Starting phenix.real_space_refine on Wed Feb 14 01:38:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eo4_31226/02_2024/7eo4_31226_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eo4_31226/02_2024/7eo4_31226.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eo4_31226/02_2024/7eo4_31226_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eo4_31226/02_2024/7eo4_31226_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eo4_31226/02_2024/7eo4_31226_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eo4_31226/02_2024/7eo4_31226.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eo4_31226/02_2024/7eo4_31226.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eo4_31226/02_2024/7eo4_31226_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eo4_31226/02_2024/7eo4_31226_neut_updated.pdb" } resolution = 2.86 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= 0.078 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 58 5.16 5 C 5311 2.51 5 N 1399 2.21 5 O 1531 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 9": "OD1" <-> "OD2" Residue "B GLU 28": "OE1" <-> "OE2" Residue "C ASP 76": "OD1" <-> "OD2" Residue "C ASP 153": "OD1" <-> "OD2" Residue "C ASP 154": "OD1" <-> "OD2" Residue "C PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8302 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2247 Classifications: {'peptide': 282} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 6, 'TRANS': 275} Chain breaks: 3 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 3} Unresolved non-hydrogen planarities: 15 Chain: "B" Number of atoms: 1205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1205 Classifications: {'peptide': 151} Link IDs: {'TRANS': 150} Chain breaks: 4 Chain: "C" Number of atoms: 2607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2607 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 333} Chain: "D" Number of atoms: 429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 429 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 4, 'TRANS': 51} Chain: "E" Number of atoms: 1777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1777 Classifications: {'peptide': 231} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220} Chain breaks: 1 Chain: "A" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 37 Unusual residues: {'J8C': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.09, per 1000 atoms: 0.61 Number of scatterers: 8302 At special positions: 0 Unit cell: (93.5, 123.2, 129.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 58 16.00 F 3 9.00 O 1531 8.00 N 1399 7.00 C 5311 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 184 " - pdb=" SG CYS A 191 " distance=2.04 Simple disulfide: pdb=" SG CYS A 282 " - pdb=" SG CYS A 287 " distance=2.03 Simple disulfide: pdb=" SG CYS E 147 " - pdb=" SG CYS E 217 " distance=2.04 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: 3.15 Conformation dependent library (CDL) restraints added in 1.5 seconds 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1980 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 25 helices and 12 sheets defined 31.6% alpha, 21.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.86 Creating SS restraints... Processing helix chain 'A' and resid 23 through 32 Processing helix chain 'A' and resid 47 through 71 Processing helix chain 'A' and resid 74 through 76 No H-bonds generated for 'chain 'A' and resid 74 through 76' Processing helix chain 'A' and resid 79 through 104 removed outlier: 3.615A pdb=" N VAL A 96 " --> pdb=" O LEU A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 108 No H-bonds generated for 'chain 'A' and resid 106 through 108' Processing helix chain 'A' and resid 114 through 145 removed outlier: 4.004A pdb=" N ALA A 127 " --> pdb=" O SER A 123 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N LEU A 128 " --> pdb=" O MET A 124 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU A 136 " --> pdb=" O VAL A 132 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N TYR A 143 " --> pdb=" O ALA A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 178 removed outlier: 3.644A pdb=" N GLY A 176 " --> pdb=" O LEU A 172 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N LEU A 177 " --> pdb=" O ILE A 173 " (cutoff:3.500A) Proline residue: A 178 - end of helix Processing helix chain 'A' and resid 188 through 190 No H-bonds generated for 'chain 'A' and resid 188 through 190' Processing helix chain 'A' and resid 200 through 232 Processing helix chain 'A' and resid 255 through 281 removed outlier: 3.938A pdb=" N ILE A 260 " --> pdb=" O LYS A 256 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA