Starting phenix.real_space_refine on Mon Mar 11 16:00:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g46_29714/03_2024/8g46_29714_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g46_29714/03_2024/8g46_29714.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g46_29714/03_2024/8g46_29714_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g46_29714/03_2024/8g46_29714_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g46_29714/03_2024/8g46_29714_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g46_29714/03_2024/8g46_29714.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g46_29714/03_2024/8g46_29714.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g46_29714/03_2024/8g46_29714_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g46_29714/03_2024/8g46_29714_updated.pdb" } resolution = 2.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.071 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 Zn 1 6.06 5 S 57 5.16 5 C 5415 2.51 5 N 1433 2.21 5 O 1697 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 65": "OE1" <-> "OE2" Residue "A GLU 127": "OE1" <-> "OE2" Residue "A GLU 210": "OE1" <-> "OE2" Residue "A GLU 235": "OE1" <-> "OE2" Residue "A GLU 277": "OE1" <-> "OE2" Residue "A GLU 288": "OE1" <-> "OE2" Residue "A ASP 299": "OD1" <-> "OD2" Residue "A GLU 307": "OE1" <-> "OE2" Residue "A TYR 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 719": "OE1" <-> "OE2" Residue "A TYR 726": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 728": "OE1" <-> "OE2" Residue "A GLU 939": "OE1" <-> "OE2" Residue "A GLU 1095": "OE1" <-> "OE2" Residue "B GLU 50": "OE1" <-> "OE2" Residue "B TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 137": "OD1" <-> "OD2" Residue "C GLU 383": "OE1" <-> "OE2" Residue "C ASP 421": "OD1" <-> "OD2" Residue "C PHE 426": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 438": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 8603 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 6180 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 782, 6150 Classifications: {'peptide': 782} Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 755} Chain breaks: 6 Conformer: "B" Number of residues, atoms: 782, 6150 Classifications: {'peptide': 782} Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 755} Chain breaks: 6 bond proxies already assigned to first conformer: 6221 Chain: "B" Number of atoms: 1260 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 158, 1246 Classifications: {'peptide': 158} Link IDs: {'PTRANS': 17, 'TRANS': 140} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 158, 1246 Classifications: {'peptide': 158} Link IDs: {'PTRANS': 17, 'TRANS': 140} Chain breaks: 1 bond proxies already assigned to first conformer: 1266 Chain: "C" Number of atoms: 859 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 859 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "E" Number of atoms: 157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 157 Classifications: {'peptide': 19} Link IDs: {'PTRANS': 1, 'TRANS': 17} Chain: "B" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 37 Unusual residues: {' ZN': 1, 'YK3': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 95 Classifications: {'water': 95} Link IDs: {None: 94} Chain: "B" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 6635 SG CYS B 100 40.352 30.235 52.256 1.00 55.81 S ATOM 6657 SG CYS B 103 42.977 32.717 50.994 1.00 59.48 S ATOM 7131 SG CYS B 177 41.272 30.475 48.590 1.00 54.63 S ATOM 7143 SG CYS B 179 39.096 33.155 50.131 1.00 56.71 S Residues with excluded nonbonded symmetry interactions: 5 residue: pdb=" N AASN A 16 " occ=0.50 ... (14 atoms not shown) pdb=" ND2BASN A 16 " occ=0.50 residue: pdb=" N AHIS A 711 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS A 711 " occ=0.50 residue: pdb=" N ACYS A 725 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS A 725 " occ=0.50 residue: pdb=" N ACYS A1008 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS A1008 " occ=0.50 residue: pdb=" N ATRP B 54 " occ=0.50 ... (26 atoms not shown) pdb=" CH2BTRP B 54 " occ=0.50 Time building chain proxies: 8.12, per 1000 atoms: 0.94 Number of scatterers: 8603 At special positions: 0 Unit cell: (86.7623, 91.189, 138.997, 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) Zn 1 29.99 S 57 16.00 O 1697 8.00 N 1433 7.00 C 5415 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 - 3.50 Amino acid : False - 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: 3.32 Conformation dependent library (CDL) restraints added in 2.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B1001 " pdb="ZN ZN B1001 " - pdb=" SG CYS B 103 " pdb="ZN ZN B1001 " - pdb=" SG CYS B 100 " pdb="ZN ZN B1001 " - pdb=" SG CYS B 177 " pdb="ZN ZN B1001 " - pdb=" SG CYS B 179 " Number of angles added : 6 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2010 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 23 helices and 15 sheets defined 20.0% alpha, 31.