Starting phenix.real_space_refine on Wed Mar 4 15:12:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7lj9_23389/03_2026/7lj9_23389.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lj9_23389/03_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_23389/03_2026/7lj9_23389.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lj9_23389/03_2026/7lj9_23389.map" model { file = "/net/cci-nas-00/data/ceres_data/7lj9_23389/03_2026/7lj9_23389.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lj9_23389/03_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/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: 4.33, per 1000 atoms: 0.30 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: 1.10 Conformation dependent library (CDL) restraints added in 931.4 milliseconds 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: 0.46 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: 2.30 Time building geometry restraints manager: 1.48 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: 7956 17.93 - 35.87: 745 35.87 - 53.80: 139 53.80 - 71.74: 27 71.74 - 89.67: 12 Dihedral angle restraints: 8879 sinusoidal: 3577 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 8876 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: 0.700 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: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.910 Find NCS groups from input model: 0.150 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:7.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 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 : 14.818 89.670 5507 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 covalent geometry : bond 0.01298 (14824) covalent geometry : angle 1.33055 (20044) hydrogen bonds : bond 0.16590 ( 679) hydrogen bonds : angle 7.55824 ( 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 : 0.400 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: 0.5805 time to fit residues: 138.4380 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 : 0.566 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3745 r_free = 0.3745 target = 0.130127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.097974 restraints weight = 30784.774| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 2.84 r_work: 0.3182 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3185 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3185 r_free = 0.3185 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 = 0.3185 r_free = 0.3185 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3185 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.1602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 14824 Z= 0.170 Angle : 0.701 8.999 20044 Z= 0.362 Chirality : 0.046 0.251 2221 Planarity : 0.006 0.123 2569 Dihedral : 8.372 88.363 2086 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 1.83 % Allowed : 9.44 % Favored : 88.73 % 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: -1.92 (0.18), residues: 1855 helix: -0.75 (0.15), residues: 990 sheet: -1.39 (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 B 829 TYR 0.046 0.002 TYR D 304 PHE 0.013 0.001 PHE D 105 TRP 0.026 0.001 TRP D 49 HIS 0.004 0.001 HIS C 900 Details of bonding type rmsd covalent geometry : bond 0.00401 (14824) covalent geometry : angle 0.70098 (20044) hydrogen bonds : bond 0.04138 ( 679) hydrogen bonds : angle 4.86829 ( 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 219 residues out of total 1549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 192 time to evaluate : 0.576 Fit side-chains REVERT: A 919 ASP cc_start: 0.7860 (m-30) cc_final: 0.7537 (m-30) REVERT: B 976 ARG cc_start: 0.6952 (ptm160) cc_final: 0.6233 (ptp-110) REVERT: B 1050 GLU cc_start: 0.8257 (OUTLIER) cc_final: 0.7779 (tp30) REVERT: C 965 LYS cc_start: 0.8336 (mtpt) cc_final: 0.7986 (tmmm) REVERT: C 969 LEU cc_start: 0.6944 (OUTLIER) cc_final: 0.6541 (mm) REVERT: D 194 ASP cc_start: 0.7791 (m-30) cc_final: 0.7307 (m-30) REVERT: D 210 ASP cc_start: 0.7850 (t70) cc_final: 0.7616 (t0) REVERT: D 269 LEU cc_start: 0.7928 (mm) cc_final: 0.7356 (tm) REVERT: D 408 GLU cc_start: 0.7406 (tp30) cc_final: 0.7041 (tp30) REVERT: D 690 ASP cc_start: 0.7889 (t70) cc_final: 0.7639 (t70) REVERT: D 976 ARG cc_start: 0.8351 (mpt180) cc_final: 0.8035 (ttp80) REVERT: D 1035 ASP cc_start: 0.8242 (t0) cc_final: 0.8005 (t0) outliers start: 27 outliers final: 12 residues processed: 210 average time/residue: 0.5263 time to fit residues: 122.8238 Evaluate side-chains 181 residues out of total 1549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 167 time to