A 270 " --> pdb=" O ILE A 266 " (cutoff:3.500A) Proline residue: A 271 - end of helix removed outlier: 3.903A pdb=" N VAL A 280 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N GLY A 281 " --> pdb=" O LEU A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 292 No H-bonds generated for 'chain 'A' and resid 290 through 292' Processing helix chain 'A' and resid 297 through 313 removed outlier: 3.777A pdb=" N ASN A 303 " --> pdb=" O LEU A 299 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N SER A 304 " --> pdb=" O ALA A 300 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N GLY A 305 " --> pdb=" O VAL A 301 " (cutoff:3.500A) Proline residue: A 308 - end of helix Processing helix chain 'A' and resid 316 through 322 Processing helix chain 'B' and resid 7 through 32 removed outlier: 4.049A pdb=" N ALA B 11 " --> pdb=" O ALA B 7 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA B 12 " --> pdb=" O GLU B 8 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N ARG B 32 " --> pdb=" O GLU B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 50 No H-bonds generated for 'chain 'B' and resid 47 through 50' Processing helix chain 'B' and resid 251 through 254 No H-bonds generated for 'chain 'B' and resid 251 through 254' Processing helix chain 'B' and resid 329 through 350 removed outlier: 4.196A pdb=" N PHE B 334 " --> pdb=" O ASN B 331 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 25 removed outlier: 3.973A pdb=" N CYS C 25 " --> pdb=" O ALA C 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 34 Processing helix chain 'D' and resid 8 through 23 Processing helix chain 'D' and resid 30 through 43 Processing helix chain 'D' and resid 49 through 51 No H-bonds generated for 'chain 'D' and resid 49 through 51' Processing helix chain 'D' and resid 56 through 58 No H-bonds generated for 'chain 'D' and resid 56 through 58' Processing helix chain 'E' and resid 29 through 31 No H-bonds generated for 'chain 'E' and resid 29 through 31' Processing helix chain 'E' and resid 74 through 76 No H-bonds generated for 'chain 'E' and resid 74 through 76' Processing sheet with id= A, first strand: chain 'B' and resid 220 through 222 removed outlier: 4.191A pdb=" N ALA B 220 " --> pdb=" O LYS B 35 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU B 37 " --> pdb=" O ALA B 220 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N HIS B 195 " --> pdb=" O VAL B 34 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N LEU B 36 " --> pdb=" O HIS B 195 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N LYS B 197 " --> pdb=" O LEU B 36 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N LEU B 38 " --> pdb=" O LYS B 197 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N PHE B 199 " --> pdb=" O LEU B 38 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N VAL B 185 " --> pdb=" O ASP B 200 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'C' and resid 58 through 63 removed outlier: 7.109A pdb=" N ALA C 73 " --> pdb=" O TYR C 59 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N MET C 61 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N VAL C 71 " --> pdb=" O MET C 61 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N TRP C 63 " --> pdb=" O LEU C 69 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N LEU C 69 " --> pdb=" O TRP C 63 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N SER C 74 " --> pdb=" O LYS C 78 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N HIS C 91 " --> pdb=" O ILE C 81 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N ASP C 83 " --> pdb=" O LYS C 89 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N LYS C 89 " --> pdb=" O ASP C 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 100 through 105 removed outlier: 6.867A pdb=" N GLY C 115 " --> pdb=" O MET C 101 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N CYS C 103 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N ALA C 113 " --> pdb=" O CYS C 103 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N TYR C 105 " --> pdb=" O TYR C 111 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N TYR C 111 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N GLY C 116 " --> pdb=" O ILE C 120 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N ILE C 120 " --> pdb=" O GLY C 116 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ARG C 137 " --> pdb=" O ILE C 123 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N ASN C 125 " --> pdb=" O VAL C 135 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N VAL C 135 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 146 through 151 removed outlier: 6.762A pdb=" N