Starting phenix.real_space_refine (version: 1.21rc1) on Fri Apr 21 19:03:04 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sj7_10213/04_2023/6sj7_10213_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sj7_10213/04_2023/6sj7_10213.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sj7_10213/04_2023/6sj7_10213_ligands.cif 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 { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sj7_10213/04_2023/6sj7_10213_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sj7_10213/04_2023/6sj7_10213_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sj7_10213/04_2023/6sj7_10213.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sj7_10213/04_2023/6sj7_10213.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sj7_10213/04_2023/6sj7_10213_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sj7_10213/04_2023/6sj7_10213_updated.pdb" } resolution = 3.54 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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-1.21rc1-4938/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: 5.45, per 1000 atoms: 0.54 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: 3.80 Conformation dependent library (CDL) restraints added in 1.4 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: 1.30 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: 4.09 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=" C2 EF6 A 701 " pdb=" C3 EF6 A 701 " ideal model delta sigma weight residual 1.365 1.489 -0.124 2.00e-02 2.50e+03 3.82e+01 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=" N2 EF6 A 701 " pdb=" S1 EF6 A 701 " ideal model delta sigma weight residual 1.707 1.628 0.079 2.00e-02 2.50e+03 1.56e+01 bond pdb=" N EF6 A 701 " pdb=" S EF6 A 701 " ideal model delta sigma weight residual 1.709 1.633 0.076 2.00e-02 2.50e+03 1.44e+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 ... (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=" O EF6 A 701 " pdb=" S EF6 A 701 " pdb=" O3 EF6 A 701 " ideal model delta sigma weight residual 101.20 117.96 -16.76 3.00e+00 1.11e-01 3.12e+01 angle pdb=" O1 EF6 A 701 " pdb=" S1 EF6 A 701 " pdb=" O2 EF6 A 701 " ideal model delta sigma weight residual 101.20 117.48 -16.28 3.00e+00 1.11e-01 2.95e+01 angle pdb=" C2 EF6 A 701 " pdb=" C3 EF6 A 701 " pdb="CL EF6 A 701 " ideal model delta sigma weight residual 139.63 123.71 15.92 3.00e+00 1.11e-01 2.82e+01 angle pdb=" C4 EF6 A 701 " pdb=" C3 EF6 A 701 " pdb="CL EF6 A 701 " ideal model delta sigma weight residual 112.34 127.81 -15.47 3.00e+00 1.11e-01 2.66e+01 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 ... (remaining 13776 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.09: 5297 18.09 - 36.18: 634 36.18 - 54.27: 114 54.27 - 72.37: 27 72.37 - 90.46: 11 Dihedral angle restraints: 6083 sinusoidal: 2441 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 6080 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: 1.320 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: 0.000 Extract box with map and model: 5.430 Check model and map are aligned: 0.150 Set scattering table: 0.090 Process input model: 28.210 Find NCS groups from input model: 0.270 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:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.210 ------------------------------------------------------------------------------- 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 0.124 10194 Z= 0.670 Angle : 1.072 16.756 13781 Z= 0.573 Chirality : 0.060 0.277 1572 Planarity : 0.006 0.062 1742 Dihedral : 16.351 90.457 3720 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 % 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 *********************** 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 : 1.264 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 4 residues processed: 154 average time/residue: 0.2784 time to fit residues: 57.5916 Evaluate side-chains 112 residues out of total 1124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 108 time to evaluate : 1.182 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2143 time to fit residues: 2.9079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 32 optimal weight: 7.9990 chunk 63 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 97 optimal weight: 0.6980 chunk 37 optimal weight: 3.9990 chunk 59 optimal weight: 8.9990 chunk 72 optimal weight: 0.6980 chunk 112 optimal weight: 10.0000 overall best weight: 1.8786 ------------------------------------------------------------------------------- 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 16 ASN ** B 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 0.7918 moved from start: 0.1269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 10194 Z= 0.277 Angle : 0.611 6.414 13781 Z= 0.322 Chirality : 0.044 0.176 1572 Planarity : 0.004 0.054 1742 Dihedral : 6.013 42.222 1344 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 13.