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.07 Creating SS restraints... Processing helix chain 'A' and resid 251 through 255 removed outlier: 4.073A pdb=" N GLN A 255 " --> pdb=" O ILE A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 384 No H-bonds generated for 'chain 'A' and resid 382 through 384' Processing helix chain 'A' and resid 986 through 990 Processing helix chain 'A' and resid 1045 through 1061 Processing helix chain 'A' and resid 1070 through 1073 No H-bonds generated for 'chain 'A' and resid 1070 through 1073' Processing helix chain 'A' and resid 1091 through 1099 removed outlier: 3.619A pdb=" N PHE A1097 " --> pdb=" O LEU A1093 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N LEU A1098 " --> pdb=" O ILE A1094 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N ASP A1099 " --> pdb=" O GLU A1095 " (cutoff:3.500A) Processing helix chain 'A' and resid 1102 through 1109 Processing helix chain 'A' and resid 1126 through 1137 Processing helix chain 'B' and resid 48 through 62 removed outlier: 4.942A pdb=" N TYR B 62 " --> pdb=" O CYS B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 77 No H-bonds generated for 'chain 'B' and resid 74 through 77' Processing helix chain 'B' and resid 86 through 94 Processing helix chain 'B' and resid 116 through 119 No H-bonds generated for 'chain 'B' and resid 116 through 119' Processing helix chain 'B' and resid 131 through 140 removed outlier: 3.929A pdb=" N THR B 140 " --> pdb=" O ARG B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 158 removed outlier: 4.215A pdb=" N ARG B 158 " --> pdb=" O ARG B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 186 Processing helix chain 'B' and resid 201 through 215 Processing helix chain 'C' and resid 354 through 365 Processing helix chain 'C' and resid 370 through 376 Proline residue: C 375 - end of helix Processing helix chain 'C' and resid 390 through 393 No H-bonds generated for 'chain 'C' and resid 390 through 393' Processing helix chain 'C' and resid 400 through 408 Processing helix chain 'C' and resid 415 through 432 Processing helix chain 'C' and resid 439 through 454 removed outlier: 3.628A pdb=" N VAL C 449 " --> pdb=" O LYS C 445 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 5 No H-bonds generated for 'chain 'E' and resid 3 through 5' Processing sheet with id= A, first strand: chain 'A' and resid 1088 through 1090 removed outlier: 6.941A pdb=" N ASN A 4 " --> pdb=" O ILE A1089 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N ILE A1037 " --> pdb=" O ALA A 9 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 17 through 21 removed outlier: 3.680A pdb=" N LYS A 53 " --> pdb=" O ILE A 41 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N VAL A 43 " --> pdb=" O PRO A 51 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N THR A 45 " --> pdb=" O LEU A 49 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N LEU A 49 " --> pdb=" O THR A 45 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 61 through 67 removed outlier: 6.544A pdb=" N LEU A 80 " --> pdb=" O ALA A 62 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N MET A 64 " --> pdb=" O PHE A 78 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N PHE A 78 " --> pdb=" O MET A 64 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N LEU A 66 " --> pdb=" O LEU A 76 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N LEU A 76 " --> pdb=" O LEU A 66 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ASN A 85 " --> pdb=" O THR A 81 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N GLU A 90 " --> pdb=" O THR A 102 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N THR A 102 " --> pdb=" O GLU A 90 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N LYS A 92 " --> pdb=" O ILE A 100 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N ILE A 100 " --> pdb=" O LYS A 92 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 121 through 124 removed outlier: 4.201A pdb=" N LEU A 135 " --> pdb=" O LEU A 139 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N LEU A 139 " --> pdb=" O LEU A 135 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 201 through 204 removed outlier: 6.528A pdb=" N GLN A 183 " --> pdb=" O VAL A 164 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N VAL A 164 " --> pdb=" O GLN A 183 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 218 through 221 Processing sheet with id= G, first strand: chain 'A' and resid 258 through 263 removed outlier: 6.913A pdb=" N GLY A 274 " --> pdb=" O VAL A 259 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N HIS A 261 " --> pdb=" O LEU A 272 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N LEU A 272 " --> pdb=" O HIS A 261 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N ARG A 263 " --> pdb=" O ARG A 270 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N ARG A 270 " --> pdb=" O ARG A 263 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ARG A 279 " --> pdb=" O ASP A 275 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N MET A 282 " --> pdb=" O LEU A 304 " (cutoff:3.500A) removed outlier: 5.770A pdb=" N LEU A 304 " --> pdb=" O MET A 282 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N LEU A 284 " --> pdb=" O VAL A 302 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N VAL A 302 " --> pdb=" O LEU A 284 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 287 through 289 Processing sheet with id= I, first strand: chain 'A' and resid 313 through 318 removed outlier: 6.666A pdb=" N VAL A 321 " --> pdb=" O LEU A 317 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N LYS A 335 " --> pdb=" O ALA A 349 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N ALA A 349 " --> pdb=" O LYS A 335 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 711 through 716 removed outlier: 3.984A pdb=" N ASP A 361 " --> pdb=" O CYS A 378 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'A' and resid 720 through 727 removed outlier: 6.332A pdb=" N LEU A 736 " --> pdb=" O ARG A 722 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N ILE A 724 " --> pdb=" O GLY A 734 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N GLY A 734 " --> pdb=" O ILE A 724 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N TYR A 726 " --> pdb=" O CYS A 732 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N CYS A 732 " --> pdb=" O TYR A 726 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ASP A 795 " --> pdb=" O VAL A 801 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N VAL A 801 " --> pdb=" O ASP A 795 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N SER A 762 " --> pdb=" O ALA A 804 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N GLN A 806 " --> pdb=" O SER A 762 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N SER A 764 " --> pdb=" O GLN A 806 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'A' and resid 811 through 820 removed outlier: 6.492A pdb=" N GLY A 832 " --> pdb=" O LEU A 814 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N LEU A 816 " --> pdb=" O ILE A 830 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ILE A 830 " --> pdb=" O LEU A 816 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N SER A 818 " --> pdb=" O TYR A 828 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N TYR A 828 " --> pdb=" O SER A 818 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N THR A 827 " --> pdb=" O TYR A 853 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N TYR A 853 " --> pdb=" O THR A 827 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ARG A 847 " --> pdb=" O THR A 833 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N GLN A 852 " --> pdb=" O THR A 860 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N THR A 860 " --> pdb=" O GLN A 852 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N SER A 854 " --> pdb=" O LEU A 858 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N LEU A 858 " --> pdb=" O SER A 854 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'A' and resid 870 through 876 removed outlier: 6.682A pdb=" N SER A 883 " --> pdb=" O TYR A 871 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N MET A 873 " --> pdb=" O LEU A 881 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N LEU A 881 " --> pdb=" O MET A 873 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N GLU A 875 " --> pdb=" O LYS A 879 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N LYS A 879 " --> pdb=" O GLU A 875 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N GLU A 892 " --> pdb=" O THR A 901 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N THR A 901 " --> pdb=" O GLU A 892 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'A' and resid 911 through 917 removed outlier: 6.568A pdb=" N GLY A 924 " --> pdb=" O LEU A 912 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N LEU A 914 " --> pdb=" O LEU A 922 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N LEU A 922 " --> pdb=" O LEU A 914 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N THR A 916 " --> pdb=" O PHE A 920 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N PHE A 920 " --> pdb=" O THR A 916 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA A 946 " --> pdb=" O LEU A 932 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N ALA A 934 " --> pdb=" O GLU A 944 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N GLU A 944 " --> pdb=" O ALA A 934 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N LYS A 936 " --> pdb=" O PHE A 942 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N PHE A 942 " --> pdb=" O LYS A 936 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'A' and resid 954 through 959 removed outlier: 6.869A pdb=" N ALA A 968 " --> pdb=" O SER A 955 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N VAL A 957 " --> pdb=" O LEU A 966 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N LEU A 966 " --> pdb=" O VAL A 957 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N ILE A 959 " --> pdb=" O ASN A 964 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N ASN A 964 " --> pdb=" O ILE A 959 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ASN A 973 " --> pdb=" O GLU A 969 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N GLN A 978 " --> pdb=" O GLU A 994 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N GLU A 994 " --> pdb=" O GLN A 978 " (cutoff:3.500A) 297 hydrogen bonds defined for protein. 808 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: 3.29 Time building geometry restraints manager: 3.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1820 1.33 - 1.46: 2666 1.46 - 1.58: 4100 1.58 - 1.71: 1 1.71 - 1.84: 85 Bond restraints: 8672 Sorted by residual: bond pdb=" C1 YK3 B1002 " pdb=" S1 YK3 B1002 " ideal model delta sigma weight residual 1.577 1.735 -0.158 2.00e-02 2.50e+03 6.26e+01 bond pdb=" C2 YK3 B1002 " pdb=" C4 YK3 B1002 " ideal model delta sigma weight residual 1.606 1.449 0.157 2.00e-02 2.50e+03 6.17e+01 bond pdb=" C21 YK3 B1002 " pdb=" S1 YK3 B1002 " ideal model delta sigma weight residual 1.568 1.716 -0.148 2.00e-02 2.50e+03 5.46e+01 bond pdb=" C5 YK3 B1002 " pdb=" N1 YK3 B1002 " ideal model delta sigma weight residual 1.421 1.283 0.138 2.00e-02 2.50e+03 4.76e+01 bond pdb=" C4 YK3 B1002 " pdb=" C5 YK3 B1002 " ideal model delta sigma weight residual 1.586 1.470 0.116 2.00e-02 2.50e+03 3.36e+01 ... (remaining 8667 not shown) Histogram of bond angle deviations from ideal: 94.52 - 102.48: 56 102.48 - 110.44: 2011 110.44 - 118.40: 4927 118.40 - 126.36: 4636 126.36 - 134.33: 121 Bond angle restraints: 11751 Sorted by residual: angle pdb=" N MET C 442 " pdb=" CA MET C 442 " pdb=" C MET C 442 " ideal model delta sigma weight residual 113.38 105.14 8.24 1.23e+00 6.61e-01 4.48e+01 angle pdb=" C2 YK3 B1002 " pdb=" C4 YK3 B1002 " pdb=" C5 YK3 B1002 " ideal model delta sigma weight residual 104.75 124.76 -20.01 3.00e+00 1.11e-01 4.45e+01 angle pdb=" O YK3 B1002 " pdb=" S YK3 B1002 " pdb=" O1 YK3 B1002 " ideal model delta sigma weight residual 101.24 118.80 -17.56 3.00e+00 1.11e-01 3.43e+01 angle pdb=" N2 YK3 B1002 " pdb=" C21 YK3 B1002 " pdb=" S1 YK3 B1002 " ideal model delta