Starting phenix.real_space_refine on Fri Mar 6 12:50:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6uia_20784/03_2026/6uia_20784.cif Found real_map, /net/cci-nas-00/data/ceres_data/6uia_20784/03_2026/6uia_20784.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6uia_20784/03_2026/6uia_20784.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6uia_20784/03_2026/6uia_20784.map" model { file = "/net/cci-nas-00/data/ceres_data/6uia_20784/03_2026/6uia_20784.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6uia_20784/03_2026/6uia_20784.cif" } resolution = 4.3 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 ------------------------------------------------------------------------------- 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= 0.001 sd= 0.003 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 6 5.49 5 S 178 5.16 5 C 20298 2.51 5 N 5374 2.21 5 O 5864 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 92 residue(s): 0.03s 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: 31720 Number of models: 1 Model: "" Number of chains: 6 Chain: "C" Number of atoms: 7906 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1021, 7898 Classifications: {'peptide': 1021} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 48, 'TRANS': 971} Chain breaks: 2 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 Conformer: "B" Number of residues, atoms: 1021, 7898 Classifications: {'peptide': 1021} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 48, 'TRANS': 971} Chain breaks: 2 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 bond proxies already assigned to first conformer: 8059 Chain: "D" Number of atoms: 7906 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1021, 7898 Classifications: {'peptide': 1021} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 48, 'TRANS': 971} Chain breaks: 2 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 Conformer: "B" Number of residues, atoms: 1021, 7898 Classifications: {'peptide': 1021} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 48, 'TRANS': 971} Chain breaks: 2 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 bond proxies already assigned to first conformer: 8059 Chain: "A" Number of atoms: 7906 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1021, 7898 Classifications: {'peptide': 1021} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 48, 'TRANS': 971} Chain breaks: 3 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 Conformer: "B" Number of residues, atoms: 1021, 7898 Classifications: {'peptide': 1021} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 48, 'TRANS': 971} Chain breaks: 3 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 bond proxies already assigned to first conformer: 8058 Chain: "B" Number of atoms: 7906 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1021, 7898 Classifications: {'peptide': 1021} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 48, 'TRANS': 971} Chain breaks: 2 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 Conformer: "B" Number of residues, atoms: 1021, 7898 Classifications: {'peptide': 1021} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 48, 'TRANS': 971} Chain breaks: 2 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 bond proxies already assigned to first conformer: 8059 Chain: "A" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'COA': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'COA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 12.99, per 1000 atoms: 0.41 Number of scatterers: 31720 At special positions: 0 Unit cell: (187.05, 171.39, 140.07, 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 178 16.00 P 6 15.00 O 5864 8.00 N 5374 7.00 C 20298 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.47 Conformation dependent library (CDL) restraints added in 2.0 seconds 8132 Ramachandran restraints generated. 4066 Oldfield, 0 Emsley, 4066 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7392 Finding SS restraints... Secondary structure from input PDB file: 157 helices and 30 sheets defined 44.4% alpha, 12.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.90 Creating SS restraints... Processing helix chain 'C' and resid 7 through 19 Processing helix chain 'C' and resid 39 through 47 removed outlier: 3.604A pdb=" N LEU C 43 " --> pdb=" O ASP C 39 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 52 removed outlier: 3.892A pdb=" N SER C 52 " --> pdb=" O TRP C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 77 through 86 Processing helix chain 'C' and resid 139 through 143 removed outlier: 3.738A pdb=" N VAL C 142 " --> pdb=" O GLY C 139 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N GLY C 143 " --> pdb=" O VAL C 140 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 139 through 143' Processing helix chain 'C' and resid 161 through 169 Processing helix chain 'C' and resid 174 through 176 No H-bonds generated for 'chain 'C' and resid 174 through 176' Processing helix chain 'C' and resid 177 through 194 removed outlier: 3.725A pdb=" N LEU C 181 " --> pdb=" O LYS C 177 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ALA C 182 " --> pdb=" O LYS C 178 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N SER C 183 " --> pdb=" O GLU C 179 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASP C 194 " --> pdb=" O ASN C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 234 removed outlier: 6.228A pdb=" N VAL C 231 " --> pdb=" O TYR C 227 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N LYS C 232 " --> pdb=" O ILE C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 260 Processing helix chain 'C' and resid 281 through 295 Processing helix chain 'C' and resid 312 through 327 removed outlier: 3.598A pdb=" N MET C 327 " --> pdb=" O ILE C 323 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 362 removed outlier: 3.621A pdb=" N ARG C 362 " --> pdb=" O VAL C 358 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 371 removed outlier: 3.706A pdb=" N LEU C 368 " --> pdb=" O TYR C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 399 Processing helix chain 'C' and resid 412 through 419 removed outlier: 3.511A pdb=" N GLY C 416 " --> pdb=" O THR C 412 " (cutoff:3.500A) Processing helix chain 'C' and resid 505 through 519 Processing helix chain 'C' and resid 555 through 563 Processing helix chain 'C' and resid 577 through 587 removed outlier: 3.781A pdb=" N ASN C 587 " --> pdb=" O MET C 583 " (cutoff:3.500A) Processing helix chain 'C' and resid 602 through 617 Processing helix chain 'C' and resid 642 through 649 Processing helix chain 'C' and resid 664 through 678 removed outlier: 3.608A pdb=" N ASN C 668 " --> pdb=" O GLY C 664 " (cutoff:3.500A) Processing helix chain 'C' and resid 696 through 707 removed outlier: 3.637A pdb=" N HIS C 700 " --> pdb=" O THR C 696 " (cutoff:3.500A) Processing helix chain 'C' and resid 723 through 733 removed outlier: 3.537A pdb=" N ILE C 727 " --> pdb=" O GLU C 723 " (cutoff:3.500A) Processing helix chain 'C' and resid 771 through 781 Processing helix chain 'C' and resid 790 through 805 Processing helix chain 'C' and resid 824 through 831 removed outlier: 3.539A 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 removed outlier: 3.534A pdb=" N SER C 923 " --> pdb=" O ASP C 919 " (cutoff:3.500A) Processing helix chain 'C' and resid 937 through 951 removed outlier: 3.985A pdb=" N PHE C 946 " --> pdb=" O ALA C 942 " (cutoff:3.500A) Processing helix chain 'C' and resid 955 through 965 removed outlier: 4.814A pdb=" N ASN C 961 " --> pdb=" O MET C 957 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 997 removed outlier: 4.055A pdb=" N ILE C 989 " --> pdb=" O MET C 985 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LEU C 990 " --> pdb=" O ARG C 986 " (cutoff:3.500A) Processing helix chain 'C' and resid 1001 through 1015 Processing helix chain 'C' and resid 1024 through 1040 removed outlier: 4.091A pdb=" N GLY C1030 " --> pdb=" O ASP C1026 " (cutoff:3.500A) Processing helix chain 'C' and resid 1045 through 1055 removed outlier: 3.566A pdb=" N ILE C1052 " --> pdb=" O ALA C1048 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLY C1055 " --> pdb=" O TYR C1051 " (cutoff:3.500A) Processing helix chain 'C' and resid 1057 through 1079 removed outlier: 3.959A pdb=" N PHE C1061 " --> pdb=" O LEU C1057 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N MET C1067 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLY C1068 " --> pdb=" O GLY C1064 " (cutoff:3.500A) Processing helix chain 'D' and resid 7 through 18 Processing helix chain 'D' and resid 41 through 46 Processing helix chain 'D' and resid 47 through 51 Processing helix chain 'D' and resid 78 through 86 Processing helix chain 'D' and resid 144 through 149 removed outlier: 4.083A pdb=" N LYS D 148 " --> pdb=" O ASP D 144 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA D 149 " --> pdb=" O VAL D 145 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 144 through 149' Processing helix chain 'D' and resid 161 through 169 Processing helix chain 'D' and resid 174 through 176 No H-bonds generated for 'chain 'D' and resid 174 through 176' Processing helix chain 'D' and resid 177 through 194 removed outlier: 4.015A pdb=" N LEU D 181 " --> pdb=" O LYS D 177 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ALA D 182 " --> pdb=" O LYS D 178 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N SER D 183 " --> pdb=" O GLU D 179 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N PHE D 184 " --> pdb=" O ILE D 180 " (cutoff:3.500A) Processing helix chain 'D' and resid 225 through 234 removed outlier: 6.271A pdb=" N VAL D 231 " --> pdb=" O TYR D 227 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N LYS D 232 " --> pdb=" O ILE D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 247 through 260 Processing helix chain 'D' and resid 281 through 295 removed outlier: 3.729A pdb=" N SER D 285 " --> pdb=" O GLY D 281 " (cutoff:3.500A) Processing helix chain 'D' and resid 312 through 327 removed outlier: 3.783A pdb=" N MET D 327 " --> pdb=" O ILE D 323 " (cutoff:3.500A) Processing helix chain 'D' and resid 349 through 362 Processing helix chain 'D' and resid 364 through 371 removed outlier: 4.025A pdb=" N LEU D 368 " --> pdb=" O TYR D 364 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N HIS D 371 " --> pdb=" O PRO D 367 " (cutoff:3.500A) Processing helix chain 'D' and resid 384 through 399 Processing helix chain 'D' and resid 410 through 412 No H-bonds generated for 'chain 'D' and resid 410 through 412' Processing helix chain 'D' and resid 413 through 419 Processing helix chain 'D' and resid 505 through 519 Processing helix chain 'D' and resid 555 through 563 Processing helix chain 'D' and resid 577 through 587 removed outlier: 4.105A pdb=" N ASN D 587 " --> pdb=" O MET D 583 " (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 664 through 677 Processing helix chain 'D' and resid 697 through 707 removed outlier: 3.989A pdb=" N ARG D 703 " --> pdb=" O ASP D 699 " (cutoff:3.500A) Processing helix chain 'D' and resid 724 through 733 Processing helix chain 'D' and resid 771 through 781 Processing helix chain 'D' and resid 791 through 807 removed outlier: 4.124A pdb=" N GLU D 795 " --> pdb=" O ASP D 791 " (cutoff:3.500A) Processing helix chain 'D' and resid 824 through 831 Processing helix chain 'D' and resid 858 through 866 Processing helix chain 'D' and resid 868 through 877 Processing helix chain 'D' and resid 883 through 897 removed outlier: 3.563A pdb=" N GLN D 888 " --> pdb=" O LYS D 884 " (cutoff:3.500A) Processing helix chain 'D' and resid 904 through 916 Processing helix chain 'D' and resid 919 through 929 removed outlier: 3.738A pdb=" N SER D 923 " --> pdb=" O ASP D 919 " (cutoff:3.500A) Processing helix chain 'D' and resid 937 through 952 removed