Starting phenix.real_space_refine on Sun Apr 7 11:48:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sj7_10213/04_2024/6sj7_10213_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sj7_10213/04_2024/6sj7_10213.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sj7_10213/04_2024/6sj7_10213.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sj7_10213/04_2024/6sj7_10213.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sj7_10213/04_2024/6sj7_10213_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sj7_10213/04_2024/6sj7_10213_updated.pdb" } resolution = 3.54 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 416 atoms to isotropic. 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 S 57 5.16 5 Cl 1 4.86 5 C 6393 2.51 5 N 1683 2.21 5 O 1873 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 132": "OE1" <-> "OE2" Residue "A TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 213": "NH1" <-> "NH2" Residue "A ARG 425": "NH1" <-> "NH2" Residue "A ASP 461": "OD1" <-> "OD2" Residue "A PHE 471": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 474": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 528": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 65": "OE1" <-> "OE2" Residue "B TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 99": "OD1" <-> "OD2" Residue "B ASP 146": "OD1" <-> "OD2" Residue "B PHE 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 224": "OE1" <-> "OE2" Residue "B ASP 243": "OD1" <-> "OD2" Residue "B TYR 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 289": "OE1" <-> "OE2" Residue "B ASP 299": "OD1" <-> "OD2" Residue "B ASP 339": "OD1" <-> "OD2" Residue "B GLU 342": "OE1" <-> "OE2" Residue "B PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 722": "NH1" <-> "NH2" Residue "B TYR 812": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 837": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 865": "OE1" <-> "OE2" Residue "B TYR 891": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 906": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 920": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 965": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 975": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 988": "OE1" <-> "OE2" Residue "B PHE 1003": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1053": "OD1" <-> "OD2" Residue "B PHE 1076": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1090": "OD1" <-> "OD2" Residue "B GLU 1107": "OE1" <-> "OE2" Residue "C ASP 264": "OD1" <-> "OD2" Residue "C PHE 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 319": "NH1" <-> "NH2" Residue "D TYR 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 10007 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 355, 2845 Classifications: {'peptide': 355} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 15, 'TRANS': 339} Chain breaks: 12 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 41 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 2, 'ARG:plan': 2, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 32 Chain: "B" Number of atoms: 6095 Number of conformers: 1 Conformer: "" Number of residues, atoms: 774, 6095 Classifications: {'peptide': 774} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 750} Chain breaks: 9 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 619 Classifications: {'peptide': 79} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 76} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 424 Classifications: {'peptide': 52} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 4, 'TRANS': 47} Chain breaks: 1 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 17 Chain: "A" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'EF6': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.55, per 1000 atoms: 0.55 Number of scatterers: 10007 At special positions: 0 Unit cell: (90.3, 95.46, 114.38, 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) Cl 1 17.00 S 57 16.00 O 1873 8.00 N 1683 7.00 C 6393 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 18 " - pdb=" SG CYS B 313 " distance=2.02 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=0, symmetry=0 Time building additional restraints: 3.82 Conformation dependent library (CDL) restraints added in 1.7 seconds 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2360 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 15 helices and 24 sheets defined 9.1% alpha, 31.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.31 Creating SS restraints... Processing helix chain 'A' and resid 37 through 46 Processing helix chain 'A' and resid 450 through 460 Processing helix chain 'A' and resid 546 through 561 Processing helix chain 'B' and resid 253 through 255 No H-bonds generated for 'chain 'B' and resid 253 through 255' Processing helix chain 'B' and resid 318 through 320 No H-bonds generated for 'chain 'B' and resid 318 through 320' Processing helix chain 'B' and resid 757 through 759 No H-bonds generated for 'chain 'B' and resid 757 through 759' Processing helix chain 'B' and resid 986 through 989 No H-bonds generated for 'chain 'B' and resid 986 through 989' Processing helix chain 'B' and resid 1046 through 1058 Processing helix chain 'B' and resid 1070 through 1073 No H-bonds generated for 'chain 'B' and resid 1070 through 1073' Processing helix chain 'B' and resid 1091 through 1095 Processing helix chain 'B' and resid 1102 through 1107 Processing helix chain 'B' and resid 1127 through 1136 Processing helix chain 'C' and resid 263 through 271 Processing helix chain 'C' and resid 303 through 310 removed outlier: 3.824A pdb=" N GLU C 309 " --> pdb=" O LYS C 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 54 through 63 Processing sheet with id= A, first strand: chain 'A' and resid 61 through 63 Processing sheet with id= B, first strand: chain 'A' and resid 78 through 83 removed outlier: 6.818A pdb=" N LEU A 91 " --> pdb=" O LEU A 81 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N PHE A 83 " --> pdb=" O TYR A 89 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N TYR A 89 " --> pdb=" O PHE A 83 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N GLU A 113 " --> pdb=" O LEU A 122 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N LEU A 122 " --> pdb=" O GLU A 113 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 