resid 902 through 918 removed outlier: 3.550A pdb=" N GLY A 906 " --> pdb=" O VAL A 902 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N GLY A 909 " --> pdb=" O LEU A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 922 through 954 removed outlier: 4.417A pdb=" N PHE A 946 " --> pdb=" O LEU A 942 " (cutoff:3.500A) Processing helix chain 'A' and resid 956 through 988 removed outlier: 4.975A pdb=" N ARG A 970 " --> pdb=" O ARG A 966 " (cutoff:3.500A) Proline residue: A 971 - end of helix Proline residue: A 985 - end of helix Processing helix chain 'A' and resid 993 through 1030 removed outlier: 4.332A pdb=" N GLY A1003 " --> pdb=" O ALA A 999 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N VAL A1004 " --> pdb=" O VAL A1000 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N TYR A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) Proline residue: A1020 - end of helix Processing helix chain 'B' and resid 2 through 7 removed outlier: 3.586A pdb=" N ASP B 7 " --> pdb=" O ASN B 3 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 29 removed outlier: 3.584A pdb=" N ALA B 12 " --> pdb=" O ARG B 8 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 61 Processing helix chain 'B' and resid 61 through 70 Processing helix chain 'B' and resid 99 through 116 removed outlier: 4.620A pdb=" N ARG B 116 " --> pdb=" O GLN B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 126 Processing helix chain 'B' and resid 150 through 162 Processing helix chain 'B' and resid 162 through 168 removed outlier: 3.513A pdb=" N ARG B 168 " --> pdb=" O ASP B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 196 Processing helix chain 'B' and resid 199 through 211 Processing helix chain 'B' and resid 242 through 248 removed outlier: 3.624A pdb=" N PHE B 246 " --> pdb=" O THR B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 261 through 265 Processing helix chain 'B' and resid 298 through 315 Processing helix chain 'B' and resid 329 through 359 Processing helix chain 'B' and resid 361 through 386 Proline residue: B 368 - end of helix removed outlier: 3.874A pdb=" N ALA B 371 " --> pdb=" O ILE B 367 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N VAL B 372 " --> pdb=" O PRO B 368 " (cutoff:3.500A) Proline residue: B 373 - end of helix Processing helix chain 'B' and resid 391 through 423 removed outlier: 4.380A pdb=" N GLY B 403 " --> pdb=" O VAL B 399 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LEU B 404 " --> pdb=" O LEU B 400 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ASP B 407 " --> pdb=" O GLY B 403 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N ASP B 408 " --> pdb=" O LEU B 404 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N ALA B 409 " --> pdb=" O LEU B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 452 removed outlier: 5.716A pdb=" N GLY B 440 " --> pdb=" O GLY B 436 " (cutoff:3.500A) removed outlier: 5.309A pdb=" N ALA B 441 " --> pdb=" O GLN B 437 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N VAL B 452 " --> pdb=" O VAL B 448 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 457 removed outlier: 4.572A pdb=" N MET B 456 " --> pdb=" O VAL B 452 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ALA B 457 " --> pdb=" O PHE B 453 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 452 through 457' Processing helix chain 'B' and resid 460 through 486 Processing helix chain 'B' and resid 487 through 496 removed outlier: 3.941A pdb=" N ALA B 491 " --> pdb=" O ILE B 487 " (cutoff:3.500A) Processing helix chain 'B' and resid 510 through 536 Processing helix chain 'B' and resid 536 through 558 removed outlier: 3.976A pdb=" N TRP B 540 " --> pdb=" O ARG B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 582 through 600 Processing helix chain 'B' and resid 642 through 657 removed outlier: 3.527A pdb=" N ALA B 653 " --> pdb=" O ARG B 649 " (cutoff:3.500A) Processing helix chain 'B' and resid 690 through 708 Processing helix chain 'B' and resid 730 through 738 Processing helix chain 'B' and resid 740 through 753 Processing helix chain 'B' and resid 782 through 786 removed outlier: 4.058A pdb=" N ASN B 785 " --> pdb=" O ASP B 782 " (cutoff:3.500A) Processing helix chain 'B' and resid 799 through 802 No H-bonds generated for 'chain 'B' and resid 799 through 802' Processing helix chain 'B' and resid 834 through 849 Processing helix chain 'B' and resid 858 through 891 Proline residue: B 872 - end of helix Processing helix chain 'B' and resid 893 through 901 removed outlier: 3.514A pdb=" N LEU B 901 " --> pdb=" O PHE B 897 " (cutoff:3.500A) Processing helix chain 'B' and resid 902 through 918 removed outlier: 3.685A pdb=" N GLY B 906 " --> pdb=" O VAL B 902 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N GLY B 909 " --> pdb=" O LEU B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 922 through 954 removed outlier: 4.435A pdb=" N PHE B 946 " --> pdb=" O LEU B 942 " (cutoff:3.500A) Processing helix chain 'B' and resid 956 through 988 removed outlier: 5.111A pdb=" N ARG B 970 " --> pdb=" O ARG B 966 " (cutoff:3.500A) Proline residue: B 971 - end of helix Proline residue: B 985 - end of helix Processing helix chain 'B' and resid 993 through 1030 removed outlier: 4.285A pdb=" N GLY B1003 " --> pdb=" O ALA B 999 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N VAL B1004 " --> pdb=" O VAL B1000 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N TYR B1017 " --> pdb=" O ILE B1013 " (cutoff:3.500A) Proline residue: B1020 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 128 through 131 removed outlier: 4.035A pdb=" N GLN A 87 " --> pdb=" O SER A 83 " (cutoff:3.500A) removed outlier: 12.362A pdb=" N ARG A 813 " --> pdb=" O GLU A 824 " (cutoff:3.500A) removed outlier: 8.766A pdb=" N GLU A 824 " --> pdb=" O ARG A 813 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N GLU A 815 " --> pdb=" O ALA A 822 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N GLU A 