Starting phenix.real_space_refine on Tue Dec 31 20:07:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yzo_14391/12_2024/7yzo_14391.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yzo_14391/12_2024/7yzo_14391.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7yzo_14391/12_2024/7yzo_14391.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yzo_14391/12_2024/7yzo_14391.map" model { file = "/net/cci-nas-00/data/ceres_data/7yzo_14391/12_2024/7yzo_14391.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yzo_14391/12_2024/7yzo_14391.cif" } resolution = 3.4 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 4287 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: 7 Type Number sf(0) Gaussians Mn 4 7.51 5 P 66 5.49 5 Mg 2 5.21 5 S 34 5.16 5 C 8019 2.51 5 N 2303 2.21 5 O 2640 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 13068 Number of models: 1 Model: "" Number of chains: 10 Chain: "C" Number of atoms: 2916 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 2916 Classifications: {'peptide': 374} Link IDs: {'PTRANS': 7, 'TRANS': 366} Chain breaks: 1 Chain: "D" Number of atoms: 2914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 2914 Classifications: {'peptide': 374} Link IDs: {'PTRANS': 7, 'TRANS': 366} Chain breaks: 1 Chain: "A" Number of atoms: 3010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 3010 Classifications: {'peptide': 381} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 360} Chain breaks: 1 Chain: "B" Number of atoms: 2897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 368, 2897 Classifications: {'peptide': 368} Link IDs: {'PTRANS': 20, 'TRANS': 347} Chain breaks: 2 Chain: "E" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 638 Classifications: {'DNA': 31} Link IDs: {'rna3p': 30} Chain: "F" Number of atoms: 633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 633 Classifications: {'DNA': 31} Link IDs: {'rna3p': 30} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 22 residue: pdb=" N GLY A 284 " occ=0.50 ... (2 atoms not shown) pdb=" O GLY A 284 " occ=0.50 residue: pdb=" N ALA A 287 " occ=0.60 ... (3 atoms not shown) pdb=" CB ALA A 287 " occ=0.60 residue: pdb=" N THR A 290 " occ=0.70 ... (5 atoms not shown) pdb=" CG2 THR A 290 " occ=0.70 residue: pdb=" N ALA A 291 " occ=0.60 ... (3 atoms not shown) pdb=" CB ALA A 291 " occ=0.60 residue: pdb=" N GLN A 292 " occ=0.70 ... (7 atoms not shown) pdb=" NE2 GLN A 292 " occ=0.70 residue: pdb=" N LEU A 293 " occ=0.80 ... (6 atoms not shown) pdb=" CD2 LEU A 293 " occ=0.80 residue: pdb=" N PRO A 303 " occ=0.61 ... (5 atoms not shown) pdb=" CD PRO A 303 " occ=0.61 residue: pdb=" N PRO A 304 " occ=0.68 ... (5 atoms not shown) pdb=" CD PRO A 304 " occ=0.68 residue: pdb=" N VAL A 305 " occ=0.88 ... (5 atoms not shown) pdb=" CG2 VAL A 305 " occ=0.88 residue: pdb=" N TRP A 306 " occ=0.97 ... (12 atoms not shown) pdb=" CH2 TRP A 306 " occ=0.97 residue: pdb=" N LEU A 307 " occ=0.87 ... (6 atoms not shown) pdb=" CD2 LEU A 307 " occ=0.87 residue: pdb=" N ILE A 309 " occ=0.89 ... (6 atoms not shown) pdb=" CD1 ILE A 309 " occ=0.89 ... (remaining 10 not shown) Time building chain proxies: 8.64, per 1000 atoms: 0.66 Number of scatterers: 13068 At special positions: 0 Unit cell: (108.018, 98.487, 134.493, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Mn 4 24.99 S 34 16.00 P 66 15.00 Mg 2 11.99 O 2640 8.00 N 2303 7.00 C 8019 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.64 Conformation dependent library (CDL) restraints added in 1.7 seconds 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2812 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 17 sheets defined 43.4% alpha, 17.9% beta 31 base pairs and 54 stacking pairs defined. Time for finding SS restraints: 5.36 Creating SS restraints... Processing helix chain 'C' and resid 42 through 56 removed outlier: 3.831A pdb=" N LEU C 47 " --> pdb=" O LYS C 43 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ILE C 50 " --> pdb=" O LEU C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 104 Processing helix chain 'C' and resid 128 through 141 Processing helix chain 'C' and resid 143 through 151 removed outlier: 4.345A pdb=" N ARG C 149 " --> pdb=" O GLY C 145 " (cutoff:3.500A) Processing helix chain 'C' and resid 159 through 164 Processing helix chain 'C' and resid 165 through 178 Processing helix chain 'C' and resid 180 through 201 Processing helix chain 'C' and resid 876 through 887 Processing helix chain 'C' and resid 889 through 891 No H-bonds generated for 'chain 'C' and resid 889 through 891' Processing helix chain 'C' and resid 892 through 900 Processing helix chain 'C' and resid 900 through 919 removed outlier: 3.591A pdb=" N LEU C 910 " --> pdb=" O ASN C 906 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ARG C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 947 through 951 removed outlier: 3.544A pdb=" N THR C 950 " --> pdb=" O ASP C 947 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU C 951 " --> pdb=" O THR C 948 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 947 through 951' Processing helix chain 'C' and resid 952 through 970 Processing helix chain 'C' and resid 985 through 989 removed outlier: 3.801A pdb=" N THR C 988 " --> pdb=" O GLY C 985 " (cutoff:3.500A) Processing helix chain 'C' and resid 990 through 1006 removed outlier: 3.615A pdb=" N ASP C 995 " --> pdb=" O SER C 991 " (cutoff:3.500A) Processing helix chain 'C' and resid 1017 through 1024 Processing helix chain 'C' and resid 1042 through 1046 Processing helix chain 'D' and resid 42 through 56 removed outlier: 3.865A pdb=" N LEU D 47 " --> pdb=" O LYS D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 104 Processing helix chain 'D' and resid 128 through 141 Processing helix chain 'D' and resid 143 