139 through 144 Processing sheet with id= D, first strand: chain 'A' and resid 242 through 246 Processing sheet with id= E, first strand: chain 'A' and resid 474 through 482 removed outlier: 6.587A pdb=" N LEU A 489 " --> pdb=" O LEU A 479 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N VAL A 481 " --> pdb=" O GLN A 487 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N GLN A 487 " --> pdb=" O VAL A 481 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N ALA A 520 " --> pdb=" O VAL A 531 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N VAL A 531 " --> pdb=" O ALA A 520 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ASP A 522 " --> pdb=" O GLU A 529 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N GLU A 529 " --> pdb=" O ASP A 522 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 495 through 498 Processing sheet with id= G, first strand: chain 'B' and resid 1088 through 1090 removed outlier: 7.412A pdb=" N ASN B 4 " --> pdb=" O ILE B1089 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N ILE B1037 " --> pdb=" O ALA B 9 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 17 through 22 removed outlier: 5.021A pdb=" N LEU B 29 " --> pdb=" O VAL B 44 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 61 through 67 removed outlier: 6.603A pdb=" N LEU B 80 " --> pdb=" O ALA B 62 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N MET B 64 " --> pdb=" O PHE B 78 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N PHE B 78 " --> pdb=" O MET B 64 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N LEU B 66 " --> pdb=" O LEU B 76 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N LEU B 76 " --> pdb=" O LEU B 66 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ASN B 85 " --> pdb=" O THR B 81 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N GLU B 90 " --> pdb=" O THR B 102 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N THR B 102 " --> pdb=" O GLU B 90 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 121 through 124 Processing sheet with id= K, first strand: chain 'B' and resid 210 through 212 removed outlier: 3.802A pdb=" N ARG B 188 " --> pdb=" O VAL B 212 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ASP B 166 " --> pdb=" O VAL B 181 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 193 through 196 Processing sheet with id= M, first strand: chain 'B' and resid 218 through 221 Processing sheet with id= N, first strand: chain 'B' and resid 258 through 263 removed outlier: 6.656A pdb=" N GLY B 274 " --> pdb=" O VAL B 259 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N HIS B 261 " --> pdb=" O LEU B 272 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N LEU B 272 " --> pdb=" O HIS B 261 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N ARG B 263 " --> pdb=" O ARG B 270 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N ARG B 270 " --> pdb=" O ARG B 263 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ASP B 275 " --> pdb=" O ARG B 279 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ARG B 279 " --> pdb=" O ASP B 275 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU B 280 " --> pdb=" O GLY B 306 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLY B 306 " --> pdb=" O LEU B 280 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N MET B 282 " --> pdb=" O LEU B 304 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N LEU B 304 " --> pdb=" O MET B 282 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N LEU B 284 " --> pdb=" O VAL B 302 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N VAL B 302 " --> pdb=" O LEU B 284 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'B' and resid 321 through 324 removed outlier: 5.553A pdb=" N LYS B 335 " --> pdb=" O ALA B 349 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N ALA B 349 " --> pdb=" O LYS B 335 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'B' and resid 362 through 365 removed outlier: 3.745A pdb=" N CYS B 363 " --> pdb=" O VAL B 376 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N VAL B 376 " --> pdb=" O CYS B 363 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL B 365 " --> pdb=" O GLN B 374 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'B' and resid 724 through 727 removed outlier: 3.669A pdb=" N HIS B 803 " --> pdb=" O ILE B 793 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N ASP B 795 " --> pdb=" O VAL B 801 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N VAL B 801 " --> pdb=" O ASP B 795 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N SER B 762 " --> pdb=" O ALA B 804 " (cutoff:3.500A) removed outlier: 8.060A pdb=" N GLN B 806 " --> pdb=" O SER B 762 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N SER B 764 " --> pdb=" O GLN B 806 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'B' and resid 741 through 743 removed outlier: 4.237A pdb=" N VAL B 742 " --> pdb=" O THR B 750 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N THR B 750 " --> pdb=" O VAL B 742 " (cutoff:3.500A) No H-bonds generated for sheet with id= R Processing sheet with id= S, first strand: chain 'B' and resid 811 through 820 removed outlier: 6.240A pdb=" N GLY B 832 " --> pdb=" O LEU B 814 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N LEU B 816 " --> pdb=" O ILE B 830 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ILE B 830 " --> pdb=" O LEU B 816 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N SER B 818 " --> pdb=" O TYR B 828 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N TYR B 828 " --> pdb=" O SER B 818 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N THR B 827 " --> pdb=" O TYR B 853 " (cutoff:3.500A) removed outlier: 5.249A pdb=" N TYR B 853 " --> pdb=" O THR B 827 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N GLN B 845 " --> pdb=" O MET B 835 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N GLN B 852 " --> pdb=" O THR B 860 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N THR B 860 " --> pdb=" O GLN B 852 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'B' and resid 872 through 875 removed outlier: 3.775A pdb=" N SER B 872 " --> pdb=" O SER B 883 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N GLU B 898 " --> pdb=" O THR B 894 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'B' and resid 931 through 933 removed outlier: 