828 " --> pdb=" O ARG A 713 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N ARG A 713 " --> pdb=" O GLU A 828 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 128 through 131 removed outlier: 4.035A pdb=" N GLN A 87 " --> pdb=" O SER A 83 " (cutoff:3.500A) removed outlier: 12.362A pdb=" N ARG A 813 " --> pdb=" O GLU A 824 " (cutoff:3.500A) removed outlier: 8.766A pdb=" N GLU A 824 " --> pdb=" O ARG A 813 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N GLU A 815 " --> pdb=" O ALA A 822 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N SER A 821 " --> pdb=" O ASP A 685 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 172 through 177 removed outlier: 3.821A pdb=" N LEU A 138 " --> pdb=" O VAL A 291 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N LEU A 293 " --> pdb=" O ASN A 136 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N ASN A 136 " --> pdb=" O LEU A 293 " (cutoff:3.500A) removed outlier: 8.517A pdb=" N ILE A 137 " --> pdb=" O GLU A 328 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N GLU A 328 " --> pdb=" O ILE A 137 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N THR A 139 " --> pdb=" O ALA A 326 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 266 through 272 removed outlier: 7.993A pdb=" N TYR A 182 " --> pdb=" O VAL A 766 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N LYS A 768 " --> pdb=" O TYR A 182 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ASN A 758 " --> pdb=" O VAL A 769 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N VAL A 771 " --> pdb=" O TYR A 756 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N TYR A 756 " --> pdb=" O VAL A 771 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 250 through 253 removed outlier: 3.744A pdb=" N ARG A 252 " --> pdb=" O VAL A 260 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 284 through 285 Processing sheet with id=AA7, first strand: chain 'A' and resid 803 through 810 removed outlier: 3.829A pdb=" N THR B 233 " --> pdb=" O PRO A 723 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLY B 217 " --> pdb=" O ILE B 234 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 788 through 790 Processing sheet with id=AA9, first strand: chain 'B' and resid 128 through 131 removed outlier: 4.044A pdb=" N GLN B 87 " --> pdb=" O SER B 83 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 172 through 177 removed outlier: 3.579A pdb=" N ASP B 174 " --> pdb=" O LYS B 292 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N SER B 144 " --> pdb=" O PRO B 285 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU B 138 " --> pdb=" O VAL B 291 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N LEU B 293 " --> pdb=" O ASN B 136 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ASN B 136 " --> pdb=" O LEU B 293 " (cutoff:3.500A) removed outlier: 8.715A pdb=" N ILE B 137 " --> pdb=" O GLU B 328 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N GLU B 328 " --> pdb=" O ILE B 137 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N THR B 139 " --> pdb=" O ALA B 326 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 172 through 177 removed outlier: 3.579A pdb=" N ASP B 174 " --> pdb=" O LYS B 292 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N SER B 279 " --> pdb=" O ALA B 286 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL B 612 " --> pdb=" O LEU B 278 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 266 through 269 removed outlier: 3.970A pdb=" N ASN B 758 " --> pdb=" O VAL B 769 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N VAL B 771 " --> pdb=" O TYR B 756 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N TYR B 756 " --> pdb=" O VAL B 771 " (cutoff:3.500A) removed outlier: 8.207A pdb=" N ALA B 773 " --> pdb=" O SER B 754 " (cutoff:3.500A) removed outlier: 8.203A pdb=" N SER B 754 " --> pdb=" O ALA B 773 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 711 through 716 removed outlier: 4.872A pdb=" N ARG B 713 " --> pdb=" O GLU B 828 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N GLU B 828 " --> pdb=" O ARG B 713 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 722 through 729 removed outlier: 3.639A pdb=" N ARG B 806 " --> pdb=" O GLN B 726 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 788 through 790 1088 hydrogen bonds defined for protein. 3186 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: 6.80 Time building geometry restraints manager: 4.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5118 1.34 - 1.46: 2193 1.46 - 1.57: 8455 1.57 - 1.69: 0 1.69 - 1.80: 168 Bond restraints: 15934 Sorted by residual: bond pdb=" CA VAL B 306 " pdb=" C VAL B 306 " ideal model delta sigma weight residual 1.524 1.504 0.020 1.22e-02 6.72e+03 2.60e+00 bond pdb=" CA GLU B 66 " pdb=" C GLU B 66 " ideal model delta sigma weight residual 1.524 1.505 0.019 1.27e-02 6.20e+03 2.16e+00 bond pdb=" CA LEU A 737 " pdb=" C LEU A 737 " ideal model delta sigma weight residual 1.523 1.502 0.020 1.41e-02 5.03e+03 2.08e+00 bond pdb=" CA ASP B 922 " pdb=" C ASP B 922 " ideal model delta sigma weight residual 1.528 1.507 0.021 1.45e-02 4.76e+03 2.06e+00 bond pdb=" N LEU B 307 " pdb=" CA LEU B 307 " ideal model delta sigma weight residual 1.459 1.442 0.017 1.21e-02 6.83e+03 1.99e+00 ... (remaining 15929 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.82: 21289 1.82 - 3.64: 298 3.64 - 5.46: 41 5.46 - 7.28: 9 7.28 - 9.10: 2 Bond angle restraints: 21639 Sorted by residual: angle pdb=" C ALA B 859 " pdb=" CA ALA B 859 " pdb=" CB ALA B 859 " ideal model delta sigma weight residual 116.63 110.03 6.60 1.16e+00 7.43e-01 3.23e+01 angle pdb=" C VAL B 61 " pdb=" CA VAL B 61 " pdb=" CB VAL B 61 " ideal model delta sigma weight residual 111.71 107.76 3.95 8.50e-01 1.38e+00 2.16e+01 angle pdb=" CA ALA B 859 " pdb=" C ALA B 859 " pdb=" N MET B 860 " ideal model delta sigma weight residual 119.63 116.20 3.43 8.10e-01 1.52e+00 1.80e+01 angle pdb=" N VAL B 61 " pdb=" CA