outlier: 3.701A pdb=" N ALA D 941 " --> pdb=" O GLY D 937 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N PHE D 946 " --> pdb=" O ALA D 942 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N SER D 952 " --> pdb=" O LYS D 948 " (cutoff:3.500A) Processing helix chain 'D' and resid 955 through 963 removed outlier: 4.690A pdb=" N ASN D 961 " --> pdb=" O MET D 957 " (cutoff:3.500A) Processing helix chain 'D' and resid 986 through 995 Processing helix chain 'D' and resid 1001 through 1018 removed outlier: 3.679A pdb=" N SER D1016 " --> pdb=" O LYS D1012 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N LYS D1017 " --> pdb=" O ILE D1013 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N LYS D1018 " --> pdb=" O THR D1014 " (cutoff:3.500A) Processing helix chain 'D' and resid 1024 through 1040 removed outlier: 4.200A pdb=" N GLY D1030 " --> pdb=" O ASP D1026 " (cutoff:3.500A) Processing helix chain 'D' and resid 1047 through 1055 removed outlier: 3.544A pdb=" N ILE D1052 " --> pdb=" O ALA D1048 " (cutoff:3.500A) Processing helix chain 'D' and resid 1057 through 1079 removed outlier: 3.979A pdb=" N PHE D1061 " --> pdb=" O LEU D1057 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N MET D1067 " --> pdb=" O LEU D1063 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLY D1068 " --> pdb=" O GLY D1064 " (cutoff:3.500A) Processing helix chain 'A' and resid 7 through 18 Processing helix chain 'A' and resid 40 through 47 Processing helix chain 'A' and resid 48 through 52 Processing helix chain 'A' and resid 77 through 89 Proline residue: A 87 - end of helix Processing helix chain 'A' and resid 139 through 143 removed outlier: 3.788A pdb=" N VAL A 142 " --> pdb=" O GLY A 139 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N GLY A 143 " --> pdb=" O VAL A 140 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 139 through 143' Processing helix chain 'A' and resid 161 through 169 removed outlier: 3.741A pdb=" N LEU A 169 " --> pdb=" O ILE A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 190 removed outlier: 5.461A pdb=" N SER A 183 " --> pdb=" O GLU A 179 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N PHE A 184 " --> pdb=" O ILE A 180 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASN A 190 " --> pdb=" O SER A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 196 removed outlier: 6.100A pdb=" N ASP A 194 " --> pdb=" O PHE A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 228 removed outlier: 4.469A pdb=" N TYR A 227 " --> pdb=" O THR A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 260 Processing helix chain 'A' and resid 282 through 294 Processing helix chain 'A' and resid 312 through 323 Processing helix chain 'A' and resid 352 through 362 Processing helix chain 'A' and resid 384 through 398 removed outlier: 3.508A pdb=" N VAL A 394 " --> pdb=" O VAL A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 505 through 519 removed outlier: 3.590A pdb=" N CYS A 519 " --> pdb=" O PHE A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 563 Processing helix chain 'A' and resid 579 through 587 Processing helix chain 'A' and resid 604 through 616 Processing helix chain 'A' and resid 643 through 648 Processing helix chain 'A' and resid 664 through 677 removed outlier: 4.069A pdb=" N GLU A 669 " --> pdb=" O GLY A 665 " (cutoff:3.500A) Processing helix chain 'A' and resid 697 through 706 removed outlier: 3.761A pdb=" N ARG A 703 " --> pdb=" O ASP A 699 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ASP A 706 " --> pdb=" O LEU A 702 " (cutoff:3.500A) Processing helix chain 'A' and resid 723 through 732 removed outlier: 3.598A pdb=" N ILE A 727 " --> pdb=" O GLU A 723 " (cutoff:3.500A) Processing helix chain 'A' and resid 771 through 781 removed outlier: 3.664A pdb=" N GLU A 781 " --> pdb=" O GLN A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 790 through 807 removed outlier: 4.475A pdb=" N GLY A 794 " --> pdb=" O PHE A 790 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N GLU A 795 " --> pdb=" O ASP A 791 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ASN A 807 " --> pdb=" O ASP A 803 " (cutoff:3.500A) Processing helix chain 'A' and resid 824 through 831 Processing helix chain 'A' and resid 858 through 865 Processing helix chain 'A' and resid 868 through 877 removed outlier: 3.542A pdb=" N VAL A 872 " --> pdb=" O GLY A 868 " (cutoff:3.500A) Processing helix chain 'A' and resid 883 through 897 removed outlier: 3.791A pdb=" N GLN A 888 " --> pdb=" O LYS A 884 " (cutoff:3.500A) Processing helix chain 'A' and resid 904 through 916 Processing helix chain 'A' and resid 919 through 929 removed outlier: 3.681A pdb=" N SER A 923 " --> pdb=" O ASP A 919 " (cutoff:3.500A) Processing helix chain 'A' and resid 937 through 951 removed outlier: 3.601A pdb=" N ALA A 943 " --> pdb=" O LEU A 939 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N PHE A 946 " --> pdb=" O ALA A 942 " (cutoff:3.500A) Processing helix chain 'A' and resid 955 through 966 removed outlier: 4.532A pdb=" N ASN A 961 " --> pdb=" O MET A 957 " (cutoff:3.500A) Processing helix chain 'A' and resid 986 through 995 Processing helix chain 'A' and resid 1001 through 1015 Processing helix chain 'A' and resid 1024 through 1040 removed outlier: 4.218A pdb=" N GLY A1030 " --> pdb=" O ASP A1026 " (cutoff:3.500A) Processing helix chain 'A' and resid 1047 through 1055 Processing helix chain 'A' and resid 1057 through 1079 removed outlier: 3.956A pdb=" N PHE A1061 " --> pdb=" O LEU A1057 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N MET A1067 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLY A1068 " --> pdb=" O GLY A1064 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 15 Processing helix chain 'B' and resid 41 through 46 Processing helix chain 'B' and resid 47 through 52 removed outlier: 3.854A pdb=" N LEU B 50 " --> pdb=" O HIS B 47 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N SER B 52 " --> pdb=" O TRP B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 86 Processing helix chain 'B' and resid 139 through 143 removed outlier: 3.816A pdb=" N VAL B 142 " --> pdb=" O GLY B 139 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N GLY B 143 " --> pdb=" O VAL B 140 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 139 through 143' Processing helix chain 'B' and resid 144 through 148 removed outlier: 4.072A pdb=" N ALA B 147 " --> pdb=" O ASP B 144 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LYS B 148 " --> pdb=" O VAL B 145 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 144 through 148' Processing helix chain 'B' and resid 161 through 169 Processing helix chain 'B' and resid 174 through 178 Processing helix chain 'B' and resid 180 through 194 removed outlier: 4.060A pdb=" N PHE B 184 " --> pdb=" O ILE B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 230 Processing helix chain 'B' and resid 247 through 260 removed outlier: 3.573A pdb=" N SER B 260 " --> pdb=" O LEU B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 293 Processing helix chain 'B' and resid 312 through 327 removed outlier: 3.998A pdb=" N MET B 327 " --> pdb=" O ILE B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 362 Processing helix chain 'B' and resid 364 through 372 removed outlier: 3.811A pdb=" N LEU B 368 " --> pdb=" O TYR B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 399 Processing helix chain 'B' and resid 410 through 412 No H-bonds generated for 'chain 'B' and resid 410 through 412' Processing helix chain 'B' and resid 413 through 419 removed outlier: 3.547A pdb=" N LEU B 419 " --> pdb=" O VAL B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 505 through 519 Processing helix chain 'B' and resid 555 through 563 Processing helix chain 'B' and resid 574 through 587 removed outlier: 4.706A pdb=" N TYR B 579 " --> pdb=" O LEU B 575 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N ASP B 580 " --> pdb=" O ARG B 576 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ASN B 587 " --> pdb=" O MET B 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 602 through 617 Processing helix chain 'B' and resid 642 through 649 Processing helix chain 'B' and resid 663 through 677 Processing helix chain 'B' and resid 696 through 705 Processing helix chain 'B' and resid 723 through 732 Processing helix chain 'B' and resid 771 through 781 Processing helix chain 'B' and resid 790 through 807 removed outlier: 3.897A pdb=" N GLU B 795 " --> pdb=" O ASP B 791 " (cutoff:3.500A) Processing helix chain 'B' and resid 824 through 832 Processing helix chain 'B' and resid 858 through 866 Processing helix chain 'B' and resid 868 through 877 Processing helix chain 'B' and resid 885 through 897 Processing helix chain 'B' and resid 904 through 916 Processing helix chain 'B' and resid 919 through 929 removed outlier: 3.513A pdb=" N SER B 923 " --> pdb=" O ASP B 919 " (cutoff:3.500A) Processing helix chain 'B' and resid 937 through 951 removed outlier: 3.967A pdb=" N PHE B 946 " --> pdb=" O ALA B 942 " (cutoff:3.500A) Processing helix chain 'B' and resid 955 through 965 removed outlier: 4.623A pdb=" N ASN B 961 " --> pdb=" O MET B 957 " (cutoff:3.500A) Processing helix chain 'B' and resid 986 through 997 Processing helix chain 'B' and resid 1001 through 1015 Processing helix chain 'B' and resid 1024 through 1040 removed outlier: 4.368A pdb=" N GLY B1030 " --> pdb=" O ASP B1026 " (cutoff:3.500A) Processing helix chain 'B' and resid 1045 through 1055 removed outlier: 3.517A pdb=" N GLU B1050 " --> pdb=" O GLU B1046 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLY B1055 " --> pdb=" O TYR B1051 " (cutoff:3.500A) Processing helix chain 'B' and resid 1057 through 1079 removed outlier: 4.086A pdb=" N PHE B1061 " --> pdb=" O LEU B1057 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N MET B1067 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLY B1068 " --> pdb=" O GLY B1064 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 3 through 5 removed outlier: 5.400A pdb=" N ASP C 222 " --> pdb=" O PHE C 197 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N PHE C 197 " --> pdb=" O ASP C 222 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N TYR C 199 " --> pdb=" O ALA C 125 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N ALA C 125 " --> pdb=" O TYR C 199 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N GLU C 201 " --> pdb=" O ILE C 123 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N ILE C 123 " --> pdb=" O GLU C 201 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N ASN C 203 " --> pdb=" O VAL C 121 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N VAL C 121 " --> pdb=" O ASN C 203 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 3 through 5 removed outlier: 5.400A pdb=" N ASP C 222 " --> pdb=" O PHE C 197 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N PHE C 197 " --> pdb=" O ASP C 222 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 32 through 34 removed outlier: 6.513A pdb=" N LEU C 55 " --> pdb=" O ASN C 75 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 93 through 95 Processing sheet with id=AA5, first strand: chain 'C' and resid 263 through 268 Processing sheet with id=AA6, first strand: chain 'C' and resid 275 through 277 Processing sheet with id=AA7, first strand: chain 'C' and resid 537 through 543 removed outlier: 7.118A pdb=" N ALA C 527 " --> pdb=" O PRO C 551 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N PHE C 553 " --> pdb=" O ALA C 527 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N MET C 529 " --> pdb=" O PHE C 553 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N ALA C 499 " --> pdb=" O ALA C 527 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N MET C 529 " --> pdb=" O ALA C 499 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N VAL C 501 " --> pdb=" O