sigma weight residual 140.49 123.88 16.61 3.00e+00 1.11e-01 3.06e+01 angle pdb=" C4 YK3 B1002 " pdb=" C21 YK3 B1002 " pdb=" N2 YK3 B1002 " ideal model delta sigma weight residual 111.20 127.22 -16.02 3.00e+00 1.11e-01 2.85e+01 ... (remaining 11746 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.24: 4987 29.24 - 58.47: 210 58.47 - 87.70: 30 87.70 - 116.94: 1 116.94 - 146.17: 1 Dihedral angle restraints: 5229 sinusoidal: 2118 harmonic: 3111 Sorted by residual: dihedral pdb=" C14 YK3 B1002 " pdb=" C15 YK3 B1002 " pdb=" C16 YK3 B1002 " pdb=" O3 YK3 B1002 " ideal model delta sinusoidal sigma weight residual 259.88 113.71 146.17 1 3.00e+01 1.11e-03 1.95e+01 dihedral pdb=" CA GLN A 332 " pdb=" C GLN A 332 " pdb=" N LEU A 333 " pdb=" CA LEU A 333 " ideal model delta harmonic sigma weight residual 180.00 162.05 17.95 0 5.00e+00 4.00e-02 1.29e+01 dihedral pdb=" CA PRO A 223 " pdb=" C PRO A 223 " pdb=" N GLU A 224 " pdb=" CA GLU A 224 " ideal model delta harmonic sigma weight residual 180.00 162.28 17.72 0 5.00e+00 4.00e-02 1.26e+01 ... (remaining 5226 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 581 0.037 - 0.074: 416 0.074 - 0.111: 233 0.111 - 0.148: 81 0.148 - 0.185: 13 Chirality restraints: 1324 Sorted by residual: chirality pdb=" CA TRP C 374 " pdb=" N TRP C 374 " pdb=" C TRP C 374 " pdb=" CB TRP C 374 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.55e-01 chirality pdb=" CA VAL A 874 " pdb=" N VAL A 874 " pdb=" C VAL A 874 " pdb=" CB VAL A 874 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 7.44e-01 chirality pdb=" CB VAL C 439 " pdb=" CA VAL C 439 " pdb=" CG1 VAL C 439 " pdb=" CG2 VAL C 439 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.17 2.00e-01 2.50e+01 6.99e-01 ... (remaining 1321 not shown) Planarity restraints: 1500 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA C 441 " -0.020 2.00e-02 2.50e+03 4.00e-02 1.60e+01 pdb=" C ALA C 441 " 0.069 2.00e-02 2.50e+03 pdb=" O ALA C 441 " -0.026 2.00e-02 2.50e+03 pdb=" N MET C 442 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL C 440 " 0.020 2.00e-02 2.50e+03 3.97e-02 1.57e+01 pdb=" C VAL C 440 " -0.069 2.00e-02 2.50e+03 pdb=" O VAL C 440 " 0.026 2.00e-02 2.50e+03 pdb=" N ALA C 441 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET C 442 " -0.014 2.00e-02 2.50e+03 2.85e-02 8.13e+00 pdb=" C MET C 442 " 0.049 2.00e-02 2.50e+03 pdb=" O MET C 442 " -0.019 2.00e-02 2.50e+03 pdb=" N ALA C 443 " -0.016 2.00e-02 2.50e+03 ... (remaining 1497 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 748 2.75 - 3.28: 8336 3.28 - 3.82: 15266 3.82 - 4.36: 18896 4.36 - 4.90: 31153 Nonbonded interactions: 74399 Sorted by model distance: nonbonded pdb=" OH TYR B 62 " pdb=" OE2 GLU C 438 " model vdw 2.207 2.440 nonbonded pdb=" ND1 HIS C 369 " pdb=" OH TYR C 372 " model vdw 2.210 2.520 nonbonded pdb=" OG1 THR A 118 " pdb=" NH2 ARG A 134 " model vdw 2.302 2.520 nonbonded pdb=" OE2 GLU B 193 " pdb=" OH TYR B 199 " model vdw 2.303 2.440 nonbonded pdb=" ND2 ASN A 950 " pdb=" OE1 GLU A 994 " model vdw 2.306 2.520 ... (remaining 74394 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.50 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 6.090 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 33.730 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.060 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:12.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 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 : 0.009 0.158 8672 Z= 0.598 Angle : 0.981 20.014 11751 Z= 0.574 Chirality : 0.061 0.185 1324 Planarity : 0.006 0.057 1500 Dihedral : 15.972 146.174 3219 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 1.70 % Allowed : 12.42 % Favored : 85.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.25), residues: 1057 helix: 0.23 (0.37), residues: 217 sheet: 0.00 (0.26), residues: 384 loop : -0.34 (0.28), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.007 TRP A 953 HIS 0.011 0.004 HIS B 138 PHE 0.030 0.006 PHE A 942 TYR 0.023 0.006 TYR B 76 ARG 0.019 0.002 ARG A 753 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 112 time to evaluate : 1.085 Fit side-chains REVERT: A 150 LYS cc_start: 0.5626 (tptt) cc_final: 0.4650 (tptp) REVERT: A 224 GLU cc_start: 0.7583 (mt-10) cc_final: 0.6971 (mm-30) REVERT: A 254 LYS cc_start: 0.6884 (mttt) cc_final: 0.6222 (ptpp) REVERT: A 267 ASN cc_start: 0.8138 (p0) cc_final: 0.7689 (p0) REVERT: A 847 ARG cc_start: 0.8144 (mtm180) cc_final: 0.7938 (mtm180) outliers start: 14 outliers final: 8 residues processed: 121 average time/residue: 1.6546 time to fit residues: 210.2294 Evaluate side-chains 112 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 104 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 204 LYS Chi-restraints excluded: chain A residue 1043 LEU Chi-restraints excluded: chain A residue 1071 SER Chi-restraints excluded: chain B residue 51 SER Chi-restraints excluded: chain B residue 58 CYS Chi-restraints excluded: chain C residue 439 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 87 optimal weight: 0.8980 chunk 78 optimal weight: 0.6980 chunk 43 optimal weight: 10.0000 chunk 26 optimal weight: 0.3980 chunk 53 optimal weight: 0.4980 chunk 42 optimal weight: 3.9990 chunk 81 optimal weight: 0.8980 chunk 31 optimal weight: 0.7980 chunk 49 optimal weight: 2.9990 chunk 60 optimal weight: 0.8980 chunk 94 optimal weight: 9.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 396 HIS C 428 ASN C 447 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.0573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 8672 Z= 0.155 Angle : 0.614 15.201 11751 Z= 0.300 Chirality : 0.043 0.169 1324 Planarity : 0.004 0.036 1500 Dihedral : 8.103 139.180 1170 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.12 % Allowed : 13.06 % Favored : 84.