VAL B 61 " pdb=" C VAL B 61 " ideal model delta sigma weight residual 111.48 115.35 -3.87 9.40e-01 1.13e+00 1.70e+01 angle pdb=" N THR B 462 " pdb=" CA THR B 462 " pdb=" C THR B 462 " ideal model delta sigma weight residual 111.28 107.16 4.12 1.09e+00 8.42e-01 1.43e+01 ... (remaining 21634 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.59: 8842 13.59 - 27.17: 498 27.17 - 40.76: 132 40.76 - 54.34: 36 54.34 - 67.93: 9 Dihedral angle restraints: 9517 sinusoidal: 3661 harmonic: 5856 Sorted by residual: dihedral pdb=" CA ILE B 249 " pdb=" C ILE B 249 " pdb=" N THR B 250 " pdb=" CA THR B 250 " ideal model delta harmonic sigma weight residual -180.00 -163.45 -16.55 0 5.00e+00 4.00e-02 1.10e+01 dihedral pdb=" CA ASP A 311 " pdb=" CB ASP A 311 " pdb=" CG ASP A 311 " pdb=" OD1 ASP A 311 " ideal model delta sinusoidal sigma weight residual -30.00 -87.08 57.08 1 2.00e+01 2.50e-03 1.10e+01 dihedral pdb=" CB ARG B 661 " pdb=" CG ARG B 661 " pdb=" CD ARG B 661 " pdb=" NE ARG B 661 " ideal model delta sinusoidal sigma weight residual 180.00 120.27 59.73 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 9514 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1671 0.029 - 0.058: 556 0.058 - 0.087: 167 0.087 - 0.115: 110 0.115 - 0.144: 8 Chirality restraints: 2512 Sorted by residual: chirality pdb=" CA THR B 489 " pdb=" N THR B 489 " pdb=" C THR B 489 " pdb=" CB THR B 489 " both_signs ideal model delta sigma weight residual False 2.53 2.38 0.14 2.00e-01 2.50e+01 5.20e-01 chirality pdb=" CA THR A 489 " pdb=" N THR A 489 " pdb=" C THR A 489 " pdb=" CB THR A 489 " both_signs ideal model delta sigma weight residual False 2.53 2.38 0.14 2.00e-01 2.50e+01 5.08e-01 chirality pdb=" CB VAL A 482 " pdb=" CA VAL A 482 " pdb=" CG1 VAL A 482 " pdb=" CG2 VAL A 482 " both_signs ideal model delta sigma weight residual False -2.63 -2.50 -0.13 2.00e-01 2.50e+01 4.22e-01 ... (remaining 2509 not shown) Planarity restraints: 2786 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN A 921 " -0.008 2.00e-02 2.50e+03 1.62e-02 2.61e+00 pdb=" C ASN A 921 " 0.028 2.00e-02 2.50e+03 pdb=" O ASN A 921 " -0.011 2.00e-02 2.50e+03 pdb=" N ASP A 922 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 250 " 0.008 2.00e-02 2.50e+03 1.51e-02 2.27e+00 pdb=" C THR B 250 " -0.026 2.00e-02 2.50e+03 pdb=" O THR B 250 " 0.010 2.00e-02 2.50e+03 pdb=" N LEU B 251 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 454 " -0.007 2.00e-02 2.50e+03 1.50e-02 2.26e+00 pdb=" C VAL B 454 " 0.026 2.00e-02 2.50e+03 pdb=" O VAL B 454 " -0.010 2.00e-02 2.50e+03 pdb=" N PRO B 455 " -0.009 2.00e-02 2.50e+03 ... (remaining 2783 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1621 2.74 - 3.28: 16429 3.28 - 3.82: 27105 3.82 - 4.36: 31663 4.36 - 4.90: 55207 Nonbonded interactions: 132025 Sorted by model distance: nonbonded pdb=" OH TYR B 756 " pdb=" OD1 ASP B 759 " model vdw 2.200 3.040 nonbonded pdb=" OE2 GLU A 601 " pdb=" ND2 ASN A 604 " model vdw 2.202 3.120 nonbonded pdb=" OG SER B 279 " pdb=" O ALA B 286 " model vdw 2.213 3.040 nonbonded pdb=" OG SER A 279 " pdb=" O ALA A 286 " model vdw 2.276 3.040 nonbonded pdb=" OD1 ASN A 415 " pdb=" NH1 ARG A 418 " model vdw 2.281 3.120 ... (remaining 132020 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 508 or (resid 509 and (name N or name CA or name \ C or name O or name CB )) or resid 510 through 1032)) selection = (chain 'B' and (resid 1 through 211 or resid 237 through 505 or (resid 506 and ( \ name N or name CA or name C or name O or name CB )) or resid 507 through 1032)) } 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: 2.360 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: 0.010 Extract box with map and model: 0.540 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 38.730 Find NCS groups from input model: 0.790 Set up NCS constraints: 0.080 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:13.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7224 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 : 0.004 0.036 15934 Z= 0.266 Angle : 0.557 9.097 21639 Z= 0.327 Chirality : 0.036 0.144 2512 Planarity : 0.003 0.029 2786 Dihedral : 9.889 67.925 5757 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.64 % Allowed : 4.61 % Favored : 92.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.81 (0.19), residues: 2033 helix: 2.22 (0.15), residues: 1165 sheet: -0.18 (0.32), residues: 282 loop : -0.11 (0.26), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 540 HIS 0.002 0.001 HIS A 686 PHE 0.011 0.001 PHE B 958 TYR 0.009 0.001 TYR A 77 ARG 0.003 0.000 ARG B 636 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4066 Ramachandran restraints generated. 2033 Oldfield, 0 Emsley, 2033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4066 Ramachandran restraints generated. 2033 Oldfield, 0 Emsley, 2033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 539 residues out of total 1671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 495 time to evaluate : 1.633 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 106 GLN cc_start: 0.7049 (mt0) cc_final: 0.6792 (mt0) REVERT: B 184 MET cc_start: 0.7433 (tpp) cc_final: 0.7154 (tpp) REVERT: B 395 MET cc_start: 0.8094 (mmm) cc_final: 0.7760 (mmm) REVERT: B 900 MET cc_start: 0.6754 (mmm) cc_final: 0.6390 (mmp) outliers start: 44 outliers final: 8 residues processed: 525 average time/residue: 1.1998 time to fit residues: 700.9913 Evaluate side-chains 269 residues out of total 1671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 261 time to evaluate : 1.