3.709A pdb=" N PHE B 920 " --> pdb=" O LYS B 917 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LYS B 917 " --> pdb=" O PHE B 920 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N TYR B 913 " --> pdb=" O GLY B 924 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'B' and resid 954 through 959 removed outlier: 6.921A pdb=" N ALA B 968 " --> pdb=" O SER B 955 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N VAL B 957 " --> pdb=" O LEU B 966 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N LEU B 966 " --> pdb=" O VAL B 957 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ASN B 973 " --> pdb=" O GLU B 969 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N GLN B 978 " --> pdb=" O GLU B 994 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N GLU B 994 " --> pdb=" O GLN B 978 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'C' and resid 251 through 253 Processing sheet with id= X, first strand: chain 'C' and resid 314 through 316 301 hydrogen bonds defined for protein. 810 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: 3.60 Time building geometry restraints manager: 4.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3223 1.34 - 1.46: 2370 1.46 - 1.59: 4512 1.59 - 1.71: 2 1.71 - 1.83: 87 Bond restraints: 10194 Sorted by residual: bond pdb=" CA HIS A 214 " pdb=" CB HIS A 214 " ideal model delta sigma weight residual 1.526 1.455 0.071 1.51e-02 4.39e+03 2.19e+01 bond pdb=" C4 EF6 A 701 " pdb=" N1 EF6 A 701 " ideal model delta sigma weight residual 1.376 1.307 0.069 2.00e-02 2.50e+03 1.20e+01 bond pdb=" C GLU B 54 " pdb=" N VAL B 55 " ideal model delta sigma weight residual 1.329 1.279 0.049 1.69e-02 3.50e+03 8.52e+00 bond pdb=" C2 EF6 A 701 " pdb=" C3 EF6 A 701 " ideal model delta sigma weight residual 1.431 1.489 -0.058 2.00e-02 2.50e+03 8.31e+00 bond pdb=" N ARG B 928 " pdb=" CA ARG B 928 " ideal model delta sigma weight residual 1.456 1.487 -0.032 1.18e-02 7.18e+03 7.19e+00 ... (remaining 10189 not shown) Histogram of bond angle deviations from ideal: 96.41 - 103.99: 128 103.99 - 111.58: 4519 111.58 - 119.17: 3843 119.17 - 126.76: 5163 126.76 - 134.34: 128 Bond angle restraints: 13781 Sorted by residual: angle pdb=" N VAL A 36 " pdb=" CA VAL A 36 " pdb=" C VAL A 36 " ideal model delta sigma weight residual 112.96 107.94 5.02 1.00e+00 1.00e+00 2.52e+01 angle pdb=" C ILE B 884 " pdb=" N ASN B 885 " pdb=" CA ASN B 885 " ideal model delta sigma weight residual 121.54 130.16 -8.62 1.91e+00 2.74e-01 2.04e+01 angle pdb=" C THR A 247 " pdb=" N SER A 248 " pdb=" CA SER A 248 " ideal model delta sigma weight residual 121.54 129.75 -8.21 1.91e+00 2.74e-01 1.85e+01 angle pdb=" C GLU B 289 " pdb=" N GLN B 290 " pdb=" CA GLN B 290 " ideal model delta sigma weight residual 121.54 128.69 -7.15 1.91e+00 2.74e-01 1.40e+01 angle pdb=" C GLN A 130 " pdb=" N ASP A 131 " pdb=" CA ASP A 131 " ideal model delta sigma weight residual 122.46 127.60 -5.14 1.41e+00 5.03e-01 1.33e+01 ... (remaining 13776 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.09: 5297 18.09 - 36.18: 646 36.18 - 54.27: 114 54.27 - 72.37: 27 72.37 - 90.46: 11 Dihedral angle restraints: 6095 sinusoidal: 2453 harmonic: 3642 Sorted by residual: dihedral pdb=" CA GLU C 271 " pdb=" C GLU C 271 " pdb=" N PRO C 272 " pdb=" CA PRO C 272 " ideal model delta harmonic sigma weight residual -180.00 -150.92 -29.08 0 5.00e+00 4.00e-02 3.38e+01 dihedral pdb=" CA LEU C 316 " pdb=" C LEU C 316 " pdb=" N ALA C 317 " pdb=" CA ALA C 317 " ideal model delta harmonic sigma weight residual 180.00 151.45 28.55 0 5.00e+00 4.00e-02 3.26e+01 dihedral pdb=" CA PRO B 225 " pdb=" C PRO B 225 " pdb=" N PHE B 226 " pdb=" CA PHE B 226 " ideal model delta harmonic sigma weight residual 180.00 152.98 27.02 0 5.00e+00 4.00e-02 2.92e+01 ... (remaining 6092 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1083 0.055 - 0.111: 373 0.111 - 0.166: 94 0.166 - 0.222: 17 0.222 - 0.277: 5 Chirality restraints: 1572 Sorted by residual: chirality pdb=" CB VAL B1033 " pdb=" CA VAL B1033 " pdb=" CG1 VAL B1033 " pdb=" CG2 VAL B1033 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 1.92e+00 chirality pdb=" CB ILE B 390 " pdb=" CA ILE B 390 " pdb=" CG1 ILE B 390 " pdb=" CG2 ILE B 390 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.27 2.00e-01 2.50e+01 1.79e+00 chirality pdb=" CB THR A 141 " pdb=" CA THR A 141 " pdb=" OG1 THR A 141 " pdb=" CG2 THR A 141 " both_signs ideal model delta sigma weight residual False 2.55 2.32 0.23 2.00e-01 2.50e+01 1.32e+00 ... (remaining 1569 not shown) Planarity restraints: 1742 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU C 316 " -0.016 2.00e-02 2.50e+03 3.22e-02 1.03e+01 pdb=" C LEU C 316 " 0.056 2.00e-02 2.50e+03 pdb=" O LEU C 316 " -0.021 2.00e-02 2.50e+03 pdb=" N ALA C 317 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B1047 " 0.024 2.00e-02 2.50e+03 1.85e-02 8.54e+00 pdb=" CG TRP B1047 " -0.050 2.00e-02 2.50e+03 pdb=" CD1 TRP B1047 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 TRP B1047 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP B1047 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP B1047 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B1047 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP B1047 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP B1047 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP B1047 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN B 731 " 0.013 2.00e-02 2.50e+03 2.68e-02 7.16e+00 pdb=" CD GLN B 731 " -0.046 2.00e-02 2.50e+03 pdb=" OE1 GLN B 731 " 0.018 2.00e-02 2.50e+03 pdb=" NE2 GLN B 731 " 0.015 2.00e-02 2.50e+03 ... (remaining 1739 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 2794 2.80 - 3.33: 8729 3.33 - 3.85: 16520 3.85 - 4.38: 18760 4.38 - 4.90: 33014 Nonbonded interactions: 79817 Sorted by model distance: nonbonded pdb=" OH TYR B 726 " pdb=" OE1 GLN B 796 " model vdw 2.280 2.440 nonbonded pdb=" OG1 THR B 13 " pdb=" OD1 ASN B 355 " model vdw 2.285 2.440 nonbonded pdb=" OG SER B 872 " pdb=" O LEU B 912 " model vdw 2.286 2.440 nonbonded pdb=" OG SER B 883 " pdb=" O ALA B 911 " model vdw 2.290 2.440 nonbonded pdb=" OG SER B 94 " pdb=" OG SER B 97 " model vdw 2.292 2.440 ... (remaining 79812 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=1.00 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: 1.