evaluate : 0.542 ------------------------------------------------------------------------------- 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: 6.9990 chunk 113 optimal weight: 9.9990 chunk 72 optimal weight: 1.9990 chunk 115 optimal weight: 10.0000 chunk 73 optimal weight: 0.0570 chunk 5 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 22 optimal weight: 0.0670 chunk 124 optimal weight: 10.0000 chunk 68 optimal weight: 5.9990 chunk 170 optimal weight: 9.9990 overall best weight: 1.4242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 C1024 ASN D 113 HIS D 168 HIS D 385 GLN D1020 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.131193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.098394 restraints weight = 32495.033| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 2.94 r_work: 0.3186 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3192 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3192 r_free = 0.3192 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3192 r_free = 0.3192 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3192 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.1987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14824 Z= 0.141 Angle : 0.624 8.125 20044 Z= 0.323 Chirality : 0.045 0.183 2221 Planarity : 0.005 0.105 2569 Dihedral : 7.598 86.216 2086 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 2.42 % Allowed : 12.84 % Favored : 84.73 % 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: -1.38 (0.19), residues: 1855 helix: -0.22 (0.16), residues: 999 sheet: -1.36 (0.45), residues: 139 loop : -1.72 (0.23), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 976 TYR 0.029 0.002 TYR D 307 PHE 0.008 0.001 PHE B 889 TRP 0.027 0.001 TRP D 49 HIS 0.006 0.001 HIS D 113 Details of bonding type rmsd covalent geometry : bond 0.00332 (14824) covalent geometry : angle 0.62419 (20044) hydrogen bonds : bond 0.03728 ( 679) hydrogen bonds : angle 4.51324 ( 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 218 residues out of total 1549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 182 time to evaluate : 0.553 Fit side-chains REVERT: A 919 ASP cc_start: 0.7856 (m-30) cc_final: 0.7582 (m-30) REVERT: A 925 THR cc_start: 0.9099 (OUTLIER) cc_final: 0.8858 (m) REVERT: B 888 GLN cc_start: 0.8538 (OUTLIER) cc_final: 0.8290 (tm-30) REVERT: B 965 LYS cc_start: 0.9075 (tppt) cc_final: 0.8690 (mptm) REVERT: B 976 ARG cc_start: 0.6972 (ptm160) cc_final: 0.6274 (ptp-110) REVERT: B 1050 GLU cc_start: 0.8194 (OUTLIER) cc_final: 0.7905 (tt0) REVERT: C 965 LYS cc_start: 0.8350 (mtpt) cc_final: 0.7934 (tmmm) REVERT: C 969 LEU cc_start: 0.6205 (OUTLIER) cc_final: 0.5656 (mm) REVERT: D 210 ASP cc_start: 0.7873 (t70) cc_final: 0.7629 (t0) REVERT: D 269 LEU cc_start: 0.7989 (mm) cc_final: 0.7366 (tm) REVERT: D 408 GLU cc_start: 0.7364 (tp30) cc_final: 0.6963 (tp30) REVERT: D 690 ASP cc_start: 0.7908 (t70) cc_final: 0.7688 (t70) REVERT: D 976 ARG cc_start: 0.8318 (mpt180) cc_final: 0.8019 (ttp80) REVERT: D 1009 GLU cc_start: 0.8143 (OUTLIER) cc_final: 0.7872 (mp0) REVERT: D 1035 ASP cc_start: 0.8220 (t0) cc_final: 0.8001 (t0) outliers start: 36 outliers final: 9 residues processed: 204 average time/residue: 0.5398 time to fit residues: 122.2601 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 : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 925 THR 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 696 THR Chi-restraints excluded: chain D residue 1009 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 63 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 6 optimal weight: 7.9990 chunk 153 optimal weight: 0.9980 chunk 56 optimal weight: 7.9990 chunk 74 optimal weight: 7.9990 chunk 62 optimal weight: 2.9990 chunk 79 optimal weight: 0.8980 chunk 126 optimal weight: 3.9990 chunk 174 optimal weight: 3.9990 chunk 182 optimal weight: 1.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 888 GLN C 996 GLN 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 = 0.3746 r_free = 0.3746 target = 0.129256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.096644 restraints weight = 36108.625| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 3.33 r_work: 0.3156 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3155 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3155 r_free = 0.3155 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3155 r_free = 0.3155 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3155 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.2238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 14824 