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 789 VAL Chi-restraints excluded: chain A residue 799 PHE Chi-restraints excluded: chain A residue 877 ILE Chi-restraints excluded: chain A residue 941 ILE Chi-restraints excluded: chain B residue 170 ASN Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 1021 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 171 optimal weight: 3.9990 chunk 153 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 52 optimal weight: 0.2980 chunk 103 optimal weight: 0.0040 chunk 82 optimal weight: 2.9990 chunk 159 optimal weight: 0.9980 chunk 61 optimal weight: 0.8980 chunk 96 optimal weight: 0.5980 chunk 118 optimal weight: 3.9990 chunk 184 optimal weight: 0.8980 overall best weight: 0.5392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 GLN A 108 GLN A 152 GLN A 197 GLN A 254 ASN A 308 ASN A 319 HIS A 517 GLN A 584 GLN A 655 ASN A 686 HIS A 691 HIS A 716 HIS ** A 726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 848 GLN A 926 GLN A 955 HIS A 967 GLN B 55 GLN B 63 GLN B 81 GLN B 108 GLN B 112 GLN B 213 GLN B 228 GLN B 237 GLN B 254 ASN B 255 GLN B 361 ASN B 437 GLN B 576 GLN B 604 ASN B 699 ASN B 708 ASN B 863 GLN B 926 GLN B 955 HIS Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7437 moved from start: 0.2642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 15934 Z= 0.195 Angle : 0.548 8.286 21639 Z= 0.287 Chirality : 0.039 0.156 2512 Planarity : 0.004 0.054 2786 Dihedral : 4.400 58.088 2201 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 4.73 % Allowed : 15.64 % Favored : 79.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.81 (0.19), residues: 2033 helix: 2.22 (0.15), residues: 1179 sheet: -0.14 (0.30), residues: 296 loop : -0.20 (0.27), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 540 HIS 0.005 0.001 HIS A 319 PHE 0.020 0.001 PHE A 4 TYR 0.015 0.002 TYR A 467 ARG 0.010 0.001 ARG A 732 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4066 Ramachandran restraints generated. 2033 Oldfield, 0 Emsley, 2033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4066 Ramachandran restraints generated. 2033 Oldfield, 0 Emsley, 2033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 1671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 297 time to evaluate : 1.726 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 28 PHE cc_start: 0.7300 (m-80) cc_final: 0.7055 (m-80) REVERT: A 151 LYS cc_start: 0.8448 (OUTLIER) cc_final: 0.8138 (ptmm) REVERT: B 151 LYS cc_start: 0.7978 (OUTLIER) cc_final: 0.7698 (ptpp) REVERT: B 456 MET cc_start: 0.7696 (mtm) cc_final: 0.7428 (mtm) REVERT: B 701 LEU cc_start: 0.8126 (OUTLIER) cc_final: 0.7775 (tt) outliers start: 79 outliers final: 27 residues processed: 349 average time/residue: 1.2277 time to fit residues: 478.3706 Evaluate side-chains 249 residues out of total 1671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 219 time to evaluate : 1.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 LYS Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 322 GLU Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 789 VAL Chi-restraints excluded: chain A residue 799 PHE Chi-restraints excluded: chain A residue 920 GLU Chi-restraints excluded: chain A residue 994 SER Chi-restraints excluded: chain B residue 151 LYS Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 638 SER Chi-restraints excluded: chain B residue 659 GLU Chi-restraints excluded: chain B residue 701 LEU Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 811 SER Chi-restraints excluded: chain B residue 885 CYS Chi-restraints excluded: chain B residue 941 ILE Chi-restraints excluded: chain B residue 1021 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 102 optimal weight: 6.9990 chunk 57 optimal weight: 0.0970 chunk 153 optimal weight: 0.0670 chunk 125 optimal weight: 0.8980 chunk 50 optimal weight: 7.9990 chunk 184 optimal weight: 1.9990 chunk 199 optimal weight: 2.9990 chunk 164 optimal weight: 1.9990 chunk 183 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 148 optimal weight: 2.9990 overall best weight: 1.0120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 GLN A 123 GLN A 437 GLN A 604 ASN ** A 726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 63 GLN B 67 GLN ** B 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 361 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.3662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 15934 Z= 0.229 Angle : 0.549 7.955 21639 Z= 0.286 Chirality : 0.040 0.161 2512 Planarity : 0.004 0.040 2786 Dihedral : 4.366 55.279 2194 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 4.85 % Allowed : 17.86 % Favored : 77.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.61 (0.19), residues: 2033 helix: 2.09 (0.15), residues: 1182 sheet: -0.36 (0.29), residues: 306 loop : -0.27 (0.27), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 540 HIS 0.005 0.001 HIS A 716 PHE 0.013 0.001 PHE A 760 TYR 0.012 0.001 TYR B 924 ARG 0.010 0.001 ARG A 732 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4066 Ramachandran restraints generated. 2033 Oldfield, 0 Emsley, 2033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4066 Ramachandran restraints generated. 2033 Oldfield, 0 Emsley, 2033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 1671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 262 time to evaluate : 1.766 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 656 GLN cc_start: 0.7969 (OUTLIER) cc_final: 0.7223 (mt0) REVERT: B 779 MET cc_start: 0.5156 (tpp) cc_final: 0.4818 (tpp) outliers start: 81 outliers final: 34 residues processed: 314 average time/residue: 1.2386 time to fit residues: 432.3175 Evaluate side-chains 246 residues out of total 1671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 211 time to evaluate : 1.