MET C 529 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N LYS C 498 " --> pdb=" O VAL C 566 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N VAL C 568 " --> pdb=" O LYS C 498 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 634 through 635 removed outlier: 6.687A pdb=" N VAL C 657 " --> pdb=" O TYR C 682 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N GLY C 684 " --> pdb=" O VAL C 657 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N TYR C 659 " --> pdb=" O GLY C 684 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N ALA C 686 " --> pdb=" O TYR C 659 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N SER C 661 " --> pdb=" O ALA C 686 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N ILE C 713 " --> pdb=" O VAL C 741 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N TRP C 743 " --> pdb=" O ILE C 713 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N VAL C 715 " --> pdb=" O TRP C 743 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ILE C 745 " --> pdb=" O VAL C 715 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N GLY C 717 " --> pdb=" O ILE C 745 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 32 through 34 removed outlier: 3.805A pdb=" N GLU D 108 " --> pdb=" O VAL D 56 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 150 through 155 removed outlier: 7.880A pdb=" N VAL D 121 " --> pdb=" O ASN D 203 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N ASN D 203 " --> pdb=" O VAL D 121 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N ILE D 123 " --> pdb=" O GLU D 201 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N GLU D 201 " --> pdb=" O ILE D 123 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N ALA D 125 " --> pdb=" O TYR D 199 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N TYR D 199 " --> pdb=" O ALA D 125 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 150 through 155 removed outlier: 7.880A pdb=" N VAL D 121 " --> pdb=" O ASN D 203 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N ASN D 203 " --> pdb=" O VAL D 121 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N ILE D 123 " --> pdb=" O GLU D 201 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N GLU D 201 " --> pdb=" O ILE D 123 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N ALA D 125 " --> pdb=" O TYR D 199 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N TYR D 199 " --> pdb=" O ALA D 125 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N LYS D 220 " --> pdb=" O THR D 198 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N ALA D 218 " --> pdb=" O LEU D 200 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 263 through 268 removed outlier: 8.000A pdb=" N ILE D 275 " --> pdb=" O ASN D 303 " (cutoff:3.500A) removed outlier: 8.787A pdb=" N GLY D 305 " --> pdb=" O ILE D 275 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N THR D 277 " --> pdb=" O GLY D 305 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N TYR D 307 " --> pdb=" O THR D 277 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N VAL D 279 " --> pdb=" O TYR D 307 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 537 through 543 removed outlier: 7.054A pdb=" N ALA D 527 " --> pdb=" O PRO D 551 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N PHE D 553 " --> pdb=" O ALA D 527 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N MET D 529 " --> pdb=" O PHE D 553 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N ALA D 499 " --> pdb=" O ALA D 527 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N MET D 529 " --> pdb=" O ALA D 499 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N VAL D 501 " --> pdb=" O MET D 529 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N LYS D 498 " --> pdb=" O VAL D 566 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL D 568 " --> pdb=" O LYS D 498 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ASP D 567 " --> pdb=" O THR D 593 " (cutoff:3.500A) removed outlier: 8.099A pdb=" N ALA D 595 " --> pdb=" O ASP D 567 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N LEU D 569 " --> pdb=" O ALA D 595 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 634 through 635 removed outlier: 4.644A pdb=" N GLY D 627 " --> pdb=" O ALA D 686 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ALA D 686 " --> pdb=" O GLY D 627 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N VAL D 657 " --> pdb=" O TYR D 682 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N GLY D 684 " --> pdb=" O VAL D 657 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N TYR D 659 " --> pdb=" O GLY D 684 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N ALA D 686 " --> pdb=" O TYR D 659 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N SER D 661 " --> pdb=" O ALA D 686 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N ILE D 713 " --> pdb=" O VAL D 741 " (cutoff:3.500A) removed outlier: 8.058A pdb=" N TRP D 743 " --> pdb=" O ILE D 713 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N VAL D 715 " --> pdb=" O TRP D 743 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 32 through 34 Processing sheet with id=AB7, first strand: chain 'A' and resid 93 through 95 Processing sheet with id=AB8, first strand: chain 'A' and resid 120 through 124 removed outlier: 3.567A pdb=" N TYR A 120 " --> pdb=" O HIS A 135 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 199 through 201 Processing sheet with id=AC1, first strand: chain 'A' and resid 263 through 268 Processing sheet with id=AC2, first strand: chain 'A' and resid 275 through 277 removed outlier: 6.324A pdb=" N LEU A 338 " --> pdb=" O PHE A 376 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 499 through 502 removed outlier: 6.567A pdb=" N LEU A 569 " --> pdb=" O ALA A 595 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 537 through 543 Processing sheet with id=AC5, first strand: chain 'A' and resid 681 through 686 removed outlier: 5.237A pdb=" N VAL A 657 " --> pdb=" O VAL A 681 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N GLU A 683 " --> pdb=" O VAL A 657 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 32 through 34 Processing sheet with id=AC7, first strand: chain 'B' and resid 93 through 95 Processing sheet with id=AC8, first strand: chain 'B' and resid 150 through 155 removed outlier: 5.261A pdb=" N PHE B 119 " --> pdb=" O PRO B 204 " (cutoff:3.500A) removed outlier: 8.497A pdb=" N THR B 198 " --> pdb=" O ALA B 125 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 150 through 155 removed outlier: 5.261A pdb=" N PHE B 119 " --> pdb=" O PRO B 204 " (cutoff:3.500A) removed outlier: 8.497A pdb=" N THR B 198 " --> pdb=" O ALA B 125 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N LYS B 220 " --> pdb=" O THR B 198 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LEU B 200 " --> pdb=" O ALA B 218 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N ALA B 218 " --> pdb=" O LEU B 200 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 263 through 268 removed outlier: 8.019A pdb=" N ILE B 275 " --> pdb=" O ASN B 303 " (cutoff:3.500A) removed outlier: 8.780A pdb=" N GLY B 305 " --> pdb=" O ILE B 275 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N THR B 277 " --> pdb=" O GLY B 305 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N TYR B 307 " --> pdb=" O THR B 277 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N VAL B 279 " --> pdb=" O TYR B 307 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLY B 341 " --> pdb=" O MET B 278 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ALA B 280 " --> pdb=" O GLY B 341 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N LYS B 336 " --> pdb=" O THR B 374 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N PHE B 376 " --> pdb=" O LYS B 336 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N LEU B 338 " --> pdb=" O PHE B 376 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N ARG B 378 " --> pdb=" O LEU B 338 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ILE B 340 " --> pdb=" O ARG B 378 " (cutoff:3.500A) removed outlier: 8.536A pdb=" N HIS B 403 " --> pdb=" O VAL B 373 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ILE B 375 " --> pdb=" O HIS B 403 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N PHE B 405 " --> pdb=" O ILE B 375 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N VAL B 377 " --> pdb=" O PHE B 405 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 537 through 543 removed outlier: 8.971A pdb=" N ALA B 527 " --> pdb=" O LEU B 549 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N ALA B 499 " --> pdb=" O ALA B 527 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N MET B 529 " --> pdb=" O ALA B 499 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N VAL B 501 " --> pdb=" O MET B 529 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE B 500 " --> pdb=" O VAL B 568 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 634 through 635 removed outlier: 4.445A pdb=" N GLY B 627 " --> pdb=" O ALA B 686 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N VAL B 657 " --> pdb=" O TYR B 682 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N GLY B 684 " --> pdb=" O VAL B 657 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N TYR B 659 " --> pdb=" O GLY B 684 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N ALA B 686 " --> pdb=" O TYR B 659 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N SER B 661 " --> pdb=" O ALA B 686 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N ALA B 658 " --> pdb=" O VAL B 714 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N LEU B 716 " --> pdb=" O ALA B 658 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N VAL B 660 " --> pdb=" O LEU B 716 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N GLU B 718 " --> pdb=" O VAL B 660 " (cutoff:3.500A) 1384 hydrogen bonds defined for protein. 3990 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.46 Time building geometry restraints manager: 3.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.62: 32089 1.62 - 2.06: 320 2.06 - 2.50: 4 2.50 - 2.94: 0 2.94 - 3.39: 2 Bond restraints: 32415 Sorted by residual: bond pdb=" CD1 TYR A 692 " pdb=" CE1 TYR A 692 " ideal model delta sigma weight residual 1.382 3.387 -2.005 3.00e-02 1.11e+03 4.47e+03 bond pdb=" CD2 TYR A 692 " pdb=" CE2 TYR A 692 " ideal model delta sigma weight residual 1.382 2.958 -1.576 3.00e-02 1.11e+03 2.76e+03 bond pdb=" C ARG A 127 " pdb=" N GLU A 128 " ideal model delta sigma weight residual 1.333 1.844 -0.511 1.24e-02 6.50e+03 1.70e+03 bond pdb=" CE1 TYR A 692 " pdb=" CZ TYR A 692 " ideal model delta sigma weight residual 1.378 2.344 -0.966 2.40e-02 1.74e+03 1.62e+03 bond pdb=" CE2 TYR A 692 " pdb=" CZ TYR A 692 " ideal model delta sigma weight residual 1.378 2.290 -0.912 2.40e-02 1.74e+03 1.44e+03 ... (remaining 32410 not shown) Histogram of bond angle deviations from ideal: 0.00 - 12.72: 43817 12.72 - 25.45: 82 25.45 - 38.17: 6 38.17 - 50.89: 1 50.89 - 63.62: 1 Bond angle restraints: 43907 Sorted by residual: angle pdb=" C ARG A 127 " pdb=" N GLU A 128 " pdb=" CA GLU A 128 " ideal model delta sigma weight residual 120.89 165.48 -44.59 1.50e+00 4.44e-01 8.84e+02 angle pdb=" O PRO C 817 " pdb=" C PRO C 817 " pdb=" N PRO C 818 " ideal model delta sigma weight residual 121.15 130.82 -9.67 4.70e-01 4.53e+00 4.23e+02 angle pdb=" CA LEU A 368 " pdb=" CB LEU A 368 " pdb=" CG LEU A 368 " ideal model delta sigma weight residual 116.30 179.92 -63.62 3.50e+00 8.16e-02 3.30e+02 angle pdb=" C LEU A 368 " pdb=" N LYS A 369 " pdb=" CA LYS A 369 " ideal model delta sigma weight residual 122.24 150.14 -27.90 1.57e+00 4.06e-01 3.16e+02 angle pdb=" CD1 LEU A 368 " pdb=" CG LEU A 368 " pdb=" CD2 LEU A 368 " ideal model delta sigma weight residual 110.80 73.90 36.90 2.20e+00 2.07e-01 2.81e+02 ... (remaining 