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.010 Extract box with map and model: 4.930 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 30.160 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 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 : 0.010 0.071 10194 Z= 0.662 Angle : 1.031 9.490 13781 Z= 0.564 Chirality : 0.060 0.277 1572 Planarity : 0.006 0.062 1742 Dihedral : 16.416 90.457 3732 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.08 % Allowed : 11.26 % Favored : 88.66 % Rotamer: Outliers : 0.81 % Allowed : 13.53 % Favored : 85.66 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 2.38 % 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: -3.72 (0.20), residues: 1208 helix: -2.78 (0.32), residues: 134 sheet: -1.27 (0.23), residues: 437 loop : -3.38 (0.19), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.004 TRP B1047 HIS 0.006 0.002 HIS B1140 PHE 0.042 0.003 PHE B1030 TYR 0.021 0.003 TYR B 245 ARG 0.007 0.001 ARG B 111 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 148 time to evaluate : 1.229 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 560 MET cc_start: 0.8151 (mmm) cc_final: 0.7796 (mmm) REVERT: B 16 ASN cc_start: 0.8480 (t0) cc_final: 0.8162 (t0) REVERT: B 787 GLU cc_start: 0.8444 (mp0) cc_final: 0.8161 (mp0) REVERT: B 958 GLU cc_start: 0.7727 (tp30) cc_final: 0.7334 (tp30) outliers start: 9 outliers final: 4 residues processed: 154 average time/residue: 0.2714 time to fit residues: 56.1186 Evaluate side-chains 114 residues out of total 1124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 110 time to evaluate : 1.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ARG Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain D residue 36 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 0.9990 chunk 93 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 32 optimal weight: 6.9990 chunk 63 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 37 optimal weight: 4.9990 chunk 59 optimal weight: 7.9990 chunk 72 optimal weight: 0.6980 chunk 112 optimal weight: 9.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 ASN A 445 GLN A 542 GLN B 4 ASN ** B 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 203 ASN B 261 HIS B 262 ASN ** B 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 964 ASN B1034 ASN B1106 GLN C 280 GLN C 310 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.1249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 10194 Z= 0.309 Angle : 0.624 6.609 13781 Z= 0.328 Chirality : 0.044 0.176 1572 Planarity : 0.004 0.055 1742 Dihedral : 6.873 52.949 1364 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 14.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.19 % Favored : 90.81 % Rotamer: Outliers : 3.07 % Allowed : 18.49 % Favored : 78.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: -3.06 (0.21), residues: 1208 helix: -1.23 (0.42), residues: 137 sheet: -0.95 (0.24), residues: 431 loop : -3.11 (0.20), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 111 HIS 0.004 0.001 HIS A 460 PHE 0.019 0.002 PHE B1030 TYR 0.017 0.001 TYR B 42 ARG 0.007 0.000 ARG D 18 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 121 time to evaluate : 1.301 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 ARG cc_start: 0.8152 (ttm-80) cc_final: 0.7687 (mtt90) REVERT: A 560 MET cc_start: 0.8162 (mmm) cc_final: 0.7820 (mmm) REVERT: A 562 TRP cc_start: 0.8442 (m100) cc_final: 0.8126 (m100) REVERT: A 575 MET cc_start: 0.6900 (mmm) cc_final: 0.6488 (mmp) REVERT: B 16 ASN cc_start: 0.8321 (t0) cc_final: 0.8033 (t0) REVERT: B 787 GLU cc_start: 0.8353 (mp0) cc_final: 0.8060 (mp0) REVERT: B 966 LEU cc_start: 0.8378 (OUTLIER) cc_final: 0.8091 (tp) outliers start: 34 outliers final: 21 residues processed: 143 average time/residue: 0.2641 time to fit residues: 53.3315 Evaluate side-chains 130 residues out of total 1124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 108 time to evaluate : 1.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 490 ILE Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 377 THR Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 929 SER Chi-restraints excluded: chain B residue 930 VAL Chi-restraints excluded: chain B residue 949 PHE Chi-restraints excluded: chain B residue 959 ILE Chi-restraints excluded: chain B residue 964 ASN Chi-restraints excluded: chain B residue 966 LEU Chi-restraints excluded: chain B residue 1065 VAL Chi-restraints excluded: chain B residue 1139 ILE Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 263 GLU Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 52 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 62 optimal weight: 3.9990 chunk 34 optimal weight: 20.0000 chunk 93 optimal weight: 2.9990 chunk 76 optimal weight: 0.9990 chunk 31 optimal weight: 0.7980 chunk 112 optimal weight: 9.9990 chunk 121 optimal weight: 7.9990 chunk 100 optimal weight: 4.9990 chunk 111 optimal weight: 4.9990 chunk 38 optimal weight: 0.8980 chunk 90 optimal weight: 0.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 16 ASN ** B 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 964 ASN C 280 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.1539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 10194 Z= 0.221 Angle : 0.574 9.006 13781 Z= 0.300 Chirality : 0.043 0.166 1572 Planarity : 0.004 0.043 1742 Dihedral : 6.142 55.225 1360 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 13.96 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.36 % Favored : 91.56 % Rotamer: Outliers : 2.98 % Allowed : 19.93 % Favored : 77.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -2.66 (0.22), residues: 1208 helix: -0.55 (0.46), residues: 139 sheet: -0.73 (0.24), residues: 429 loop : -2.90 (0.21), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 111 HIS 0.003 0.001 HIS A 219 PHE 0.019 0.001 PHE A 157 TYR 0.011 0.001 TYR B 42 ARG 0.007 0.000 ARG D 18 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 126 time to evaluate : 1.180 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 ARG cc_start: 0.8162 (ttm-80) cc_final: 0.7531 (mtm-85) REVERT: A 562 TRP cc_start: 0.8376 (m100) cc_final: 0.8110 (m100) REVERT: B 16 ASN cc_start: 0.8232 (t0) cc_final: 0.7935 (t0) REVERT: B 714 THR cc_start: 0.8757 (m) cc_final: 0.8465 (p) REVERT: B 787 GLU cc_start: 0.8307 (mp0) cc_final: 0.8026 (mp0) REVERT: B 1002 GLU cc_start: 0.8144 (mm-30) cc_final: 0.7866 (mm-30) REVERT: D 62 GLN cc_start: 0.8251 (tt0) cc_final: 0.8014 (tt0) outliers start: 33 outliers final: 24 residues processed: 148 average time/residue: 0.2568 time to fit residues: 53.3419 Evaluate side-chains 142 residues out of total 1124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 118 time to evaluate : 1.