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.86 % Favored : 91.14 % Rotamer Outliers : 2.80 % 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: -3.02 (0.21), residues: 1208 helix: -1.21 (0.42), residues: 137 sheet: -0.87 (0.24), residues: 424 loop : -3.11 (0.20), residues: 647 *********************** 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 154 residues out of total 1124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 123 time to evaluate : 1.148 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 31 outliers final: 20 residues processed: 143 average time/residue: 0.2421 time to fit residues: 48.4801 Evaluate side-chains 128 residues out of total 1124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 108 time to evaluate : 1.229 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.0999 time to fit residues: 5.2605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 7.9990 chunk 93 optimal weight: 3.9990 chunk 76 optimal weight: 4.9990 chunk 31 optimal weight: 0.7980 chunk 112 optimal weight: 9.9990 chunk 121 optimal weight: 8.9990 chunk 100 optimal weight: 3.9990 chunk 111 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 chunk 90 optimal weight: 0.1980 overall best weight: 1.9784 ------------------------------------------------------------------------------- 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 203 ASN ** B 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 280 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.1519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.042 10194 Z= 0.284 Angle : 0.598 6.206 13781 Z= 0.315 Chirality : 0.044 0.170 1572 Planarity : 0.004 0.044 1742 Dihedral : 5.703 35.211 1344 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 14.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.60 % Favored : 90.40 % Rotamer Outliers : 1.98 % 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: -2.70 (0.22), residues: 1208 helix: -0.54 (0.46), residues: 139 sheet: -0.82 (0.24), residues: 435 loop : -2.91 (0.21), residues: 634 *********************** 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 142 residues out of total 1124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 120 time to evaluate : 1.248 Fit side-chains revert: symmetry clash outliers start: 22 outliers final: 10 residues processed: 134 average time/residue: 0.2639 time to fit residues: 48.9915 Evaluate side-chains 121 residues out of total 1124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 111 time to evaluate : 1.275 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1018 time to fit residues: 3.7301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 111 optimal weight: 2.9990 chunk 84 optimal weight: 0.3980 chunk 58 optimal weight: 6.9990 chunk 12 optimal weight: 6.9990 chunk 53 optimal weight: 0.5980 chunk 75 optimal weight: 2.9990 chunk 113 optimal weight: 6.9990 chunk 119 optimal weight: 0.0020 chunk 59 optimal weight: 2.9990 chunk 107 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 overall best weight: 1.3992 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.1761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 10194 Z= 0.228 Angle : 0.587 9.498 13781 Z= 0.302 Chirality : 0.044 0.158 1572 Planarity : 0.004 0.102 1742 Dihedral : 5.447 32.386 1344 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 14.31 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.69 % Favored : 91.23 % Rotamer Outliers : 2.25 % 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: -2.35 (0.23), residues: 1208 helix: -0.15 (0.47), residues: 136 sheet: -0.56 (0.24), residues: 434 loop : -2.71 (0.22), residues: 638 *********************** 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 142 residues out of total 1124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 117 time to evaluate : 1.889 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 14 residues processed: 134 average time/residue: 0.2605 time to fit residues: 48.3206 Evaluate side-chains 120 residues out of total 1124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 106 time to evaluate : 1.210 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1492 time to fit residues: 4.9803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 99 optimal weight: 9.9990 chunk 68 optimal weight: 5.9990 chunk 1 optimal weight: 0.9980 chunk 89 optimal weight: 0.0570 chunk 49 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 chunk 82 optimal weight: 0.0010 chunk 0 optimal weight: 7.9990 chunk 61 optimal weight: 4.9990 chunk 107 optimal weight: 0.8980 chunk 30 optimal weight: 7.9990 overall best weight: 0.7906 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 105 HIS B 107 ASN B 267 ASN ** B 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.2062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 10194 Z= 0.172 Angle : 0.558 9.893 13781 Z= 0.287 Chirality : 0.043 0.161 1572 Planarity : 0.004 0.038 1742 Dihedral : 5.128 31.155 1344 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 13.16 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.78 % Favored : 92.14 % Rotamer Outliers : 1.26 % 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: -2.14 (0.23), residues: 1208 helix: -0.09 (0.47), residues: 136 sheet: -0.41 (0.25), residues: 419 loop : -2.51 (0.22), residues: 653 *********************** 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 145 residues out of