Z= 0.147 Angle : 0.601 9.555 20044 Z= 0.309 Chirality : 0.044 0.173 2221 Planarity : 0.004 0.081 2569 Dihedral : 7.015 78.513 2086 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 2.42 % Allowed : 14.74 % 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: -0.99 (0.19), residues: 1855 helix: 0.18 (0.16), residues: 999 sheet: -1.43 (0.45), residues: 141 loop : -1.62 (0.23), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 507 TYR 0.031 0.002 TYR D 307 PHE 0.009 0.001 PHE B 889 TRP 0.028 0.001 TRP D 49 HIS 0.006 0.001 HIS D 113 Details of bonding type rmsd covalent geometry : bond 0.00350 (14824) covalent geometry : angle 0.60107 (20044) hydrogen bonds : bond 0.03528 ( 679) hydrogen bonds : angle 4.32110 ( 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 215 residues out of total 1549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 179 time to evaluate : 0.479 Fit side-chains REVERT: A 919 ASP cc_start: 0.7929 (m-30) cc_final: 0.7727 (t0) REVERT: A 925 THR cc_start: 0.9071 (OUTLIER) cc_final: 0.8760 (m) REVERT: B 888 GLN cc_start: 0.8532 (OUTLIER) cc_final: 0.8296 (tm-30) REVERT: B 965 LYS cc_start: 0.9051 (tppt) cc_final: 0.8690 (mptm) REVERT: B 976 ARG cc_start: 0.6903 (ptm160) cc_final: 0.6184 (ptp-110) REVERT: B 1050 GLU cc_start: 0.8182 (OUTLIER) cc_final: 0.7898 (tt0) REVERT: B 1053 ASP cc_start: 0.8224 (m-30) cc_final: 0.8012 (m-30) REVERT: C 965 LYS cc_start: 0.8441 (mtpt) cc_final: 0.7997 (tmmm) REVERT: C 969 LEU cc_start: 0.6001 (OUTLIER) cc_final: 0.5193 (mm) REVERT: D 194 ASP cc_start: 0.7777 (m-30) cc_final: 0.7299 (m-30) REVERT: D 210 ASP cc_start: 0.7878 (t70) cc_final: 0.7621 (t0) REVERT: D 408 GLU cc_start: 0.7343 (tp30) cc_final: 0.6994 (tp30) REVERT: D 690 ASP cc_start: 0.7914 (t70) cc_final: 0.7710 (t70) REVERT: D 976 ARG cc_start: 0.8235 (mpt180) cc_final: 0.7993 (ttp80) REVERT: D 1009 GLU cc_start: 0.8131 (OUTLIER) cc_final: 0.7858 (mp0) REVERT: D 1035 ASP cc_start: 0.8205 (t0) cc_final: 0.7976 (t0) outliers start: 36 outliers final: 11 residues processed: 202 average time/residue: 0.5433 time to fit residues: 121.5623 Evaluate side-chains 184 residues out of total 1549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 168 time to evaluate : 0.596 ------------------------------------------------------------------------------- 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 888 GLN Chi-restraints excluded: chain B residue 891 GLU Chi-restraints excluded: chain B residue 919 ASP 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 113 HIS Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 216 ASP Chi-restraints excluded: chain D residue 593 THR Chi-restraints excluded: chain D residue 696 THR Chi-restraints excluded: chain D residue 867 MET 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: 7.9990 chunk 121 optimal weight: 9.9990 chunk 134 optimal weight: 9.9990 chunk 58 optimal weight: 3.9990 chunk 111 optimal weight: 10.0000 chunk 116 optimal weight: 6.9990 chunk 68 optimal weight: 4.9990 chunk 2 optimal weight: 5.9990 chunk 127 optimal weight: 3.9990 chunk 146 optimal weight: 7.9990 chunk 105 optimal weight: 8.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 888 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 996 GLN C1024 ASN D 45 GLN D 113 HIS ** D 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 385 GLN D1020 ASN D1024 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.127200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.095655 restraints weight = 23791.639| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 2.29 r_work: 0.3154 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3023 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3013 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3013 r_free = 0.3013 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3013 r_free = 0.3013 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3013 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.2310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.061 14824 Z= 0.306 Angle : 0.734 8.697 20044 Z= 0.374 Chirality : 0.050 0.175 2221 Planarity : 0.005 0.066 2569 Dihedral : 7.254 78.035 2084 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 3.34 % Allowed : 15.27 % Favored : 81.39 % 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: -1.03 (0.19), residues: 1855 helix: 0.11 (0.16), residues: 999 sheet: -1.37 (0.47), residues: 127 loop : -1.59 (0.23), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A1065 TYR 0.038 0.002 TYR D 692 PHE 0.016 0.002 PHE B 863 TRP 0.025 0.001 TRP D 49 HIS 0.020 0.001 HIS