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 490 ILE Chi-restraints excluded: chain A residue 514 HIS Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 209 GLN Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 929 SER Chi-restraints excluded: chain B residue 930 VAL Chi-restraints excluded: chain B residue 949 PHE Chi-restraints excluded: chain B residue 959 ILE Chi-restraints excluded: chain B residue 964 ASN Chi-restraints excluded: chain B residue 1032 THR Chi-restraints excluded: chain B residue 1065 VAL Chi-restraints excluded: chain B residue 1139 ILE Chi-restraints excluded: chain C residue 263 GLU Chi-restraints excluded: chain C residue 296 ILE Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 52 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 111 optimal weight: 3.9990 chunk 84 optimal weight: 3.9990 chunk 58 optimal weight: 7.9990 chunk 12 optimal weight: 6.9990 chunk 53 optimal weight: 0.9990 chunk 75 optimal weight: 3.9990 chunk 113 optimal weight: 1.9990 chunk 119 optimal weight: 7.9990 chunk 59 optimal weight: 7.9990 chunk 107 optimal weight: 0.0670 chunk 32 optimal weight: 2.9990 overall best weight: 2.0126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 290 GLN B 964 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.1640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10194 Z= 0.287 Angle : 0.591 8.740 13781 Z= 0.308 Chirality : 0.044 0.163 1572 Planarity : 0.004 0.040 1742 Dihedral : 6.027 57.520 1359 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 14.77 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.52 % Favored : 90.40 % Rotamer: Outliers : 3.97 % Allowed : 21.28 % Favored : 74.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -2.46 (0.23), residues: 1208 helix: -0.17 (0.48), residues: 135 sheet: -0.69 (0.24), residues: 437 loop : -2.76 (0.21), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 111 HIS 0.004 0.001 HIS A 460 PHE 0.020 0.001 PHE B1030 TYR 0.013 0.001 TYR B 42 ARG 0.006 0.000 ARG D 18 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 117 time to evaluate : 1.121 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 ARG cc_start: 0.8188 (ttm-80) cc_final: 0.7644 (mtt90) REVERT: B 16 ASN cc_start: 0.8305 (t0) cc_final: 0.8004 (t0) REVERT: B 57 MET cc_start: 0.8050 (mmm) cc_final: 0.7794 (mmm) REVERT: B 714 THR cc_start: 0.8775 (m) cc_final: 0.8465 (p) REVERT: B 787 GLU cc_start: 0.8320 (mp0) cc_final: 0.8022 (mp0) REVERT: B 966 LEU cc_start: 0.8337 (OUTLIER) cc_final: 0.8025 (tp) REVERT: B 1080 ARG cc_start: 0.7659 (mpt180) cc_final: 0.7387 (mpt180) REVERT: D 5 LEU cc_start: 0.7286 (OUTLIER) cc_final: 0.6989 (tt) outliers start: 44 outliers final: 31 residues processed: 151 average time/residue: 0.2432 time to fit residues: 50.3845 Evaluate side-chains 146 residues out of total 1124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 113 time to evaluate : 1.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 490 ILE Chi-restraints excluded: chain A residue 514 HIS Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 196 SER Chi-restraints excluded: chain B residue 209 GLN Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 369 ARG Chi-restraints excluded: chain B residue 377 THR Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 885 ASN Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 929 SER Chi-restraints excluded: chain B residue 930 VAL Chi-restraints excluded: chain B residue 959 ILE Chi-restraints excluded: chain B residue 964 ASN Chi-restraints excluded: chain B residue 966 LEU Chi-restraints excluded: chain B residue 1032 THR Chi-restraints excluded: chain B residue 1065 VAL Chi-restraints excluded: chain B residue 1139 ILE Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 263 GLU Chi-restraints excluded: chain C residue 296 ILE Chi-restraints excluded: chain D residue 5 LEU Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 52 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 99 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 1 optimal weight: 0.9990 chunk 89 optimal weight: 0.9990 chunk 49 optimal weight: 0.9990 chunk 102 optimal weight: 5.9990 chunk 82 optimal weight: 5.9990 chunk 0 optimal weight: 7.9990 chunk 61 optimal weight: 4.9990 chunk 107 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 overall best weight: 1.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 290 GLN ** B 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 964 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.1856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10194 Z= 0.203 Angle : 0.574 9.773 13781 Z= 0.296 Chirality : 0.043 0.152 1572 Planarity : 0.003 0.038 1742 Dihedral : 5.753 58.769 1359 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 14.41 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.20 % Favored : 91.72 % Rotamer: Outliers : 3.97 % Allowed : 22.09 % Favored : 73.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -2.27 (0.23), residues: 1208 helix: -0.07 (0.48), residues: 136 sheet: -0.53 (0.25), residues: 434 loop : -2.64 (0.22), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 111 HIS 0.004 0.001 HIS C 258 PHE 0.016 0.001 PHE B1030 TYR 0.010 0.001 TYR B 42 ARG 0.007 0.000 ARG D 18 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 126 time to evaluate : 1.224 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 ARG cc_start: 0.8163 (ttm-80) cc_final: 0.7534 (mtm-85) REVERT: B 16 ASN cc_start: 0.8245 (t0) cc_final: 0.7959 (t0) REVERT: B 57 MET cc_start: 0.7954 (mmm) cc_final: 0.7705 (mmm) REVERT: B 714 THR cc_start: 0.8740 (m) cc_final: 0.8435 (p) REVERT: B 787 GLU cc_start: 0.8282 (mp0) cc_final: 0.7973 (mp0) REVERT: C 250 MET cc_start: 0.6590 (ttm) cc_final: 0.6353 (ttp) REVERT: D 5 LEU cc_start: 0.7194 (OUTLIER) cc_final: 0.6880 (tt) REVERT: D 62 GLN cc_start: 0.8195 (tt0) cc_final: 0.7702 (tm-30) outliers start: 44 outliers final: 35 residues processed: 161 average time/residue: 0.2471 time to fit residues: 55.2557 Evaluate side-chains 155 residues out of total 1124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 119 time to evaluate : 1.