total 1124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 131 time to evaluate : 1.281 Fit side-chains revert: symmetry clash outliers start: 14 outliers final: 6 residues processed: 142 average time/residue: 0.2456 time to fit residues: 48.8316 Evaluate side-chains 120 residues out of total 1124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 114 time to evaluate : 1.272 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0989 time to fit residues: 2.8400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 40 optimal weight: 4.9990 chunk 107 optimal weight: 1.9990 chunk 23 optimal weight: 5.9990 chunk 70 optimal weight: 0.9980 chunk 29 optimal weight: 10.0000 chunk 119 optimal weight: 0.9980 chunk 99 optimal weight: 9.9990 chunk 55 optimal weight: 0.0670 chunk 9 optimal weight: 9.9990 chunk 39 optimal weight: 0.9990 chunk 62 optimal weight: 4.9990 overall best weight: 1.0122 ------------------------------------------------------------------------------- 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** C 280 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.2189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 10194 Z= 0.192 Angle : 0.561 9.804 13781 Z= 0.288 Chirality : 0.043 0.161 1572 Planarity : 0.003 0.037 1742 Dihedral : 5.004 30.360 1344 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.95 % Favored : 91.97 % Rotamer Outliers : 1.80 % 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: -2.03 (0.23), residues: 1208 helix: -0.09 (0.48), residues: 136 sheet: -0.31 (0.25), residues: 420 loop : -2.44 (0.22), residues: 652 *********************** 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 141 residues out of total 1124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 121 time to evaluate : 1.154 Fit side-chains revert: symmetry clash outliers start: 20 outliers final: 10 residues processed: 135 average time/residue: 0.2585 time to fit residues: 48.9397 Evaluate side-chains 125 residues out of total 1124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 115 time to evaluate : 1.164 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0977 time to fit residues: 3.4035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 115 optimal weight: 0.9980 chunk 13 optimal weight: 7.9990 chunk 68 optimal weight: 0.6980 chunk 87 optimal weight: 0.9990 chunk 67 optimal weight: 5.9990 chunk 100 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 119 optimal weight: 7.9990 chunk 74 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 55 optimal weight: 5.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 290 GLN ** B 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 280 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.2177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.034 10194 Z= 0.259 Angle : 0.595 9.754 13781 Z= 0.304 Chirality : 0.044 0.158 1572 Planarity : 0.003 0.038 1742 Dihedral : 5.149 30.337 1344 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 13.96 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.02 % Favored : 90.89 % Rotamer Outliers : 1.35 % 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: -2.02 (0.23), residues: 1208 helix: -0.01 (0.48), residues: 136 sheet: -0.35 (0.25), residues: 425 loop : -2.42 (0.22), residues: 647 *********************** 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 130 residues out of total 1124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 115 time to evaluate : 1.169 Fit side-chains revert: symmetry clash outliers start: 15 outliers final: 8 residues processed: 125 average time/residue: 0.2580 time to fit residues: 44.5739 Evaluate side-chains 117 residues out of total 1124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 109 time to evaluate : 1.326 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0934 time to fit residues: 3.1681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 71 optimal weight: 0.7980 chunk 36 optimal weight: 3.9990 chunk 23 optimal weight: 6.9990 chunk 75 optimal weight: 0.7980 chunk 81 optimal weight: 0.8980 chunk 59 optimal weight: 3.9990 chunk 11 optimal weight: 5.9990 chunk 93 optimal weight: 3.9990 chunk 108 optimal weight: 3.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- 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** C 280 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.2197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.034 10194 Z= 0.257 Angle : 0.607 9.938 13781 Z= 0.309 Chirality : 0.044 0.154 1572 Planarity : 0.003 0.037 1742 Dihedral : 5.142 30.266 1344 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 14.56 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.69 % Favored : 91.23 % Rotamer Outliers : 1.35 % 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: -2.00 (0.23), residues: 1208 helix: -0.04 (0.48), residues: 136 sheet: -0.33 (0.25), residues: 425 loop : -2.41 (0.22), residues: 647 *********************** 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 128 residues out of total 1124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 113 time to evaluate : 1.370 Fit side-chains revert: symmetry clash outliers start: 15 outliers final: 9 residues processed: 122 average time/residue: 0.2655 time to fit residues: 44.5840 Evaluate side-chains 117 residues out of total 1124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 108 time to evaluate : 1.226 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1026 time to fit residues: 3.3138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 114 optimal weight: 1.9990 chunk 104 optimal weight: 3.9990 chunk 111 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 87 optimal weight: 4.9990 chunk 34 optimal weight: 9.9990 chunk 100 optimal weight: 2.9990 chunk 105 optimal weight: 3.9990 chunk 110 optimal weight: 6.9990 chunk 73 optimal weight: 3.