through 151 removed outlier: 4.263A pdb=" N ARG D 149 " --> pdb=" O GLY D 145 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 178 removed outlier: 3.741A pdb=" N LEU D 172 " --> pdb=" O GLU D 168 " (cutoff:3.500A) Processing helix chain 'D' and resid 180 through 199 removed outlier: 3.634A pdb=" N GLN D 184 " --> pdb=" O GLU D 180 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLU D 199 " --> pdb=" O SER D 195 " (cutoff:3.500A) Processing helix chain 'D' and resid 875 through 887 Processing helix chain 'D' and resid 889 through 891 No H-bonds generated for 'chain 'D' and resid 889 through 891' Processing helix chain 'D' and resid 892 through 900 removed outlier: 3.665A pdb=" N ARG D 896 " --> pdb=" O GLY D 892 " (cutoff:3.500A) Processing helix chain 'D' and resid 900 through 919 removed outlier: 4.507A pdb=" N ARG D 917 " --> pdb=" O GLN D 913 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU D 918 " --> pdb=" O GLN D 914 " (cutoff:3.500A) Processing helix chain 'D' and resid 949 through 951 No H-bonds generated for 'chain 'D' and resid 949 through 951' Processing helix chain 'D' and resid 952 through 971 removed outlier: 4.052A pdb=" N VAL D 971 " --> pdb=" O LEU D 967 " (cutoff:3.500A) Processing helix chain 'D' and resid 990 through 1006 removed outlier: 4.528A pdb=" N THR D 996 " --> pdb=" O GLU D 992 " (cutoff:3.500A) Processing helix chain 'D' and resid 1018 through 1024 removed outlier: 4.107A pdb=" N GLU D1022 " --> pdb=" O GLU D1018 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ARG D1023 " --> pdb=" O ALA D1019 " (cutoff:3.500A) Processing helix chain 'D' and resid 1043 through 1046 Processing helix chain 'A' and resid 20 through 39 Processing helix chain 'A' and resid 56 through 70 Processing helix chain 'A' and resid 86 through 93 removed outlier: 4.365A pdb=" N SER A 93 " --> pdb=" O THR A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 99 removed outlier: 3.836A pdb=" N PHE A 99 " --> pdb=" O ASP A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 138 removed outlier: 3.650A pdb=" N ILE A 137 " --> pdb=" O ARG A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 173 removed outlier: 3.598A pdb=" N GLN A 150 " --> pdb=" O GLY A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 212 Processing helix chain 'A' and resid 245 through 249 Processing helix chain 'A' and resid 285 through 294 Processing helix chain 'A' and resid 295 through 297 No H-bonds generated for 'chain 'A' and resid 295 through 297' Processing helix chain 'A' and resid 319 through 328 removed outlier: 3.527A pdb=" N LYS A 323 " --> pdb=" O ASP A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 372 removed outlier: 3.582A pdb=" N LEU A 372 " --> pdb=" O ARG A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 394 removed outlier: 3.888A pdb=" N GLN A 381 " --> pdb=" O GLU A 377 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N ARG A 382 " --> pdb=" O SER A 378 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 39 removed outlier: 3.750A pdb=" N TRP B 30 " --> pdb=" O ALA B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 74 removed outlier: 3.573A pdb=" N ARG B 60 " --> pdb=" O PRO B 56 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLN B 71 " --> pdb=" O VAL B 67 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N GLN B 72 " --> pdb=" O VAL B 68 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N THR B 73 " --> pdb=" O ASN B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 99 removed outlier: 4.084A pdb=" N PHE B 99 " --> pdb=" O ASP B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 137 Processing helix chain 'B' and resid 154 through 173 Processing helix chain 'B' and resid 208 through 212 removed outlier: 3.744A pdb=" N PHE B 212 " --> pdb=" O ALA B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 249 removed outlier: 3.600A pdb=" N GLU B 248 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N CYS B 249 " --> pdb=" O PHE B 246 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 245 through 249' Processing helix chain 'B' and resid 285 through 293 removed outlier: 3.518A pdb=" N ALA B 291 " --> pdb=" O ALA B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 297 Processing helix chain 'B' and resid 316 through 329 removed outlier: 4.583A pdb=" N ARG B 322 " --> pdb=" O HIS B 318 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LYS B 323 " --> pdb=" O ASP B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 373 removed outlier: 3.841A pdb=" N LEU B 372 " --> pdb=" O ARG B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 376 through 395 removed outlier: 4.529A pdb=" N ARG B 382 " --> pdb=" O SER B 378 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 14 through 21 removed outlier: 6.561A pdb=" N GLY C 16 " --> pdb=" O ASN C 10 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N GLU C 84 " --> pdb=" O LEU C 4 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N LEU C 6 " --> pdb=" O GLU C 82 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N GLU C 82 " --> pdb=" O LEU C 6 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N LEU C 8 " --> pdb=" O LEU C 80 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N LEU C 80 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N ASN C 10 " --> pdb=" O GLU C 78 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N GLU C 78 " --> pdb=" O ASN C 10 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N LEU C 116 " --> pdb=" O LEU C 125 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 152 through 153 removed outlier: 6.522A pdb=" N LEU C 980 " --> pdb=" O GLY C1012 " (cutoff:3.500A) removed outlier: 8.074A pdb=" N ILE C1014 " --> pdb=" O LEU C 980 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N LEU C 982 " --> pdb=" O ILE