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 214 HIS Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 490 ILE Chi-restraints excluded: chain A residue 514 HIS Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 209 GLN Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 369 ARG Chi-restraints excluded: chain B residue 377 THR Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 885 ASN Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 929 SER Chi-restraints excluded: chain B residue 930 VAL Chi-restraints excluded: chain B residue 931 LEU Chi-restraints excluded: chain B residue 959 ILE Chi-restraints excluded: chain B residue 964 ASN Chi-restraints excluded: chain B residue 1032 THR Chi-restraints excluded: chain B residue 1065 VAL Chi-restraints excluded: chain B residue 1139 ILE Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 263 GLU Chi-restraints excluded: chain C residue 296 ILE Chi-restraints excluded: chain D residue 5 LEU Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 52 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 40 optimal weight: 3.9990 chunk 107 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 70 optimal weight: 0.9990 chunk 29 optimal weight: 4.9990 chunk 119 optimal weight: 7.9990 chunk 99 optimal weight: 9.9990 chunk 55 optimal weight: 2.9990 chunk 9 optimal weight: 20.0000 chunk 39 optimal weight: 0.9990 chunk 62 optimal weight: 5.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 290 GLN ** B 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 964 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.1891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 10194 Z= 0.331 Angle : 0.615 9.014 13781 Z= 0.318 Chirality : 0.044 0.156 1572 Planarity : 0.004 0.043 1742 Dihedral : 5.947 59.406 1359 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 16.02 Ramachandran Plot: Outliers : 0.08 % Allowed : 10.18 % Favored : 89.74 % Rotamer: Outliers : 4.51 % Allowed : 23.35 % Favored : 72.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -2.33 (0.23), residues: 1208 helix: -0.15 (0.47), residues: 136 sheet: -0.61 (0.24), residues: 440 loop : -2.65 (0.22), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 562 HIS 0.005 0.001 HIS C 258 PHE 0.023 0.001 PHE B1030 TYR 0.014 0.001 TYR B 42 ARG 0.008 0.000 ARG D 18 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 113 time to evaluate : 1.232 Fit side-chains revert: symmetry clash REVERT: B 16 ASN cc_start: 0.8373 (t0) cc_final: 0.8078 (t0) REVERT: B 207 TRP cc_start: 0.6179 (t60) cc_final: 0.5946 (t60) REVERT: B 714 THR cc_start: 0.8782 (m) cc_final: 0.8490 (p) REVERT: B 787 GLU cc_start: 0.8313 (mp0) cc_final: 0.8016 (mp0) REVERT: B 966 LEU cc_start: 0.8252 (OUTLIER) cc_final: 0.7919 (tp) REVERT: B 1080 ARG cc_start: 0.7676 (mpt180) cc_final: 0.7467 (mpt180) REVERT: C 250 MET cc_start: 0.6512 (ttm) cc_final: 0.6240 (ttp) REVERT: D 5 LEU cc_start: 0.7285 (OUTLIER) cc_final: 0.6971 (tt) outliers start: 50 outliers final: 39 residues processed: 152 average time/residue: 0.2290 time to fit residues: 49.1190 Evaluate side-chains 149 residues out of total 1124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 108 time to evaluate : 1.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 214 HIS Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 490 ILE Chi-restraints excluded: chain A residue 514 HIS Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 137 ASP Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 196 SER Chi-restraints excluded: chain B residue 209 GLN Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 377 THR Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 885 ASN Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 929 SER Chi-restraints excluded: chain B residue 930 VAL Chi-restraints excluded: chain B residue 931 LEU Chi-restraints excluded: chain B residue 949 PHE Chi-restraints excluded: chain B residue 959 ILE Chi-restraints excluded: chain B residue 964 ASN Chi-restraints excluded: chain B residue 966 LEU Chi-restraints excluded: chain B residue 1032 THR Chi-restraints excluded: chain B residue 1065 VAL Chi-restraints excluded: chain B residue 1112 LEU Chi-restraints excluded: chain B residue 1139 ILE Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 263 GLU Chi-restraints excluded: chain C residue 296 ILE Chi-restraints excluded: chain D residue 5 LEU Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 52 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 115 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 87 optimal weight: 0.7980 chunk 67 optimal weight: 3.9990 chunk 100 optimal weight: 2.9990 chunk 66 optimal weight: 0.7980 chunk 119 optimal weight: 4.9990 chunk 74 optimal weight: 2.9990 chunk 72 optimal weight: 0.6980 chunk 55 optimal weight: 0.9980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 267 ASN ** B 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 964 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.2101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10194 Z= 0.195 Angle : 0.563 8.878 13781 Z= 0.290 Chirality : 0.043 0.159 1572 Planarity : 0.003 0.037 1742 Dihedral : 5.593 58.692 1359 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 14.11 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.78 % Favored : 92.14 % Rotamer: Outliers : 4.33 % Allowed : 23.90 % Favored : 71.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -2.11 (0.23), residues: 1208 helix: -0.07 (0.48), residues: 136 sheet: -0.51 (0.25), residues: 430 loop : -2.42 (0.22), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 562 HIS 0.005 0.001 HIS C 258 PHE 0.015 0.001 PHE B1030 TYR 0.009 0.001 TYR B 42 ARG 0.008 0.000 ARG D 18 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 118 time to evaluate : 1.258 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 16 ASN cc_start: 0.8253 (t0) cc_final: 0.7968 (t0) REVERT: B 254 LYS cc_start: 0.8240 (pttt) cc_final: 0.7945 (ptmm) REVERT: B 714 THR cc_start: 0.8743 (m) cc_final: 0.8456 (p) REVERT: B 1080 ARG cc_start: 0.7629 (mpt180) cc_final: 0.7397 (mpt180) REVERT: C 250 MET cc_start: 0.6506 (ttm) cc_final: 0.6243 (ttp) REVERT: D 5 LEU cc_start: 0.7224 (OUTLIER) cc_final: 0.6903 (tt) outliers start: 48 outliers final: 39 residues processed: 155 average time/residue: 0.2328 time to fit residues: 51.0852 Evaluate side-chains 154 residues out of total 1124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 114 time to evaluate : 1.