D 113 Details of bonding type rmsd covalent geometry : bond 0.00742 (14824) covalent geometry : angle 0.73428 (20044) hydrogen bonds : bond 0.04401 ( 679) hydrogen bonds : angle 4.61778 ( 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 214 residues out of total 1549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 164 time to evaluate : 0.384 Fit side-chains REVERT: A 866 GLU cc_start: 0.8226 (mm-30) cc_final: 0.7990 (mt-10) REVERT: A 919 ASP cc_start: 0.7997 (m-30) cc_final: 0.7728 (t0) REVERT: A 925 THR cc_start: 0.9250 (OUTLIER) cc_final: 0.9021 (m) REVERT: B 888 GLN cc_start: 0.8707 (OUTLIER) cc_final: 0.8485 (mm-40) REVERT: B 965 LYS cc_start: 0.9130 (tppt) cc_final: 0.8749 (mptm) REVERT: B 976 ARG cc_start: 0.7187 (ptm160) cc_final: 0.6471 (ptp-110) REVERT: B 1035 ASP cc_start: 0.8236 (OUTLIER) cc_final: 0.7851 (m-30) REVERT: B 1046 GLU cc_start: 0.8180 (pm20) cc_final: 0.7911 (pm20) REVERT: B 1050 GLU cc_start: 0.8353 (OUTLIER) cc_final: 0.8047 (tt0) REVERT: C 965 LYS cc_start: 0.8548 (mtpt) cc_final: 0.8119 (tmmm) REVERT: C 969 LEU cc_start: 0.6048 (OUTLIER) cc_final: 0.5121 (mm) REVERT: D 210 ASP cc_start: 0.7962 (t70) cc_final: 0.7675 (t0) REVERT: D 408 GLU cc_start: 0.7426 (tp30) cc_final: 0.7075 (tp30) REVERT: D 690 ASP cc_start: 0.8066 (t70) cc_final: 0.7811 (t70) REVERT: D 976 ARG cc_start: 0.8308 (mpt180) cc_final: 0.7986 (ttp80) REVERT: D 1009 GLU cc_start: 0.8275 (OUTLIER) cc_final: 0.8016 (mp0) outliers start: 50 outliers final: 15 residues processed: 197 average time/residue: 0.5522 time to fit residues: 120.5306 Evaluate side-chains 180 residues out of total 1549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 159 time to evaluate : 0.453 ------------------------------------------------------------------------------- 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 821 VAL Chi-restraints excluded: chain B residue 888 GLN Chi-restraints excluded: chain B residue 919 ASP 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 C residue 977 VAL Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 215 LEU 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 1009 GLU Chi-restraints excluded: chain D residue 1024 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 123 optimal weight: 3.9990 chunk 96 optimal weight: 6.9990 chunk 98 optimal weight: 7.9990 chunk 146 optimal weight: 5.9990 chunk 58 optimal weight: 2.9990 chunk 129 optimal weight: 0.8980 chunk 132 optimal weight: 0.8980 chunk 91 optimal weight: 10.0000 chunk 24 optimal weight: 0.9980 chunk 154 optimal weight: 8.9990 chunk 128 optimal weight: 0.8980 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 888 GLN C 996 GLN C1024 ASN D 45 GLN D 113 HIS D 385 GLN D1020 ASN D1024 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.129178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.096513 restraints weight = 34621.009| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 3.21 r_work: 0.3163 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3164 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3164 r_free = 0.3164 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3164 r_free = 0.3164 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3164 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.2543 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= 0.132 Angle : 0.602 9.432 20044 Z= 0.310 Chirality : 0.044 0.154 2221 Planarity : 0.004 0.065 2569 Dihedral : 6.613 71.913 2084 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 2.42 % Allowed : 16.91 % Favored : 80.67 % 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: -0.78 (0.20), residues: 1855 helix: 0.38 (0.16), residues: 998 sheet: -1.35 (0.44), residues: 142 loop : -1.56 (0.23), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 976 TYR 0.027 0.002 TYR D 307 PHE 0.009 0.001 PHE A 863 TRP 0.027 0.001 TRP D 49 HIS 0.003 0.001 HIS C 900 Details of bonding type rmsd covalent geometry : bond 0.00314 (14824) covalent geometry : angle 0.60241 (20044) hydrogen bonds : bond 0.03480 ( 679) hydrogen bonds : angle 4.28334 ( 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 210 residues out of total 1549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 174 time to evaluate : 0.580 Fit side-chains REVERT: A 866 GLU cc_start: 0.7797 (mm-30) cc_final: 0.7582 (mt-10) REVERT: A 919 ASP cc_start: 0.7889 (m-30) cc_final: 0.7644 (t0) REVERT: A 925 THR cc_start: 0.9096 (OUTLIER) cc_final: 0.8824 (m) REVERT: B 976 ARG cc_start: 0.7031 (ptm160) cc_final: 0.6322 (ptp-110) REVERT: B 1035 ASP cc_start: 0.8143 (OUTLIER) cc_final: 0.7681 (m-30) REVERT: B 1046 GLU cc_start: 0.8029 (pm20) cc_final: 0.7720 (pm20) REVERT: C 965 LYS cc_start: 0.8433 (mtpt) cc_final: 0.8012 (tmmm) REVERT: C 969 LEU cc_start: 0.5959 (OUTLIER) cc_final: 0.5067 (mm) REVERT: C 1020 ASN cc_start: 0.8741 (p0) cc_final: 0.7890 (t0) REVERT: D 86 LYS cc_start: 0.6139 (mmmt) cc_final: 0.5331 (mttt) REVERT: D 194 ASP cc_start: 0.7881 (m-30) cc_final: 0.7384 (m-30) REVERT: D 210 ASP cc_start: 0.7895 (t70) cc_final: 0.7375 (t0) REVERT: D 690 ASP cc_start: 0.7968 (t70) cc_final: 0.7726 (t70) REVERT: D 976 ARG cc_start: 0.8207 (mpt180) cc_final: 0.7974 (ttp80) REVERT: D 1009 GLU cc_start: 0.8092 (OUTLIER) cc_final: 0.7829 (mp0) outliers start: 36 outliers final: 14 residues processed: 197 average time/residue: 0.5487 time to fit residues: 119.7997 Evaluate side-chains 178 residues out of total 1549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 160 time to evaluate : 0.461 ------------------------------------------------------------------------------- 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 955 ILE 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 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 1009 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 15 optimal weight: 4.9990 chunk 182 optimal weight: 5.9990 chunk 172 optimal weight: 2.9990 chunk 141 optimal weight: 10.0000 chunk 98 optimal weight: 0.9980 chunk 73 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 174 optimal weight: 4.9990 chunk 70 optimal weight: 7.9990 chunk 134 optimal weight: 9.9990 chunk 113 optimal weight: 3.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 113 HIS ** 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 = 0.3728 r_free = 0.3728 target = 0.127485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.094890 restraints weight = 32960.239| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 3.04 r_work: 0.3141 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3146 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3146 r_free = 0.3146 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3146 r_free = 0.3146 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3146 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.2585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 14824 Z= 0.190 Angle : 0.642 10.613 20044 Z= 0.328 Chirality : 0.046 0.149 2221 Planarity : 0.004 0.060 2569 Dihedral : 6.630 70.582 2084 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 2.49 % Allowed : 17.89 % Favored : 79.62 % 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: 0.45 (0.16), residues: 998 sheet: -1.28 (0.44), residues: 144 loop : -1.51 (0.23), residues: 713 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 829 TYR 0.030 0.002 TYR D 307 PHE 0.011 0.001 PHE A 863 TRP 0.020 0.001 TRP D 49 HIS 0.017 0.001 HIS D 113 Details of bonding type rmsd covalent geometry : bond 0.00463 (14824) covalent geometry : angle 0.64192 (20044) hydrogen bonds : bond 0.03701 ( 679) hydrogen bonds : angle 4.33626 ( 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 201 residues out of total 1549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 164 time to evaluate : 0.548 Fit side-chains REVERT: A 866 GLU cc_start: 0.7899 (mm-30) cc_final: 0.7689 (mt-10) REVERT: A 919 ASP cc_start: 0.7878 (m-30) cc_final: 0.7618 (t0) REVERT: A 925 THR cc_start: 0.9129 (OUTLIER) cc_final: 0.8843 (m) REVERT: B 976 ARG cc_start: 0.7073 (ptm160) cc_final: 0.6350 (ptp-110) REVERT: B 1035 ASP cc_start: 0.8149 (OUTLIER) cc_final: 0.7696 (m-30) REVERT: B 1046 GLU cc_start: 0.8010 (pm20) cc_final: 0.7673 (pm20) REVERT: C 965 LYS cc_start: 0.8476 (mtpt) cc_final: 0.8162 (tmtt) REVERT: C 969 LEU cc_start: 0.6001 (OUTLIER) cc_final: 0.5085 (mm) REVERT: D 86 LYS cc_start: 0.6146 (mmmt) cc_final: 0.5310 (mttt) REVERT: D 194 ASP cc_start: 0.7793 (m-30) cc_final: 0.7267 (m-30) REVERT: D 210 ASP cc_start: 0.7913 (t70) cc_final: 0.7623 (t0) REVERT: D 560 MET cc_start: 0.8249 (OUTLIER) cc_final: 0.7036 (mpp) REVERT: D 690 ASP cc_start: 0.7991 (t70) cc_final: 0.7743 (t70) REVERT: D 976 ARG cc_start: 0.8240 (mpt180) cc_final: 0.7970 (ttp80) REVERT: D 1009 GLU cc_start: 0.8114 (OUTLIER) cc_final: 0.7837 (mp0) outliers start: 37 outliers final: 17 residues processed: 189 average time/residue: 0.5326 time to fit residues: 111.4495 Evaluate side-chains 182 residues out of total 1549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 160 time to evaluate : 0.461 ------------------------------------------------------------------------------- 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 961 ASN 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 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 560 MET 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 Chi-restraints excluded: chain D residue 1009 GLU 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: 2.9990 chunk 143 optimal weight: 10.0000 chunk 87 optimal weight: 4.9990 chunk 150 optimal weight: 6.9990 chunk 94 optimal weight: 9.9990 chunk 75 optimal weight: 3.9990 chunk 147 optimal weight: 10.0000 chunk 79 optimal weight: 5.9990 chunk 99 optimal weight: 7.9990 chunk 58 optimal weight: 4.