43902 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.10: 17094 18.10 - 36.19: 1860 36.19 - 54.29: 387 54.29 - 72.38: 83 72.38 - 90.48: 15 Dihedral angle restraints: 19439 sinusoidal: 7800 harmonic: 11639 Sorted by residual: dihedral pdb=" CA VAL D 74 " pdb=" C VAL D 74 " pdb=" N ASN D 75 " pdb=" CA ASN D 75 " ideal model delta harmonic sigma weight residual 180.00 97.19 82.81 0 5.00e+00 4.00e-02 2.74e+02 dihedral pdb=" CA VAL D 72 " pdb=" C VAL D 72 " pdb=" N GLY D 73 " pdb=" CA GLY D 73 " ideal model delta harmonic sigma weight residual -180.00 -105.49 -74.51 0 5.00e+00 4.00e-02 2.22e+02 dihedral pdb=" CA VAL A 121 " pdb=" C VAL A 121 " pdb=" N CYS A 122 " pdb=" CA CYS A 122 " ideal model delta harmonic sigma weight residual 180.00 119.42 60.58 0 5.00e+00 4.00e-02 1.47e+02 ... (remaining 19436 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.302: 4854 0.302 - 0.603: 42 0.603 - 0.904: 1 0.904 - 1.206: 2 1.206 - 1.507: 3 Chirality restraints: 4902 Sorted by residual: chirality pdb=" CB THR A 328 " pdb=" CA THR A 328 " pdb=" OG1 THR A 328 " pdb=" CG2 THR A 328 " both_signs ideal model delta sigma weight residual False 2.55 1.04 1.51 2.00e-01 2.50e+01 5.68e+01 chirality pdb=" CB VAL D 74 " pdb=" CA VAL D 74 " pdb=" CG1 VAL D 74 " pdb=" CG2 VAL D 74 " both_signs ideal model delta sigma weight residual False -2.63 -1.18 -1.44 2.00e-01 2.50e+01 5.22e+01 chirality pdb=" CG LEU A 324 " pdb=" CB LEU A 324 " pdb=" CD1 LEU A 324 " pdb=" CD2 LEU A 324 " both_signs ideal model delta sigma weight residual False -2.59 -1.31 -1.28 2.00e-01 2.50e+01 4.10e+01 ... (remaining 4899 not shown) Planarity restraints: 5617 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 366 " -0.106 5.00e-02 4.00e+02 1.62e-01 4.19e+01 pdb=" N PRO A 367 " 0.280 5.00e-02 4.00e+02 pdb=" CA PRO A 367 " -0.095 5.00e-02 4.00e+02 pdb=" CD PRO A 367 " -0.079 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 120 " 0.030 2.00e-02 2.50e+03 6.01e-02 3.61e+01 pdb=" C TYR A 120 " -0.104 2.00e-02 2.50e+03 pdb=" O TYR A 120 " 0.039 2.00e-02 2.50e+03 pdb=" N VAL A 121 " 0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 118 " -0.027 2.00e-02 2.50e+03 5.44e-02 2.96e+01 pdb=" C GLU A 118 " 0.094 2.00e-02 2.50e+03 pdb=" O GLU A 118 " -0.034 2.00e-02 2.50e+03 pdb=" N PHE A 119 " -0.032 2.00e-02 2.50e+03 ... (remaining 5614 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 2189 2.72 - 3.26: 30878 3.26 - 3.81: 53520 3.81 - 4.35: 65433 4.35 - 4.90: 106175 Nonbonded interactions: 258195 Sorted by model distance: nonbonded pdb=" OE2 GLU B 92 " pdb=" OG1 THR B 99 " model vdw 2.172 3.040 nonbonded pdb=" CD LYS A1018 " pdb=" O1A COA A1201 " model vdw 2.175 2.752 nonbonded pdb=" O GLY C 622 " pdb=" OG1 THR C 625 " model vdw 2.179 3.040 nonbonded pdb=" O ILE A 344 " pdb=" N GLY A 381 " model vdw 2.186 3.120 nonbonded pdb=" OG1 THR A 412 " pdb=" OD1 ASP A 791 " model vdw 2.193 3.040 ... (remaining 258190 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: 0.03 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 19 or resid 21 through 225 or resid 227 through \ 1099)) selection = (chain 'B' and (resid 2 through 19 or resid 21 through 225 or resid 227 through \ 1099)) selection = (chain 'C' and (resid 2 through 19 or resid 21 through 225 or resid 227 through \ 1099)) selection = (chain 'D' and (resid 2 through 19 or resid 21 through 225 or resid 227 through \ 1099)) } 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 group one per residue 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: 0.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.030 Extract box with map and model: 0.590 Check model and map are aligned: 0.090 Set scattering table: 0.090 Process input model: 35.460 Find NCS groups from input model: 0.910 Set up NCS constraints: 0.100 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:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5066 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 : 0.021 2.005 32416 Z= 0.949 Angle : 1.748 63.616 43907 Z= 0.946 Chirality : 0.092 1.507 4902 Planarity : 0.010 0.162 5617 Dihedral : 15.870 90.480 12047 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 14.46 Ramachandran Plot: Outliers : 0.74 % Allowed : 8.40 % Favored : 90.86 % Rotamer: Outliers : 1.60 % Allowed : 8.82 % Favored : 89.58 % Cbeta Deviations : 0.49 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 3.06 % Twisted General : 1.36 % 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: -4.29 (0.10), residues: 4066 helix: -2.97 (0.09), residues: 1598 sheet: -1.81 (0.22), residues: 436 loop : -2.98 (0.11), residues: 2032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.026 0.002 ARG A 127 TYR 0.057 0.004 TYR A 692 PHE 0.079 0.004 PHE D 110 TRP 0.069 0.005 TRP D 84 HIS 0.029 0.004 HIS A 135 Details of bonding type rmsd covalent geometry : bond 0.02072 (32415) covalent geometry : angle 1.74776 (43907) hydrogen bonds : bond 0.16742 ( 1347) hydrogen bonds : angle 9.54414 ( 3990) Misc. bond : bond 0.31034 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8132 Ramachandran restraints generated. 4066 Oldfield, 0 Emsley, 4066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8132 Ramachandran restraints generated. 4066 Oldfield, 0 Emsley, 4066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 881 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 831 time to evaluate : 1.216 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 10 THR cc_start: 0.7420 (m) cc_final: 0.7189 (m) REVERT: C 194 ASP cc_start: 0.6850 (m-30) cc_final: 0.6563 (t0) REVERT: C 235 ASP cc_start: 0.7259 (p0) cc_final: 0.6809 (p0) REVERT: C 278 MET cc_start: 0.7356 (ttt) cc_final: 0.7052 (ttp) REVERT: C 391 MET cc_start: 0.6707 (ttp) cc_final: 0.6253 (ttp) REVERT: C 519 CYS cc_start: 0.7727 (m) cc_final: 0.7492 (p) REVERT: C 584 GLU cc_start: 0.7881 (tm-30) cc_final: 0.7632 (tm-30) REVERT: C 687 ILE cc_start: 0.8541 (pt) cc_final: 0.8057 (mt) REVERT: C 704 TYR cc_start: 0.7438 (m-10) cc_final: 0.7125 (m-10) REVERT: D 404 VAL cc_start: 0.7609 (m) cc_final: 0.7217 (m) REVERT: D 618 VAL cc_start: 0.7322 (t) cc_final: 0.6965 (t) REVERT: D 869 ILE cc_start: 0.8698 (OUTLIER) cc_final: 0.8453 (pt) REVERT: D 1079 LEU cc_start: 0.8460 (mp) cc_final: 0.7789 (tp) REVERT: A 208 THR cc_start: 0.3105 (OUTLIER) cc_final: 0.2306 (m) REVERT: A 625 THR cc_start: 0.4958 (t) cc_final: 0.4650 (t) REVERT: A 715 VAL cc_start: 0.3744 (OUTLIER) cc_final: 0.3150 (t) REVERT: A 867 MET cc_start: 0.6562 (ptp) cc_final: 0.6282 (mtm) REVERT: A 873 LEU cc_start: 0.7654 (OUTLIER) cc_final: 0.6513 (mt) REVERT: A 915 ARG cc_start: 0.7026 (ttt180) cc_final: 0.6647 (mtp85) REVERT: A 990 LEU cc_start: 0.9312 (tp) cc_final: 0.9098 (tp) REVERT: B 353 THR cc_start: 0.7808 (p) cc_final: 0.7512 (m) REVERT: B 497 THR cc_start: 0.6399 (m) cc_final: 0.4994 (p) REVERT: B 580 ASP cc_start: 0.7478 (m-30) cc_final: 0.6810 (m-30) REVERT: B 651 LEU cc_start: 0.8371 (mt) cc_final: 0.8113 (mt) REVERT: B 843 SER cc_start: 0.8708 (m) cc_final: 0.8426 (p) REVERT: B 869 ILE cc_start: 0.8351 (pt) cc_final: 0.7919 (pt) REVERT: B 873 LEU cc_start: 0.8706 (mp) cc_final: 0.7709 (tp) REVERT: B 959 PHE cc_start: 0.7765 (t80) cc_final: 0.7301 (t80) REVERT: B 1052 ILE cc_start: 0.8507 (mm) cc_final: 0.8175 (mm) outliers start: 50 outliers final: 12 residues processed: 871 average time/residue: 0.2071 time to fit residues: 279.9718 Evaluate side-chains 454 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 438 time to evaluate : 1.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 197 optimal weight: 0.9990 chunk 388 optimal weight: 6.9990 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 40.0000 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 40.0000 chunk 207 optimal weight: 6.9990 chunk 401 optimal weight: 6.9990 chunk 155 optimal weight: 8.9990 chunk 244 optimal weight: 7.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 45 GLN C 61 GLN C 104 ASN C 555 ASN C 638 ASN C 705 GLN C 850 GLN C 908 HIS C 961 ASN ** D 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 113 HIS D 332 HIS D 421 HIS ** D 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 777 GLN ** D 900 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 908 HIS D 961 ASN D 996 GLN D 997 HIS D1024 ASN ** D1076 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 299 ASN ** A 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 346 ASN A 587 ASN A 700 HIS A 888 GLN A 900 HIS A 908 HIS A 961 ASN ** A1072 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1076 GLN B 45 GLN ** B 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 203 ASN ** B 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 403 HIS B 505 GLN B 587 ASN B 615 GLN ** B 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 850 GLN B 900 HIS B 908 HIS ** B 975 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 988 GLN B 997 HIS Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.124338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.100337 restraints weight = 221768.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.100395 restraints weight = 195274.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.102306 restraints weight = 137467.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.102365 restraints weight = 94123.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.102576 restraints weight = 82553.499| |-----------------------------------------------------------------------------| r_work (final): 0.3907 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3907 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3907 r_free = 0.3907 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3907 r_free = 0.3907 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3907 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6697 moved from start: 0.3732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 1.704 32416 Z= 0.488 Angle : 1.080 34.236 43907 Z= 0.563 Chirality : 0.058 0.520 4902 Planarity : 0.008 0.122 5617 Dihedral : 8.522 89.295 4547 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 23.88 Ramachandran Plot: Outliers : 0.32 % Allowed : 8.45 % Favored : 91.23 % Rotamer: Outliers : 0.39 % Allowed : 4.69 % Favored : 94.92 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 1.02 % Twisted General : 0.57 % 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: -3.36 (0.11), residues: 4066 helix: -1.74 (0.11), residues: 1659 sheet: -1.78 (0.22), residues: 480 loop : -2.79 (0.12), residues: 1927 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG C 42 TYR 0.071 0.003 TYR A 692 PHE 0.044 0.003 PHE C 189 TRP 0.022 0.003 TRP D 233 HIS 0.016 0.002 HIS D 421 Details of bonding type rmsd covalent geometry : bond 0.01273 (32415) covalent geometry : angle 1.07997 (43907) hydrogen bonds : bond 0.05600 ( 1347) hydrogen bonds : angle 6.73896 ( 3990) Misc. bond : bond 0.00114 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8132 Ramachandran restraints generated. 4066 Oldfield, 0 Emsley, 4066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8132 Ramachandran restraints generated. 4066 Oldfield, 0 Emsley, 4066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 552 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 543 time to evaluate : 1.