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 447 MET Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 656 GLN Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 789 VAL Chi-restraints excluded: chain A residue 799 PHE Chi-restraints excluded: chain A residue 920 GLU Chi-restraints excluded: chain A residue 994 SER Chi-restraints excluded: chain B residue 213 GLN Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 659 GLU Chi-restraints excluded: chain B residue 676 SER Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 866 LEU Chi-restraints excluded: chain B residue 885 CYS Chi-restraints excluded: chain B residue 990 THR Chi-restraints excluded: chain B residue 1013 ILE Chi-restraints excluded: chain B residue 1021 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 182 optimal weight: 5.9990 chunk 138 optimal weight: 0.9990 chunk 95 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 88 optimal weight: 0.8980 chunk 124 optimal weight: 0.0970 chunk 185 optimal weight: 0.5980 chunk 196 optimal weight: 0.9980 chunk 96 optimal weight: 0.8980 chunk 175 optimal weight: 6.9990 chunk 52 optimal weight: 3.9990 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 GLN A 106 GLN A 319 HIS ** A 726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 59 ASN B 63 GLN B 361 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.4099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15934 Z= 0.180 Angle : 0.516 9.579 21639 Z= 0.264 Chirality : 0.039 0.177 2512 Planarity : 0.004 0.038 2786 Dihedral : 4.285 57.225 2194 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 4.01 % Allowed : 19.83 % Favored : 76.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.73 (0.19), residues: 2033 helix: 2.19 (0.15), residues: 1179 sheet: -0.18 (0.29), residues: 308 loop : -0.31 (0.26), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 540 HIS 0.003 0.001 HIS A 319 PHE 0.010 0.001 PHE A 760 TYR 0.013 0.001 TYR B 77 ARG 0.011 0.001 ARG A 732 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4066 Ramachandran restraints generated. 2033 Oldfield, 0 Emsley, 2033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4066 Ramachandran restraints generated. 2033 Oldfield, 0 Emsley, 2033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 1671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 245 time to evaluate : 1.797 Fit side-chains revert: symmetry clash REVERT: A 860 MET cc_start: 0.6925 (tmm) cc_final: 0.6561 (tmt) REVERT: B 213 GLN cc_start: 0.7259 (OUTLIER) cc_final: 0.6677 (tp40) REVERT: B 447 MET cc_start: 0.6617 (ttm) cc_final: 0.6087 (mtt) REVERT: B 659 GLU cc_start: 0.6374 (OUTLIER) cc_final: 0.6173 (mt-10) outliers start: 67 outliers final: 28 residues processed: 291 average time/residue: 1.2799 time to fit residues: 413.0884 Evaluate side-chains 252 residues out of total 1671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 222 time to evaluate : 1.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 MET Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 789 VAL Chi-restraints excluded: chain A residue 799 PHE Chi-restraints excluded: chain A residue 920 GLU Chi-restraints excluded: chain A residue 941 ILE Chi-restraints excluded: chain A residue 994 SER Chi-restraints excluded: chain B residue 176 ASP Chi-restraints excluded: chain B residue 213 GLN Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 659 GLU Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 866 LEU Chi-restraints excluded: chain B residue 941 ILE Chi-restraints excluded: chain B residue 1021 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 163 optimal weight: 0.9990 chunk 111 optimal weight: 6.9990 chunk 2 optimal weight: 0.9990 chunk 146 optimal weight: 0.6980 chunk 80 optimal weight: 3.9990 chunk 167 optimal weight: 4.9990 chunk 135 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 100 optimal weight: 3.9990 chunk 176 optimal weight: 4.9990 chunk 49 optimal weight: 6.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 ASN A 63 GLN A 67 GLN A 68 ASN A 106 GLN A 319 HIS ** A 726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 59 ASN ** B 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 361 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.4765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 15934 Z= 0.376 Angle : 0.624 9.309 21639 Z= 0.320 Chirality : 0.043 0.217 2512 Planarity : 0.004 0.045 2786 Dihedral : 4.616 57.153 2194 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 5.45 % Allowed : 19.89 % Favored : 74.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.18), residues: 2033 helix: 1.86 (0.14), residues: 1172 sheet: -0.31 (0.29), residues: 313 loop : -0.40 (0.26), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 540 HIS 0.007 0.001 HIS A 716 PHE 0.017 0.002 PHE A 981 TYR 0.015 0.002 TYR A 597 ARG 0.008 0.001 ARG A 521 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4066 Ramachandran restraints generated. 2033 Oldfield, 0 Emsley, 2033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4066 Ramachandran restraints generated. 2033 Oldfield, 0 Emsley, 2033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 1671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 242 time to evaluate : 1.748 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 34 GLN cc_start: 0.8426 (OUTLIER) cc_final: 0.8180 (tt0) REVERT: A 322 GLU cc_start: 0.6841 (OUTLIER) cc_final: 0.6362 (tt0) REVERT: A 656 GLN cc_start: 0.8158 (OUTLIER) cc_final: 0.7516 (mt0) REVERT: B 486 MET cc_start: 0.7525 (OUTLIER) cc_final: 0.7211 (mpp) REVERT: B 659 GLU cc_start: 0.6485 (OUTLIER) cc_final: 0.6090 (mp0) outliers start: 91 outliers final: 39 residues processed: 301 average time/residue: 1.3310 time to fit residues: 442.3211 Evaluate side-chains 265 residues out of total 1671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 221 time to evaluate : 1.