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 214 HIS Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 490 ILE Chi-restraints excluded: chain A residue 514 HIS Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 137 ASP Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 196 SER Chi-restraints excluded: chain B residue 209 GLN Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 377 THR Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 725 CYS Chi-restraints excluded: chain B residue 849 VAL Chi-restraints excluded: chain B residue 885 ASN Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 929 SER Chi-restraints excluded: chain B residue 930 VAL Chi-restraints excluded: chain B residue 931 LEU Chi-restraints excluded: chain B residue 949 PHE Chi-restraints excluded: chain B residue 959 ILE Chi-restraints excluded: chain B residue 964 ASN Chi-restraints excluded: chain B residue 1032 THR Chi-restraints excluded: chain B residue 1065 VAL Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 263 GLU Chi-restraints excluded: chain C residue 296 ILE Chi-restraints excluded: chain D residue 5 LEU Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 59 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 73 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 71 optimal weight: 0.8980 chunk 36 optimal weight: 0.9980 chunk 23 optimal weight: 0.7980 chunk 75 optimal weight: 4.9990 chunk 81 optimal weight: 3.9990 chunk 59 optimal weight: 5.9990 chunk 11 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 chunk 108 optimal weight: 4.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 964 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.2142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10194 Z= 0.240 Angle : 0.578 10.026 13781 Z= 0.296 Chirality : 0.044 0.155 1572 Planarity : 0.003 0.038 1742 Dihedral : 5.611 57.233 1359 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 14.97 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.53 % Favored : 91.39 % Rotamer: Outliers : 4.87 % Allowed : 23.26 % Favored : 71.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -2.04 (0.23), residues: 1208 helix: -0.00 (0.48), residues: 135 sheet: -0.43 (0.25), residues: 431 loop : -2.40 (0.22), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 562 HIS 0.004 0.001 HIS C 258 PHE 0.017 0.001 PHE B1030 TYR 0.010 0.001 TYR B 42 ARG 0.008 0.000 ARG D 18 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 114 time to evaluate : 1.266 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 562 TRP cc_start: 0.7927 (m100) cc_final: 0.7581 (m100) REVERT: B 16 ASN cc_start: 0.8289 (t0) cc_final: 0.8003 (t0) REVERT: B 254 LYS cc_start: 0.8229 (pttt) cc_final: 0.7989 (ptmm) REVERT: B 714 THR cc_start: 0.8753 (m) cc_final: 0.8465 (p) REVERT: B 966 LEU cc_start: 0.8252 (OUTLIER) cc_final: 0.7958 (tp) REVERT: B 1080 ARG cc_start: 0.7555 (mpt180) cc_final: 0.7335 (mpt180) REVERT: C 250 MET cc_start: 0.6524 (ttm) cc_final: 0.6246 (ttp) REVERT: D 5 LEU cc_start: 0.7248 (OUTLIER) cc_final: 0.6920 (tt) outliers start: 54 outliers final: 43 residues processed: 158 average time/residue: 0.2300 time to fit residues: 51.4783 Evaluate side-chains 159 residues out of total 1124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 114 time to evaluate : 1.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 214 HIS Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 490 ILE Chi-restraints excluded: chain A residue 514 HIS Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 137 ASP Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 196 SER Chi-restraints excluded: chain B residue 209 GLN Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 377 THR Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 725 CYS Chi-restraints excluded: chain B residue 849 VAL Chi-restraints excluded: chain B residue 885 ASN Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 929 SER Chi-restraints excluded: chain B residue 930 VAL Chi-restraints excluded: chain B residue 931 LEU Chi-restraints excluded: chain B residue 949 PHE Chi-restraints excluded: chain B residue 959 ILE Chi-restraints excluded: chain B residue 964 ASN Chi-restraints excluded: chain B residue 966 LEU Chi-restraints excluded: chain B residue 1032 THR Chi-restraints excluded: chain B residue 1065 VAL Chi-restraints excluded: chain B residue 1112 LEU Chi-restraints excluded: chain B residue 1139 ILE Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 263 GLU Chi-restraints excluded: chain C residue 296 ILE Chi-restraints excluded: chain D residue 5 LEU Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 52 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 114 optimal weight: 0.5980 chunk 104 optimal weight: 2.9990 chunk 111 optimal weight: 0.9980 chunk 67 optimal weight: 4.9990 chunk 48 optimal weight: 0.9990 chunk 87 optimal weight: 2.9990 chunk 34 optimal weight: 0.0060 chunk 100 optimal weight: 3.9990 chunk 105 optimal weight: 0.9990 chunk 110 optimal weight: 3.9990 chunk 73 optimal weight: 4.9990 overall best weight: 0.7200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 107 ASN ** B 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 964 ASN ** C 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.2342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10194 Z= 0.170 Angle : 0.571 10.769 13781 Z= 0.290 Chirality : 0.043 0.160 1572 Planarity : 0.003 0.037 1742 Dihedral : 5.356 54.289 1359 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.71 % Favored : 93.21 % Rotamer: Outliers : 3.43 % Allowed : 24.71 % Favored : 71.