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 10 THR cc_start: 0.8547 (m) cc_final: 0.8171 (m) REVERT: C 141 ASP cc_start: 0.6909 (t0) cc_final: 0.6646 (t70) REVERT: C 194 ASP cc_start: 0.7883 (m-30) cc_final: 0.7066 (t0) REVERT: C 412 THR cc_start: 0.7925 (p) cc_final: 0.7413 (t) REVERT: C 704 TYR cc_start: 0.7943 (m-10) cc_final: 0.7465 (m-10) REVERT: C 705 GLN cc_start: 0.6930 (OUTLIER) cc_final: 0.6507 (tm-30) REVERT: C 877 TRP cc_start: 0.7545 (m-10) cc_final: 0.7272 (m-10) REVERT: C 895 MET cc_start: 0.8409 (mtp) cc_final: 0.7889 (mtp) REVERT: C 921 VAL cc_start: 0.8909 (p) cc_final: 0.8664 (m) REVERT: D 238 PHE cc_start: 0.6742 (m-80) cc_final: 0.6259 (m-80) REVERT: D 288 TYR cc_start: 0.5336 (m-80) cc_final: 0.5011 (m-80) REVERT: D 892 MET cc_start: 0.7527 (ptp) cc_final: 0.7148 (ptp) REVERT: A 370 GLU cc_start: 0.5561 (tt0) cc_final: 0.5094 (pp20) REVERT: A 373 VAL cc_start: 0.2831 (t) cc_final: 0.2627 (t) REVERT: A 501 VAL cc_start: 0.4387 (t) cc_final: 0.4116 (p) REVERT: A 666 MET cc_start: 0.4874 (tpt) cc_final: 0.3781 (ttt) REVERT: A 682 TYR cc_start: 0.4889 (t80) cc_final: 0.4087 (t80) REVERT: B 45 GLN cc_start: 0.8089 (OUTLIER) cc_final: 0.7812 (mm110) REVERT: B 317 TYR cc_start: 0.7562 (t80) cc_final: 0.7112 (t80) REVERT: B 497 THR cc_start: 0.7464 (m) cc_final: 0.5148 (p) REVERT: B 542 TYR cc_start: 0.6936 (m-80) cc_final: 0.6310 (m-80) REVERT: B 580 ASP cc_start: 0.8977 (m-30) cc_final: 0.8668 (m-30) REVERT: B 629 ILE cc_start: 0.8958 (tt) cc_final: 0.8726 (tt) REVERT: B 843 SER cc_start: 0.8538 (m) cc_final: 0.8188 (p) REVERT: B 873 LEU cc_start: 0.8628 (mp) cc_final: 0.7649 (mt) REVERT: B 959 PHE cc_start: 0.7276 (t80) cc_final: 0.6968 (t80) REVERT: B 988 GLN cc_start: 0.7804 (OUTLIER) cc_final: 0.7330 (tp-100) outliers start: 9 outliers final: 1 residues processed: 552 average time/residue: 0.1977 time to fit residues: 175.5104 Evaluate side-chains 370 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 366 time to evaluate : 1.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 254 optimal weight: 8.9990 chunk 404 optimal weight: 3.9990 chunk 104 optimal weight: 4.9990 chunk 307 optimal weight: 8.9990 chunk 41 optimal weight: 4.9990 chunk 131 optimal weight: 0.4980 chunk 27 optimal weight: 20.0000 chunk 210 optimal weight: 40.0000 chunk 73 optimal weight: 20.0000 chunk 225 optimal weight: 0.4980 chunk 49 optimal weight: 20.0000 overall best weight: 2.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 900 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 909 ASN ** D1081 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 135 HIS ** A 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 505 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 537 HIS ** A1072 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 45 GLN ** B 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 638 ASN B 981 ASN B1024 ASN B1076 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.124295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.099111 restraints weight = 222676.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.100781 restraints weight = 188489.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.101766 restraints weight = 124071.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.102675 restraints weight = 83779.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.103184 restraints weight = 72330.124| |-----------------------------------------------------------------------------| r_work (final): 0.3936 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3936 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3936 r_free = 0.3936 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3936 r_free = 0.3936 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3936 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6712 moved from start: 0.4626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 1.743 32416 Z= 0.452 Angle : 0.944 28.848 43907 Z= 0.491 Chirality : 0.054 0.322 4902 Planarity : 0.006 0.094 5617 Dihedral : 7.914 84.672 4547 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 20.06 Ramachandran Plot: Outliers : 0.22 % Allowed : 8.92 % Favored : 90.86 % Rotamer: Outliers : 0.30 % Allowed : 3.06 % Favored : 96.64 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 2.55 % Twisted General : 0.41 % 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: -2.80 (0.12), residues: 4066 helix: -1.14 (0.12), residues: 1680 sheet: -1.45 (0.22), residues: 484 loop : -2.63 (0.12), residues: 1902 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 42 TYR 0.058 0.002 TYR A 120 PHE 0.027 0.002 PHE B 889 TRP 0.042 0.002 TRP B 877 HIS 0.010 0.001 HIS A 545 Details of bonding type rmsd covalent geometry : bond 0.01222 (32415) covalent geometry : angle 0.94416 (43907) hydrogen bonds : bond 0.04757 ( 1347) hydrogen bonds : angle 6.05743 ( 3990) Misc. bond : bond 0.00042 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8132 Ramachandran restraints generated. 4066 Oldfield, 0 Emsley, 4066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8132 Ramachandran restraints generated. 4066 Oldfield, 0 Emsley, 4066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 502 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 496 time to evaluate : 1.229 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 141 ASP cc_start: 0.6969 (t0) cc_final: 0.6603 (t70) REVERT: C 391 MET cc_start: 0.7689 (ttt) cc_final: 0.7334 (ttt) REVERT: C 704 TYR cc_start: 0.7723 (m-10) cc_final: 0.7400 (m-10) REVERT: C 895 MET cc_start: 0.8493 (mtp) cc_final: 0.7840 (mtp) REVERT: C 1067 MET cc_start: 0.7125 (tpt) cc_final: 0.6822 (tpt) REVERT: D 191 PHE cc_start: 0.5262 (t80) cc_final: 0.4375 (t80) REVERT: D 288 TYR cc_start: 0.5217 (m-80) cc_final: 0.4920 (m-80) REVERT: D 824 ASP cc_start: 0.8113 (t70) cc_final: 0.7827 (t0) REVERT: D 846 ASP cc_start: 0.8220 (t70) cc_final: 0.7939 (t0) REVERT: D 928 LEU cc_start: 0.8860 (mt) cc_final: 0.8648 (mt) REVERT: A 510 GLN cc_start: 0.7437 (mm110) cc_final: 0.7087 (mt0) REVERT: A 529 MET cc_start: 0.3655 (mpp) cc_final: 0.3140 (mpp) REVERT: A 653 ARG cc_start: 0.4917 (mmm160) cc_final: 0.3713 (mtt180) REVERT: A 666 MET cc_start: 0.5065 (tpt) cc_final: 0.4459 (ttt) REVERT: A 682 TYR cc_start: 0.5110 (t80) cc_final: 0.4493 (t80) REVERT: A 890 ILE cc_start: 0.9111 (mt) cc_final: 0.8813 (tp) REVERT: B 45 GLN cc_start: 0.7721 (OUTLIER) cc_final: 0.7446 (mm110) REVERT: B 327 MET cc_start: 0.7977 (ttt) cc_final: 0.7299 (tmm) REVERT: B 533 PHE cc_start: 0.8080 (m-80) cc_final: 0.7712 (m-80) REVERT: B 560 MET cc_start: 0.6831 (mmm) cc_final: 0.6504 (mmm) REVERT: B 580 ASP cc_start: 0.8983 (m-30) cc_final: 0.8760 (m-30) REVERT: B 674 ILE cc_start: 0.9219 (mt) cc_final: 0.8981 (mt) REVERT: B 843 SER cc_start: 0.8461 (m) cc_final: 0.8133 (p) REVERT: B 873 LEU cc_start: 0.8720 (mp) cc_final: 0.8323 (mt) REVERT: B 909 ASN cc_start: 0.9117 (m-40) cc_final: 0.8252 (t0) REVERT: B 959 PHE cc_start: 0.7331 (t80) cc_final: 0.7052 (t80) REVERT: B 1011 GLU cc_start: 0.7905 (pt0) cc_final: 0.7242 (pt0) outliers start: 6 outliers final: 1 residues processed: 502 average time/residue: 0.1865 time to fit residues: 154.2574 Evaluate side-chains 373 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 371 time to evaluate : 1.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 319 optimal weight: 20.0000 chunk 253 optimal weight: 10.0000 chunk 321 optimal weight: 4.9990 chunk 126 optimal weight: 4.9990 chunk 187 optimal weight: 4.9990 chunk 107 optimal weight: 50.0000 chunk 87 optimal weight: 0.5980 chunk 139 optimal weight: 50.0000 chunk 134 optimal weight: 20.0000 chunk 377 optimal weight: 20.0000 chunk 200 optimal weight: 6.9990 overall best weight: 4.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 45 GLN C 315 GLN C 505 GLN C1098 HIS ** D 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1081 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 150 GLN ** A 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 505 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1072 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 332 HIS ** B 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 403 HIS ** B 505 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1024 ASN B1086 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.122512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.097898 restraints weight = 261823.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.100396 restraints weight = 252760.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.102045 restraints weight = 139084.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.102194 restraints weight = 104702.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.103257 restraints weight = 83137.778| |-----------------------------------------------------------------------------| r_work (final): 0.3924 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3925 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3925 r_free = 0.3925 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3925 r_free = 0.3925 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3925 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6757 moved from start: 0.5280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 1.736 32416 Z= 0.450 Angle : 0.902 31.990 43907 Z= 0.467 Chirality : 0.052 0.450 4902 Planarity : 0.006 0.094 5617 Dihedral : 7.585 84.460 4547 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 19.99 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.92 % Favored : 90.91 % Rotamer: Outliers : 0.15 % Allowed : 2.40 % Favored : 97.45 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 1.53 % Twisted General : 0.33 % 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: -2.48 (0.12), residues: 4066 helix: -0.80 (0.12), residues: 1705 sheet: -1.36 (0.22), residues: 502 loop : -2.55 (0.13), residues: 1859 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 379 TYR 0.038 0.002 TYR C1073 PHE 0.024 0.002 PHE D 105 TRP 0.055 0.002 TRP B 877 HIS 0.009 0.001 HIS A1086 Details of bonding type rmsd covalent geometry : bond 0.01227 (32415) covalent geometry : angle 0.90238 (43907) hydrogen bonds : bond 0.04349 ( 1347) hydrogen bonds : angle 5.76052 ( 3990) Misc. bond : bond 0.00003 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8132 Ramachandran restraints generated. 4066 Oldfield, 0 Emsley, 4066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8132 Ramachandran restraints generated. 4066 Oldfield, 0 Emsley, 4066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 463 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 462 time to evaluate : 1.243 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 141 ASP cc_start: 0.7060 (t0) cc_final: 0.6665 (t70) REVERT: C 391 MET cc_start: 0.7407 (ttt) cc_final: 0.7038 (ttt) REVERT: C 560 MET cc_start: 0.8629 (mpp) cc_final: 0.8393 (mpp) REVERT: C 823 MET cc_start: 0.8520 (ppp) cc_final: 0.7970 (ppp) REVERT: C 1067 MET cc_start: 0.7200 (tpt) cc_final: 0.6896 (tpt) REVERT: D 253 ILE cc_start: 0.7660 (mm) cc_final: 0.6788 (pt) REVERT: D 288 TYR cc_start: 0.5171 (m-80) cc_final: 0.4901 (m-80) REVERT: D 678 THR cc_start: 0.8865 (m) cc_final: 0.8559 (m) REVERT: D 891 GLU cc_start: 0.7982 (mp0) cc_final: 0.7492 (mm-30) REVERT: A 417 MET cc_start: -0.2035 (ptm) cc_final: -0.2238 (ptt) REVERT: A 529 MET cc_start: 0.3738 (mpp) cc_final: 0.3248 (mpp) REVERT: A 653 ARG cc_start: 0.5222 (mmm160) cc_final: 0.4202 (mtt180) REVERT: A 666 MET cc_start: 0.5572 (tpt) cc_final: 0.5036 (ttt) REVERT: A 890 ILE cc_start: 0.9126 (mt) cc_final: 0.8771 (tp) REVERT: A 924 LEU cc_start: 0.8786 (tp) cc_final: 0.8549 (tp) REVERT: B 179 GLU cc_start: 0.7191 (tp30) cc_final: 0.5979 (pm20) REVERT: B 327 MET cc_start: 0.8285 (ttt) cc_final: 0.7911 (ttt) REVERT: B 533 PHE cc_start: 0.7998 (m-80) cc_final: 0.7532 (m-80) REVERT: B 560 MET cc_start: 0.6677 (mmm) cc_final: 0.6466 (mtp) REVERT: B 566 VAL cc_start: 0.8383 (t) cc_final: 0.8097 (m) REVERT: B 580 ASP cc_start: 0.8984 (m-30) cc_final: 0.8688 (m-30) REVERT: B 959 PHE cc_start: 0.7202 (t80) cc_final: 0.6902 (t80) REVERT: B 1011 GLU cc_start: 0.8092 (pt0) cc_final: 0.7463 (pt0) outliers start: 1 outliers final: 0 residues processed: 463 average time/residue: 0.1861 time to fit residues: 142.2316 Evaluate side-chains 338 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 338 time to evaluate : 1.