Starting phenix.real_space_refine on Fri Jul 3 13:59:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7lj9_23389/07_2026/7lj9_23389.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lj9_23389/07_2026/7lj9_23389.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7lj9_23389/07_2026/7lj9_23389.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lj9_23389/07_2026/7lj9_23389.map" model { file = "/net/cci-nas-00/data/ceres_data/7lj9_23389/07_2026/7lj9_23389.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lj9_23389/07_2026/7lj9_23389.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7lj9_23389/07_2026/7lj9_23389.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7lj9_23389/07_2026/7lj9_23389.cif" } resolution = 3.0 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= -0.005 sd= 0.129 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: 5 Type Number sf(0) Gaussians P 3 5.49 5 S 96 5.16 5 C 9288 2.51 5 N 2461 2.21 5 O 2668 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14516 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 2160 Classifications: {'peptide': 279} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 12, 'TRANS': 266} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 Chain: "B" Number of atoms: 2160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 2160 Classifications: {'peptide': 279} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 12, 'TRANS': 266} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 Chain: "C" Number of atoms: 2160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 2160 Classifications: {'peptide': 279} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 12, 'TRANS': 266} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 Chain: "D" Number of atoms: 7940 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1028, 7932 Classifications: {'peptide': 1028} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 2, 'PTRANS': 47, 'TRANS': 978} Chain breaks: 2 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'ASN:plan1': 2, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 14 Conformer: "B" Number of residues, atoms: 1028, 7932 Classifications: {'peptide': 1028} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 2, 'PTRANS': 47, 'TRANS': 978} Chain breaks: 2 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'ASN:plan1': 2, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 14 bond proxies already assigned to first conformer: 8093 Chain: "A" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'OAA': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'OAA': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'OAA': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 69 Unusual residues: {'ACO': 1, 'OAA': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 4.56, per 1000 atoms: 0.31 Number of scatterers: 14516 At special positions: 0 Unit cell: (96.57, 100.92, 142.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 96 16.00 P 3 15.00 O 2668 8.00 N 2461 7.00 C 9288 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.19 Conformation dependent library (CDL) restraints added in 1.1 seconds 3710 Ramachandran restraints generated. 1855 Oldfield, 0 Emsley, 1855 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3372 Finding SS restraints... Secondary structure from input PDB file: 83 helices and 9 sheets defined 53.8% alpha, 6.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'A' and resid 824 through 831 removed outlier: 4.173A pdb=" N LEU A 831 " --> pdb=" O TRP A 827 " (cutoff:3.500A) Processing helix chain 'A' and resid 858 through 865 Processing helix chain 'A' and resid 868 through 877 Processing helix chain 'A' and resid 883 through 897 Processing helix chain 'A' and resid 904 through 916 Processing helix chain 'A' and resid 919 through 929 Processing helix chain 'A' and resid 937 through 951 removed outlier: 3.523A pdb=" N PHE A 946 " --> pdb=" O ALA A 942 " (cutoff:3.500A) Processing helix chain 'A' and resid 955 through 966 Processing helix chain 'A' and resid 986 through 998 removed outlier: 3.530A pdb=" N LEU A 990 " --> pdb=" O ARG A 986 " (cutoff:3.500A) Processing helix chain 'A' and resid 1001 through 1018 removed outlier: 3.940A pdb=" N SER A1016 " --> pdb=" O LYS A1012 " (cutoff:3.500A) Processing helix chain 'A' and resid 1024 through 1040 removed outlier: 4.030A pdb=" N GLY A1030 " --> pdb=" O ASP A1026 " (cutoff:3.500A) Processing helix chain 'A' and resid 1046 through 1055 removed outlier: 4.127A pdb=" N ILE A1052 " --> pdb=" O ALA A1048 " (cutoff:3.500A) Processing helix chain 'A' and resid 1055 through 1079 removed outlier: 3.569A pdb=" N GLY A1059 " --> pdb=" O GLY A1055 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N PHE A1061 " --> pdb=" O LEU A1057 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N MET A1067 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N GLY A1068 " --> pdb=" O GLY A1064 " (cutoff:3.500A) Processing helix chain 'A' and resid 1087 through 1091 removed outlier: 3.619A pdb=" N ILE A1091 " --> pdb=" O TRP A1088 " (cutoff:3.500A) Processing helix chain 'B' and resid 824 through 831 Processing helix chain 'B' and resid 858 through 865 Processing helix chain 'B' and resid 868 through 877 Processing helix chain 'B' and resid 883 through 897 Processing helix chain 'B' and resid 904 through 916 Processing helix chain 'B' and resid 919 through 929 Processing helix chain 'B' and resid 937 through 951 removed outlier: 3.522A pdb=" N PHE B 946 " --> pdb=" O ALA B 942 " (cutoff:3.500A) Processing helix chain 'B' and resid 955 through 966 Processing helix chain 'B' and resid 986 through 998 removed outlier: 3.530A pdb=" N LEU B 990 " --> pdb=" O ARG B 986 " (cutoff:3.500A) Processing helix chain 'B' and resid 1001 through 1010 Processing helix chain 'B' and resid 1013 through 1018 Processing helix chain 'B' and resid 1024 through 1040 removed outlier: 4.031A pdb=" N GLY B1030 " --> pdb=" O ASP B1026 " (cutoff:3.500A) Processing helix chain 'B' and resid 1049 through 1055 Processing helix chain 'B' and resid 1055 through 1079 removed outlier: 3.569A pdb=" N GLY B1059 " --> pdb=" O GLY B1055 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N PHE B1061 " --> pdb=" O LEU B1057 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N MET B1067 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N GLY B1068 " --> pdb=" O GLY B1064 " (cutoff:3.500A) Processing helix chain 'B' and resid 1087 through 1091 removed outlier: 3.619A pdb=" N ILE B1091 " --> pdb=" O TRP B1088 " (cutoff:3.500A) Processing helix chain 'C' and resid 825 through 831 removed outlier: 3.632A pdb=" N LEU C 831 " --> pdb=" O TRP C 827 " (cutoff:3.500A) Processing helix chain 'C' and resid 858 through 865 Processing helix chain 'C' and resid 868 through 877 Processing helix chain 'C' and resid 883 through 897 Processing helix chain 'C' and resid 904 through 916 Processing helix chain 'C' and resid 919 through 929 Processing helix chain 'C' and resid 937 through 951 removed outlier: 3.522A pdb=" N PHE C 946 " --> pdb=" O ALA C 942 " (cutoff:3.500A) Processing helix chain 'C' and resid 955 through 966 Processing helix chain 'C' and resid 986 through 998 removed outlier: 3.529A pdb=" N LEU C 990 " --> pdb=" O ARG C 986 " (cutoff:3.500A) Processing helix chain 'C' and resid 1001 through 1018 Processing helix chain 'C' and resid 1024 through 1040 removed outlier: 4.031A pdb=" N GLY C1030 " --> pdb=" O ASP C1026 " (cutoff:3.500A) Processing helix chain 'C' and resid 1049 through 1055 Processing helix chain 'C' and resid 1055 through 1079 removed outlier: 3.569A pdb=" N GLY C1059 " --> pdb=" O GLY C1055 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N PHE C1061 " --> pdb=" O LEU C1057 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N MET C1067 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N GLY C1068 " --> pdb=" O GLY C1064 " (cutoff:3.500A) Processing helix chain 'C' and resid 1087 through 1091 removed outlier: 3.620A pdb=" N ILE C1091 " --> pdb=" O TRP C1088 " (cutoff:3.500A) Processing helix chain 'D' and resid 7 through 19 Processing helix chain 'D' and resid 42 through 47 removed outlier: 3.671A pdb=" N HIS D 47 " --> pdb=" O LEU