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.90 (0.24), residues: 1208 helix: -0.07 (0.48), residues: 135 sheet: -0.13 (0.26), residues: 414 loop : -2.38 (0.22), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 562 HIS 0.006 0.001 HIS C 258 PHE 0.014 0.001 PHE B1030 TYR 0.009 0.001 TYR D 35 ARG 0.008 0.000 ARG D 18 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 124 time to evaluate : 1.236 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 16 ASN cc_start: 0.8224 (t0) cc_final: 0.7937 (t0) REVERT: B 714 THR cc_start: 0.8706 (m) cc_final: 0.8424 (p) REVERT: B 1080 ARG cc_start: 0.7507 (mpt180) cc_final: 0.7284 (mpt180) REVERT: C 250 MET cc_start: 0.6364 (ttm) cc_final: 0.6131 (ttp) REVERT: D 5 LEU cc_start: 0.7126 (OUTLIER) cc_final: 0.6808 (tt) outliers start: 38 outliers final: 34 residues processed: 155 average time/residue: 0.2354 time to fit residues: 51.4089 Evaluate side-chains 151 residues out of total 1124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 116 time to evaluate : 1.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 214 HIS Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 490 ILE Chi-restraints excluded: chain A residue 514 HIS Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 196 SER Chi-restraints excluded: chain B residue 209 GLN Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 377 THR Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 849 VAL Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 929 SER Chi-restraints excluded: chain B residue 931 LEU Chi-restraints excluded: chain B residue 959 ILE Chi-restraints excluded: chain B residue 964 ASN Chi-restraints excluded: chain B residue 1065 VAL Chi-restraints excluded: chain B residue 1112 LEU Chi-restraints excluded: chain B residue 1139 ILE Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 296 ILE Chi-restraints excluded: chain D residue 5 LEU Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 52 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 117 optimal weight: 8.9990 chunk 71 optimal weight: 3.9990 chunk 55 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 chunk 123 optimal weight: 2.9990 chunk 113 optimal weight: 0.6980 chunk 98 optimal weight: 1.9990 chunk 10 optimal weight: 0.4980 chunk 75 optimal weight: 0.8980 chunk 60 optimal weight: 4.9990 chunk 78 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 964 ASN ** C 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.2430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10194 Z= 0.198 Angle : 0.586 10.595 13781 Z= 0.297 Chirality : 0.043 0.153 1572 Planarity : 0.003 0.037 1742 Dihedral : 5.331 50.871 1359 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.11 % Favored : 91.80 % Rotamer: Outliers : 3.88 % Allowed : 24.89 % Favored : 71.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.83 (0.24), residues: 1208 helix: 0.02 (0.48), residues: 135 sheet: -0.09 (0.26), residues: 414 loop : -2.35 (0.22), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 207 HIS 0.008 0.001 HIS C 258 PHE 0.015 0.001 PHE B1030 TYR 0.020 0.001 TYR A 452 ARG 0.009 0.000 ARG D 18 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 118 time to evaluate : 1.440 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 16 ASN cc_start: 0.8244 (t0) cc_final: 0.7946 (t0) REVERT: B 714 THR cc_start: 0.8710 (m) cc_final: 0.8437 (p) REVERT: B 942 PHE cc_start: 0.5715 (OUTLIER) cc_final: 0.4465 (m-80) REVERT: B 1080 ARG cc_start: 0.7504 (mpt180) cc_final: 0.7290 (mpt180) REVERT: C 250 MET cc_start: 0.6365 (ttm) cc_final: 0.6134 (ttm) REVERT: D 5 LEU cc_start: 0.7136 (OUTLIER) cc_final: 0.6822 (tt) outliers start: 43 outliers final: 37 residues processed: 153 average time/residue: 0.2370 time to fit residues: 51.2458 Evaluate side-chains 155 residues out of total 1124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 116 time to evaluate : 1.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 214 HIS Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 490 ILE Chi-restraints excluded: chain A residue 514 HIS Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 196 SER Chi-restraints excluded: chain B residue 209 GLN Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 377 THR Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 725 CYS Chi-restraints excluded: chain B residue 849 VAL Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 929 SER Chi-restraints excluded: chain B residue 931 LEU Chi-restraints excluded: chain B residue 942 PHE Chi-restraints excluded: chain B residue 959 ILE Chi-restraints excluded: chain B residue 1032 THR Chi-restraints excluded: chain B residue 1065 VAL Chi-restraints excluded: chain B residue 1112 LEU Chi-restraints excluded: chain B residue 1139 ILE Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 265 MET Chi-restraints excluded: chain C residue 296 ILE Chi-restraints excluded: chain D residue 5 LEU Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 52 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 2.9990 chunk 30 optimal weight: 10.0000 chunk 90 optimal weight: 0.5980 chunk 14 optimal weight: 0.9990 chunk 27 optimal weight: 0.1980 chunk 98 optimal weight: 3.9990 chunk 41 optimal weight: 0.5980 chunk 101 optimal weight: 0.7980 chunk 12 optimal weight: 8.9990 chunk 18 optimal weight: 1.9990 chunk 86 optimal weight: 0.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 268 GLN ** B 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 952 ASN ** C 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.119416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.098522 restraints weight = 22966.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.101314 restraints weight = 13225.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.102164 restraints weight = 9132.103| |-----------------------------------------------------------------------------| r_work (final): 0.3657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.2598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 10194 Z= 0.166 Angle : 0.574 10.907 13781 Z= 0.289 Chirality : 0.043 0.157 1572 Planarity : 0.003 0.036 1742 Dihedral : 5.126 45.213 1359 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.62 % Favored : 93.29 % Rotamer: Outliers : 3.70 % Allowed : 24.89 % Favored : 71.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.70 (0.24), residues: 1208 helix: 0.05 (0.48), residues: 135 sheet: 0.02 (0.26), residues: 415 loop : -2.27 (0.23), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 207 HIS 0.011 0.001 HIS C 258 PHE 0.014 0.001 PHE B1030 TYR 0.020 0.001 TYR A 452 ARG 0.008 0.000 ARG D 18 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2127.71 seconds wall clock time: 39 minutes 52.37 seconds (2392.37 seconds total)