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 343 optimal weight: 6.9990 chunk 258 optimal weight: 7.9990 chunk 156 optimal weight: 20.0000 chunk 203 optimal weight: 9.9990 chunk 353 optimal weight: 10.0000 chunk 115 optimal weight: 30.0000 chunk 62 optimal weight: 20.0000 chunk 81 optimal weight: 5.9990 chunk 263 optimal weight: 50.0000 chunk 30 optimal weight: 30.0000 chunk 271 optimal weight: 40.0000 overall best weight: 8.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 645 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 505 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1024 ASN A1076 GLN B 61 GLN ** B 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 403 HIS B 410 HIS ** B 505 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 645 ASN ** B 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1024 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.119001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.093862 restraints weight = 219577.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.096404 restraints weight = 203562.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.097285 restraints weight = 110579.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.097299 restraints weight = 84091.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.097440 restraints weight = 69650.124| |-----------------------------------------------------------------------------| r_work (final): 0.3807 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3807 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3807 r_free = 0.3807 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3806 r_free = 0.3806 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3806 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6990 moved from start: 0.6282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 1.702 32416 Z= 0.473 Angle : 0.938 24.853 43907 Z= 0.486 Chirality : 0.054 0.415 4902 Planarity : 0.007 0.093 5617 Dihedral : 7.491 55.942 4547 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 23.23 Ramachandran Plot: Outliers : 0.22 % Allowed : 9.41 % Favored : 90.36 % Rotamer: Outliers : 0.12 % Allowed : 2.58 % Favored : 97.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 1.02 % Twisted General : 0.41 % 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: -2.46 (0.12), residues: 4066 helix: -0.70 (0.12), residues: 1699 sheet: -1.54 (0.22), residues: 526 loop : -2.58 (0.13), residues: 1841 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG C 662 TYR 0.034 0.003 TYR C1073 PHE 0.025 0.003 PHE D1061 TRP 0.064 0.003 TRP B 877 HIS 0.014 0.002 HIS A1086 Details of bonding type rmsd covalent geometry : bond 0.01265 (32415) covalent geometry : angle 0.93762 (43907) hydrogen bonds : bond 0.04621 ( 1347) hydrogen bonds : angle 5.85955 ( 3990) Misc. bond : bond 0.00010 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8132 Ramachandran restraints generated. 4066 Oldfield, 0 Emsley, 4066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8132 Ramachandran restraints generated. 4066 Oldfield, 0 Emsley, 4066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 429 time to evaluate : 1.150 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 14 LEU cc_start: 0.8340 (tp) cc_final: 0.8040 (mm) REVERT: C 127 ARG cc_start: 0.7155 (ttt90) cc_final: 0.6353 (ttt-90) REVERT: C 141 ASP cc_start: 0.7206 (t0) cc_final: 0.6727 (t70) REVERT: C 194 ASP cc_start: 0.8427 (m-30) cc_final: 0.7706 (t0) REVERT: C 307 TYR cc_start: 0.7375 (p90) cc_final: 0.7041 (p90) REVERT: C 391 MET cc_start: 0.7691 (ttt) cc_final: 0.7300 (ttt) REVERT: C 560 MET cc_start: 0.8729 (mpp) cc_final: 0.8462 (mpp) REVERT: C 698 MET cc_start: 0.6502 (mmt) cc_final: 0.5901 (tpp) REVERT: C 704 TYR cc_start: 0.7696 (m-80) cc_final: 0.7001 (m-10) REVERT: C 895 MET cc_start: 0.7956 (mtp) cc_final: 0.7602 (mtt) REVERT: D 153 LEU cc_start: 0.8832 (tp) cc_final: 0.8376 (tp) REVERT: D 256 LEU cc_start: 0.8146 (mt) cc_final: 0.7794 (mt) REVERT: D 985 MET cc_start: 0.7056 (mtt) cc_final: 0.6719 (mmm) REVERT: D 1033 PHE cc_start: 0.8338 (t80) cc_final: 0.8116 (t80) REVERT: A 33 ARG cc_start: 0.4869 (pmt-80) cc_final: 0.4654 (ptt90) REVERT: A 529 MET cc_start: 0.4097 (mpp) cc_final: 0.3621 (mpp) REVERT: A 653 ARG cc_start: 0.5096 (mmm160) cc_final: 0.4206 (mtt180) REVERT: A 666 MET cc_start: 0.5842 (tpt) cc_final: 0.5378 (ttt) REVERT: A 890 ILE cc_start: 0.9369 (mt) cc_final: 0.9016 (tp) REVERT: B 179 GLU cc_start: 0.7250 (tp30) cc_final: 0.6242 (pm20) REVERT: B 383 ASN cc_start: 0.8298 (m-40) cc_final: 0.8006 (m-40) REVERT: B 391 MET cc_start: 0.7949 (tmm) cc_final: 0.7658 (ppp) REVERT: B 504 MET cc_start: 0.6898 (mpp) cc_final: 0.6637 (mpp) REVERT: B 514 ASP cc_start: 0.8572 (m-30) cc_final: 0.8345 (m-30) REVERT: B 580 ASP cc_start: 0.9147 (m-30) cc_final: 0.8884 (m-30) REVERT: B 582 THR cc_start: 0.8806 (m) cc_final: 0.8568 (p) REVERT: B 777 GLN cc_start: 0.8630 (mm-40) cc_final: 0.8426 (mm-40) REVERT: B 867 MET cc_start: 0.9108 (ppp) cc_final: 0.8451 (ppp) REVERT: B 959 PHE cc_start: 0.7311 (t80) cc_final: 0.6941 (t80) outliers start: 0 outliers final: 0 residues processed: 429 average time/residue: 0.1911 time to fit residues: 132.7700 Evaluate side-chains 315 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 315 time to evaluate : 1.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 248 optimal weight: 20.0000 chunk 37 optimal weight: 20.0000 chunk 183 optimal weight: 6.9990 chunk 346 optimal weight: 20.0000 chunk 304 optimal weight: 0.0270 chunk 110 optimal weight: 7.9990 chunk 327 optimal weight: 8.9990 chunk 18 optimal weight: 5.9990 chunk 317 optimal weight: 40.0000 chunk 241 optimal weight: 6.9990 chunk 26 optimal weight: 30.0000 overall best weight: 5.6046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 168 HIS ** C 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 988 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 403 HIS ** D 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 403 HIS ** B 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 850 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.119596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.095308 restraints weight = 206982.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.095787 restraints weight = 199321.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.097358 restraints weight = 126697.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.097505 restraints weight = 86292.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.097665 restraints weight = 73283.338| |-----------------------------------------------------------------------------| r_work (final): 0.3819 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3819 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3819 r_free = 0.3819 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3819 r_free = 0.3819 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3819 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6969 moved from start: 0.6708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 1.733 32416 Z= 0.445 Angle : 0.846 25.551 43907 Z= 0.438 Chirality : 0.052 0.337 4902 Planarity : 0.006 0.095 5617 Dihedral : 7.188 58.361 4547 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 20.44 Ramachandran Plot: Outliers : 0.20 % Allowed : 9.09 % Favored : 90.71 % Rotamer: Outliers : 0.12 % Allowed : 1.60 % Favored : 98.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 1.02 % Twisted General : 0.28 % 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: -2.26 (0.12), residues: 4066 helix: -0.50 (0.12), residues: 1717 sheet: -1.49 (0.22), residues: 528 loop : -2.50 (0.13), residues: 1821 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 379 TYR 0.031 0.002 TYR C1073 PHE 0.046 0.002 PHE B 354 TRP 0.046 0.002 TRP B 877 HIS 0.010 0.001 HIS B 700 Details of bonding type rmsd covalent geometry : bond 0.01223 (32415) covalent geometry : angle 0.84603 (43907) hydrogen bonds : bond 0.04210 ( 1347) hydrogen bonds : angle 5.57811 ( 3990) Misc. bond : bond 0.00007 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8132 Ramachandran restraints generated. 4066 Oldfield, 0 Emsley, 4066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8132 Ramachandran restraints generated. 4066 Oldfield, 0 Emsley, 4066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 420 time to evaluate : 1.115 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 14 LEU cc_start: 0.8308 (tp) cc_final: 0.8097 (mm) REVERT: C 141 ASP cc_start: 0.7224 (t0) cc_final: 0.6781 (t70) REVERT: C 560 MET cc_start: 0.8819 (mpp) cc_final: 0.8481 (mpp) REVERT: C 698 MET cc_start: 0.7136 (tpp) cc_final: 0.6921 (tpp) REVERT: C 704 TYR cc_start: 0.7702 (m-80) cc_final: 0.7087 (m-10) REVERT: D 77 THR cc_start: 0.8312 (t) cc_final: 0.8063 (p) REVERT: D 153 LEU cc_start: 0.8895 (tp) cc_final: 0.8429 (tp) REVERT: D 256 LEU cc_start: 0.8082 (mt) cc_final: 0.7661 (mt) REVERT: D 288 TYR cc_start: 0.6041 (m-10) cc_final: 0.5495 (m-80) REVERT: D 666 MET cc_start: 0.7385 (mmp) cc_final: 0.6872 (ptp) REVERT: D 891 GLU cc_start: 0.7929 (mp0) cc_final: 0.7610 (mp0) REVERT: D 985 MET cc_start: 0.7009 (mtt) cc_final: 0.6725 (mmm) REVERT: A 317 TYR cc_start: 0.6816 (t80) cc_final: 0.6614 (t80) REVERT: A 337 ILE cc_start: 0.2403 (mt) cc_final: 0.2107 (mt) REVERT: A 417 MET cc_start: -0.2806 (ptm) cc_final: -0.3027 (ptm) REVERT: A 529 MET cc_start: 0.4406 (mpp) cc_final: 0.3945 (mpp) REVERT: A 653 ARG cc_start: 0.5033 (mmm160) cc_final: 0.4234 (mtt180) REVERT: A 666 MET cc_start: 0.5906 (tpt) cc_final: 0.5503 (ttt) REVERT: A 890 ILE cc_start: 0.9258 (mt) cc_final: 0.8881 (tp) REVERT: B 19 ILE cc_start: 0.5638 (tp) cc_final: 0.4680 (tt) REVERT: B 327 MET cc_start: 0.8407 (ttt) cc_final: 0.7817 (tpp) REVERT: B 383 ASN cc_start: 0.8732 (m-40) cc_final: 0.8500 (m110) REVERT: B 514 ASP cc_start: 0.8601 (m-30) cc_final: 0.8359 (m-30) REVERT: B 580 ASP cc_start: 0.9089 (m-30) cc_final: 0.8886 (m-30) REVERT: B 582 THR cc_start: 0.8873 (m) cc_final: 0.8580 (p) REVERT: B 959 PHE cc_start: 0.7257 (t80) cc_final: 0.6925 (t80) REVERT: B 985 MET cc_start: 0.6277 (mtm) cc_final: 0.5520 (mmp) REVERT: B 1011 GLU cc_start: 0.8149 (pt0) cc_final: 0.7489 (pt0) outliers start: 0 outliers final: 0 residues processed: 420 average time/residue: 0.1882 time to fit residues: 129.1378 Evaluate side-chains 315 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 315 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 261 optimal weight: 6.9990 chunk 27 optimal weight: 8.9990 chunk 265 optimal weight: 5.9990 chunk 221 optimal weight: 0.1980 chunk 291 optimal weight: 9.9990 chunk 203 optimal weight: 0.0370 chunk 25 optimal weight: 7.9990 chunk 107 optimal weight: 0.0970 chunk 65 optimal weight: 20.0000 chunk 374 optimal weight: 30.0000 chunk 114 optimal weight: 50.0000 overall best weight: 2.6660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 410 HIS C 555 ASN ** C 988 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 172 HIS D 403 HIS D 671 ASN ** D1076 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 537 HIS A 545 HIS ** B 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 403 HIS ** B 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 505 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.121252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.097105 restraints weight = 188210.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.096768 restraints weight = 157583.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.098266 restraints weight = 122677.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.098889 restraints weight = 80388.