D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 52 removed outlier: 4.007A pdb=" N LEU D 51 " --> pdb=" O PRO D 48 " (cutoff:3.500A) Processing helix chain 'D' and resid 65 through 70 removed outlier: 4.125A pdb=" N LEU D 69 " --> pdb=" O ARG D 65 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 86 Processing helix chain 'D' and resid 161 through 168 Processing helix chain 'D' and resid 178 through 195 removed outlier: 3.883A pdb=" N SER D 186 " --> pdb=" O ALA D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 225 through 234 removed outlier: 6.584A pdb=" N VAL D 231 " --> pdb=" O TYR D 227 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N LYS D 232 " --> pdb=" O ILE D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 249 through 258 removed outlier: 4.358A pdb=" N ALA D 258 " --> pdb=" O ALA D 254 " (cutoff:3.500A) Processing helix chain 'D' and resid 281 through 295 removed outlier: 3.743A pdb=" N VAL D 286 " --> pdb=" O GLY D 282 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N SER D 289 " --> pdb=" O SER D 285 " (cutoff:3.500A) Processing helix chain 'D' and resid 312 through 327 removed outlier: 3.915A pdb=" N MET D 327 " --> pdb=" O ILE D 323 " (cutoff:3.500A) Processing helix chain 'D' and resid 349 through 364 removed outlier: 4.040A pdb=" N THR D 353 " --> pdb=" O ASN D 349 " (cutoff:3.500A) Processing helix chain 'D' and resid 364 through 372 removed outlier: 3.508A pdb=" N LEU D 368 " --> pdb=" O TYR D 364 " (cutoff:3.500A) Processing helix chain 'D' and resid 383 through 399 removed outlier: 3.848A pdb=" N GLY D 387 " --> pdb=" O ASN D 383 " (cutoff:3.500A) Processing helix chain 'D' and resid 412 through 420 removed outlier: 4.084A pdb=" N GLY D 416 " --> pdb=" O THR D 412 " (cutoff:3.500A) Processing helix chain 'D' and resid 505 through 519 Processing helix chain 'D' and resid 556 through 563 Processing helix chain 'D' and resid 577 through 587 removed outlier: 3.592A pdb=" N SER D 581 " --> pdb=" O SER D 577 " (cutoff:3.500A) Processing helix chain 'D' and resid 602 through 617 Processing helix chain 'D' and resid 642 through 649 Processing helix chain 'D' and resid 663 through 665 No H-bonds generated for 'chain 'D' and resid 663 through 665' Processing helix chain 'D' and resid 666 through 678 Processing helix chain 'D' and resid 696 through 707 removed outlier: 3.708A pdb=" N HIS D 700 " --> pdb=" O THR D 696 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU D 702 " --> pdb=" O MET D 698 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ARG D 703 " --> pdb=" O ASP D 699 " (cutoff:3.500A) Processing helix chain 'D' and resid 723 through 733 removed outlier: 3.588A pdb=" N ILE D 727 " --> pdb=" O GLU D 723 " (cutoff:3.500A) Processing helix chain 'D' and resid 771 through 783 removed outlier: 3.510A pdb=" N GLY D 783 " --> pdb=" O LEU D 779 " (cutoff:3.500A) Processing helix chain 'D' and resid 792 through 807 Processing helix chain 'D' and resid 824 through 831 Processing helix chain 'D' and resid 858 through 865 Processing helix chain 'D' and resid 868 through 877 Processing helix chain 'D' and resid 883 through 896 Processing helix chain 'D' and resid 904 through 916 Processing helix chain 'D' and resid 919 through 929 Processing helix chain 'D' and resid 937 through 952 removed outlier: 3.516A pdb=" N SER D 952 " --> pdb=" O LYS D 948 " (cutoff:3.500A) Processing helix chain 'D' and resid 955 through 966 removed outlier: 3.667A pdb=" N ASN D 961 " --> pdb=" O MET D 957 " (cutoff:3.500A) Processing helix chain 'D' and resid 986 through 998 removed outlier: 3.597A pdb=" N LEU D 990 " --> pdb=" O ARG D 986 " (cutoff:3.500A) Processing helix chain 'D' and resid 1001 through 1018 removed outlier: 3.950A pdb=" N SER D1016 " --> pdb=" O LYS D1012 " (cutoff:3.500A) Processing helix chain 'D' and resid 1024 through 1040 removed outlier: 4.136A pdb=" N GLY D1030 " --> pdb=" O ASP D1026 " (cutoff:3.500A) Processing helix chain 'D' and resid 1047 through 1055 removed outlier: 3.588A pdb=" N ILE D1052 " --> pdb=" O ALA D1048 " (cutoff:3.500A) Processing helix chain 'D' and resid 1055 through 1079 removed outlier: 3.525A pdb=" N PHE D1061 " --> pdb=" O LEU D1057 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N MET D1067 " --> pdb=" O LEU D1063 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N GLY D1068 " --> pdb=" O GLY D1064 " (cutoff:3.500A) Processing helix chain 'D' and resid 1087 through 1091 removed outlier: 3.615A pdb=" N ILE D1091 " --> pdb=" O TRP D1088 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 823 through 824 removed outlier: 6.002A pdb=" N MET C 823 " --> pdb=" O ARG D 835 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'D' and resid 3 through 6 removed outlier: 4.405A pdb=" N ALA D 219 " --> pdb=" O ILE D 6 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N ALA D 218 " --> pdb=" O LEU D 200 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N LEU D 200 " --> pdb=" O ALA D 218 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N LYS D 220 " --> pdb=" O THR D 198 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N THR D 198 " --> pdb=" O ALA D 125 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 73 through 74 Processing sheet with id=AA4, first strand: chain 'D' and resid 92 through 95 Processing sheet with id=AA5, first strand: chain 'D' and resid 205 through 207 Processing sheet with id=AA6, first strand: chain 'D' and resid 263 through 265 Processing sheet with id=AA7, first strand: chain 'D' and resid 275 through 277 removed outlier: 6.597A pdb=" N LYS D 336 " --> pdb=" O THR D 374 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N PHE D 376 " --> pdb=" O LYS D 336 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N LEU D 338 " --> pdb=" O PHE D 376 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N ARG D 378 " --> pdb=" O LEU D 338 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N ILE D 340 " --> pdb=" O ARG D 378 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 537 through 543 removed outlier: 3.574A pdb=" N LYS D 546 " --> pdb=" O TRP D 543 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N ALA D 527 " --> pdb=" O PRO D 551 " (cutoff:3.500A) removed outlier: 8.252A pdb=" N PHE D 553 " --> pdb=" O ALA D 527 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N MET D 529 " --> pdb=" O PHE D 553 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ALA D 499 " --> pdb=" O ALA D 528 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N VAL D 530 " --> pdb=" O ALA D 499 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N VAL D 501 " --> pdb=" O VAL D 530 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N LEU D 569 " --> pdb=" O ALA D 595 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 634 through 635 removed outlier: 7.106A pdb=" N VAL D 657 " --> pdb=" O TYR D 682 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N GLY D 684 " --> pdb=" O VAL D 657 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N TYR D 659 " --> pdb=" O GLY D 684 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N ALA D 686 " --> pdb=" O TYR D 659 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N SER D 661 " --> pdb=" O ALA D 686 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N ALA D 658 " --> pdb=" O VAL D 714 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N LEU D 716 " --> pdb=" O ALA D 658 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N VAL D 660 " --> pdb=" O LEU D 716 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N ILE D 713 " --> pdb=" O VAL D 741 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N TRP D 743 " --> pdb=" O ILE D 713 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N VAL D 715 " --> pdb=" O TRP D 743 " (cutoff:3.500A) 679 hydrogen bonds defined for protein. 1995 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: 2.44 Time building geometry restraints manager: 1.