C1014 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 922 through 926 Processing sheet with id=AA4, first strand: chain 'C' and resid 1031 through 1032 Processing sheet with id=AA5, first strand: chain 'D' and resid 14 through 21 removed outlier: 6.610A pdb=" N GLY D 16 " --> pdb=" O ASN D 10 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N ILE D 3 " --> pdb=" O GLU D 86 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N GLU D 86 " --> pdb=" O ILE D 3 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N LEU D 11 " --> pdb=" O GLU D 78 " (cutoff:3.500A) removed outlier: 11.406A pdb=" N GLU D 78 " --> pdb=" O LEU D 11 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N LEU D 116 " --> pdb=" O LEU D 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 152 through 153 removed outlier: 6.132A pdb=" N PHE D 33 " --> pdb=" O VAL D1013 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ALA D 34 " --> pdb=" O ILE D1028 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N VAL D1030 " --> pdb=" O ALA D 34 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N THR D 36 " --> pdb=" O VAL D1030 " (cutoff:3.500A) removed outlier: 8.101A pdb=" N LYS D1032 " --> pdb=" O THR D 36 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 924 through 926 Processing sheet with id=AA8, first strand: chain 'A' and resid 102 through 105 removed outlier: 6.429A pdb=" N LEU A 77 " --> pdb=" O THR A 103 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N VAL A 105 " --> pdb=" O LEU A 77 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N VAL A 79 " --> pdb=" O VAL A 105 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N ILE A 43 " --> pdb=" O VAL A 78 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N LEU A 80 " --> pdb=" O ILE A 43 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N VAL A 45 " --> pdb=" O LEU A 80 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N ARG A 2 " --> pdb=" O ALA A 42 " (cutoff:3.500A) removed outlier: 8.297A pdb=" N ILE A 44 " --> pdb=" O ARG A 2 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N LEU A 4 " --> pdb=" O ILE A 44 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N ALA A 46 " --> pdb=" O LEU A 4 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N THR A 6 " --> pdb=" O ALA A 46 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N VAL A 255 " --> pdb=" O ASN A 270 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N ASN A 270 " --> pdb=" O VAL A 255 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N LEU A 257 " --> pdb=" O VAL A 268 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N VAL A 268 " --> pdb=" O LEU A 257 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N THR A 259 " --> pdb=" O GLU A 266 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 14 through 15 Processing sheet with id=AB1, first strand: chain 'A' and resid 114 through 116 Processing sheet with id=AB2, first strand: chain 'A' and resid 180 through 182 removed outlier: 6.827A pdb=" N ALA A 181 " --> pdb=" O ALA A 219 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N VAL A 235 " --> pdb=" O ILE A 229 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE A 229 " --> pdb=" O VAL A 235 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 279 through 284 removed outlier: 6.754A pdb=" N VAL A 305 " --> pdb=" O VAL A 333 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N VAL A 335 " --> pdb=" O VAL A 305 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N LEU A 307 " --> pdb=" O VAL A 335 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU A 337 " --> pdb=" O LEU A 307 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 102 through 105 removed outlier: 6.580A pdb=" N LEU B 77 " --> pdb=" O THR B 103 " (cutoff:3.500A) removed outlier: 8.048A pdb=" N VAL B 105 " --> pdb=" O LEU B 77 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N VAL B 79 " --> pdb=" O VAL B 105 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ILE B 43 " --> pdb=" O VAL B 78 " (cutoff:3.500A) removed outlier: 8.250A pdb=" N LEU B 80 " --> pdb=" O ILE B 43 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N VAL B 45 " --> pdb=" O LEU B 80 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N ARG B 2 " --> pdb=" O ALA B 42 " (cutoff:3.500A) removed outlier: 8.204A pdb=" N ILE B 44 " --> pdb=" O ARG B 2 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N LEU B 4 " --> pdb=" O ILE B 44 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N ALA B 46 " --> pdb=" O LEU B 4 " (cutoff:3.500A) removed outlier: 7.702A pdb=" N THR B 6 " --> pdb=" O ALA B 46 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N VAL B 255 " --> pdb=" O ASN B 270 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N ASN B 270 " --> pdb=" O VAL B 255 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N LEU B 257 " --> pdb=" O VAL B 268 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N VAL B 268 " --> pdb=" O LEU B 257 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N THR B 259 " --> pdb=" O GLU B 266 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 14 through 15 Processing sheet with id=AB6, first strand: chain 'B' and resid 114 through 116 Processing sheet with id=AB7, first strand: chain 'B' and resid 180 through 183 removed outlier: 6.518A pdb=" N ALA B 181 " --> pdb=" O ALA B 219 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ILE B 218 " --> pdb=" O ARG B 236 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 279 through 284 removed outlier: 3.587A pdb=" N GLY B 284 " --> pdb=" O GLU B 310 " (cutoff:3.500A) removed outlier: 9.377A pdb=" N VAL B 305 " --> pdb=" O VAL B 335 " (cutoff:3.500A) removed outlier: 8.737A pdb=" N LEU B 337 " --> pdb=" O VAL B 305 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N LEU B 307 " --> pdb=" O LEU B 337 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N ARG B 339 " --> pdb=" O LEU B 307 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N ILE B 309 " --> pdb=" O ARG B 339 " (cutoff:3.500A) 519 hydrogen bonds defined for protein. 