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.099505 restraints weight = 72038.917| |-----------------------------------------------------------------------------| r_work (final): 0.3839 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3839 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3839 r_free = 0.3839 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3839 r_free = 0.3839 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3839 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6909 moved from start: 0.6992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 1.733 32416 Z= 0.427 Angle : 0.808 22.336 43907 Z= 0.416 Chirality : 0.051 0.310 4902 Planarity : 0.005 0.093 5617 Dihedral : 6.942 58.306 4547 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 18.21 Ramachandran Plot: Outliers : 0.20 % Allowed : 8.77 % Favored : 91.03 % Rotamer: Outliers : 0.12 % Allowed : 0.98 % Favored : 98.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.51 % Twisted General : 0.21 % 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: -2.08 (0.13), residues: 4066 helix: -0.30 (0.12), residues: 1734 sheet: -1.50 (0.23), residues: 512 loop : -2.43 (0.14), residues: 1820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 848 TYR 0.042 0.002 TYR D1093 PHE 0.034 0.002 PHE B 354 TRP 0.049 0.002 TRP B 877 HIS 0.010 0.001 HIS A 371 Details of bonding type rmsd covalent geometry : bond 0.01192 (32415) covalent geometry : angle 0.80793 (43907) hydrogen bonds : bond 0.03980 ( 1347) hydrogen bonds : angle 5.35579 ( 3990) Misc. bond : bond 0.00019 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8132 Ramachandran restraints generated. 4066 Oldfield, 0 Emsley, 4066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8132 Ramachandran restraints generated. 4066 Oldfield, 0 Emsley, 4066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 434 time to evaluate : 0.888 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 4 LYS cc_start: 0.7467 (tptp) cc_final: 0.7141 (tptp) REVERT: C 14 LEU cc_start: 0.8233 (tp) cc_final: 0.8016 (mm) REVERT: C 560 MET cc_start: 0.8694 (mpp) cc_final: 0.8416 (mpp) REVERT: C 698 MET cc_start: 0.7189 (tpp) cc_final: 0.6788 (tpp) REVERT: C 704 TYR cc_start: 0.7796 (m-10) cc_final: 0.7155 (m-10) REVERT: C 864 LYS cc_start: 0.8991 (ptmm) cc_final: 0.8718 (ptmm) REVERT: C 867 MET cc_start: 0.8124 (mmm) cc_final: 0.7757 (tpp) REVERT: C 985 MET cc_start: 0.7541 (mtt) cc_final: 0.7258 (ttm) REVERT: C 1063 LEU cc_start: 0.9218 (tt) cc_final: 0.9006 (tp) REVERT: D 153 LEU cc_start: 0.8830 (tp) cc_final: 0.8339 (tp) REVERT: D 256 LEU cc_start: 0.7913 (mt) cc_final: 0.7512 (mt) REVERT: D 666 MET cc_start: 0.7294 (mmp) cc_final: 0.6815 (ptt) REVERT: D 891 GLU cc_start: 0.7687 (mp0) cc_final: 0.7314 (mp0) REVERT: D 965 LYS cc_start: 0.8262 (pttm) cc_final: 0.7279 (tppt) REVERT: D 985 MET cc_start: 0.7124 (mtt) cc_final: 0.6887 (mmm) REVERT: A 529 MET cc_start: 0.4418 (mpp) cc_final: 0.4036 (mpp) REVERT: A 653 ARG cc_start: 0.5027 (mmm160) cc_final: 0.4062 (mtp180) REVERT: A 666 MET cc_start: 0.5692 (tpt) cc_final: 0.5353 (ttt) REVERT: A 729 ARG cc_start: 0.6006 (ppt170) cc_final: 0.5068 (mmp80) REVERT: A 890 ILE cc_start: 0.9105 (mt) cc_final: 0.8891 (tp) REVERT: A 933 ASP cc_start: 0.7347 (p0) cc_final: 0.6411 (t0) REVERT: A 963 MET cc_start: 0.8192 (mmm) cc_final: 0.7899 (mmm) REVERT: B 19 ILE cc_start: 0.5659 (tp) cc_final: 0.4669 (tt) REVERT: B 327 MET cc_start: 0.8321 (ttt) cc_final: 0.7833 (tpp) REVERT: B 391 MET cc_start: 0.7792 (tmm) cc_final: 0.7241 (ppp) REVERT: B 504 MET cc_start: 0.6733 (mpp) cc_final: 0.6487 (mpp) REVERT: B 514 ASP cc_start: 0.8584 (m-30) cc_final: 0.8361 (m-30) REVERT: B 582 THR cc_start: 0.8729 (m) cc_final: 0.8506 (p) REVERT: B 698 MET cc_start: 0.6554 (mmt) cc_final: 0.5915 (mmm) REVERT: B 841 MET cc_start: 0.8243 (mmm) cc_final: 0.7965 (mmm) REVERT: B 867 MET cc_start: 0.9305 (ppp) cc_final: 0.8974 (ppp) REVERT: B 959 PHE cc_start: 0.7287 (t80) cc_final: 0.7014 (t80) REVERT: B 985 MET cc_start: 0.6174 (mtm) cc_final: 0.5372 (mmp) REVERT: B 1011 GLU cc_start: 0.8136 (pt0) cc_final: 0.7762 (pt0) outliers start: 0 outliers final: 0 residues processed: 434 average time/residue: 0.1878 time to fit residues: 133.0764 Evaluate side-chains 327 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 327 time to evaluate : 1.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 381 optimal weight: 6.9990 chunk 350 optimal weight: 5.9990 chunk 29 optimal weight: 6.9990 chunk 155 optimal weight: 4.9990 chunk 100 optimal weight: 5.9990 chunk 336 optimal weight: 50.0000 chunk 102 optimal weight: 50.0000 chunk 241 optimal weight: 10.0000 chunk 128 optimal weight: 0.6980 chunk 19 optimal weight: 20.0000 chunk 391 optimal weight: 10.0000 overall best weight: 4.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 988 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 403 HIS D 700 HIS ** A 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 365 GLN ** B 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 403 HIS ** B 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 850 GLN B1024 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.119838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.095248 restraints weight = 241813.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.097176 restraints weight = 230333.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.098907 restraints weight = 120752.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.098627 restraints weight = 90915.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.099641 restraints weight = 72473.835| |-----------------------------------------------------------------------------| r_work (final): 0.3848 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3846 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3846 r_free = 0.3846 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3846 r_free = 0.3846 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3846 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6942 moved from start: 0.7351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 1.733 32416 Z= 0.436 Angle : 0.812 21.981 43907 Z= 0.419 Chirality : 0.051 0.328 4902 Planarity : 0.006 0.090 5617 Dihedral : 6.884 60.460 4547 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 20.02 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.99 % Favored : 90.83 % Rotamer: Outliers : 0.12 % Allowed : 1.10 % Favored : 98.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 1.02 % Twisted General : 0.18 % 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: -2.04 (0.13), residues: 4066 helix: -0.22 (0.12), residues: 1739 sheet: -1.54 (0.22), residues: 520 loop : -2.44 (0.14), residues: 1807 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 379 TYR 0.043 0.002 TYR A 213 PHE 0.033 0.002 PHE B 354 TRP 0.071 0.002 TRP B 877 HIS 0.009 0.001 HIS A 371 Details of bonding type rmsd covalent geometry : bond 0.01212 (32415) covalent geometry : angle 0.81222 (43907) hydrogen bonds : bond 0.03994 ( 1347) hydrogen bonds : angle 5.34848 ( 3990) Misc. bond : bond 0.00007 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8132 Ramachandran restraints generated. 4066 Oldfield, 0 Emsley, 4066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8132 Ramachandran restraints generated. 4066 Oldfield, 0 Emsley, 4066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 403 time to evaluate : 1.175 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 14 LEU cc_start: 0.8287 (tp) cc_final: 0.8084 (mm) REVERT: C 556 MET cc_start: 0.6745 (mmm) cc_final: 0.6378 (mmm) REVERT: C 560 MET cc_start: 0.8594 (mpp) cc_final: 0.8360 (mpp) REVERT: C 698 MET cc_start: 0.7282 (tpp) cc_final: 0.6995 (tpp) REVERT: C 704 TYR cc_start: 0.7776 (m-10) cc_final: 0.7173 (m-10) REVERT: C 864 LYS cc_start: 0.8958 (ptmm) cc_final: 0.8694 (ptmm) REVERT: C 867 MET cc_start: 0.8043 (mmm) cc_final: 0.7681 (mmm) REVERT: C 985 MET cc_start: 0.7389 (mtt) cc_final: 0.6680 (ttm) REVERT: C 1067 MET cc_start: 0.6968 (tpt) cc_final: 0.6178 (tpt) REVERT: D 153 LEU cc_start: 0.8947 (tp) cc_final: 0.8539 (tp) REVERT: D 256 LEU cc_start: 0.8049 (mt) cc_final: 0.7604 (mt) REVERT: D 327 MET cc_start: 0.3594 (ttt) cc_final: 0.2567 (tpt) REVERT: D 666 MET cc_start: 0.7470 (mmp) cc_final: 0.6791 (ptt) REVERT: D 965 LYS cc_start: 0.8468 (pttm) cc_final: 0.7560 (tppt) REVERT: A 529 MET cc_start: 0.4582 (mpp) cc_final: 0.4128 (mpp) REVERT: A 653 ARG cc_start: 0.5200 (mmm160) cc_final: 0.4130 (mtp180) REVERT: A 666 MET cc_start: 0.5856 (tpt) cc_final: 0.5643 (ttt) REVERT: A 890 ILE cc_start: 0.9140 (mt) cc_final: 0.8939 (tp) REVERT: A 933 ASP cc_start: 0.7441 (p0) cc_final: 0.6604 (t0) REVERT: A 963 MET cc_start: 0.8326 (mmm) cc_final: 0.7997 (mmm) REVERT: B 19 ILE cc_start: 0.5741 (tp) cc_final: 0.4788 (tt) REVERT: B 314 GLN cc_start: 0.8944 (tp40) cc_final: 0.8689 (tp40) REVERT: B 383 ASN cc_start: 0.8711 (m-40) cc_final: 0.8462 (m110) REVERT: B 514 ASP cc_start: 0.8629 (m-30) cc_final: 0.8367 (m-30) REVERT: B 582 THR cc_start: 0.8759 (m) cc_final: 0.8525 (p) REVERT: B 698 MET cc_start: 0.6264 (mmt) cc_final: 0.5796 (mmt) REVERT: B 841 MET cc_start: 0.8298 (mmm) cc_final: 0.7952 (mmm) REVERT: B 867 MET cc_start: 0.9238 (ppp) cc_final: 0.8987 (ppp) REVERT: B 985 MET cc_start: 0.6326 (mtm) cc_final: 0.5514 (mmp) outliers start: 0 outliers final: 0 residues processed: 403 average time/residue: 0.1847 time to fit residues: 122.3417 Evaluate side-chains 321 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 321 time to evaluate : 1.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 284 optimal weight: 4.9990 chunk 328 optimal weight: 40.0000 chunk 286 optimal weight: 0.7980 chunk 295 optimal weight: 4.9990 chunk 146 optimal weight: 7.9990 chunk 319 optimal weight: 40.0000 chunk 259 optimal weight: 7.9990 chunk 262 optimal weight: 8.9990 chunk 54 optimal weight: 4.9990 chunk 221 optimal weight: 0.7980 chunk 70 optimal weight: 10.0000 overall best weight: 3.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 988 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 172 HIS D 203 ASN D 403 HIS ** A 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 26 GLN ** B 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 403 HIS B 410 HIS B1024 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.121372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.096547 restraints weight = 225181.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.097250 restraints weight = 191490.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.098587 restraints weight = 135593.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.099121 restraints weight = 92199.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.099277 restraints weight = 77053.104| |-----------------------------------------------------------------------------| r_work (final): 0.3842 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3841 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3841 r_free = 0.3841 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3841 r_free = 0.3841 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3841 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6913 moved from start: 0.7588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 1.733 32416 Z= 0.425 Angle : 0.788 21.883 43907 Z= 0.406 Chirality : 0.051 0.333 4902 Planarity : 0.005 0.088 5617 Dihedral : 6.753 61.269 4547 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 18.86 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.43 % Favored : 91.42 % Rotamer: Outliers : 0.15 % Allowed : 0.42 % Favored : 99.