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 2420 1.30 - 1.43: 3748 1.43 - 1.56: 8473 1.56 - 1.69: 23 1.69 - 1.81: 160 Bond restraints: 14824 Sorted by residual: bond pdb=" N PRO D 36 " pdb=" CD PRO D 36 " ideal model delta sigma weight residual 1.473 1.330 0.143 1.40e-02 5.10e+03 1.04e+02 bond pdb=" C5A ACO D1201 " pdb=" N7A ACO D1201 " ideal model delta sigma weight residual 1.387 1.297 0.090 1.00e-02 1.00e+04 8.11e+01 bond pdb=" C VAL D 34 " pdb=" O VAL D 34 " ideal model delta sigma weight residual 1.236 1.342 -0.106 1.19e-02 7.06e+03 7.89e+01 bond pdb=" CA GLU B1011 " pdb=" C GLU B1011 " ideal model delta sigma weight residual 1.523 1.424 0.099 1.34e-02 5.57e+03 5.48e+01 bond pdb=" C2P ACO D1201 " pdb=" S1P ACO D1201 " ideal model delta sigma weight residual 1.818 1.756 0.062 1.00e-02 1.00e+04 3.82e+01 ... (remaining 14819 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.81: 19588 3.81 - 7.61: 382 7.61 - 11.42: 65 11.42 - 15.23: 5 15.23 - 19.04: 4 Bond angle restraints: 20044 Sorted by residual: angle pdb=" P1A ACO D1201 " pdb=" O3A ACO D1201 " pdb=" P2A ACO D1201 " ideal model delta sigma weight residual 136.83 123.13 13.70 1.00e+00 1.00e+00 1.88e+02 angle pdb=" N GLY D 832 " pdb=" CA GLY D 832 " pdb=" C GLY D 832 " ideal model delta sigma weight residual 113.48 129.42 -15.94 1.46e+00 4.69e-01 1.19e+02 angle pdb=" C5A ACO D1201 " pdb=" C4A ACO D1201 " pdb=" N3A ACO D1201 " ideal model delta sigma weight residual 126.80 116.77 10.03 1.00e+00 1.00e+00 1.01e+02 angle pdb=" C2B ACO D1201 " pdb=" C1B ACO D1201 " pdb=" O4B ACO D1201 " ideal model delta sigma weight residual 106.53 95.02 11.51 1.18e+00 7.24e-01 9.60e+01 angle pdb=" CA GLU A1011 " pdb=" CB GLU A1011 " pdb=" CG GLU A1011 " ideal model delta sigma weight residual 114.10 133.14 -19.04 2.00e+00 2.50e-01 9.06e+01 ... (remaining 20039 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 7936 17.93 - 35.87: 741 35.87 - 53.80: 125 53.80 - 71.74: 26 71.74 - 89.67: 10 Dihedral angle restraints: 8838 sinusoidal: 3536 harmonic: 5302 Sorted by residual: dihedral pdb=" CA MET A 985 " pdb=" C MET A 985 " pdb=" N ARG A 986 " pdb=" CA ARG A 986 " ideal model delta harmonic sigma weight residual 180.00 150.36 29.64 0 5.00e+00 4.00e-02 3.51e+01 dihedral pdb=" CA MET C 985 " pdb=" C MET C 985 " pdb=" N ARG C 986 " pdb=" CA ARG C 986 " ideal model delta harmonic sigma weight residual 180.00 150.38 29.62 0 5.00e+00 4.00e-02 3.51e+01 dihedral pdb=" CA MET B 985 " pdb=" C MET B 985 " pdb=" N ARG B 986 " pdb=" CA ARG B 986 " ideal model delta harmonic sigma weight residual 180.00 150.38 29.62 0 5.00e+00 4.00e-02 3.51e+01 ... (remaining 8835 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.103: 1929 0.103 - 0.206: 250 0.206 - 0.308: 29 0.308 - 0.411: 6 0.411 - 0.514: 7 Chirality restraints: 2221 Sorted by residual: chirality pdb=" CA ARG B1045 " pdb=" N ARG B1045 " pdb=" C ARG B1045 " pdb=" CB ARG B1045 " both_signs ideal model delta sigma weight residual False 2.51 2.00 0.51 2.00e-01 2.50e+01 6.61e+00 chirality pdb=" CA PRO D 36 " pdb=" N PRO D 36 " pdb=" C PRO D 36 " pdb=" CB PRO D 36 " both_signs ideal model delta sigma weight residual False 2.72 2.23 0.49 2.00e-01 2.50e+01 5.91e+00 chirality pdb=" CB VAL D 904 " pdb=" CA VAL D 904 " pdb=" CG1 VAL D 904 " pdb=" CG2 VAL D 904 " both_signs ideal model delta sigma weight residual False -2.63 -2.15 -0.48 2.00e-01 2.50e+01 5.69e+00 ... (remaining 2218 not shown) Planarity restraints: 2569 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C3P ACO D1201 " 0.315 2.00e-02 2.50e+03 2.65e-01 8.76e+02 pdb=" C5P ACO D1201 " -0.083 2.00e-02 2.50e+03 pdb=" C6P ACO D1201 " 0.184 2.00e-02 2.50e+03 pdb=" N4P ACO D1201 " -0.457 2.00e-02 2.50e+03 pdb=" O5P ACO D1201 " 0.041 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C7P ACO D1201 " -0.188 2.00e-02 2.50e+03 1.51e-01 2.86e+02 pdb=" C9P ACO D1201 " 0.037 2.00e-02 2.50e+03 pdb=" CAP ACO D1201 " -0.132 2.00e-02 2.50e+03 pdb=" N8P ACO D1201 " 0.242 2.00e-02 2.50e+03 pdb=" O9P ACO D1201 " 0.040 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS D 86 " 0.123 5.00e-02 4.00e+02 1.89e-01 5.69e+01 pdb=" N PRO D 87 " -0.326 5.00e-02 4.00e+02 pdb=" CA PRO D 87 " 0.099 5.00e-02 4.00e+02 pdb=" CD PRO D 87 " 0.104 5.00e-02 4.00e+02 ... (remaining 2566 not shown) Histogram of nonbonded interaction distances: 1.17 - 1.92: 9 1.92 - 2.66: 352 2.66 - 3.41: 20090 3.41 - 4.15: 34925 4.15 - 4.90: 64822 Nonbonded interactions: 120198 Sorted by model distance: nonbonded pdb=" O ASN D 190 " pdb=" OD2 ASP D 194 " model vdw 1.171 3.040 nonbonded pdb=" OE2 GLU C 966 " pdb=" NZ LYS C 968 " model vdw 1.305 3.120 nonbonded pdb=" CG PRO D 36 " pdb=" CD1 LEU D 89 " model vdw 1.507 3.860 nonbonded pdb=" CH2 TRP D 49 " pdb=" CG PRO D 109 " model vdw 1.545 3.740 nonbonded pdb=" CB PRO D 36 " pdb=" CD1 LEU D 89 " model vdw 1.598 3.860 ... (remaining 120193 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' 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=0.40 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: 0.910 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: 0.240 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 15.930 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 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 : 0.013 0.143 14824 Z= 0.622 Angle : 1.331 19.035 20044 Z= 0.742 Chirality : 0.076 0.514 2221 Planarity : 0.010 0.265 2569 Dihedral : 14.570 89.670 5466 Min Nonbonded Distance : 1.171 Molprobity Statistics. All-atom Clashscore : 14.97 Ramachandran Plot: Outliers : 0.32 % Allowed : 6.53 % Favored : 93.15 % Rotamer: Outliers : 0.07 % Allowed : 0.13 % Favored : 99.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % 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: -3.16 (0.17), residues: 1855 helix: -2.10 (0.13), residues: 951 sheet: -1.16 (0.45), residues: 142 loop : -2.08 (0.20), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG A1045 TYR 0.042 0.004 TYR D 692 PHE 0.036 0.004 PHE A 840 TRP 0.031 0.002 TRP D 49 HIS 0.008 0.002 HIS D 908 Details of bonding type rmsd/Z covalent geometry : bond 0.01298 / 0.62 (14824) covalent geometry : angle 1.33055 / 0.74 (20044) hydrogen bonds : bond 0.16590 / 10.90 ( 679) hydrogen bonds : angle 7.55824 / 5.24 ( 1995) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3710 Ramachandran restraints generated. 1855 Oldfield, 0 Emsley, 1855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3710 Ramachandran restraints generated. 1855 Oldfield, 0 Emsley, 1855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 217 time to evaluate : 0.461 Fit side-chains REVERT: B 865 GLU cc_start: 0.7387 (tt0) cc_final: 0.7127 (tm-30) REVERT: D 210 ASP cc_start: 0.7695 (t70) cc_final: 0.7192 (t0) REVERT: D 269 LEU cc_start: 0.7505 (mm) cc_final: 0.7152 (tm) REVERT: D 888 GLN cc_start: 0.7513 (tp-100) cc_final: 0.7263 (tm-30) outliers start: 0 outliers final: 1 residues processed: 217 average time/residue: 0.5282 time to fit residues: 126.3861 Evaluate side-chains 159 residues out of total 1549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 158 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 522 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 98 optimal weight: 8.9990 chunk 107 optimal weight: 20.0000 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 5.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1098 HIS ** C 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 888 GLN C 961 ASN ** C1072 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 172 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.129977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.097866 restraints weight = 30785.956| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 2.83 r_work: 0.3178 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3182 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3182 r_free = 0.3182 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3182 r_free = 0.3182 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (8 function evaluations) r_final: 0.3182 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.1571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 14824 Z= 0.176 Angle : 0.707 9.089 20044 Z= 0.365 Chirality : 0.047 0.249 2221 Planarity : 0.006 0.123 2569 Dihedral : 7.292 79.656 2045 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 1.90 % Allowed : 9.50 % Favored : 88.