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.26), residues: 1057 helix: 0.84 (0.36), residues: 218 sheet: -0.01 (0.26), residues: 374 loop : -0.18 (0.29), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 207 HIS 0.004 0.001 HIS C 396 PHE 0.018 0.002 PHE A1030 TYR 0.017 0.001 TYR A 891 ARG 0.006 0.000 ARG A 158 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 108 time to evaluate : 0.913 Fit side-chains REVERT: A 70 LYS cc_start: 0.7182 (mtpm) cc_final: 0.6218 (mppt) REVERT: A 150 LYS cc_start: 0.5755 (tptt) cc_final: 0.4715 (tptp) REVERT: A 158 ARG cc_start: 0.7701 (ttt-90) cc_final: 0.7224 (ttp-170) REVERT: A 224 GLU cc_start: 0.7614 (mt-10) cc_final: 0.6985 (mm-30) REVERT: A 254 LYS cc_start: 0.6693 (mttt) cc_final: 0.6039 (ptpp) REVERT: A 267 ASN cc_start: 0.8187 (p0) cc_final: 0.7654 (p0) REVERT: A 847 ARG cc_start: 0.8013 (mtm180) cc_final: 0.7595 (mtm180) REVERT: C 364 MET cc_start: 0.5531 (mtp) cc_final: 0.4628 (mmm) outliers start: 18 outliers final: 5 residues processed: 117 average time/residue: 1.7057 time to fit residues: 209.3270 Evaluate side-chains 108 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 103 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 1043 LEU Chi-restraints excluded: chain A residue 1071 SER Chi-restraints excluded: chain C residue 439 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 52 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 78 optimal weight: 6.9990 chunk 64 optimal weight: 9.9990 chunk 26 optimal weight: 0.2980 chunk 94 optimal weight: 10.0000 chunk 102 optimal weight: 2.9990 chunk 84 optimal weight: 5.9990 chunk 93 optimal weight: 6.9990 chunk 32 optimal weight: 6.9990 chunk 75 optimal weight: 5.9990 overall best weight: 2.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 209 ASN ** C 428 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.1003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 8672 Z= 0.357 Angle : 0.744 16.592 11751 Z= 0.374 Chirality : 0.048 0.169 1324 Planarity : 0.005 0.040 1500 Dihedral : 8.607 143.976 1164 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 1.91 % Allowed : 13.69 % Favored : 84.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.25), residues: 1057 helix: 0.77 (0.36), residues: 218 sheet: -0.00 (0.26), residues: 363 loop : -0.38 (0.28), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.004 TRP A 207 HIS 0.008 0.002 HIS A1077 PHE 0.022 0.003 PHE A 169 TYR 0.017 0.002 TYR A 718 ARG 0.005 0.001 ARG C 444 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 108 time to evaluate : 1.091 Fit side-chains REVERT: A 70 LYS cc_start: 0.7188 (mtpm) cc_final: 0.6250 (mppt) REVERT: A 150 LYS cc_start: 0.5794 (tptt) cc_final: 0.4587 (tptp) REVERT: A 224 GLU cc_start: 0.7640 (mt-10) cc_final: 0.6987 (mm-30) REVERT: A 254 LYS cc_start: 0.6704 (mttt) cc_final: 0.6035 (ptpp) REVERT: A 267 ASN cc_start: 0.8210 (p0) cc_final: 0.7696 (p0) REVERT: A 1106 GLN cc_start: 0.4948 (tp40) cc_final: 0.4736 (tp-100) REVERT: A 1107 GLU cc_start: 0.5934 (OUTLIER) cc_final: 0.5506 (tt0) REVERT: C 364 MET cc_start: 0.5568 (mtp) cc_final: 0.4703 (mmm) REVERT: C 378 LYS cc_start: 0.7329 (OUTLIER) cc_final: 0.7092 (mmtm) REVERT: C 407 LEU cc_start: 0.4368 (OUTLIER) cc_final: 0.4097 (mp) outliers start: 17 outliers final: 9 residues processed: 116 average time/residue: 1.7716 time to fit residues: 215.8862 Evaluate side-chains 119 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 107 time to evaluate : 1.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain A residue 204 LYS Chi-restraints excluded: chain A residue 859 GLN Chi-restraints excluded: chain A residue 1043 LEU Chi-restraints excluded: chain A residue 1071 SER Chi-restraints excluded: chain A residue 1107 GLU Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain C residue 439 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 93 optimal weight: 0.7980 chunk 71 optimal weight: 4.9990 chunk 49 optimal weight: 6.9990 chunk 10 optimal weight: 6.9990 chunk 45 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 94 optimal weight: 6.9990 chunk 100 optimal weight: 1.9990 chunk 89 optimal weight: 0.0370 chunk 27 optimal weight: 4.9990 chunk 83 optimal weight: 2.9990 overall best weight: 1.5664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 428 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.0982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 8672 Z= 0.238 Angle : 0.662 15.871 11751 Z= 0.330 Chirality : 0.045 0.155 1324 Planarity : 0.004 0.037 1500 Dihedral : 8.364 140.870 1164 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.23 % Allowed : 13.80 % Favored : 83.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.25), residues: 1057 helix: 0.85 (0.36), residues: 224 sheet: 0.01 (0.26), residues: 363 loop : -0.35 (0.28), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP A 207 HIS 0.005 0.001 HIS A 789 PHE 0.019 0.002 PHE A 169 TYR 0.016 0.002 TYR A 891 ARG 0.004 0.000 ARG C 444 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 108 time to evaluate : 1.035 Fit side-chains REVERT: A 70 LYS cc_start: 0.7200 (mtpm) cc_final: 0.6227 (mppt) REVERT: A 150 LYS cc_start: 0.5586 (tptt) cc_final: 0.4564 (tptp) REVERT: A 224 GLU cc_start: 0.7618 (mt-10) cc_final: 0.6975 (mm-30) REVERT: A 254 LYS cc_start: 0.6710 (mttt) cc_final: 0.6041 (ptpp) REVERT: A 267 ASN cc_start: 0.8207 (p0) cc_final: 0.7684 (p0) REVERT: A 1106 GLN cc_start: 0.4903 (tp40) cc_final: 0.4683 (tp-100) REVERT: A 1107 GLU cc_start: 0.5960 (OUTLIER) cc_final: 0.5533 (tt0) REVERT: C 360 ILE cc_start: 0.4907 (OUTLIER) cc_final: 