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- 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** C 280 GLN D 53 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.2152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.049 10194 Z= 0.355 Angle : 0.657 10.043 13781 Z= 0.336 Chirality : 0.045 0.161 1572 Planarity : 0.004 0.038 1742 Dihedral : 5.442 30.259 1344 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 16.47 Ramachandran Plot: Outliers : 0.08 % Allowed : 10.02 % Favored : 89.90 % Rotamer Outliers : 0.90 % 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: -2.14 (0.23), residues: 1208 helix: -0.22 (0.47), residues: 136 sheet: -0.33 (0.25), residues: 429 loop : -2.57 (0.22), residues: 643 *********************** 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 118 residues out of total 1124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 108 time to evaluate : 1.278 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 6 residues processed: 114 average time/residue: 0.2699 time to fit residues: 42.5740 Evaluate side-chains 112 residues out of total 1124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 106 time to evaluate : 1.282 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1095 time to fit residues: 2.9476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 117 optimal weight: 6.9990 chunk 71 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 chunk 81 optimal weight: 0.5980 chunk 123 optimal weight: 0.9980 chunk 113 optimal weight: 5.9990 chunk 98 optimal weight: 4.9990 chunk 10 optimal weight: 0.0970 chunk 75 optimal weight: 0.9980 chunk 60 optimal weight: 0.3980 chunk 78 optimal weight: 7.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 290 GLN ** B 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 280 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.2443 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= 0.173 Angle : 0.603 12.957 13781 Z= 0.302 Chirality : 0.043 0.151 1572 Planarity : 0.003 0.036 1742 Dihedral : 4.979 29.971 1344 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.87 % Favored : 93.05 % Rotamer Outliers : 0.27 % 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: -1.90 (0.24), residues: 1208 helix: -0.07 (0.47), residues: 136 sheet: -0.19 (0.26), residues: 418 loop : -2.36 (0.22), residues: 654 ********************** 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 125 residues out of total 1124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 122 time to evaluate : 1.259 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 122 average time/residue: 0.2665 time to fit residues: 44.9529 Evaluate side-chains 116 residues out of total 1124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 114 time to evaluate : 1.284 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0981 time to fit residues: 2.1226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 6.9990 chunk 90 optimal weight: 4.9990 chunk 14 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 chunk 98 optimal weight: 0.6980 chunk 41 optimal weight: 1.9990 chunk 101 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 18 optimal weight: 4.9990 chunk 86 optimal weight: 0.9980 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 290 GLN ** B 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 952 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.117340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.096237 restraints weight = 23147.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.098793 restraints weight = 13545.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.099698 restraints weight = 9509.211| |-----------------------------------------------------------------------------| r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.2445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 10194 Z= 0.223 Angle : 0.605 11.151 13781 Z= 0.305 Chirality : 0.044 0.155 1572 Planarity : 0.003 0.037 1742 Dihedral : 4.990 30.216 1344 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 13.31 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.20 % Favored : 91.72 % Rotamer Outliers : 0.27 % 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: -1.87 (0.24), residues: 1208 helix: -0.11 (0.47), residues: 136 sheet: -0.15 (0.26), residues: 417 loop : -2.33 (0.22), residues: 655 =============================================================================== Job complete usr+sys time: 1980.85 seconds wall clock time: 37 minutes 10.94 seconds (2230.94 seconds total)