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 1.18 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.95 (0.18), residues: 1855 helix: -0.79 (0.15), residues: 990 sheet: -1.38 (0.47), residues: 129 loop : -1.86 (0.22), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 33 TYR 0.045 0.002 TYR D 304 PHE 0.012 0.001 PHE B 863 TRP 0.025 0.001 TRP D 49 HIS 0.004 0.001 HIS C 900 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.18 (14824) covalent geometry : angle 0.70693 / 0.37 (20044) hydrogen bonds : bond 0.04261 / 2.79 ( 679) hydrogen bonds : angle 4.91479 / 3.41 ( 1995) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3710 Ramachandran restraints generated. 1855 Oldfield, 0 Emsley, 1855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3710 Ramachandran restraints generated. 1855 Oldfield, 0 Emsley, 1855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 189 time to evaluate : 0.578 Fit side-chains REVERT: A 919 ASP cc_start: 0.7849 (m-30) cc_final: 0.7519 (m-30) REVERT: B 976 ARG cc_start: 0.6910 (ptm160) cc_final: 0.6186 (ptp-110) REVERT: B 1050 GLU cc_start: 0.8254 (OUTLIER) cc_final: 0.7774 (tp30) REVERT: C 965 LYS cc_start: 0.8340 (mtpt) cc_final: 0.7988 (tmmm) REVERT: C 969 LEU cc_start: 0.6940 (OUTLIER) cc_final: 0.6540 (mm) REVERT: D 194 ASP cc_start: 0.7794 (m-30) cc_final: 0.7319 (m-30) REVERT: D 210 ASP cc_start: 0.7849 (t70) cc_final: 0.7610 (t0) REVERT: D 269 LEU cc_start: 0.7930 (mm) cc_final: 0.7360 (tm) REVERT: D 408 GLU cc_start: 0.7410 (tp30) cc_final: 0.7042 (tp30) REVERT: D 690 ASP cc_start: 0.7880 (t70) cc_final: 0.7633 (t70) REVERT: D 976 ARG cc_start: 0.8349 (mpt180) cc_final: 0.8036 (ttp80) outliers start: 28 outliers final: 12 residues processed: 208 average time/residue: 0.4913 time to fit residues: 113.8004 Evaluate side-chains 179 residues out of total 1549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 165 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 888 GLN Chi-restraints excluded: chain B residue 891 GLU Chi-restraints excluded: chain B residue 955 ILE Chi-restraints excluded: chain B residue 987 VAL Chi-restraints excluded: chain B residue 1050 GLU Chi-restraints excluded: chain C residue 833 LEU Chi-restraints excluded: chain C residue 848 ARG Chi-restraints excluded: chain C residue 969 LEU Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 230 LYS Chi-restraints excluded: chain D residue 522 ASP Chi-restraints excluded: chain D residue 593 THR Chi-restraints excluded: chain D residue 696 THR Chi-restraints excluded: chain D residue 1053 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 142 optimal weight: 4.9990 chunk 113 optimal weight: 9.9990 chunk 72 optimal weight: 2.9990 chunk 115 optimal weight: 10.0000 chunk 73 optimal weight: 3.9990 chunk 5 optimal weight: 0.7980 chunk 3 optimal weight: 0.9990 chunk 22 optimal weight: 4.9990 chunk 124 optimal weight: 9.9990 chunk 68 optimal weight: 5.9990 chunk 170 optimal weight: 9.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1024 ASN ** C 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 888 GLN C 996 GLN D 113 HIS D 168 HIS D1020 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.129073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.096479 restraints weight = 32654.780| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 2.91 r_work: 0.3154 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3163 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3163 r_free = 0.3163 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3163 r_free = 0.3163 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3163 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8709 moved from start: 0.1913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 14824 Z= 0.192 Angle : 0.667 8.284 20044 Z= 0.342 Chirality : 0.046 0.188 2221 Planarity : 0.005 0.108 2569 Dihedral : 6.878 70.633 2045 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 2.42 % Allowed : 13.37 % Favored : 84.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 1.18 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.42 (0.19), residues: 1855 helix: -0.26 (0.16), residues: 994 sheet: -1.42 (0.45), residues: 139 loop : -1.70 (0.23), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 976 TYR 0.030 0.002 TYR D 307 PHE 0.012 0.001 PHE B 863 TRP 0.027 0.001 TRP D 49 HIS 0.005 0.001 HIS D 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00459 / 0.19 (14824) covalent geometry : angle 0.66690 / 0.34 (20044) hydrogen bonds : bond 0.04021 / 2.63 ( 679) hydrogen bonds : angle 4.62505 / 3.21 ( 1995) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3710 Ramachandran restraints generated. 1855 Oldfield, 0 Emsley, 1855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3710 Ramachandran restraints generated. 1855 Oldfield, 0 Emsley, 1855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 179 time to evaluate : 0.487 Fit side-chains REVERT: A 919 ASP cc_start: 0.7851 (m-30) cc_final: 0.7619 (t0) REVERT: A 925 THR cc_start: 0.9143 (OUTLIER) cc_final: 0.8887 (m) REVERT: B 888 GLN cc_start: 0.8583 (OUTLIER) cc_final: 0.8322 (tm-30) REVERT: B 965 LYS cc_start: 0.9097 (tppt) cc_final: 0.8696 (mptm) REVERT: B 976 ARG cc_start: 0.7012 (ptm160) cc_final: 0.6306 (ptp-110) REVERT: B 1050 GLU cc_start: 0.8235 (OUTLIER) cc_final: 0.7925 (tt0) REVERT: C 965 LYS cc_start: 0.8378 (mtpt) cc_final: 0.7982 (tmmm) REVERT: C 969 LEU cc_start: 0.5986 (OUTLIER) cc_final: 0.5324 (mm) REVERT: D 210 ASP cc_start: 0.7879 (t70) cc_final: 0.7624 (t0) REVERT: D 408 GLU cc_start: 0.7387 (tp30) cc_final: 0.6968 (tp30) REVERT: D 690 ASP cc_start: 0.7952 (t70) cc_final: 0.7695 (t70) REVERT: D 976 ARG cc_start: 0.8336 (mpt180) cc_final: 0.8055 (ttp80) outliers start: 36 outliers final: 11 residues processed: 204 average time/residue: 0.4695 time to fit residues: 107.2180 Evaluate side-chains 177 residues out of total 1549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 162 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 925 THR Chi-restraints excluded: chain B residue 821 VAL Chi-restraints excluded: chain B residue 888 GLN Chi-restraints excluded: chain B residue 891 GLU Chi-restraints excluded: chain B residue 919 ASP Chi-restraints excluded: chain B residue 955 ILE Chi-restraints excluded: chain B residue 987 VAL Chi-restraints excluded: chain B residue 1050 GLU Chi-restraints excluded: chain C residue 848 ARG Chi-restraints excluded: chain C residue 969 LEU Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 216 ASP Chi-restraints excluded: chain D residue 522 ASP Chi-restraints excluded: chain D residue 593 THR Chi-restraints excluded: chain D residue 696 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 63 optimal weight: 0.8980 chunk 37 optimal weight: 0.7980 chunk 6 optimal weight: 6.9990 chunk 153 optimal weight: 0.9980 chunk 56 optimal weight: 0.0070 chunk 74 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 79 optimal weight: 0.9990 chunk 126 optimal weight: 3.9990 chunk 174 optimal weight: 3.9990 chunk 182 optimal weight: 2.9990 overall best weight: 0.6998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 888 GLN C1024 ASN D 113 HIS D 385 GLN D1020 ASN D1024 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.131703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.099164 restraints weight = 35968.271| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 3.31 r_work: 0.3203 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3202 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3202 r_free = 0.3202 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3202 r_free = 0.3202 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3202 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.2349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14824 Z= 0.115 Angle : 0.581 9.716 20044 Z= 0.300 Chirality : 0.044 0.184 2221 Planarity : 0.004 0.085 2569 Dihedral : 6.295 71.398 2045 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 2.36 % Allowed : 14.81 % Favored : 82.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 1.18 % 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: -0.94 (0.19), residues: 1855 helix: 0.20 (0.16), residues: 999 sheet: -1.32 (0.45), residues: 140 loop : -1.58 (0.23), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 976 TYR 0.032 0.002 TYR D 307 PHE 0.008 0.001 PHE D 105 TRP 0.029 0.001 TRP D 49 HIS 0.006 0.001 HIS D 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.11 (14824) covalent geometry : angle 0.58104 / 0.30 (20044) hydrogen bonds : bond 0.03297 / 2.19 ( 679) hydrogen bonds : angle 4.24576 / 2.94 ( 1995) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3710 Ramachandran restraints generated. 