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 34 GLN Chi-restraints excluded: chain A residue 76 MET Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 322 GLU Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 447 MET Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain A residue 656 GLN Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 789 VAL Chi-restraints excluded: chain A residue 799 PHE Chi-restraints excluded: chain A residue 920 GLU Chi-restraints excluded: chain A residue 941 ILE Chi-restraints excluded: chain A residue 994 SER Chi-restraints excluded: chain B residue 149 MET Chi-restraints excluded: chain B residue 201 LYS Chi-restraints excluded: chain B residue 213 GLN Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 300 MET Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 486 MET Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 659 GLU Chi-restraints excluded: chain B residue 676 SER Chi-restraints excluded: chain B residue 731 GLN Chi-restraints excluded: chain B residue 784 ILE Chi-restraints excluded: chain B residue 866 LEU Chi-restraints excluded: chain B residue 986 MET Chi-restraints excluded: chain B residue 990 THR Chi-restraints excluded: chain B residue 1021 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 66 optimal weight: 0.9990 chunk 176 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 115 optimal weight: 0.7980 chunk 48 optimal weight: 0.0170 chunk 196 optimal weight: 0.9980 chunk 163 optimal weight: 0.9980 chunk 90 optimal weight: 0.6980 chunk 16 optimal weight: 2.9990 chunk 64 optimal weight: 0.0470 chunk 103 optimal weight: 3.9990 overall best weight: 0.5116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 GLN A 67 GLN ** A 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 319 HIS ** A 726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 731 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 735 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.4966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 15934 Z= 0.172 Angle : 0.531 8.937 21639 Z= 0.273 Chirality : 0.040 0.199 2512 Planarity : 0.004 0.040 2786 Dihedral : 4.417 58.919 2194 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 3.71 % Allowed : 22.11 % Favored : 74.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.19), residues: 2033 helix: 2.08 (0.15), residues: 1180 sheet: -0.21 (0.29), residues: 313 loop : -0.49 (0.26), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 540 HIS 0.003 0.001 HIS B 691 PHE 0.008 0.001 PHE A 571 TYR 0.009 0.001 TYR B 277 ARG 0.006 0.001 ARG A 130 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4066 Ramachandran restraints generated. 2033 Oldfield, 0 Emsley, 2033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4066 Ramachandran restraints generated. 2033 Oldfield, 0 Emsley, 2033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 242 time to evaluate : 1.755 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 GLN cc_start: 0.8436 (OUTLIER) cc_final: 0.8136 (tt0) REVERT: A 860 MET cc_start: 0.6903 (tmm) cc_final: 0.6522 (tmt) REVERT: B 167 SER cc_start: 0.8030 (OUTLIER) cc_final: 0.7765 (m) REVERT: B 659 GLU cc_start: 0.6322 (OUTLIER) cc_final: 0.6085 (mt-10) REVERT: B 779 MET cc_start: 0.5203 (tpp) cc_final: 0.4974 (tpp) REVERT: B 1029 ARG cc_start: 0.5820 (OUTLIER) cc_final: 0.4898 (ttp-170) outliers start: 62 outliers final: 33 residues processed: 286 average time/residue: 1.2916 time to fit residues: 409.4588 Evaluate side-chains 256 residues out of total 1671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 219 time to evaluate : 1.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 34 GLN Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 626 MET Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 789 VAL Chi-restraints excluded: chain A residue 799 PHE Chi-restraints excluded: chain A residue 920 GLU Chi-restraints excluded: chain A residue 941 ILE Chi-restraints excluded: chain A residue 994 SER Chi-restraints excluded: chain B residue 89 SER Chi-restraints excluded: chain B residue 167 SER Chi-restraints excluded: chain B residue 174 ASP Chi-restraints excluded: chain B residue 176 ASP Chi-restraints excluded: chain B residue 213 GLN Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 659 GLU Chi-restraints excluded: chain B residue 676 SER Chi-restraints excluded: chain B residue 866 LEU Chi-restraints excluded: chain B residue 990 THR Chi-restraints excluded: chain B residue 1021 LEU Chi-restraints excluded: chain B residue 1029 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 189 optimal weight: 0.7980 chunk 22 optimal weight: 0.0570 chunk 111 optimal weight: 5.9990 chunk 143 optimal weight: 0.9980 chunk 165 optimal weight: 0.6980 chunk 109 optimal weight: 4.9990 chunk 195 optimal weight: 0.4980 chunk 122 optimal weight: 0.0270 chunk 119 optimal weight: 0.0770 chunk 90 optimal weight: 0.5980 chunk 121 optimal weight: 3.9990 overall best weight: 0.2514 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 GLN A 67 GLN A 106 GLN A 319 HIS ** A 726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 731 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.5091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 15934 Z= 0.151 Angle : 0.523 9.333 21639 Z= 0.267 Chirality : 0.039 0.196 2512 Planarity : 0.004 0.042 2786 Dihedral : 4.286 59.142 2194 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 3.18 % Allowed : 23.73 % Favored : 73.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.77 (0.19), residues: 2033 helix: 2.26 (0.15), residues: 1173 sheet: -0.10 (0.30), residues: 300 loop : -0.41 (0.26), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 540 HIS 0.003 0.001 HIS B 955 PHE 0.008 0.001 PHE A 5 TYR 0.009 0.001 TYR A 327 ARG 0.005 0.000 ARG A 130 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4066 Ramachandran restraints generated. 2033 Oldfield, 0 Emsley, 2033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4066 Ramachandran restraints generated. 2033 Oldfield, 0 Emsley, 2033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 236 time to evaluate : 1.715 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 328 GLU cc_start: 0.5626 (tp30) cc_final: 0.5357 (tp30) REVERT: A 860 MET cc_start: 0.6895 (tmm) cc_final: 0.6540 (tmt) REVERT: B 167 SER cc_start: 0.8038 (OUTLIER) cc_final: 0.7768 (m) REVERT: B 398 MET cc_start: 0.7675 (mmt) cc_final: 0.7157 (mmt) REVERT: B 779 MET cc_start: 0.5153 (tpp) cc_final: 0.4806 (tpp) REVERT: B 1029 ARG cc_start: 0.5832 (OUTLIER) cc_final: 0.4882 (ttp-170) outliers start: 53 outliers final: 30 residues processed: 278 average time/residue: 1.2838 time to fit residues: 396.4733 Evaluate side-chains 254 residues out of total 1671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 222 time to evaluate : 1.