0.4683 (mp) REVERT: C 364 MET cc_start: 0.6003 (mtp) cc_final: 0.4741 (mmm) REVERT: C 378 LYS cc_start: 0.7424 (OUTLIER) cc_final: 0.7189 (mmtm) REVERT: C 383 GLU cc_start: 0.7526 (OUTLIER) cc_final: 0.7280 (tp30) REVERT: C 407 LEU cc_start: 0.4360 (OUTLIER) cc_final: 0.4084 (mp) outliers start: 20 outliers final: 6 residues processed: 120 average time/residue: 1.6197 time to fit residues: 204.2107 Evaluate side-chains 117 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 106 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 204 LYS Chi-restraints excluded: chain A residue 1071 SER Chi-restraints excluded: chain A residue 1107 GLU Chi-restraints excluded: chain C residue 360 ILE Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 383 GLU Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain C residue 439 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 57 optimal weight: 4.9990 chunk 1 optimal weight: 2.9990 chunk 74 optimal weight: 0.9990 chunk 41 optimal weight: 0.7980 chunk 85 optimal weight: 0.9980 chunk 69 optimal weight: 0.4980 chunk 0 optimal weight: 0.6980 chunk 51 optimal weight: 3.9990 chunk 90 optimal weight: 6.9990 chunk 25 optimal weight: 0.3980 chunk 33 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.0912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8672 Z= 0.154 Angle : 0.604 15.435 11751 Z= 0.294 Chirality : 0.043 0.144 1324 Planarity : 0.003 0.034 1500 Dihedral : 7.748 135.699 1162 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.38 % Allowed : 14.33 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.26), residues: 1057 helix: 1.21 (0.36), residues: 218 sheet: 0.01 (0.26), residues: 382 loop : -0.24 (0.29), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 207 HIS 0.003 0.001 HIS A 789 PHE 0.018 0.002 PHE A1030 TYR 0.017 0.001 TYR A 891 ARG 0.007 0.000 ARG A 158 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 112 time to evaluate : 0.996 Fit side-chains REVERT: A 70 LYS cc_start: 0.7200 (mtpm) cc_final: 0.6223 (mppt) REVERT: A 150 LYS cc_start: 0.5775 (tptt) cc_final: 0.4624 (tptp) REVERT: A 153 LYS cc_start: 0.6572 (OUTLIER) cc_final: 0.6340 (mmmm) REVERT: A 224 GLU cc_start: 0.7560 (mt-10) cc_final: 0.6975 (mm-30) REVERT: A 254 LYS cc_start: 0.6685 (mttt) cc_final: 0.6018 (ptpp) REVERT: A 267 ASN cc_start: 0.8191 (p0) cc_final: 0.7672 (p0) REVERT: A 298 LYS cc_start: 0.7600 (tmtm) cc_final: 0.6623 (ttpt) REVERT: A 1081 LYS cc_start: 0.7747 (ttmt) cc_final: 0.7480 (ttpt) REVERT: A 1106 GLN cc_start: 0.4852 (tp40) cc_final: 0.4636 (tp-100) REVERT: C 364 MET cc_start: 0.5923 (mtp) cc_final: 0.4770 (mmm) REVERT: C 378 LYS cc_start: 0.7420 (OUTLIER) cc_final: 0.7184 (mmtm) REVERT: C 407 LEU cc_start: 0.4298 (OUTLIER) cc_final: 0.3931 (mp) outliers start: 12 outliers final: 4 residues processed: 117 average time/residue: 1.7211 time to fit residues: 211.0319 Evaluate side-chains 115 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 108 time to evaluate : 1.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 153 LYS Chi-restraints excluded: chain A residue 204 LYS Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain C residue 439 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 90 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 59 optimal weight: 0.0070 chunk 24 optimal weight: 0.0070 chunk 100 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 46 optimal weight: 4.9990 chunk 8 optimal weight: 7.9990 chunk 33 optimal weight: 2.9990 chunk 52 optimal weight: 4.9990 chunk 97 optimal weight: 1.9990 overall best weight: 1.2022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.0973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8672 Z= 0.201 Angle : 0.634 15.694 11751 Z= 0.312 Chirality : 0.044 0.146 1324 Planarity : 0.004 0.035 1500 Dihedral : 7.816 136.571 1159 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 1.70 % Allowed : 14.86 % Favored : 83.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.25), residues: 1057 helix: 1.14 (0.36), residues: 218 sheet: 0.06 (0.26), residues: 363 loop : -0.34 (0.28), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 207 HIS 0.004 0.001 HIS A 789 PHE 0.019 0.002 PHE A1030 TYR 0.016 0.001 TYR A 891 ARG 0.006 0.000 ARG A 158 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 107 time to evaluate : 1.014 Fit side-chains REVERT: A 70 LYS cc_start: 0.7189 (mtpm) cc_final: 0.6209 (mppt) REVERT: A 150 LYS cc_start: 0.5763 (tptt) cc_final: 0.4554 (tptp) REVERT: A 153 LYS cc_start: 0.6541 (OUTLIER) cc_final: 0.6317 (mmmm) REVERT: A 210 GLU cc_start: 0.5499 (tm-30) cc_final: 0.5210 (tm-30) REVERT: A 224 GLU cc_start: 0.7604 (mt-10) cc_final: 0.7000 (mm-30) REVERT: A 254 LYS cc_start: 0.6697 (mttt) cc_final: 0.6020 (ptpp) REVERT: A 267 ASN cc_start: 0.8192 (p0) cc_final: 0.7676 (p0) REVERT: A 1106 GLN cc_start: 0.4878 (tp40) cc_final: 0.4665 (tp-100) REVERT: C 364 MET cc_start: 0.5969 (mtp) cc_final: 0.4758 (mmm) REVERT: C 378 LYS cc_start: 0.7424 (OUTLIER) cc_final: 0.7188 (mmtm) REVERT: C 383 GLU cc_start: 0.7576 (OUTLIER) cc_final: 0.7291 (tp30) REVERT: C 421 ASP cc_start: 0.6529 (OUTLIER) cc_final: 0.5956 (t0) REVERT: E 1 MET cc_start: 0.2043 (OUTLIER) cc_final: 0.1842 (ttt) outliers start: 15 outliers final: 4 residues processed: 112 average time/residue: 1.7679 time to fit residues: 207.5721 Evaluate side-chains 117 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 108 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 153 LYS Chi-restraints excluded: chain A residue 204 LYS Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 383 GLU Chi-restraints excluded: chain C residue 421 ASP Chi-restraints excluded: chain C residue 439 VAL Chi-restraints excluded: chain E residue 1 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 11 optimal weight: 0.9990 chunk 57 optimal weight: 4.9990 chunk 73 optimal weight: 0.8980 chunk 56 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 100 optimal weight: 2.9990 chunk 62 optimal weight: 5.9990 chunk 61 optimal weight: 0.7980 chunk 46 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 59 optimal weight: 0.6980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.1028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8672 Z= 0.207 Angle : 0.638 15.777 11751 Z= 0.314 Chirality : 0.044 0.149 1324 Planarity : 0.004 0.035 1500 Dihedral : 7.856 136.749 1159 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.02 % Allowed : 14.54 % Favored : 83.