SER C 160 " --> pdb=" O SER C 147 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N CYS C 149 " --> pdb=" O VAL C 158 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N VAL C 158 " --> pdb=" O CYS C 149 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ILE C 157 " --> pdb=" O TRP C 169 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N THR C 165 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N THR C 178 " --> pdb=" O LEU C 168 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ASP C 170 " --> pdb=" O GLN C 176 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N GLN C 176 " --> pdb=" O ASP C 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 187 through 192 removed outlier: 6.548A pdb=" N GLY C 202 " --> pdb=" O MET C 188 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N LEU C 190 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N VAL C 200 " --> pdb=" O LEU C 190 " (cutoff:3.500A) removed outlier: 5.363A pdb=" N LEU C 192 " --> pdb=" O LEU C 198 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N LEU C 198 " --> pdb=" O LEU C 192 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N SER C 201 " --> pdb=" O LYS C 209 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLN C 220 " --> pdb=" O LEU C 210 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N ASP C 212 " --> pdb=" O CYS C 218 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N CYS C 218 " --> pdb=" O ASP C 212 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 229 through 234 removed outlier: 6.883A pdb=" N GLY C 244 " --> pdb=" O ASN C 230 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N ILE C 232 " --> pdb=" O ALA C 242 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ALA C 242 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N PHE C 241 " --> pdb=" O PHE C 253 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N PHE C 253 " --> pdb=" O PHE C 241 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N THR C 249 " --> pdb=" O SER C 245 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N MET C 262 " --> pdb=" O LEU C 252 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N ASP C 254 " --> pdb=" O GLU C 260 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N GLU C 260 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 295 through 297 removed outlier: 3.533A pdb=" N ALA C 287 " --> pdb=" O ASN C 295 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N SER C 275 " --> pdb=" O GLY C 288 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 47 through 51 removed outlier: 6.803A pdb=" N ILE C 338 " --> pdb=" O ARG C 48 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N THR C 50 " --> pdb=" O LEU C 336 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N LEU C 336 " --> pdb=" O THR C 50 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N CYS C 317 " --> pdb=" O GLY C 330 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 3 through 7 Processing sheet with id= J, first strand: chain 'E' and resid 10 through 12 removed outlier: 3.547A pdb=" N TRP E 36 " --> pdb=" O ALA E 49 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ALA E 49 " --> pdb=" O TRP E 36 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N TYR E 59 " --> pdb=" O TYR E 50 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'E' and resid 128 through 130 removed outlier: 3.505A pdb=" N CYS E 147 " --> pdb=" O PHE E 200 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N PHE E 200 " --> pdb=" O CYS E 147 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'E' and resid 134 through 136 removed outlier: 6.554A pdb=" N LYS E 232 " --> pdb=" O VAL E 135 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N GLY E 213 " --> pdb=" O LEU E 233 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ILE E 177 " --> pdb=" O TRP E 164 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N LEU E 166 " --> pdb=" O LEU E 175 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N LEU E 175 " --> pdb=" O LEU E 166 " (cutoff:3.500A) 336 hydrogen bonds defined for protein. 