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 888 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 996 GLN C1072 HIS D 45 GLN D 113 HIS D 385 GLN ** D 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1020 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.129259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.098080 restraints weight = 37365.233| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 2.95 r_work: 0.3106 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3121 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3121 r_free = 0.3121 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3121 r_free = 0.3121 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3121 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.2606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 14824 Z= 0.256 Angle : 0.698 10.915 20044 Z= 0.354 Chirality : 0.048 0.158 2221 Planarity : 0.005 0.061 2569 Dihedral : 6.810 71.115 2084 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 2.75 % Allowed : 18.48 % Favored : 78.77 % 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: -0.74 (0.20), residues: 1855 helix: 0.39 (0.16), residues: 998 sheet: -1.23 (0.45), residues: 139 loop : -1.53 (0.23), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 829 TYR 0.035 0.002 TYR D 692 PHE 0.013 0.002 PHE A 863 TRP 0.017 0.001 TRP D 49 HIS 0.015 0.001 HIS D 113 Details of bonding type rmsd covalent geometry : bond 0.00622 (14824) covalent geometry : angle 0.69832 (20044) hydrogen bonds : bond 0.04048 ( 679) hydrogen bonds : angle 4.46236 ( 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 202 residues out of total 1549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 161 time to evaluate : 0.585 Fit side-chains REVERT: A 925 THR cc_start: 0.9148 (OUTLIER) cc_final: 0.8904 (m) REVERT: A 1012 LYS cc_start: 0.8182 (ttmt) cc_final: 0.7957 (tptp) REVERT: B 873 LEU cc_start: 0.8706 (OUTLIER) cc_final: 0.8270 (mp) REVERT: B 976 ARG cc_start: 0.7136 (ptm160) cc_final: 0.6416 (ptp-110) REVERT: B 1046 GLU cc_start: 0.7996 (pm20) cc_final: 0.7686 (pm20) REVERT: C 965 LYS cc_start: 0.8503 (mtpt) cc_final: 0.8278 (tmtt) REVERT: C 969 LEU cc_start: 0.5919 (OUTLIER) cc_final: 0.4984 (mm) REVERT: D 210 ASP cc_start: 0.7913 (t70) cc_final: 0.7614 (t0) REVERT: D 560 MET cc_start: 0.8376 (OUTLIER) cc_final: 0.7221 (mpp) REVERT: D 690 ASP cc_start: 0.7999 (t70) cc_final: 0.7745 (t70) REVERT: D 976 ARG cc_start: 0.8242 (mpt180) cc_final: 0.8004 (ttp80) outliers start: 41 outliers final: 18 residues processed: 187 average time/residue: 0.5500 time to fit residues: 113.9694 Evaluate side-chains 181 residues out of total 1549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 159 time to evaluate : 0.549 ------------------------------------------------------------------------------- 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 821 VAL Chi-restraints excluded: chain B residue 873 LEU 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 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 C residue 977 VAL 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 560 MET 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 Chi-restraints excluded: chain D residue 867 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 64 optimal weight: 0.7980 chunk 177 optimal weight: 1.9990 chunk 43 optimal weight: 0.0060 chunk 124 optimal weight: 8.9990 chunk 50 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 120 optimal weight: 0.7980 chunk 145 optimal weight: 0.9980 chunk 53 optimal weight: 4.9990 chunk 56 optimal weight: 0.7980 chunk 136 optimal weight: 4.9990 overall best weight: 0.6796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 888 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 996 GLN D 45 GLN D 113 HIS D 385 GLN ** D 879 GLN ** 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 = 0.3761 r_free = 0.3761 target = 0.130561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.097756 restraints weight = 