1855 Oldfield, 0 Emsley, 1855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3710 Ramachandran restraints generated. 1855 Oldfield, 0 Emsley, 1855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 183 time to evaluate : 0.463 Fit side-chains REVERT: A 919 ASP cc_start: 0.7880 (m-30) cc_final: 0.7562 (m-30) REVERT: A 925 THR cc_start: 0.9050 (OUTLIER) cc_final: 0.8747 (m) REVERT: A 1075 ASP cc_start: 0.8689 (t0) cc_final: 0.8439 (t0) REVERT: B 965 LYS cc_start: 0.8996 (tppt) cc_final: 0.8689 (mptt) REVERT: B 976 ARG cc_start: 0.6855 (ptm160) cc_final: 0.6107 (ptp-110) REVERT: B 1050 GLU cc_start: 0.8073 (OUTLIER) cc_final: 0.7841 (tt0) REVERT: B 1053 ASP cc_start: 0.8197 (m-30) cc_final: 0.7961 (m-30) REVERT: C 965 LYS cc_start: 0.8393 (mtpt) cc_final: 0.7937 (tmmm) REVERT: C 969 LEU cc_start: 0.5865 (OUTLIER) cc_final: 0.5109 (mm) REVERT: D 86 LYS cc_start: 0.6345 (mmmt) cc_final: 0.5559 (mttt) REVERT: D 194 ASP cc_start: 0.7687 (m-30) cc_final: 0.7181 (m-30) REVERT: D 210 ASP cc_start: 0.7854 (t70) cc_final: 0.7324 (t0) REVERT: D 269 LEU cc_start: 0.7726 (mm) cc_final: 0.7159 (tm) REVERT: D 690 ASP cc_start: 0.7923 (t70) cc_final: 0.7712 (t70) REVERT: D 976 ARG cc_start: 0.8233 (mpt180) cc_final: 0.7918 (ttp80) REVERT: D 1009 GLU cc_start: 0.8135 (OUTLIER) cc_final: 0.7836 (mp0) REVERT: D 1035 ASP cc_start: 0.8170 (t0) cc_final: 0.7931 (t0) outliers start: 35 outliers final: 7 residues processed: 205 average time/residue: 0.4607 time to fit residues: 105.4545 Evaluate side-chains 179 residues out of total 1549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 168 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 925 THR Chi-restraints excluded: chain B residue 891 GLU Chi-restraints excluded: chain B residue 925 THR Chi-restraints excluded: chain B residue 987 VAL Chi-restraints excluded: chain B residue 1050 GLU Chi-restraints excluded: chain C residue 848 ARG Chi-restraints excluded: chain C residue 969 LEU Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 216 ASP Chi-restraints excluded: chain D residue 1009 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 18 optimal weight: 0.4980 chunk 121 optimal weight: 0.0980 chunk 134 optimal weight: 10.0000 chunk 58 optimal weight: 1.9990 chunk 111 optimal weight: 8.9990 chunk 116 optimal weight: 5.9990 chunk 68 optimal weight: 4.9990 chunk 2 optimal weight: 6.9990 chunk 127 optimal weight: 10.0000 chunk 146 optimal weight: 9.9990 chunk 105 optimal weight: 0.0030 overall best weight: 1.5194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 888 GLN D 45 GLN D 113 HIS D 385 GLN D1020 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.131313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.099085 restraints weight = 24207.710| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 2.57 r_work: 0.3217 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3086 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3091 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3091 r_free = 0.3091 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3091 r_free = 0.3091 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.3091 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 moved from start: 0.2454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14824 Z= 0.136 Angle : 0.583 8.849 20044 Z= 0.300 Chirality : 0.044 0.164 2221 Planarity : 0.004 0.071 2569 Dihedral : 6.005 70.718 2043 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 2.56 % Allowed : 15.73 % Favored : 81.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 1.18 % 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: -0.68 (0.20), residues: 1855 helix: 0.44 (0.17), residues: 999 sheet: -1.18 (0.45), residues: 142 loop : -1.53 (0.23), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 507 TYR 0.030 0.002 TYR D 307 PHE 0.010 0.001 PHE B 889 TRP 0.027 0.001 TRP D 49 HIS 0.007 0.001 HIS D 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.14 (14824) covalent geometry : angle 0.58325 / 0.30 (20044) hydrogen bonds : bond 0.03370 / 2.23 ( 679) hydrogen bonds : angle 4.20041 / 2.92 ( 1995) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3710 Ramachandran restraints generated. 1855 Oldfield, 0 Emsley, 1855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3710 Ramachandran restraints generated. 1855 Oldfield, 0 Emsley, 1855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 170 time to evaluate : 0.563 Fit side-chains REVERT: A 904 VAL cc_start: 0.8249 (OUTLIER) cc_final: 0.8026 (m) REVERT: A 919 ASP cc_start: 0.8078 (m-30) cc_final: 0.7819 (t0) REVERT: A 925 THR cc_start: 0.9117 (OUTLIER) cc_final: 0.8830 (m) REVERT: A 1075 ASP cc_start: 0.8831 (t0) cc_final: 0.8586 (t0) REVERT: B 965 LYS cc_start: 0.9081 (tppt) cc_final: 0.8784 (mptt) REVERT: B 976 ARG cc_start: 0.6943 (ptm160) cc_final: 0.6170 (ptp-110) REVERT: B 1035 ASP cc_start: 0.8264 (OUTLIER) cc_final: 0.7725 (m-30) REVERT: B 1050 GLU cc_start: 0.8167 (OUTLIER) cc_final: 0.7943 (tt0) REVERT: B 1053 ASP cc_start: 0.8319 (m-30) cc_final: 0.8092 (m-30) REVERT: C 904 VAL cc_start: 0.8545 (OUTLIER) cc_final: 0.8298 (m) REVERT: C 969 LEU cc_start: 0.5736 (OUTLIER) cc_final: 0.4826 (mm) REVERT: D 194 ASP cc_start: 0.7740 (m-30) cc_final: 0.7265 (m-30) REVERT: D 210 ASP cc_start: 0.7911 (t70) cc_final: 0.7383 (t0) REVERT: D 408 GLU cc_start: 0.7634 (tp30) cc_final: 0.7256 (tp30) REVERT: D 690 ASP cc_start: 0.7997 (t70) cc_final: 0.7613 (t70) REVERT: D 919 ASP cc_start: 0.8285 (m-30) cc_final: 0.8017 (p0) REVERT: D 976 ARG cc_start: 0.8217 (mpt180) cc_final: 0.7856 (ttp80) REVERT: D 1009 GLU cc_start: 0.8300 (OUTLIER) cc_final: 0.8040 (mp0) REVERT: D 1035 ASP cc_start: 0.8337 (t0) cc_final: 0.8110 (t0) outliers start: 38 outliers final: 14 residues processed: 196 average time/residue: 0.4846 time to fit residues: 105.9271 Evaluate side-chains 185 residues out of total 1549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 164 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 904 VAL Chi-restraints excluded: chain A residue 925 THR Chi-restraints excluded: chain A residue 945 MET Chi-restraints excluded: chain B residue 891 GLU Chi-restraints excluded: chain B residue 919 ASP Chi-restraints excluded: chain B residue 955 ILE Chi-restraints excluded: chain B residue 987 VAL Chi-restraints excluded: chain B residue 1035 ASP Chi-restraints excluded: chain B residue 1050 GLU Chi-restraints excluded: chain C residue 848 ARG Chi-restraints excluded: chain C residue 904 VAL Chi-restraints excluded: chain C residue 940 ASP Chi-restraints excluded: chain C residue 969 LEU Chi-restraints excluded: chain D residue 113 HIS Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 216 ASP Chi-restraints excluded: chain D residue 522 ASP Chi-restraints excluded: chain D residue 741 VAL Chi-restraints excluded: chain D residue 867 MET Chi-restraints excluded: chain D residue 1009 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 123 optimal weight: 6.9990 chunk 96 optimal weight: 6.9990 chunk 98 optimal weight: 6.9990 chunk 146 optimal weight: 9.9990 chunk 58 optimal weight: 3.9990 chunk 129 optimal weight: 0.9990 chunk 132 optimal weight: 9.9990 chunk 91 optimal weight: 9.9990 chunk 24 optimal weight: 5.9990 chunk 154 optimal weight: 8.9990 chunk 128 optimal weight: 0.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 879 GLN C 888 GLN C 996 GLN D 45 GLN D 385 GLN D1020 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.126229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.092620 restraints weight = 34918.256| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 3.15 r_work: 0.3124 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3153 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3153 r_free = 0.3153 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3153 r_free = 0.3153 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3153 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8702 moved from start: 0.2411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 14824 Z= 0.237 Angle : 0.666 9.718 20044 Z= 0.338 Chirality : 0.047 0.154 2221 Planarity : 0.005 0.063 2569 Dihedral : 6.169 69.032 2043 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 2.88 % Allowed : 16.38 % Favored : 80.