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 626 MET Chi-restraints excluded: chain A residue 757 VAL Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 789 VAL Chi-restraints excluded: chain A residue 799 PHE Chi-restraints excluded: chain A residue 941 ILE Chi-restraints excluded: chain A residue 994 SER Chi-restraints excluded: chain B residue 167 SER Chi-restraints excluded: chain B residue 201 LYS Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 676 SER Chi-restraints excluded: chain B residue 915 TRP Chi-restraints excluded: chain B residue 990 THR Chi-restraints excluded: chain B residue 1021 LEU Chi-restraints excluded: chain B residue 1029 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 78 optimal weight: 3.9990 chunk 116 optimal weight: 0.9990 chunk 58 optimal weight: 5.9990 chunk 38 optimal weight: 0.8980 chunk 37 optimal weight: 0.0980 chunk 124 optimal weight: 0.6980 chunk 133 optimal weight: 0.6980 chunk 96 optimal weight: 1.9990 chunk 18 optimal weight: 5.9990 chunk 153 optimal weight: 0.8980 chunk 177 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 GLN ** A 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 106 GLN A 319 HIS ** A 726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 731 GLN ** B 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 735 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.5192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15934 Z= 0.178 Angle : 0.531 9.077 21639 Z= 0.270 Chirality : 0.040 0.192 2512 Planarity : 0.004 0.049 2786 Dihedral : 4.269 58.356 2194 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 3.24 % Allowed : 23.85 % Favored : 72.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.73 (0.19), residues: 2033 helix: 2.27 (0.15), residues: 1173 sheet: -0.25 (0.29), residues: 305 loop : -0.43 (0.26), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 540 HIS 0.003 0.001 HIS B 955 PHE 0.027 0.001 PHE B 883 TYR 0.009 0.001 TYR B 277 ARG 0.012 0.000 ARG A 732 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4066 Ramachandran restraints generated. 2033 Oldfield, 0 Emsley, 2033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4066 Ramachandran restraints generated. 2033 Oldfield, 0 Emsley, 2033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 226 time to evaluate : 1.685 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 799 PHE cc_start: 0.8751 (OUTLIER) cc_final: 0.8428 (t80) REVERT: A 860 MET cc_start: 0.6876 (tmm) cc_final: 0.6542 (tmt) REVERT: B 398 MET cc_start: 0.7689 (mmt) cc_final: 0.7159 (mmt) REVERT: B 779 MET cc_start: 0.4901 (tpp) cc_final: 0.4599 (tpp) REVERT: B 1029 ARG cc_start: 0.5795 (OUTLIER) cc_final: 0.4827 (ttp-170) outliers start: 54 outliers final: 34 residues processed: 264 average time/residue: 1.2549 time to fit residues: 368.6813 Evaluate side-chains 255 residues out of total 1671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 219 time to evaluate : 1.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 626 MET Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 789 VAL Chi-restraints excluded: chain A residue 799 PHE Chi-restraints excluded: chain A residue 804 THR Chi-restraints excluded: chain A residue 941 ILE Chi-restraints excluded: chain A residue 994 SER Chi-restraints excluded: chain B residue 76 MET Chi-restraints excluded: chain B residue 89 SER Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 201 LYS Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 676 SER Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 915 TRP Chi-restraints excluded: chain B residue 990 THR Chi-restraints excluded: chain B residue 1013 ILE Chi-restraints excluded: chain B residue 1021 LEU Chi-restraints excluded: chain B residue 1029 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 187 optimal weight: 0.7980 chunk 171 optimal weight: 0.0370 chunk 182 optimal weight: 0.0870 chunk 109 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 143 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 164 optimal weight: 0.9980 chunk 172 optimal weight: 0.0070 chunk 181 optimal weight: 5.9990 chunk 119 optimal weight: 0.8980 overall best weight: 0.3654 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 GLN ** A 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 319 HIS ** A 726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 415 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.5283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 15934 Z= 0.158 Angle : 0.530 9.254 21639 Z= 0.269 Chirality : 0.039 0.163 2512 Planarity : 0.004 0.047 2786 Dihedral : 4.225 56.958 2194 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 2.76 % Allowed : 24.45 % Favored : 72.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.75 (0.19), residues: 2033 helix: 2.27 (0.15), residues: 1174 sheet: -0.21 (0.30), residues: 300 loop : -0.41 (0.26), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A 540 HIS 0.002 0.001 HIS A 686 PHE 0.022 0.001 PHE B 883 TYR 0.009 0.001 TYR A 327 ARG 0.012 0.000 ARG A 732 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4066 Ramachandran restraints generated. 2033 Oldfield, 0 Emsley, 2033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4066 Ramachandran restraints generated. 2033 Oldfield, 0 Emsley, 2033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 234 time to evaluate : 1.736 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 799 PHE cc_start: 0.8700 (OUTLIER) cc_final: 0.8429 (t80) REVERT: A 860 MET cc_start: 0.6858 (tmm) cc_final: 0.6538 (tmt) REVERT: A 970 ARG cc_start: 0.8128 (OUTLIER) cc_final: 0.7578 (ttm-80) REVERT: B 398 MET cc_start: 0.7652 (mmt) cc_final: 0.7119 (mmt) REVERT: B 779 MET cc_start: 0.4887 (tpp) cc_final: 0.4590 (tpp) REVERT: B 1029 ARG cc_start: 0.5755 (OUTLIER) cc_final: 0.4771 (ttp-170) outliers start: 46 outliers final: 35 residues processed: 266 average time/residue: 1.3090 time to fit residues: 389.4655 Evaluate side-chains 260 residues out of total 1671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 222 time to evaluate : 1.