1470 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 80 hydrogen bonds 160 hydrogen bond angles 0 basepair planarities 31 basepair parallelities 54 stacking parallelities Total time for adding SS restraints: 4.96 Time building geometry restraints manager: 3.88 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: 3897 1.34 - 1.45: 2323 1.45 - 1.57: 7028 1.57 - 1.69: 128 1.69 - 1.81: 52 Bond restraints: 13428 Sorted by residual: bond pdb=" C4 ADP D1101 " pdb=" C5 ADP D1101 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 2.98e+01 bond pdb=" C4 ADP C1101 " pdb=" C5 ADP C1101 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 2.98e+01 bond pdb=" C5 ADP D1101 " pdb=" C6 ADP D1101 " ideal model delta sigma weight residual 1.490 1.407 0.083 2.00e-02 2.50e+03 1.74e+01 bond pdb=" C5 ADP C1101 " pdb=" C6 ADP C1101 " ideal model delta sigma weight residual 1.490 1.408 0.082 2.00e-02 2.50e+03 1.69e+01 bond pdb=" N ILE A 223 " pdb=" CA ILE A 223 " ideal model delta sigma weight residual 1.458 1.495 -0.037 1.17e-02 7.31e+03 1.01e+01 ... (remaining 13423 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.69: 18281 2.69 - 5.37: 172 5.37 - 8.06: 18 8.06 - 10.75: 6 10.75 - 13.44: 4 Bond angle restraints: 18481 Sorted by residual: angle pdb=" C ASN D 12 " pdb=" CA ASN D 12 " pdb=" CB ASN D 12 " ideal model delta sigma weight residual 116.54 109.97 6.57 1.15e+00 7.56e-01 3.26e+01 angle pdb=" CA GLY A 221 " pdb=" C GLY A 221 " pdb=" O GLY A 221 " ideal model delta sigma weight residual 121.61 115.82 5.79 1.05e+00 9.07e-01 3.04e+01 angle pdb=" CA GLY B 221 " pdb=" C GLY B 221 " pdb=" O GLY B 221 " ideal model delta sigma weight residual 121.78 117.04 4.74 9.10e-01 1.21e+00 2.71e+01 angle pdb=" PA ADP C1101 " pdb=" O3A ADP C1101 " pdb=" PB ADP C1101 " ideal model delta sigma weight residual 120.50 133.94 -13.44 3.00e+00 1.11e-01 2.01e+01 angle pdb=" PA ADP D1101 " pdb=" O3A ADP D1101 " pdb=" PB ADP D1101 " ideal model delta sigma weight residual 120.50 133.52 -13.02 3.00e+00 1.11e-01 1.88e+01 ... (remaining 18476 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.22: 7212 25.22 - 50.44: 568 50.44 - 75.66: 115 75.66 - 100.88: 10 100.88 - 126.09: 3 Dihedral angle restraints: 7908 sinusoidal: 3573 harmonic: 4335 Sorted by residual: dihedral pdb=" C5' ADP D1101 " pdb=" O5' ADP D1101 " pdb=" PA ADP D1101 " pdb=" O2A ADP D1101 " ideal model delta sinusoidal sigma weight residual -60.00 66.10 -126.09 1 2.00e+01 2.50e-03 3.81e+01 dihedral pdb=" O2A ADP D1101 " pdb=" O3A ADP D1101 " pdb=" PA ADP D1101 " pdb=" PB ADP D1101 " ideal model delta sinusoidal sigma weight residual -60.00 65.40 -125.40 1 2.00e+01 2.50e-03 3.79e+01 dihedral pdb=" O1B ADP D1101 " pdb=" O3A ADP D1101 " pdb=" PB ADP D1101 " pdb=" PA ADP D1101 " ideal model delta sinusoidal sigma weight residual -60.00 57.79 -117.80 1 2.00e+01 2.50e-03 3.52e+01 ... (remaining 7905 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 1827 0.058 - 0.115: 272 0.115 - 0.173: 23 0.173 - 0.231: 3 0.231 - 0.288: 4 Chirality restraints: 2129 Sorted by residual: chirality pdb=" CA TYR A 237 " pdb=" N TYR A 237 " pdb=" C TYR A 237 " pdb=" CB TYR A 237 " both_signs ideal model delta sigma weight residual False 2.51 2.80 -0.29 2.00e-01 2.50e+01 2.08e+00 chirality pdb=" C3' ADP C1101 " pdb=" C2' ADP C1101 " pdb=" C4' ADP C1101 " pdb=" O3' ADP C1101 " both_signs ideal model delta sigma weight residual False -2.51 -2.76 0.25 2.00e-01 2.50e+01 1.52e+00 chirality pdb=" C3' ADP D1101 " pdb=" C2' ADP D1101 " pdb=" C4' ADP D1101 " pdb=" O3' ADP D1101 " both_signs ideal model delta sigma weight residual False -2.51 -2.75 0.24 2.00e-01 2.50e+01 1.44e+00 ... (remaining 2126 not shown) Planarity restraints: 2167 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR D 58 " 0.032 5.00e-02 4.00e+02 4.80e-02 3.68e+00 pdb=" N PRO D 59 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO D 59 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO D 59 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 47 " -0.007 2.00e-02 2.50e+03 1.38e-02 1.91e+00 pdb=" C GLY A 47 " 0.024 2.00e-02 2.50e+03 pdb=" O GLY A 47 " -0.009 2.00e-02 2.50e+03 pdb=" N ASP A 48 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA D 41 " 0.007 2.00e-02 2.50e+03 1.33e-02 1.76e+00 pdb=" C ALA D 41 " -0.023 2.00e-02 2.50e+03 pdb=" O ALA D 41 " 0.008 2.00e-02 2.50e+03 pdb=" N GLY D 42 " 0.008 2.00e-02 2.50e+03 ... (remaining 2164 not shown) Histogram of nonbonded interaction distances: 1.50 - 2.18: 12 2.18 - 2.86: 4382 2.86 - 3.54: 18347 3.54 - 4.22: 30527 4.22 - 4.90: 52538 Nonbonded interactions: 105806 Sorted by model distance: nonbonded pdb=" OD2 ASP A 48 " pdb="MN MN A 501 " model vdw 1.498 2.320 nonbonded pdb=" OD2 ASP A 48 " pdb="MN MN A 502 " model vdw 1.600 2.320 nonbonded pdb=" OD1 ASN B 83 " pdb="MN MN B 502 " model vdw 1.806 2.320 nonbonded pdb=" O3B ADP C1101 " pdb="MG MG C1102 " model vdw 1.816 2.170 nonbonded pdb=" OD2 ASP B 48 " pdb="MN MN B 502 " model vdw 1.931 2.320 ... (remaining 105801 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 137 or resid 153 through 343 or resid 356 throug \ h 395 or resid 501 through 502)) selection = (chain 'B' and (resid 1 through 189 or resid 204 through 395 or resid 501 throug \ h 502)) } ncs_group { reference = (chain 'C' and (resid 1 through 200 or resid 875 through 1047 or resid 1101 thro \ ugh 1102)) selection = (chain 'D' and (resid 1 through 200 or resid 875 through 1047 or resid 1101 thro \ ugh 1102)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.110 