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 1.18 % 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: -0.73 (0.20), residues: 1855 helix: 0.40 (0.16), residues: 999 sheet: -1.17 (0.45), residues: 144 loop : -1.54 (0.23), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1065 TYR 0.032 0.002 TYR D 692 PHE 0.013 0.002 PHE B 863 TRP 0.026 0.001 TRP D 49 HIS 0.025 0.001 HIS D 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00575 / 0.24 (14824) covalent geometry : angle 0.66622 / 0.34 (20044) hydrogen bonds : bond 0.03877 / 2.55 ( 679) hydrogen bonds : angle 4.37038 / 3.03 ( 1995) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3710 Ramachandran restraints generated. 1855 Oldfield, 0 Emsley, 1855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3710 Ramachandran restraints generated. 1855 Oldfield, 0 Emsley, 1855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 168 time to evaluate : 0.396 Fit side-chains REVERT: A 866 GLU cc_start: 0.7935 (mm-30) cc_final: 0.7697 (mt-10) REVERT: A 904 VAL cc_start: 0.8242 (OUTLIER) cc_final: 0.7983 (m) REVERT: A 919 ASP cc_start: 0.7909 (m-30) cc_final: 0.7664 (t0) REVERT: A 925 THR cc_start: 0.9164 (OUTLIER) cc_final: 0.8875 (m) REVERT: B 873 LEU cc_start: 0.8597 (OUTLIER) cc_final: 0.8140 (mp) REVERT: B 976 ARG cc_start: 0.7126 (ptm160) cc_final: 0.6351 (ptp-110) REVERT: B 1035 ASP cc_start: 0.8098 (OUTLIER) cc_final: 0.7685 (m-30) REVERT: B 1044 THR cc_start: 0.8563 (p) cc_final: 0.8317 (p) REVERT: B 1050 GLU cc_start: 0.8166 (OUTLIER) cc_final: 0.7915 (tt0) REVERT: C 965 LYS cc_start: 0.8458 (mtpt) cc_final: 0.8032 (tmmm) REVERT: C 969 LEU cc_start: 0.5858 (OUTLIER) cc_final: 0.4949 (mm) REVERT: D 86 LYS cc_start: 0.6371 (mmmt) cc_final: 0.5314 (mttt) REVERT: D 194 ASP cc_start: 0.7805 (m-30) cc_final: 0.7323 (m-30) REVERT: D 210 ASP cc_start: 0.7919 (t70) cc_final: 0.7636 (t0) REVERT: D 408 GLU cc_start: 0.7510 (tp30) cc_final: 0.7176 (tp30) REVERT: D 560 MET cc_start: 0.8386 (tpp) cc_final: 0.7294 (mpp) REVERT: D 690 ASP cc_start: 0.8029 (t70) cc_final: 0.7811 (t70) REVERT: D 976 ARG cc_start: 0.8081 (mpt180) cc_final: 0.7852 (ttp80) outliers start: 43 outliers final: 20 residues processed: 196 average time/residue: 0.4946 time to fit residues: 107.6836 Evaluate side-chains 188 residues out of total 1549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 162 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 904 VAL Chi-restraints excluded: chain A residue 925 THR Chi-restraints excluded: chain A residue 945 MET Chi-restraints excluded: chain A residue 1067 MET Chi-restraints excluded: chain B residue 821 VAL Chi-restraints excluded: chain B residue 873 LEU Chi-restraints excluded: chain B residue 891 GLU Chi-restraints excluded: chain B residue 919 ASP Chi-restraints excluded: chain B residue 925 THR Chi-restraints excluded: chain B residue 977 VAL Chi-restraints excluded: chain B residue 987 VAL Chi-restraints excluded: chain B residue 1035 ASP Chi-restraints excluded: chain B residue 1050 GLU Chi-restraints excluded: chain C residue 834 ILE Chi-restraints excluded: chain C residue 848 ARG Chi-restraints excluded: chain C residue 940 ASP Chi-restraints excluded: chain C residue 969 LEU Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 215 LEU Chi-restraints excluded: chain D residue 216 ASP Chi-restraints excluded: chain D residue 522 ASP Chi-restraints excluded: chain D residue 696 THR Chi-restraints excluded: chain D residue 741 VAL Chi-restraints excluded: chain D residue 831 LEU Chi-restraints excluded: chain D residue 867 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 15 optimal weight: 1.9990 chunk 182 optimal weight: 4.9990 chunk 172 optimal weight: 0.8980 chunk 141 optimal weight: 7.9990 chunk 98 optimal weight: 5.9990 chunk 73 optimal weight: 3.9990 chunk 7 optimal weight: 6.9990 chunk 174 optimal weight: 1.9990 chunk 70 optimal weight: 0.7980 chunk 134 optimal weight: 9.9990 chunk 113 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 888 GLN C 996 GLN D 45 GLN D 385 GLN D 814 GLN D1020 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.129231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.095713 restraints weight = 32627.441| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 3.07 r_work: 0.3174 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3197 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3197 r_free = 0.3197 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3197 r_free = 0.3197 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.3197 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.2610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14824 Z= 0.135 Angle : 0.599 10.558 20044 Z= 0.307 Chirality : 0.044 0.156 2221 Planarity : 0.004 0.058 2569 Dihedral : 5.973 68.525 2043 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 2.56 % Allowed : 17.17 % Favored : 80.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 1.18 % 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 (0.20), residues: 1855 helix: 0.59 (0.17), residues: 998 sheet: -1.12 (0.45), residues: 142 loop : -1.51 (0.23), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 848 TYR 0.030 0.002 TYR D 307 PHE 0.010 0.001 PHE A 863 TRP 0.025 0.001 TRP D 49 HIS 0.003 0.001 HIS C 900 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.13 (14824) covalent geometry : angle 0.59929 / 0.31 (20044) hydrogen bonds : bond 0.03410 / 2.26 ( 679) hydrogen bonds : angle 4.20695 / 2.92 ( 1995) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3710 Ramachandran restraints generated. 1855 Oldfield, 0 Emsley, 1855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3710 Ramachandran restraints generated. 1855 Oldfield, 0 Emsley, 1855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 169 time to evaluate : 0.379 Fit side-chains REVERT: A 866 GLU cc_start: 0.7769 (mm-30) cc_final: 0.7525 (mt-10) REVERT: A 925 THR cc_start: 0.9097 (OUTLIER) cc_final: 0.8823 (m) REVERT: B 965 LYS cc_start: 0.9112 (ttmm) cc_final: 0.8649 (mtmp) REVERT: B 976 ARG cc_start: 0.7023 (ptm160) cc_final: 0.6255 (ptp-110) REVERT: B 1035 ASP cc_start: 0.8102 (OUTLIER) cc_final: 0.7576 (m-30) REVERT: B 1044 THR cc_start: 0.8501 (p) cc_final: 0.8257 (p) REVERT: C 965 LYS cc_start: 0.8425 (mtpt) cc_final: 0.7998 (tmmm) REVERT: C 969 LEU cc_start: 0.5924 (OUTLIER) cc_final: 0.5020 (mm) REVERT: D 86 LYS cc_start: 0.6358 (mmmt) cc_final: 0.5447 (mttt) REVERT: D 194 ASP cc_start: 0.7733 (m-30) cc_final: 0.7257 (m-30) REVERT: D 210 ASP cc_start: 0.7891 (t70) cc_final: 0.7610 (t0) REVERT: D 560 MET cc_start: 0.8314 (tpp) cc_final: 0.7264 (mpp) REVERT: D 690 ASP cc_start: 0.7935 (t70) cc_final: 0.7559 (t70) REVERT: D 1035 ASP cc_start: 0.8210 (t0) cc_final: 0.7962 (t0) outliers start: 38 outliers final: 17 residues processed: 194 average time/residue: 0.5130 time to fit residues: 110.1796 Evaluate side-chains 182 residues out of total 1549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 162 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 925 THR Chi-restraints excluded: chain A residue 945 MET Chi-restraints excluded: chain A residue 1067 MET Chi-restraints excluded: chain B residue 919 ASP Chi-restraints excluded: chain B residue 925 THR Chi-restraints excluded: chain B residue 987 VAL Chi-restraints excluded: chain B residue 1035 ASP Chi-restraints excluded: chain C residue 834 ILE Chi-restraints excluded: chain C residue 848 ARG Chi-restraints excluded: chain C residue 940 ASP Chi-restraints excluded: chain C residue 969 LEU Chi-restraints excluded: chain D residue 45 GLN Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 215 LEU Chi-restraints excluded: chain D residue 216 ASP Chi-restraints excluded: chain D residue 522 ASP Chi-restraints excluded: chain D residue 593 THR Chi-restraints excluded: chain D residue 696 THR Chi-restraints excluded: chain D residue 741 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 39 optimal weight: 3.9990 chunk 175 optimal weight: 0.8980 chunk 143 optimal weight: 8.9990 chunk 87 optimal weight: 3.9990 chunk 150 optimal weight: 0.0070 chunk 94 optimal weight: 10.0000 chunk 75 optimal weight: 2.9990 chunk 147 optimal weight: 8.9990 chunk 79 optimal weight: 0.6980 chunk 99 optimal weight: 4.9990 chunk 58 optimal weight: 3.9990 overall best weight: 1.7202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 888 GLN C 996 GLN ** C1072 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 45 GLN D 385 GLN ** D 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1020 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.128980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.095739 restraints weight = 37977.856| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 3.42 r_work: 0.3157 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3182 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3182 r_free = 0.3182 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3182 r_free = 0.3182 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3182 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.2700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14824 Z= 0.145 Angle : 0.607 10.407 20044 Z= 0.310 Chirality : 0.044 0.149 2221 Planarity : 0.004 0.058 2569 Dihedral : 5.911 68.051 2043 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 2.29 % Allowed : 17.96 % Favored : 79.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 1.18 % 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: -0.48 (0.20), residues: 1855 helix: 0.64 (0.17), residues: 998 sheet: -1.14 (0.45), residues: 142 loop : -1.48 (0.23), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 42 TYR 0.028 0.002 TYR D 307 PHE 0.010 0.001 PHE B 889 TRP 0.023 0.001 TRP D 49 HIS 0.003 0.001 HIS C 900 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.14 (14824) covalent geometry : angle 0.60732 / 0.31 (20044) hydrogen bonds : bond 0.03415 / 2.26 ( 679) hydrogen bonds : angle 4.18603 / 2.90 ( 1995) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3710 Ramachandran restraints generated. 1855 Oldfield, 0 Emsley, 1855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3710 Ramachandran restraints generated. 1855 Oldfield, 0 Emsley, 1855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 167 time to evaluate : 0.585 Fit side-chains revert: symmetry clash REVERT: A 925 THR cc_start: 0.9102 (OUTLIER) cc_final: 0.8821 (m) REVERT: B 888 GLN cc_start: 0.8517 (OUTLIER) cc_final: 0.8270 (tm-30) REVERT: B 976 ARG cc_start: 0.7039 (ptm160) cc_final: 0.6263 (ptp-110) REVERT: B 1035 ASP cc_start: 0.8118 (OUTLIER) cc_final: 0.7585 (m-30) REVERT: B 1044 THR cc_start: 0.8480 (p) cc_final: 0.8229 (p) REVERT: C 965 LYS cc_start: 0.8459 (mtpt) cc_final: 0.8131 (tmtt) REVERT: C 969 LEU cc_start: 0.5871 (OUTLIER) cc_final: 0.4963 (mm) REVERT: C 1020 ASN cc_start: 0.8700 (p0) cc_final: 0.8001 (t0) REVERT: D 86 LYS cc_start: 0.6447 (mmmt) cc_final: 0.5983 (mttt) REVERT: D 89 LEU cc_start: 0.5252 (OUTLIER) cc_final: 0.4348 (pp) REVERT: D 194 ASP cc_start: 0.7720 (m-30) cc_final: 0.7255 (m-30) REVERT: D 210 ASP cc_start: 0.7889 (t70) cc_final: 0.7599 (t0) REVERT: D 662 ARG cc_start: 0.8007 (ttt180) cc_final: 0.7796 (tpp80) REVERT: D 690 ASP cc_start: 0.7950 (t70) cc_final: 0.7533 (t70) REVERT: D 780 LYS cc_start: 0.8352 (tttt) cc_final: 0.7775 (tptt) REVERT: D 1009 GLU cc_start: 0.7985 (mp0) cc_final: 0.7764 (mp0) REVERT: D 1035 ASP cc_start: 0.8244 (t0) cc_final: 0.8003 (t0) outliers start: 34 outliers final: 20 residues processed: 189 average time/residue: 0.5178 time to fit residues: 108.4478 Evaluate side-chains 191 residues out of total 1549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 166 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 925 THR Chi-restraints excluded: chain A residue 945 MET Chi-restraints excluded: chain A residue 955 ILE Chi-restraints excluded: chain A residue 1067 MET Chi-restraints excluded: chain B residue 888 GLN Chi-restraints excluded: chain B residue 891 GLU Chi-restraints excluded: chain B residue 919 ASP Chi-restraints excluded: chain B residue 925 THR Chi-restraints excluded: chain B residue 977 VAL Chi-restraints excluded: chain B residue 987 VAL Chi-restraints excluded: chain B residue 1035 ASP Chi-restraints excluded: chain C residue 834 ILE Chi-restraints excluded: chain C residue 848 ARG Chi-restraints excluded: chain C residue 940 ASP Chi-restraints excluded: chain C residue 969 LEU Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 215 LEU Chi-restraints excluded: chain D residue 216 ASP Chi-restraints excluded: chain D residue 522 ASP Chi-restraints excluded: chain D residue 593 THR Chi-restraints excluded: chain D residue 696 THR Chi-restraints excluded: chain D residue 741 VAL Chi-restraints excluded: chain D residue 831 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 64 optimal weight: 5.9990 chunk 177 optimal weight: 3.9990 chunk 43 optimal weight: 0.6980 chunk 124 optimal weight: 6.9990 chunk 50 optimal weight: 0.1980 chunk 61 optimal weight: 0.9980 chunk 120 optimal weight: 0.0980 chunk 145 optimal weight: 0.6980 chunk 53 optimal weight: 0.7980 chunk 56 optimal weight: 3.9990 chunk 136 optimal weight: 2.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1072 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 888 GLN C 996 GLN D 45 GLN D 385 GLN D 814 GLN ** D 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1020 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.132526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.099584 restraints weight = 32653.654| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 3.30 r_work: 0.3218 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3240 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3240 r_free = 0.3240 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3240 r_free = 0.3240 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3240 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.2971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14824 Z= 0.110 Angle : 0.575 10.808 20044 Z= 0.295 Chirality : 0.043 0.144 2221 Planarity : 0.004 0.056 2569 Dihedral : 5.683 67.872 2043 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 2.10 % Allowed : 18.35 % Favored : 79.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % 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: -0.30 (0.20), residues: 1855 helix: 0.82 (0.17), residues: 998 sheet: -1.02 (0.46), residues: 142 loop : -1.46 (0.23), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 244 TYR 0.028 0.001 TYR D 307 PHE 0.009 0.001 PHE B 889 TRP 0.023 0.001 TRP D 49 HIS 0.003 0.001 HIS D 997 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 (14824) covalent geometry : angle 0.57542 / 0.29 (20044) hydrogen bonds : bond 0.03078 / 2.04 ( 679) hydrogen bonds : angle 4.05145 / 2.81 ( 1995) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3710 Ramachandran restraints generated. 1855 Oldfield, 0 Emsley, 1855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3710 Ramachandran restraints generated. 