32571.633| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 3.02 r_work: 0.3196 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3204 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3204 r_free = 0.3204 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3204 r_free = 0.3204 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3204 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.2878 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= 0.119 Angle : 0.602 10.823 20044 Z= 0.308 Chirality : 0.044 0.157 2221 Planarity : 0.004 0.065 2569 Dihedral : 6.247 65.618 2084 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 2.10 % Allowed : 19.33 % Favored : 78.57 % 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: -0.50 (0.20), residues: 1855 helix: 0.61 (0.17), residues: 1000 sheet: -1.12 (0.45), residues: 142 loop : -1.48 (0.23), residues: 713 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 829 TYR 0.024 0.001 TYR D 307 PHE 0.007 0.001 PHE D 189 TRP 0.022 0.001 TRP D 49 HIS 0.005 0.001 HIS C1072 Details of bonding type rmsd covalent geometry : bond 0.00278 (14824) covalent geometry : angle 0.60188 (20044) hydrogen bonds : bond 0.03277 ( 679) hydrogen bonds : angle 4.19695 ( 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 207 residues out of total 1549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 176 time to evaluate : 0.587 Fit side-chains revert: symmetry clash REVERT: A 925 THR cc_start: 0.9039 (OUTLIER) cc_final: 0.8760 (m) REVERT: A 1075 ASP cc_start: 0.8604 (t0) cc_final: 0.8355 (t0) REVERT: B 976 ARG cc_start: 0.7061 (ptm160) cc_final: 0.6262 (ptp-110) REVERT: C 965 LYS cc_start: 0.8434 (mtpt) cc_final: 0.8154 (tmtt) REVERT: C 969 LEU cc_start: 0.5791 (OUTLIER) cc_final: 0.4888 (mm) REVERT: D 86 LYS cc_start: 0.6024 (mmmt) cc_final: 0.5115 (mttt) REVERT: D 194 ASP cc_start: 0.7794 (m-30) cc_final: 0.7298 (m-30) REVERT: D 210 ASP cc_start: 0.7911 (t70) cc_final: 0.7384 (t0) REVERT: D 355 LYS cc_start: 0.5838 (mmtm) cc_final: 0.5027 (tppt) REVERT: D 408 GLU cc_start: 0.7436 (tp30) cc_final: 0.7031 (tp30) REVERT: D 560 MET cc_start: 0.8106 (OUTLIER) cc_final: 0.6943 (mpp) REVERT: D 690 ASP cc_start: 0.7897 (t70) cc_final: 0.7456 (t70) REVERT: D 780 LYS cc_start: 0.8299 (tttt) cc_final: 0.7746 (tptt) REVERT: D 976 ARG cc_start: 0.8136 (mpt180) cc_final: 0.7893 (ttp80) REVERT: D 1035 ASP cc_start: 0.8176 (t0) cc_final: 0.7940 (t0) outliers start: 31 outliers final: 16 residues processed: 196 average time/residue: 0.5289 time to fit residues: 115.1017 Evaluate side-chains 182 residues out of total 1549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 163 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 925 THR 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 C residue 834 ILE Chi-restraints excluded: chain C residue 848 ARG Chi-restraints excluded: chain C residue 969 LEU Chi-restraints excluded: chain C residue 977 VAL Chi-restraints excluded: chain D residue 45 GLN Chi-restraints excluded: chain D residue 113 HIS 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 560 MET Chi-restraints excluded: chain D residue 614 ASP Chi-restraints excluded: chain D residue 741 VAL Chi-restraints excluded: chain D residue 831 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 44 optimal weight: 0.9990 chunk 69 optimal weight: 5.9990 chunk 59 optimal weight: 2.9990 chunk 49 optimal weight: 6.9990 chunk 110 optimal weight: 0.0870 chunk 103 optimal weight: 6.9990 chunk 139 optimal weight: 0.2980 chunk 101 optimal weight: 9.9990 chunk 80 optimal weight: 9.9990 chunk 53 optimal weight: 0.0050 chunk 147 optimal weight: 10.0000 overall best weight: 0.8776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 888 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 45 GLN D 113 HIS ** D 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1020 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.130519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.098808 restraints weight = 26585.137| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 2.66 r_work: 0.3224 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3090 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3101 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3101 r_free = 0.3101 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3101 r_free = 0.3101 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3101 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.2936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14824 Z= 0.124 Angle : 0.618 11.441 20044 Z= 0.313 Chirality : 0.044 0.149 2221 Planarity : 