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 626 MET Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 789 VAL Chi-restraints excluded: chain A residue 799 PHE Chi-restraints excluded: chain A residue 804 THR Chi-restraints excluded: chain A residue 920 GLU Chi-restraints excluded: chain A residue 970 ARG Chi-restraints excluded: chain A residue 994 SER Chi-restraints excluded: chain B residue 76 MET Chi-restraints excluded: chain B residue 110 GLN Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 176 ASP Chi-restraints excluded: chain B residue 201 LYS Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 676 SER Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 915 TRP Chi-restraints excluded: chain B residue 990 THR Chi-restraints excluded: chain B residue 1021 LEU Chi-restraints excluded: chain B residue 1029 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 192 optimal weight: 3.9990 chunk 117 optimal weight: 3.9990 chunk 91 optimal weight: 0.8980 chunk 134 optimal weight: 0.9980 chunk 202 optimal weight: 0.6980 chunk 186 optimal weight: 0.5980 chunk 161 optimal weight: 0.3980 chunk 16 optimal weight: 1.9990 chunk 124 optimal weight: 0.5980 chunk 98 optimal weight: 2.9990 chunk 127 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 GLN ** A 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 319 HIS ** A 726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 921 ASN B 59 ASN ** B 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 735 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.5349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15934 Z= 0.179 Angle : 0.542 9.759 21639 Z= 0.273 Chirality : 0.040 0.182 2512 Planarity : 0.004 0.047 2786 Dihedral : 4.221 55.712 2194 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.64 % Allowed : 24.87 % Favored : 72.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.76 (0.19), residues: 2033 helix: 2.30 (0.15), residues: 1173 sheet: -0.19 (0.30), residues: 292 loop : -0.46 (0.26), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A 540 HIS 0.003 0.001 HIS B 955 PHE 0.022 0.001 PHE B 883 TYR 0.009 0.001 TYR B 182 ARG 0.012 0.000 ARG A 732 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4066 Ramachandran restraints generated. 2033 Oldfield, 0 Emsley, 2033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4066 Ramachandran restraints generated. 2033 Oldfield, 0 Emsley, 2033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 222 time to evaluate : 1.876 Fit side-chains revert: symmetry clash REVERT: A 860 MET cc_start: 0.6846 (tmm) cc_final: 0.6551 (tmt) REVERT: A 970 ARG cc_start: 0.8221 (OUTLIER) cc_final: 0.7614 (ttm-80) REVERT: B 398 MET cc_start: 0.7628 (mmt) cc_final: 0.7087 (mmt) REVERT: B 779 MET cc_start: 0.4858 (tpp) cc_final: 0.4540 (tpp) REVERT: B 1029 ARG cc_start: 0.5779 (OUTLIER) cc_final: 0.4798 (ttp-170) outliers start: 44 outliers final: 36 residues processed: 255 average time/residue: 1.3125 time to fit residues: 370.2977 Evaluate side-chains 254 residues out of total 1671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 216 time to evaluate : 1.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 626 MET Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 789 VAL Chi-restraints excluded: chain A residue 804 THR Chi-restraints excluded: chain A residue 920 GLU Chi-restraints excluded: chain A residue 970 ARG Chi-restraints excluded: chain A residue 994 SER Chi-restraints excluded: chain B residue 76 MET Chi-restraints excluded: chain B residue 89 SER Chi-restraints excluded: chain B residue 110 GLN Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 176 ASP Chi-restraints excluded: chain B residue 201 LYS Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 676 SER Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 915 TRP Chi-restraints excluded: chain B residue 990 THR Chi-restraints excluded: chain B residue 1021 LEU Chi-restraints excluded: chain B residue 1029 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 171 optimal weight: 5.9990 chunk 49 optimal weight: 3.9990 chunk 148 optimal weight: 3.9990 chunk 23 optimal weight: 0.6980 chunk 44 optimal weight: 0.9990 chunk 161 optimal weight: 5.9990 chunk 67 optimal weight: 3.9990 chunk 165 optimal weight: 0.5980 chunk 20 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 141 optimal weight: 0.9980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 GLN A 106 GLN A 112 GLN A 319 HIS ** A 726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 59 ASN ** B 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.131472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.110589 restraints weight = 20624.629| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 1.50 r_work: 0.3143 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3034 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.5410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15934 Z= 0.203 Angle : 0.560 9.652 21639 Z= 0.281 Chirality : 0.040 0.338 2512 Planarity : 0.004 0.047 2786 Dihedral : 4.104 47.802 2192 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.70 % Allowed : 24.99 % Favored : 72.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.70 (0.19), residues: 2033 helix: 2.24 (0.15), residues: 1174 sheet: -0.27 (0.29), residues: 306 loop : -0.42 (0.26), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP A 540 HIS 0.004 0.001 HIS B 955 PHE 0.021 0.001 PHE B 883 TYR 0.009 0.001 TYR B 277 ARG 0.012 0.001 ARG A 732 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6697.54 seconds wall clock time: 120 minutes 27.37 seconds (7227.37 seconds total)