1855 Oldfield, 0 Emsley, 1855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 181 time to evaluate : 0.563 Fit side-chains REVERT: A 925 THR cc_start: 0.9039 (OUTLIER) cc_final: 0.8798 (m) REVERT: A 1075 ASP cc_start: 0.8610 (t0) cc_final: 0.8355 (t0) REVERT: B 961 ASN cc_start: 0.8716 (m-40) cc_final: 0.8490 (m-40) REVERT: B 965 LYS cc_start: 0.9054 (ttmm) cc_final: 0.8632 (mtmp) REVERT: B 976 ARG cc_start: 0.6988 (ptm160) cc_final: 0.6194 (ptp-110) REVERT: C 965 LYS cc_start: 0.8451 (mtpt) cc_final: 0.8125 (tmtt) REVERT: C 969 LEU cc_start: 0.5839 (OUTLIER) cc_final: 0.4936 (mm) REVERT: C 1020 ASN cc_start: 0.8509 (p0) cc_final: 0.8225 (t0) REVERT: D 86 LYS cc_start: 0.6433 (mmmt) cc_final: 0.6056 (mttt) REVERT: D 89 LEU cc_start: 0.5203 (OUTLIER) cc_final: 0.4292 (pp) REVERT: D 194 ASP cc_start: 0.7584 (m-30) cc_final: 0.7143 (m-30) REVERT: D 210 ASP cc_start: 0.7874 (t70) cc_final: 0.7590 (t0) REVERT: D 355 LYS cc_start: 0.5726 (mmtm) cc_final: 0.4974 (tppt) REVERT: D 408 GLU cc_start: 0.7464 (tp30) cc_final: 0.7061 (tp30) REVERT: D 662 ARG cc_start: 0.7910 (ttt180) cc_final: 0.7687 (ttp80) REVERT: D 690 ASP cc_start: 0.7896 (t70) cc_final: 0.7095 (t0) REVERT: D 780 LYS cc_start: 0.8306 (tttt) cc_final: 0.7773 (tptt) REVERT: D 1009 GLU cc_start: 0.7984 (OUTLIER) cc_final: 0.7756 (mp0) REVERT: D 1035 ASP cc_start: 0.8110 (t0) cc_final: 0.7887 (t0) outliers start: 31 outliers final: 15 residues processed: 203 average time/residue: 0.5416 time to fit residues: 122.0968 Evaluate side-chains 188 residues out of total 1549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 169 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 925 THR Chi-restraints excluded: chain A residue 955 ILE Chi-restraints excluded: chain A residue 1067 MET Chi-restraints excluded: chain B residue 925 THR Chi-restraints excluded: chain B residue 977 VAL Chi-restraints excluded: chain B residue 987 VAL Chi-restraints excluded: chain B residue 1067 MET Chi-restraints excluded: chain C residue 834 ILE Chi-restraints excluded: chain C residue 848 ARG Chi-restraints excluded: chain C residue 969 LEU Chi-restraints excluded: chain D residue 45 GLN Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 216 ASP Chi-restraints excluded: chain D residue 614 ASP Chi-restraints excluded: chain D residue 696 THR Chi-restraints excluded: chain D residue 741 VAL Chi-restraints excluded: chain D residue 831 LEU Chi-restraints excluded: chain D residue 1009 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 44 optimal weight: 2.9990 chunk 69 optimal weight: 9.9990 chunk 59 optimal weight: 2.9990 chunk 49 optimal weight: 0.4980 chunk 110 optimal weight: 7.9990 chunk 103 optimal weight: 8.9990 chunk 139 optimal weight: 0.0270 chunk 101 optimal weight: 1.9990 chunk 80 optimal weight: 5.9990 chunk 53 optimal weight: 0.9990 chunk 147 optimal weight: 9.9990 overall best weight: 1.3044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 879 GLN C 888 GLN ** C1072 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 45 GLN D 850 GLN ** D 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1020 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.131537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.098778 restraints weight = 26734.596| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 2.76 r_work: 0.3235 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3254 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3254 r_free = 0.3254 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3254 r_free = 0.3254 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3254 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.2979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14824 Z= 0.130 Angle : 0.611 11.361 20044 Z= 0.309 Chirality : 0.044 0.147 2221 Planarity : 0.004 0.057 2569 Dihedral : 5.678 67.233 2043 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 1.64 % Allowed : 19.46 % Favored : 78.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % 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: -0.25 (0.20), residues: 1855 helix: 0.86 (0.17), residues: 997 sheet: -1.06 (0.45), residues: 147 loop : -1.41 (0.23), residues: 711 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 976 TYR 0.027 0.002 TYR D 307 PHE 0.010 0.001 PHE B 889 TRP 0.023 0.001 TRP D 49 HIS 0.003 0.001 HIS D 997 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.13 (14824) covalent geometry : angle 0.61138 / 0.31 (20044) hydrogen bonds : bond 0.03248 / 2.16 ( 679) hydrogen bonds : angle 4.10770 / 2.85 ( 1995) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3710 Ramachandran restraints generated. 1855 Oldfield, 0 Emsley, 1855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3710 Ramachandran restraints generated. 1855 Oldfield, 0 Emsley, 1855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 170 time to evaluate : 0.599 Fit side-chains revert: symmetry clash REVERT: A 925 THR cc_start: 0.9038 (OUTLIER) cc_final: 0.8766 (m) REVERT: A 1020 ASN cc_start: 0.8485 (p0) cc_final: 0.7705 (t0) REVERT: A 1075 ASP cc_start: 0.8582 (t0) cc_final: 0.8316 (t0) REVERT: B 965 LYS cc_start: 0.9044 (ttmm) cc_final: 0.8627 (mtmp) REVERT: B 976 ARG cc_start: 0.6970 (ptm160) cc_final: 0.6197 (ptp-110) REVERT: C 965 LYS cc_start: 0.8452 (mtpt) cc_final: 0.8145 (tmtt) REVERT: C 969 LEU cc_start: 0.5888 (OUTLIER) cc_final: 0.4990 (mm) REVERT: D 86 LYS cc_start: 0.6357 (mmmt) cc_final: 0.5986 (mttt) REVERT: D 89 LEU cc_start: 0.5159 (OUTLIER) cc_final: 0.4269 (pp) REVERT: D 210 ASP cc_start: 0.7880 (t70) cc_final: 0.7371 (t0) REVERT: D 355 LYS cc_start: 0.5769 (mmtm) cc_final: 0.4932 (tppt) REVERT: D 408 GLU cc_start: 0.7443 (tp30) cc_final: 0.7049 (tp30) REVERT: D 560 MET cc_start: 0.8172 (mpp) cc_final: 0.6838 (mpp) REVERT: D 662 ARG cc_start: 0.7920 (ttt180) cc_final: 0.7716 (ttp80) REVERT: D 690 ASP cc_start: 0.7904 (t70) cc_final: 0.7106 (t0) REVERT: D 780 LYS cc_start: 0.8319 (tttt) cc_final: 0.7809 (tptt) REVERT: D 1009 GLU cc_start: 0.7977 (OUTLIER) cc_final: 0.7738 (mp0) REVERT: D 1035 ASP cc_start: 0.8092 (t0) cc_final: 0.7878 (t0) outliers start: 24 outliers final: 14 residues processed: 188 average time/residue: 0.5519 time to fit residues: 115.0218 Evaluate side-chains 176 residues out of total 1549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 158 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 925 THR Chi-restraints excluded: chain A residue 955 ILE Chi-restraints excluded: chain A residue 1067 MET Chi-restraints excluded: chain B residue 891 GLU Chi-restraints excluded: chain B residue 925 THR Chi-restraints excluded: chain B residue 977 VAL Chi-restraints excluded: chain B residue 987 VAL Chi-restraints excluded: chain C residue 834 ILE Chi-restraints excluded: chain C residue 848 ARG Chi-restraints excluded: chain C residue 940 ASP Chi-restraints excluded: chain C residue 969 LEU Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 216 ASP Chi-restraints excluded: chain D residue 696 THR Chi-restraints excluded: chain D residue 741 VAL Chi-restraints excluded: chain D residue 831 LEU Chi-restraints excluded: chain D residue 1009 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 132 optimal weight: 1.9990 chunk 153 optimal weight: 1.9990 chunk 57 optimal weight: 0.6980 chunk 127 optimal weight: 0.5980 chunk 98 optimal weight: 0.9990 chunk 37 optimal weight: 0.9980 chunk 141 optimal weight: 8.9990 chunk 147 optimal weight: 10.0000 chunk 104 optimal weight: 3.9990 chunk 142 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 888 GLN ** C1072 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 45 GLN D 814 GLN ** D 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1020 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.131936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.099103 restraints weight = 29506.080| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 3.15 r_work: 0.3220 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3241 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3241 r_free = 0.3241 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3241 r_free = 0.3241 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3241 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.3063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14824 Z= 0.123 Angle : 0.606 10.762 20044 Z= 0.307 Chirality : 0.043 0.149 2221 Planarity : 0.004 0.056 2569 Dihedral : 5.556 66.166 2043 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 1.83 % Allowed : 19.33 % Favored : 78.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % 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: -0.21 (0.20), residues: 1855 helix: 0.90 (0.17), residues: 996 sheet: -1.04 (0.45), residues: 147 loop : -1.40 (0.23), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 976 TYR 0.025 0.001 TYR D 307 PHE 0.010 0.001 PHE B 889 TRP 0.021 0.001 TRP D 49 HIS 0.003 0.001 HIS D 997 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.12 (14824) covalent geometry : angle 0.60610 / 0.31 (20044) hydrogen bonds : bond 0.03130 / 2.08 ( 679) hydrogen bonds : angle 4.05994 / 2.82 ( 1995) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4151.75 seconds wall clock time: 71 minutes 45.60 seconds (4305.60 seconds total)