0.004 0.059 2569 Dihedral : 6.150 65.249 2084 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 1.44 % Allowed : 20.31 % Favored : 78.24 % 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: -0.37 (0.20), residues: 1855 helix: 0.74 (0.17), residues: 998 sheet: -1.05 (0.45), residues: 142 loop : -1.45 (0.23), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 829 TYR 0.024 0.001 TYR D 307 PHE 0.009 0.001 PHE B 889 TRP 0.020 0.001 TRP D 49 HIS 0.005 0.001 HIS D 113 Details of bonding type rmsd covalent geometry : bond 0.00293 (14824) covalent geometry : angle 0.61827 (20044) hydrogen bonds : bond 0.03287 ( 679) hydrogen bonds : angle 4.18414 ( 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 189 residues out of total 1549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 168 time to evaluate : 0.514 Fit side-chains REVERT: A 925 THR cc_start: 0.9109 (OUTLIER) cc_final: 0.8829 (m) REVERT: A 1075 ASP cc_start: 0.8779 (t0) cc_final: 0.8552 (t0) REVERT: B 976 ARG cc_start: 0.7063 (ptm160) cc_final: 0.6275 (ptp-110) REVERT: C 965 LYS cc_start: 0.8436 (mtpt) cc_final: 0.8155 (tmtt) REVERT: C 969 LEU cc_start: 0.5778 (OUTLIER) cc_final: 0.4866 (mm) REVERT: C 1020 ASN cc_start: 0.8791 (p0) cc_final: 0.7940 (t0) REVERT: D 86 LYS cc_start: 0.6019 (mmmt) cc_final: 0.5126 (mttt) REVERT: D 194 ASP cc_start: 0.7784 (m-30) cc_final: 0.7301 (m-30) REVERT: D 210 ASP cc_start: 0.7942 (t70) cc_final: 0.7423 (t0) REVERT: D 355 LYS cc_start: 0.5858 (mmtm) cc_final: 0.5035 (tppt) REVERT: D 408 GLU cc_start: 0.7522 (tp30) cc_final: 0.7180 (tp30) REVERT: D 560 MET cc_start: 0.8089 (OUTLIER) cc_final: 0.6914 (mpp) REVERT: D 690 ASP cc_start: 0.7981 (t70) cc_final: 0.7603 (t70) REVERT: D 780 LYS cc_start: 0.8347 (tttt) cc_final: 0.7791 (tptt) REVERT: D 976 ARG cc_start: 0.8210 (mpt180) cc_final: 0.7867 (ttp80) REVERT: D 1035 ASP cc_start: 0.8346 (t0) cc_final: 0.8116 (t0) outliers start: 21 outliers final: 13 residues processed: 184 average time/residue: 0.5448 time to fit residues: 111.2917 Evaluate side-chains 176 residues out of total 1549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 160 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 925 THR 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 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 154 VAL Chi-restraints excluded: chain D residue 216 ASP Chi-restraints excluded: chain D residue 278 MET Chi-restraints excluded: chain D residue 522 ASP Chi-restraints excluded: chain D residue 560 MET Chi-restraints excluded: chain D residue 741 VAL Chi-restraints excluded: chain D residue 831 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 132 optimal weight: 20.0000 chunk 153 optimal weight: 0.6980 chunk 57 optimal weight: 5.9990 chunk 127 optimal weight: 3.9990 chunk 98 optimal weight: 7.9990 chunk 37 optimal weight: 0.7980 chunk 141 optimal weight: 0.9980 chunk 147 optimal weight: 10.0000 chunk 104 optimal weight: 0.0970 chunk 142 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 888 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1020 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.130368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.098165 restraints weight = 29379.710| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 2.83 r_work: 0.3204 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3215 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3215 r_free = 0.3215 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3215 r_free = 0.3215 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3215 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.2961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.155 14824 Z= 0.166 Angle : 0.853 59.170 20044 Z= 0.473 Chirality : 0.046 0.674 2221 Planarity : 0.004 0.059 2569 Dihedral : 6.153 65.239 2084 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 1.70 % Allowed : 20.31 % Favored : 77.98 % Cbeta Deviations : 0.06 % 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: -0.35 (0.20), residues: 1855 helix: 0.76 (0.17), residues: 997 sheet: -1.05 (0.45), residues: 142 loop : -1.44 (0.23), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 829 TYR 0.023 0.001 TYR D 307 PHE 0.016 0.001 PHE D 790 TRP 0.019 0.001 TRP D 49 HIS 0.003 0.001 HIS D 997 Details of bonding type rmsd covalent geometry : bond 0.00367 (14824) covalent geometry : angle 0.85281 (20044) hydrogen bonds : bond 0.03284 ( 679) hydrogen bonds : angle 4.18354 ( 1995) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4607.54 seconds wall clock time: 79 minutes 16.89 seconds (4756.89 seconds total)