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.25), residues: 1057 helix: 1.14 (0.36), residues: 218 sheet: -0.01 (0.26), residues: 368 loop : -0.30 (0.28), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 207 HIS 0.004 0.001 HIS A 789 PHE 0.019 0.002 PHE A1030 TYR 0.016 0.002 TYR A 891 ARG 0.006 0.000 ARG A 158 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 107 time to evaluate : 1.051 Fit side-chains REVERT: A 70 LYS cc_start: 0.7201 (mtpm) cc_final: 0.6229 (mppt) REVERT: A 150 LYS cc_start: 0.5586 (tttt) cc_final: 0.4532 (tptp) REVERT: A 153 LYS cc_start: 0.6546 (OUTLIER) cc_final: 0.6322 (mmmm) REVERT: A 224 GLU cc_start: 0.7534 (mt-10) cc_final: 0.6935 (mm-30) REVERT: A 254 LYS cc_start: 0.6701 (mttt) cc_final: 0.6001 (ptpp) REVERT: A 267 ASN cc_start: 0.8201 (p0) cc_final: 0.7690 (p0) REVERT: A 1106 GLN cc_start: 0.4799 (tp40) cc_final: 0.4593 (tp-100) REVERT: C 364 MET cc_start: 0.5994 (mtp) cc_final: 0.4783 (mmm) REVERT: C 378 LYS cc_start: 0.7403 (OUTLIER) cc_final: 0.7160 (mmtm) REVERT: C 383 GLU cc_start: 0.7579 (OUTLIER) cc_final: 0.7313 (tp30) REVERT: C 407 LEU cc_start: 0.4391 (OUTLIER) cc_final: 0.4077 (mp) REVERT: E 1 MET cc_start: 0.2043 (OUTLIER) cc_final: 0.1808 (ttt) outliers start: 18 outliers final: 4 residues processed: 116 average time/residue: 1.7199 time to fit residues: 209.8002 Evaluate side-chains 115 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 106 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 153 LYS Chi-restraints excluded: chain A residue 204 LYS Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 383 GLU Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain C residue 439 VAL Chi-restraints excluded: chain E residue 1 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 30 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 chunk 63 optimal weight: 3.9990 chunk 68 optimal weight: 6.9990 chunk 49 optimal weight: 3.9990 chunk 9 optimal weight: 8.9990 chunk 78 optimal weight: 0.0970 chunk 91 optimal weight: 1.9990 chunk 96 optimal weight: 7.9990 chunk 87 optimal weight: 0.9990 chunk 93 optimal weight: 0.0270 overall best weight: 0.6038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 428 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.1014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8672 Z= 0.146 Angle : 0.591 15.395 11751 Z= 0.288 Chirality : 0.043 0.143 1324 Planarity : 0.003 0.034 1500 Dihedral : 7.578 131.983 1159 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 0.96 % Allowed : 15.71 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.26), residues: 1057 helix: 1.33 (0.36), residues: 218 sheet: 0.06 (0.26), residues: 379 loop : -0.21 (0.29), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 207 HIS 0.003 0.001 HIS A 789 PHE 0.018 0.002 PHE A1030 TYR 0.016 0.001 TYR A 891 ARG 0.007 0.000 ARG A 158 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 110 time to evaluate : 1.058 Fit side-chains REVERT: A 70 LYS cc_start: 0.7219 (mtpm) cc_final: 0.6236 (mppt) REVERT: A 150 LYS cc_start: 0.5801 (tttt) cc_final: 0.4571 (tptp) REVERT: A 224 GLU cc_start: 0.7528 (mt-10) cc_final: 0.6942 (mm-30) REVERT: A 254 LYS cc_start: 0.6693 (mttt) cc_final: 0.5984 (ptpp) REVERT: A 267 ASN cc_start: 0.8196 (p0) cc_final: 0.7681 (p0) REVERT: A 298 LYS cc_start: 0.7609 (tmtm) cc_final: 0.6579 (ttpp) REVERT: A 969 GLU cc_start: 0.8168 (pp20) cc_final: 0.7021 (pt0) REVERT: A 1081 LYS cc_start: 0.7766 (ttmt) cc_final: 0.7468 (ttpt) REVERT: A 1106 GLN cc_start: 0.4720 (tp40) cc_final: 0.4510 (tp-100) REVERT: C 364 MET cc_start: 0.5931 (mtp) cc_final: 0.4800 (mmm) REVERT: C 378 LYS cc_start: 0.7407 (OUTLIER) cc_final: 0.7162 (mmtm) REVERT: C 407 LEU cc_start: 0.4452 (OUTLIER) cc_final: 0.4161 (mp) REVERT: C 421 ASP cc_start: 0.6450 (OUTLIER) cc_final: 0.5893 (t0) outliers start: 8 outliers final: 4 residues processed: 114 average time/residue: 1.7050 time to fit residues: 203.8008 Evaluate side-chains 114 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 107 time to evaluate : 1.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 204 LYS Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain C residue 421 ASP Chi-restraints excluded: chain C residue 439 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 96 optimal weight: 9.9990 chunk 56 optimal weight: 4.9990 chunk 40 optimal weight: 0.9990 chunk 73 optimal weight: 0.5980 chunk 28 optimal weight: 3.9990 chunk 84 optimal weight: 0.9980 chunk 88 optimal weight: 0.7980 chunk 93 optimal weight: 9.9990 chunk 61 optimal weight: 0.1980 chunk 98 optimal weight: 6.9990 chunk 60 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.1043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8672 Z= 0.148 Angle : 0.591 15.567 11751 Z= 0.287 Chirality : 0.043 0.143 1324 Planarity : 0.003 0.034 1500 Dihedral : 7.471 129.368 1159 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.06 % Allowed : 15.71 % Favored : 83.