Construct map_model_manager: 0.020 Extract box with map and model: 0.550 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 36.310 Find NCS groups from input model: 0.640 Set up NCS constraints: 0.070 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: 0.010 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 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 : 0.004 0.109 13428 Z= 0.254 Angle : 0.703 13.436 18481 Z= 0.399 Chirality : 0.042 0.288 2129 Planarity : 0.003 0.048 2167 Dihedral : 17.730 126.095 5096 Min Nonbonded Distance : 1.498 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 0.08 % Allowed : 0.31 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.23), residues: 1479 helix: 1.66 (0.23), residues: 547 sheet: 0.38 (0.34), residues: 231 loop : -0.29 (0.25), residues: 701 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 9 HIS 0.009 0.001 HIS A 392 PHE 0.014 0.001 PHE C 895 TYR 0.014 0.001 TYR C 882 ARG 0.009 0.000 ARG D 976 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 139 time to evaluate : 1.470 Fit side-chains REVERT: C 179 THR cc_start: 0.7860 (p) cc_final: 0.7607 (p) REVERT: A 185 LEU cc_start: 0.9070 (OUTLIER) cc_final: 0.8831 (pp) outliers start: 1 outliers final: 0 residues processed: 140 average time/residue: 0.2514 time to fit residues: 52.1561 Evaluate side-chains 100 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 99 time to evaluate : 1.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 130 optimal weight: 7.9990 chunk 116 optimal weight: 2.9990 chunk 64 optimal weight: 0.5980 chunk 39 optimal weight: 2.9990 chunk 78 optimal weight: 0.8980 chunk 62 optimal weight: 0.4980 chunk 120 optimal weight: 0.5980 chunk 46 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 89 optimal weight: 0.8980 chunk 139 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1005 ASN A 110 HIS A 318 HIS A 392 HIS B 84 GLN B 222 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.0878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13428 Z= 0.209 Angle : 0.578 7.957 18481 Z= 0.302 Chirality : 0.041 0.171 2129 Planarity : 0.004 0.051 2167 Dihedral : 18.774 135.971 2299 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.02 % Allowed : 6.83 % Favored : 92.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.23), residues: 1479 helix: 1.65 (0.23), residues: 548 sheet: -0.05 (0.32), residues: 260 loop : -0.25 (0.26), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 296 HIS 0.011 0.001 HIS A 392 PHE 0.014 0.001 PHE C 85 TYR 0.014 0.001 TYR B 237 ARG 0.005 0.000 ARG C 149 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 115 time to evaluate : 1.428 Fit side-chains REVERT: D 66 GLN cc_start: 0.8542 (tm-30) cc_final: 0.7855 (tm-30) REVERT: D 167 LYS cc_start: 0.8267 (ttpp) cc_final: 0.8058 (ptmm) REVERT: A 51 ASP cc_start: 0.8254 (t0) cc_final: 0.8009 (t0) REVERT: A 185 LEU cc_start: 0.9074 (OUTLIER) cc_final: 0.8745 (pp) REVERT: B 373 GLU cc_start: 0.7871 (tp30) cc_final: 0.7615 (tp30) outliers start: 13 outliers final: 6 residues processed: 124 average time/residue: 0.2591 time to fit residues: 47.2494 Evaluate side-chains 111 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 104 time to evaluate : 1.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 910 LEU Chi-restraints excluded: chain C residue 983 ASP Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 168 GLU Chi-restraints excluded: chain D residue 1026 VAL Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 392 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 77 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 chunk 116 optimal weight: 0.3980 chunk 95 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 140 optimal weight: 4.9990 chunk 151 optimal weight: 6.9990 chunk 124 optimal weight: 1.9990 chunk 138 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 112 optimal weight: 1.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 HIS A 224 HIS A 318 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.1264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 13428 Z= 0.347 Angle : 0.622 7.328 18481 Z= 0.324 Chirality : 0.043 0.163 2129 Planarity : 0.004 0.050 2167 Dihedral : 19.098 141.869 2299 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 1.18 % Allowed : 10.44 % Favored : 88.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.23), residues: 1479 helix: 1.47 (0.22), residues: 548 sheet: -0.14 (0.33), residues: 262 loop : -0.42 (0.26), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 9 HIS 0.022 0.001 HIS A 392 PHE 0.017 0.002 PHE C 85 TYR 0.013 0.002 TYR B 63 ARG 0.006 0.000 ARG C 149 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 104 time to evaluate : 1.613 Fit side-chains REVERT: A 185 LEU cc_start: 0.9197 (OUTLIER) cc_final: 0.8847 (pp) outliers start: 15 outliers final: 11 residues processed: 118 average time/residue: 0.2779 time to fit residues: 49.2194 Evaluate side-chains 108 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 96 time to evaluate : 1.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 115 GLU Chi-restraints excluded: chain C residue 983 ASP Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 168 GLU Chi-restraints excluded: chain D residue 1026 VAL Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain B residue 205 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 138 optimal weight: 0.6980 chunk 105 optimal weight: 0.9990 chunk 72 optimal weight: 0.0370 chunk 15 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 140 optimal weight: 0.9990 chunk 148 optimal weight: 3.9990 chunk 73 optimal weight: 0.7980 chunk 133 optimal weight: 0.0050 chunk 40 optimal weight: 0.9990 overall best weight: 0.5074 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 110 HIS ** A 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 227 GLN A 318 HIS A 392 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.1385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13428 Z= 0.177 Angle : 0.545 6.693 18481 Z= 0.286 Chirality : 0.039 0.153 2129 Planarity : 0.003 0.051 2167 Dihedral : 18.872 128.650 2299 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.26 % Allowed : 12.40 % Favored : 86.