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 1.02 % Twisted General : 0.21 % 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: -1.91 (0.13), residues: 4066 helix: -0.09 (0.12), residues: 1734 sheet: -1.46 (0.23), residues: 518 loop : -2.39 (0.14), residues: 1814 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 379 TYR 0.031 0.002 TYR C 304 PHE 0.029 0.002 PHE B 354 TRP 0.070 0.002 TRP B 877 HIS 0.010 0.001 HIS A 371 Details of bonding type rmsd covalent geometry : bond 0.01193 (32415) covalent geometry : angle 0.78778 (43907) hydrogen bonds : bond 0.03809 ( 1347) hydrogen bonds : angle 5.25084 ( 3990) Misc. bond : bond 0.00024 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8132 Ramachandran restraints generated. 4066 Oldfield, 0 Emsley, 4066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8132 Ramachandran restraints generated. 4066 Oldfield, 0 Emsley, 4066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 408 time to evaluate : 1.064 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 4 LYS cc_start: 0.7514 (tptp) cc_final: 0.7163 (tptp) REVERT: C 12 LYS cc_start: 0.8090 (pttt) cc_final: 0.7846 (mttm) REVERT: C 510 GLN cc_start: 0.8103 (tp40) cc_final: 0.7703 (tp40) REVERT: C 514 ASP cc_start: 0.8131 (m-30) cc_final: 0.7893 (m-30) REVERT: C 556 MET cc_start: 0.6692 (mmm) cc_final: 0.6411 (mmm) REVERT: C 560 MET cc_start: 0.8653 (mpp) cc_final: 0.8441 (mpp) REVERT: C 698 MET cc_start: 0.7118 (tpp) cc_final: 0.6760 (tpp) REVERT: C 704 TYR cc_start: 0.7735 (m-10) cc_final: 0.7053 (m-10) REVERT: C 864 LYS cc_start: 0.8989 (ptmm) cc_final: 0.8721 (ptmm) REVERT: C 873 LEU cc_start: 0.8577 (mm) cc_final: 0.8283 (mm) REVERT: C 895 MET cc_start: 0.7242 (mtt) cc_final: 0.7037 (mtt) REVERT: C 985 MET cc_start: 0.7415 (mtt) cc_final: 0.7206 (ttm) REVERT: D 153 LEU cc_start: 0.8956 (tp) cc_final: 0.8569 (tp) REVERT: D 161 ASN cc_start: 0.8930 (t0) cc_final: 0.8716 (t0) REVERT: D 163 GLU cc_start: 0.8328 (tt0) cc_final: 0.7905 (tm-30) REVERT: D 256 LEU cc_start: 0.8063 (mt) cc_final: 0.7586 (mt) REVERT: D 327 MET cc_start: 0.3470 (ttt) cc_final: 0.2405 (tpt) REVERT: D 666 MET cc_start: 0.7395 (mmp) cc_final: 0.6761 (ptt) REVERT: D 698 MET cc_start: 0.8535 (mmp) cc_final: 0.8299 (mmt) REVERT: D 965 LYS cc_start: 0.8372 (pttm) cc_final: 0.7807 (tppt) REVERT: D 985 MET cc_start: 0.6965 (mmm) cc_final: 0.6666 (mmm) REVERT: A 653 ARG cc_start: 0.5335 (mmm160) cc_final: 0.4328 (mtp180) REVERT: A 829 ARG cc_start: 0.7324 (mmp-170) cc_final: 0.7091 (mmp-170) REVERT: A 890 ILE cc_start: 0.9237 (mt) cc_final: 0.8944 (tp) REVERT: A 933 ASP cc_start: 0.7185 (p0) cc_final: 0.6412 (t0) REVERT: A 963 MET cc_start: 0.8311 (mmm) cc_final: 0.7990 (mmm) REVERT: B 19 ILE cc_start: 0.5538 (tp) cc_final: 0.4509 (tt) REVERT: B 327 MET cc_start: 0.8247 (tpp) cc_final: 0.7700 (mmm) REVERT: B 514 ASP cc_start: 0.8735 (m-30) cc_final: 0.8496 (m-30) REVERT: B 582 THR cc_start: 0.8764 (m) cc_final: 0.8543 (p) REVERT: B 597 ILE cc_start: 0.8840 (mp) cc_final: 0.8510 (mp) REVERT: B 698 MET cc_start: 0.6255 (mmt) cc_final: 0.6009 (mmm) REVERT: B 841 MET cc_start: 0.8157 (mmm) cc_final: 0.7843 (mmm) REVERT: B 850 GLN cc_start: 0.7688 (mm-40) cc_final: 0.7315 (tm-30) REVERT: B 867 MET cc_start: 0.9263 (ppp) cc_final: 0.9013 (ppp) REVERT: B 985 MET cc_start: 0.6213 (mtm) cc_final: 0.5425 (mmp) outliers start: 1 outliers final: 0 residues processed: 409 average time/residue: 0.1812 time to fit residues: 122.4837 Evaluate side-chains 311 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 311 time to evaluate : 1.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 196 optimal weight: 0.0010 chunk 161 optimal weight: 7.9990 chunk 253 optimal weight: 30.0000 chunk 24 optimal weight: 0.5980 chunk 273 optimal weight: 9.9990 chunk 139 optimal weight: 8.9990 chunk 165 optimal weight: 0.0970 chunk 388 optimal weight: 0.9990 chunk 344 optimal weight: 2.9990 chunk 96 optimal weight: 10.0000 chunk 42 optimal weight: 0.0970 overall best weight: 0.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 315 GLN ** C 988 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 172 HIS D 403 HIS D 671 ASN ** D1076 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1076 GLN ** B 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1024 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.122939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.097510 restraints weight = 176377.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.096798 restraints weight = 130362.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.098368 restraints weight = 92404.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.098464 restraints weight = 64635.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.099472 restraints weight = 61890.535| |-----------------------------------------------------------------------------| r_work (final): 0.3858 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3856 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3856 r_free = 0.3856 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3856 r_free = 0.3856 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3856 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6905 moved from start: 0.7814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 1.736 32416 Z= 0.418 Angle : 0.774 21.738 43907 Z= 0.396 Chirality : 0.051 0.323 4902 Planarity : 0.005 0.090 5617 Dihedral : 6.548 62.775 4547 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 16.38 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.84 % Favored : 92.07 % Rotamer: Outliers : 0.15 % Allowed : 0.27 % Favored : 99.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.51 % Twisted General : 0.23 % 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: -1.78 (0.13), residues: 4066 helix: 0.03 (0.12), residues: 1737 sheet: -1.38 (0.23), residues: 527 loop : -2.35 (0.14), residues: 1802 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 379 TYR 0.034 0.002 TYR C 304 PHE 0.027 0.001 PHE D1061 TRP 0.063 0.002 TRP B 877 HIS 0.009 0.001 HIS A 371 Details of bonding type rmsd covalent geometry : bond 0.01178 (32415) covalent geometry : angle 0.77355 (43907) hydrogen bonds : bond 0.03724 ( 1347) hydrogen bonds : angle 5.08643 ( 3990) Misc. bond : bond 0.00031 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8132 Ramachandran restraints generated. 4066 Oldfield, 0 Emsley, 4066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8132 Ramachandran restraints generated. 4066 Oldfield, 0 Emsley, 4066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 445 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 444 time to evaluate : 1.161 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 4 LYS cc_start: 0.7305 (tptp) cc_final: 0.7044 (tptp) REVERT: C 12 LYS cc_start: 0.8245 (pttt) cc_final: 0.7835 (mttm) REVERT: C 386 GLU cc_start: 0.7986 (mt-10) cc_final: 0.7744 (tm-30) REVERT: C 510 GLN cc_start: 0.8182 (tp40) cc_final: 0.7913 (tp40) REVERT: C 514 ASP cc_start: 0.8027 (m-30) cc_final: 0.7794 (m-30) REVERT: C 555 ASN cc_start: 0.8091 (m-40) cc_final: 0.7700 (m-40) REVERT: C 556 MET cc_start: 0.6812 (mmm) cc_final: 0.6564 (mmm) REVERT: C 698 MET cc_start: 0.7496 (tpp) cc_final: 0.7177 (tpp) REVERT: C 704 TYR cc_start: 0.7780 (m-10) cc_final: 0.7102 (m-10) REVERT: C 823 MET cc_start: 0.7962 (ppp) cc_final: 0.7693 (ppp) REVERT: C 985 MET cc_start: 0.7330 (mtt) cc_final: 0.7106 (ttm) REVERT: C 1067 MET cc_start: 0.6775 (tpt) cc_final: 0.5992 (tpt) REVERT: D 153 LEU cc_start: 0.8948 (tp) cc_final: 0.8466 (tp) REVERT: D 163 GLU cc_start: 0.8294 (tt0) cc_final: 0.7917 (tm-30) REVERT: D 256 LEU cc_start: 0.7945 (mt) cc_final: 0.7463 (mt) REVERT: D 286 VAL cc_start: 0.8060 (t) cc_final: 0.7847 (m) REVERT: D 327 MET cc_start: 0.3541 (ttt) cc_final: 0.2392 (tpt) REVERT: D 666 MET cc_start: 0.7075 (mmp) cc_final: 0.6642 (ptp) REVERT: D 985 MET cc_start: 0.6890 (mmm) cc_final: 0.6651 (mmm) REVERT: A 411 MET cc_start: 0.3245 (ttm) cc_final: 0.1822 (mmm) REVERT: A 543 TRP cc_start: 0.4817 (t-100) cc_final: 0.3770 (t-100) REVERT: A 653 ARG cc_start: 0.5384 (mmm160) cc_final: 0.4603 (mtp180) REVERT: A 729 ARG cc_start: 0.5822 (ppt170) cc_final: 0.4965 (mmt-90) REVERT: A 829 ARG cc_start: 0.7280 (mmp-170) cc_final: 0.7022 (mmp-170) REVERT: A 933 ASP cc_start: 0.6826 (p0) cc_final: 0.6188 (t0) REVERT: A 963 MET cc_start: 0.8327 (mmm) cc_final: 0.8046 (mmm) REVERT: B 19 ILE cc_start: 0.5363 (tp) cc_final: 0.4338 (tt) REVERT: B 327 MET cc_start: 0.8264 (tpp) cc_final: 0.7408 (tpt) REVERT: B 514 ASP cc_start: 0.8696 (m-30) cc_final: 0.8443 (m-30) REVERT: B 582 THR cc_start: 0.8659 (m) cc_final: 0.8439 (p) REVERT: B 850 GLN cc_start: 0.7741 (mm-40) cc_final: 0.7354 (tm-30) REVERT: B 867 MET cc_start: 0.9239 (ppp) cc_final: 0.8936 (ppp) REVERT: B 909 ASN cc_start: 0.9110 (m-40) cc_final: 0.8080 (t0) REVERT: B 985 MET cc_start: 0.6190 (mtm) cc_final: 0.5545 (mmp) outliers start: 1 outliers final: 0 residues processed: 445 average time/residue: 0.1803 time to fit residues: 130.6050 Evaluate side-chains 323 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 323 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 198 optimal weight: 6.9990 chunk 74 optimal weight: 0.0060 chunk 227 optimal weight: 5.9990 chunk 232 optimal weight: 50.0000 chunk 250 optimal weight: 30.0000 chunk 220 optimal weight: 7.9990 chunk 88 optimal weight: 20.0000 chunk 347 optimal weight: 20.0000 chunk 397 optimal weight: 1.9990 chunk 251 optimal weight: 2.9990 chunk 258 optimal weight: 5.9990 overall best weight: 3.4004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 900 HIS ** C 988 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 172 HIS D 403 HIS D 668 ASN ** D 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 909 ASN ** D1076 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1076 GLN ** B 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 383 ASN B 403 HIS B 671 ASN B1024 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.121483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.096990 restraints weight = 243491.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.098273 restraints weight = 218448.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.100257 restraints weight = 129410.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.100269 restraints weight = 90531.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.101338 restraints weight = 74482.504| |-----------------------------------------------------------------------------| r_work (final): 0.3955 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3958 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3958 r_free = 0.3958 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3957 r_free = 0.3957 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3957 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6800 moved from start: 0.7991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 1.733 32416 Z= 0.425 Angle : 0.783 21.984 43907 Z= 0.401 Chirality : 0.051 0.330 4902 Planarity : 0.005 0.100 5617 Dihedral : 6.528 62.656 4547 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 18.35 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.33 % Favored : 91.57 % Rotamer: Outliers : 0.15 % Allowed : 0.42 % Favored : 99.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.51 % Twisted General : 0.23 % 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: -1.73 (0.13), residues: 4066 helix: 0.05 (0.13), residues: 1739 sheet: -1.37 (0.23), residues: 527 loop : -2.30 (0.14), residues: 1800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 607 TYR 0.035 0.002 TYR A 192 PHE 0.033 0.002 PHE D 18 TRP 0.077 0.002 TRP B 877 HIS 0.018 0.001 HIS D 997 Details of bonding type rmsd covalent geometry : bond 0.01193 (32415) covalent geometry : angle 0.78259 (43907) hydrogen bonds : bond 0.03684 ( 1347) hydrogen bonds : angle 5.11653 ( 3990) Misc. bond : bond 0.00005 ( 1) =============================================================================== Job complete usr+sys time: 5511.95 seconds wall clock time: 96 minutes 16.44 seconds (5776.44 seconds total)