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.26), residues: 1057 helix: 1.38 (0.37), residues: 218 sheet: 0.04 (0.26), residues: 389 loop : -0.20 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A1073 HIS 0.003 0.001 HIS A 789 PHE 0.018 0.002 PHE A1030 TYR 0.015 0.001 TYR A 891 ARG 0.007 0.000 ARG A 158 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 107 time to evaluate : 0.960 Fit side-chains REVERT: A 70 LYS cc_start: 0.7228 (mtpm) cc_final: 0.6240 (mppt) REVERT: A 101 ILE cc_start: 0.7056 (OUTLIER) cc_final: 0.6855 (mt) REVERT: A 150 LYS cc_start: 0.5804 (tttt) cc_final: 0.4565 (tptp) REVERT: A 153 LYS cc_start: 0.6582 (OUTLIER) cc_final: 0.6353 (mmmm) REVERT: A 224 GLU cc_start: 0.7550 (mt-10) cc_final: 0.6963 (mm-30) REVERT: A 254 LYS cc_start: 0.6770 (mttt) cc_final: 0.6011 (ptpp) REVERT: A 267 ASN cc_start: 0.8205 (p0) cc_final: 0.7686 (p0) REVERT: A 969 GLU cc_start: 0.8195 (pp20) cc_final: 0.7082 (pt0) REVERT: A 1081 LYS cc_start: 0.7778 (ttmt) cc_final: 0.7473 (ttpt) REVERT: A 1106 GLN cc_start: 0.4706 (tp40) cc_final: 0.4504 (tp-100) REVERT: C 364 MET cc_start: 0.5942 (mtp) cc_final: 0.4840 (mmm) REVERT: C 378 LYS cc_start: 0.7399 (OUTLIER) cc_final: 0.7147 (mmtm) REVERT: C 383 GLU cc_start: 0.7563 (OUTLIER) cc_final: 0.7278 (tp30) REVERT: C 421 ASP cc_start: 0.6472 (OUTLIER) cc_final: 0.5963 (t0) outliers start: 9 outliers final: 2 residues processed: 111 average time/residue: 1.7023 time to fit residues: 198.3411 Evaluate side-chains 112 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 105 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 153 LYS Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 383 GLU Chi-restraints excluded: chain C residue 421 ASP Chi-restraints excluded: chain C residue 439 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 46 optimal weight: 2.9990 chunk 68 optimal weight: 6.9990 chunk 103 optimal weight: 0.7980 chunk 95 optimal weight: 0.5980 chunk 82 optimal weight: 3.9990 chunk 8 optimal weight: 7.9990 chunk 63 optimal weight: 1.9990 chunk 50 optimal weight: 5.9990 chunk 65 optimal weight: 0.9980 chunk 87 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.1094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8672 Z= 0.226 Angle : 0.649 15.915 11751 Z= 0.321 Chirality : 0.044 0.152 1324 Planarity : 0.004 0.035 1500 Dihedral : 7.787 134.388 1159 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 1.27 % Allowed : 15.50 % Favored : 83.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.26), residues: 1057 helix: 1.19 (0.36), residues: 218 sheet: 0.03 (0.26), residues: 384 loop : -0.29 (0.29), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP A1073 HIS 0.005 0.001 HIS A 789 PHE 0.019 0.002 PHE A1030 TYR 0.015 0.002 TYR A 891 ARG 0.006 0.000 ARG A 158 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 106 time to evaluate : 0.903 Fit side-chains REVERT: A 65 GLU cc_start: 0.7745 (tp30) cc_final: 0.7338 (tp30) REVERT: A 70 LYS cc_start: 0.7207 (mtpm) cc_final: 0.6226 (mppt) REVERT: A 150 LYS cc_start: 0.5608 (tttt) cc_final: 0.4546 (tptp) REVERT: A 153 LYS cc_start: 0.6546 (OUTLIER) cc_final: 0.6319 (mmmm) REVERT: A 224 GLU cc_start: 0.7525 (mt-10) cc_final: 0.6963 (mm-30) REVERT: A 254 LYS cc_start: 0.6759 (mttt) cc_final: 0.6016 (ptpp) REVERT: A 267 ASN cc_start: 0.8184 (p0) cc_final: 0.7674 (p0) REVERT: A 969 GLU cc_start: 0.8347 (pp20) cc_final: 0.8006 (pm20) REVERT: C 364 MET cc_start: 0.5979 (mtp) cc_final: 0.4823 (mmm) REVERT: C 378 LYS cc_start: 0.7397 (OUTLIER) cc_final: 0.7167 (mmtm) REVERT: C 383 GLU cc_start: 0.7580 (OUTLIER) cc_final: 0.7289 (tp30) outliers start: 11 outliers final: 4 residues processed: 110 average time/residue: 1.6929 time to fit residues: 195.5292 Evaluate side-chains 113 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 106 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 153 LYS Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 383 GLU Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 439 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 76 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 82 optimal weight: 0.9990 chunk 34 optimal weight: 7.9990 chunk 84 optimal weight: 0.0370 chunk 10 optimal weight: 0.0060 chunk 15 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 59 optimal weight: 0.6980 overall best weight: 0.5076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.185748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.140817 restraints weight = 29838.359| |-----------------------------------------------------------------------------| r_work (start): 0.3641 rms_B_bonded: 3.33 r_work: 0.3515 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3519 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3519 r_free = 0.3519 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3519 r_free = 0.3519 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3519 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.1075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8672 Z= 0.140 Angle : 0.586 15.417 11751 Z= 0.285 Chirality : 0.042 0.144 1324 Planarity : 0.003 0.035 1500 Dihedral : 7.424 129.157 1159 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 0.85 % Allowed : 15.82 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.26), residues: 1057 helix: 1.40 (0.37), residues: 218 sheet: 0.04 (0.26), residues: 385 loop : -0.21 (0.29), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 207 HIS 0.003 0.001 HIS A 789 PHE 0.017 0.002 PHE A1030 TYR 0.016 0.001 TYR A 891 ARG 0.007 0.000 ARG A 158 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4166.62 seconds wall clock time: 74 minutes 34.91 seconds (4474.91 seconds total)