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.23), residues: 1479 helix: 1.71 (0.23), residues: 547 sheet: -0.06 (0.33), residues: 253 loop : -0.36 (0.25), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 96 HIS 0.008 0.001 HIS A 392 PHE 0.012 0.001 PHE C 85 TYR 0.012 0.001 TYR B 237 ARG 0.006 0.000 ARG D 926 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 109 time to evaluate : 1.461 Fit side-chains REVERT: A 51 ASP cc_start: 0.8229 (t0) cc_final: 0.8011 (t0) REVERT: A 185 LEU cc_start: 0.9145 (OUTLIER) cc_final: 0.8882 (pp) REVERT: A 285 ASP cc_start: 0.6094 (p0) cc_final: 0.5661 (p0) REVERT: B 394 LEU cc_start: 0.6977 (OUTLIER) cc_final: 0.6725 (mp) outliers start: 16 outliers final: 10 residues processed: 123 average time/residue: 0.2481 time to fit residues: 45.3178 Evaluate side-chains 114 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 102 time to evaluate : 1.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 115 GLU Chi-restraints excluded: chain C residue 910 LEU Chi-restraints excluded: chain C residue 983 ASP Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 168 GLU Chi-restraints excluded: chain D residue 1026 VAL Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 164 HIS Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain B residue 394 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 123 optimal weight: 0.7980 chunk 84 optimal weight: 1.9990 chunk 2 optimal weight: 0.4980 chunk 110 optimal weight: 3.9990 chunk 61 optimal weight: 0.9980 chunk 127 optimal weight: 2.9990 chunk 102 optimal weight: 7.9990 chunk 0 optimal weight: 1.9990 chunk 76 optimal weight: 0.9980 chunk 133 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 HIS ** A 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 227 GLN A 318 HIS A 392 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.1545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13428 Z= 0.267 Angle : 0.578 8.337 18481 Z= 0.300 Chirality : 0.041 0.156 2129 Planarity : 0.004 0.050 2167 Dihedral : 18.973 123.924 2299 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.20 % Allowed : 13.11 % Favored : 84.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.23), residues: 1479 helix: 1.70 (0.23), residues: 541 sheet: -0.14 (0.33), residues: 259 loop : -0.39 (0.25), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 296 HIS 0.012 0.001 HIS A 392 PHE 0.015 0.001 PHE C 147 TYR 0.011 0.001 TYR A 58 ARG 0.005 0.000 ARG D 976 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 105 time to evaluate : 1.533 Fit side-chains REVERT: D 197 ARG cc_start: 0.7363 (tpp80) cc_final: 0.6933 (tpt-90) REVERT: A 51 ASP cc_start: 0.8247 (t0) cc_final: 0.7978 (t0) REVERT: A 185 LEU cc_start: 0.9160 (OUTLIER) cc_final: 0.8878 (pp) REVERT: B 394 LEU cc_start: 0.7099 (OUTLIER) cc_final: 0.6811 (mp) outliers start: 28 outliers final: 20 residues processed: 126 average time/residue: 0.2615 time to fit residues: 48.7808 Evaluate side-chains 122 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 100 time to evaluate : 1.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 115 GLU Chi-restraints excluded: chain C residue 910 LEU Chi-restraints excluded: chain C residue 983 ASP Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 68 GLN Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 168 GLU Chi-restraints excluded: chain D residue 1026 VAL Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 164 HIS Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 392 HIS Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain B residue 169 CYS Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 394 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 50 optimal weight: 0.5980 chunk 134 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 87 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 149 optimal weight: 3.9990 chunk 123 optimal weight: 2.9990 chunk 68 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 chunk 49 optimal weight: 0.5980 chunk 78 optimal weight: 1.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 HIS ** A 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 392 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.1634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 13428 Z= 0.252 Angle : 0.577 7.666 18481 Z= 0.299 Chirality : 0.041 0.152 2129 Planarity : 0.003 0.051 2167 Dihedral : 18.958 120.435 2299 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.35 % Allowed : 14.13 % Favored : 83.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.23), residues: 1479 helix: 1.68 (0.23), residues: 542 sheet: -0.18 (0.33), residues: 259 loop : -0.43 (0.25), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 296 HIS 0.015 0.001 HIS A 392 PHE 0.014 0.001 PHE C 85 TYR 0.011 0.001 TYR B 237 ARG 0.006 0.000 ARG D 976 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 101 time to evaluate : 1.484 Fit side-chains REVERT: D 197 ARG cc_start: 0.7361 (tpp80) cc_final: 0.6955 (tpt-90) REVERT: A 51 ASP cc_start: 0.8241 (t0) cc_final: 0.7975 (t0) REVERT: A 185 LEU cc_start: 0.9170 (OUTLIER) cc_final: 0.8928 (pp) outliers start: 30 outliers final: 20 residues processed: 127 average time/residue: 0.2622 time to fit residues: 49.6357 Evaluate side-chains 122 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 101 time to evaluate : 1.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 115 GLU Chi-restraints excluded: chain C residue 910 LEU Chi-restraints excluded: chain C residue 1043 SER Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 68 GLN Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 168 GLU Chi-restraints excluded: chain D residue 1026 VAL Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 164 HIS Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain B residue 169 CYS Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 275 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 143 optimal weight: 0.0670 chunk 16 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 chunk 125 optimal weight: 0.8980 chunk 83 optimal weight: 0.7980 chunk 148 optimal weight: 3.9990 chunk 92 optimal weight: 0.0270 chunk 90 optimal weight: 2.9990 chunk 68 optimal weight: 4.9990 chunk 91 optimal weight: 3.9990 overall best weight: 0.7578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 HIS ** A 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 318 HIS A 392 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.1709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13428 Z= 0.216 Angle : 0.568 12.773 18481 Z= 0.293 Chirality : 0.040 0.172 2129 Planarity : 0.003 0.050 2167 Dihedral : 18.865 117.863 2299 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.88 % Allowed : 15.07 % Favored : 83.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.23), residues: 1479 helix: 1.72 (0.23), residues: 542 sheet: -0.19 (0.32), residues: 259 loop : -0.42 (0.25), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 296 HIS 0.012 0.001 HIS A 392 PHE 0.013 0.001 PHE C 33 TYR 0.011 0.001 TYR B 237 ARG 0.007 0.000 ARG D 976 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 108 time to evaluate : 1.468 Fit side-chains REVERT: C 998 LEU cc_start: 0.8322 (OUTLIER) cc_final: 0.7897 (mt) REVERT: D 197 ARG cc_start: 0.7274 (tpp80) cc_final: 0.6866 (tpt-90) REVERT: A 51 ASP cc_start: 0.8226 (t0) cc_final: 0.8018 (t0) REVERT: A 185 LEU cc_start: 0.9169 (OUTLIER) cc_final: 0.8961 (pp) outliers start: 24 outliers final: 19 residues processed: 130 average time/residue: 0.2595 time to fit residues: 49.9532 Evaluate side-chains 123 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 102 time to evaluate : 1.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 115 GLU Chi-restraints excluded: chain C residue 910 LEU Chi-restraints excluded: chain C residue 983 ASP Chi-restraints excluded: chain C residue 998 LEU Chi-restraints excluded: chain C residue 1043 SER Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 68 GLN Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 168 GLU Chi-restraints excluded: chain D residue 1026 VAL Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 164 HIS Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 392 HIS Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 275 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 59 optimal weight: 1.9990 chunk 88 optimal weight: 0.7980 chunk 44 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 101 optimal weight: 0.7980 chunk 73 optimal weight: 0.0770 chunk 13 optimal weight: 0.6980 chunk 116 optimal weight: 1.9990 chunk 135 optimal weight: 0.0980 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 HIS ** A 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 227 GLN A 392 HIS B 211 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.1780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13428 Z= 0.179 Angle : 0.558 11.299 18481 Z= 0.288 Chirality : 0.040 0.155 2129 Planarity : 0.003 0.051 2167 Dihedral : 18.781 116.282 2299 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.96 % Allowed : 15.38 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.23), residues: 1479 helix: 1.75 (0.23), residues: 542 sheet: -0.10 (0.33), residues: 255 loop : -0.41 (0.25), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 296 HIS 0.018 0.001 HIS A 392 PHE 0.013 0.001 PHE C 33 TYR 0.011 0.001 TYR B 237 ARG 0.008 0.000 ARG D 976 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 105 time to evaluate : 1.377 Fit side-chains REVERT: C 998 LEU cc_start: 0.8311 (OUTLIER) cc_final: 0.7939 (mt) REVERT: D 197 ARG cc_start: 0.7261 (tpp80) cc_final: 0.6848 (tpt-90) REVERT: A 51 ASP cc_start: 0.8211 (t0) cc_final: 0.8001 (t0) outliers start: 25 outliers final: 19 residues processed: 126 average time/residue: 0.2623 time to fit residues: 49.0121 Evaluate side-chains 123 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 103 time to evaluate : 1.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 115 GLU Chi-restraints excluded: chain C residue 910 LEU Chi-restraints excluded: chain C residue 998 LEU Chi-restraints excluded: chain C residue 1043 SER Chi-restraints excluded: chain D residue 68 GLN Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 168 GLU Chi-restraints excluded: chain D residue 1026 VAL Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 164 HIS Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 392 HIS Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 275 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 142 optimal weight: 0.6980 chunk 129 optimal weight: 1.9990 chunk 138 optimal weight: 0.6980 chunk 83 optimal weight: 1.9990 chunk 60 optimal weight: 0.5980 chunk 108 optimal weight: 0.0980 chunk 42 optimal weight: 1.9990 chunk 124 optimal weight: 0.7980 chunk 130 optimal weight: 0.9990 chunk 137 optimal weight: 3.9990 chunk 90 optimal weight: 2.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 HIS ** A 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 392 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.1831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13428 Z= 0.189 Angle : 0.562 10.145 18481 Z= 0.290 Chirality : 0.040 0.154 2129 Planarity : 0.003 0.051 2167 Dihedral : 18.746 115.417 2297 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.88 % Allowed : 15.62 % Favored : 82.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.23), residues: 1479 helix: 1.73 (0.23), residues: 548 sheet: -0.14 (0.33), residues: 257 loop : -0.40 (0.25), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 296 HIS 0.023 0.001 HIS A 392 PHE 0.013 0.001 PHE C 33 TYR 0.011 0.001 TYR B 237 ARG 0.008 0.000 ARG D 976 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 104 time to evaluate : 1.417 Fit side-chains REVERT: C 180 GLU cc_start: 0.8019 (mp0) cc_final: 0.7657 (mp0) REVERT: C 927 LYS cc_start: 0.7920 (tppt) cc_final: 0.7385 (tppt) REVERT: C 998 LEU cc_start: 0.8329 (OUTLIER) cc_final: 0.7955 (mt) REVERT: D 197 ARG cc_start: 0.7042 (tpp80) cc_final: 0.6687 (tpt-90) REVERT: A 51 ASP cc_start: 0.8218 (t0) cc_final: 0.8001 (t0) outliers start: 24 outliers final: 20 residues processed: 125 average time/residue: 0.2587 time to fit residues: 47.6585 Evaluate side-chains 124 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 103 time to evaluate : 1.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 115 GLU Chi-restraints excluded: chain C residue 910 LEU Chi-restraints excluded: chain C residue 998 LEU Chi-restraints excluded: chain C residue 1043 SER Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 168 GLU Chi-restraints excluded: chain D residue 1026 VAL Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 164 HIS Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 392 HIS Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 275 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 146 optimal weight: 6.9990 chunk 89 optimal weight: 0.3980 chunk 69 optimal weight: 2.9990 chunk 101 optimal weight: 0.8980 chunk 153 optimal weight: 3.9990 chunk 141 optimal weight: 1.9990 chunk 122 optimal weight: 4.9990 chunk 12 optimal weight: 0.8980 chunk 94 optimal weight: 0.2980 chunk 74 optimal weight: 0.5980 chunk 97 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 HIS ** A 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 392 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.1879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13428 Z= 0.196 Angle : 0.565 9.428 18481 Z= 0.291 Chirality : 0.040 0.150 2129 Planarity : 0.003 0.051 2167 Dihedral : 18.728 114.542 2297 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.96 % Allowed : 15.54 % Favored : 82.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.23), residues: 1479 helix: 1.74 (0.23), residues: 548 sheet: -0.17 (0.33), residues: 259 loop : -0.41 (0.25), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 296 HIS 0.019 0.001 HIS A 392 PHE 0.013 0.001 PHE C 33 TYR 0.011 0.001 TYR B 237 ARG 0.009 0.000 ARG D 976 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 101 time to evaluate : 1.418 Fit side-chains REVERT: C 180 GLU cc_start: 0.8037 (mp0) cc_final: 0.7691 (mp0) REVERT: C 998 LEU cc_start: 0.8289 (OUTLIER) cc_final: 0.7893 (mt) REVERT: D 197 ARG cc_start: 0.7076 (tpp80) cc_final: 0.6706 (tpt-90) REVERT: A 51 ASP cc_start: 0.8219 (t0) cc_final: 0.8002 (t0) REVERT: A 393 THR cc_start: 0.9024 (OUTLIER) cc_final: 0.8818 (m) outliers start: 25 outliers final: 21 residues processed: 122 average time/residue: 0.2656 time to fit residues: 47.5176 Evaluate side-chains 123 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 100 time to evaluate : 1.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 115 GLU Chi-restraints excluded: chain C residue 910 LEU Chi-restraints excluded: chain C residue 998 LEU Chi-restraints excluded: chain C residue 1043 SER Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 168 GLU Chi-restraints excluded: chain D residue 1011 ILE Chi-restraints excluded: chain D residue 1026 VAL Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 164 HIS Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 275 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 130 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 112 optimal weight: 4.9990 chunk 18 optimal weight: 0.8980 chunk 33 optimal weight: 0.6980 chunk 122 optimal weight: 4.9990 chunk 51 optimal weight: 0.9980 chunk 125 optimal weight: 0.3980 chunk 15 optimal weight: 3.9990 chunk 22 optimal weight: 0.9990 chunk 107 optimal weight: 0.0970 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 HIS ** A 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 392 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.129594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.099648 restraints weight = 19484.360| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 2.22 r_work: 0.3084 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3082 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3082 r_free = 0.3082 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3065 r_free = 0.3065 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3065 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.1958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13428 Z= 0.194 Angle : 0.557 9.282 18481 Z= 0.289 Chirality : 0.040 0.150 2129 Planarity : 0.003 0.051 2167 Dihedral : 18.672 111.632 2297 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.81 % Allowed : 15.70 % Favored : 82.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.23), residues: 1479 helix: 1.81 (0.23), residues: 548 sheet: -0.15 (0.33), residues: 259 loop : -0.41 (0.25), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 296 HIS 0.014 0.001 HIS A 392 PHE 0.013 0.001 PHE C 33 TYR 0.011 0.001 TYR B 237 ARG 0.009 0.000 ARG D 976 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2528.80 seconds wall clock time: 47 minutes 16.16 seconds (2836.16 seconds total)