912 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: 2.50 Time building geometry restraints manager: 3.36 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: 2587 1.34 - 1.46: 1992 1.46 - 1.58: 3806 1.58 - 1.71: 3 1.71 - 1.83: 81 Bond restraints: 8469 Sorted by residual: bond pdb=" C16 J8C A 401 " pdb=" C19 J8C A 401 " ideal model delta sigma weight residual 0.000 1.576 -1.576 2.00e-02 2.50e+03 6.21e+03 bond pdb=" C12 J8C A 401 " pdb=" C13 J8C A 401 " ideal model delta sigma weight residual 1.958 1.584 0.374 2.00e-02 2.50e+03 3.49e+02 bond pdb=" C02 J8C A 401 " pdb=" C03 J8C A 401 " ideal model delta sigma weight residual 1.428 1.563 -0.135 2.00e-02 2.50e+03 4.53e+01 bond pdb=" C19 J8C A 401 " pdb=" C20 J8C A 401 " ideal model delta sigma weight residual 1.457 1.585 -0.128 2.00e-02 2.50e+03 4.10e+01 bond pdb=" N10 J8C A 401 " pdb=" O11 J8C A 401 " ideal model delta sigma weight residual 1.523 1.408 0.115 2.00e-02 2.50e+03 3.33e+01 ... (remaining 8464 not shown) Histogram of bond angle deviations from ideal: 87.26 - 96.64: 4 96.64 - 106.02: 138 106.02 - 115.39: 5192 115.39 - 124.77: 5976 124.77 - 134.15: 162 Bond angle restraints: 11472 Sorted by residual: angle pdb=" C12 J8C A 401 " pdb=" C13 J8C A 401 " pdb=" C14 J8C A 401 " ideal model delta sigma weight residual 105.15 120.45 -15.30 3.00e+00 1.11e-01 2.60e+01 angle pdb=" N MET E 180 " pdb=" CA MET E 180 " pdb=" CB MET E 180 " ideal model delta sigma weight residual 114.17 108.76 5.41 1.14e+00 7.69e-01 2.25e+01 angle pdb=" N ASP C 303 " pdb=" CA ASP C 303 " pdb=" C ASP C 303 " ideal model delta sigma weight residual 107.48 117.67 -10.19 2.29e+00 1.91e-01 1.98e+01 angle pdb=" N ASP E 211 " pdb=" CA ASP E 211 " pdb=" C ASP E 211 " ideal model delta sigma weight residual 110.80 101.34 9.46 2.13e+00 2.20e-01 1.97e+01 angle pdb=" N PHE C 292 " pdb=" CA PHE C 292 " pdb=" CB PHE C 292 " ideal model delta sigma weight residual 114.17 109.11 5.06 1.14e+00 7.69e-01 1.97e+01 ... (remaining 11467 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.93: 4719 22.93 - 45.86: 243 45.86 - 68.79: 25 68.79 - 91.72: 6 91.72 - 114.65: 4 Dihedral angle restraints: 4997 sinusoidal: 1932 harmonic: 3065 Sorted by residual: dihedral pdb=" C ASP E 211 " pdb=" N ASP E 211 " pdb=" CA ASP E 211 " pdb=" CB ASP E 211 " ideal model delta harmonic sigma weight residual -122.60 -112.23 -10.37 0 2.50e+00 1.60e-01 1.72e+01 dihedral pdb=" CA THR B 187 " pdb=" C THR B 187 " pdb=" N HIS B 188 " pdb=" CA HIS B 188 " ideal model delta harmonic sigma weight residual -180.00 -160.09 -19.91 0 5.00e+00 4.00e-02 1.59e+01 dihedral pdb=" CA TRP C 339 " pdb=" C TRP C 339 " pdb=" N ASN C 340 " pdb=" CA ASN C 340 " ideal model delta harmonic sigma weight residual 180.00 160.10 19.90 0 5.00e+00 4.00e-02 1.58e+01 ... (remaining 4994 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.173: 1323 1.173 - 2.347: 0 2.347 - 3.520: 0 3.520 - 4.693: 0 4.693 - 5.866: 1 Chirality restraints: 1324 Sorted by residual: chirality pdb=" C33 J8C A 401 " pdb=" C32 J8C A 401 " pdb=" C34 J8C A 401 " pdb=" C35 J8C A 401 " both_signs ideal model delta sigma weight residual False -2.82 3.05 -5.87 2.00e-01 2.50e+01 8.60e+02 chirality pdb=" CA ASP E 211 " pdb=" N ASP E 211 " pdb=" C ASP E 211 " pdb=" CB ASP E 211 " both_signs ideal model delta sigma weight residual False 2.51 2.87 -0.36 2.00e-01 2.50e+01 3.20e+00 chirality pdb=" CA ALA E 209 " pdb=" N ALA E 209 " pdb=" C ALA E 209 " pdb=" CB ALA E 209 " both_signs ideal model delta sigma weight residual False 2.48 2.74 -0.25 2.00e-01 2.50e+01 1.62e+00 ... (remaining 1321 not shown) Planarity restraints: 1424 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 292 " -0.291 9.50e-02 1.11e+02 1.31e-01 1.05e+01 pdb=" NE ARG A 292 " 0.017 2.00e-02 2.50e+03 pdb=" CZ ARG A 292 " 0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG A 292 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 292 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE C 235 " -0.046 5.00e-02 4.00e+02 6.95e-02 7.74e+00 pdb=" N PRO C 236 " 0.120 5.00e-02 4.00e+02 pdb=" CA PRO C 236 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO C 236 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 177 " 0.046 5.00e-02 4.00e+02 6.89e-02 7.61e+00 pdb=" N PRO A 178 " -0.119 5.00e-02 4.00e+02 pdb=" CA PRO A 178 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 178 " 0.039 5.00e-02 4.00e+02 ... (remaining 1421 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1250 2.76 - 3.29: 7641 3.29 - 3.83: 12511 3.83 - 4.36: 14972 4.36 - 4.90: 26009 Nonbonded interactions: 62383 Sorted by model distance: nonbonded pdb=" N GLY C 144 " pdb=" OD1 ASP C 163 " model vdw 2.220 2.520 nonbonded pdb=" O GLY E 197 " pdb=" OG1 THR E 198 " model vdw 2.242 2.440 nonbonded pdb=" OG1 THR C 86 " pdb=" OD1 ASN C 88 " model vdw 2.244 2.440 nonbonded pdb=" O LEU C 30 " pdb=" OG1 THR C 34 " model vdw 2.274 2.440 nonbonded pdb=" O ASP C 163 " pdb=" OG1 THR C 164 " model vdw 2.297 2.440 ... (remaining 62378 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 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: 0.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 4.090 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 26.580 Find NCS groups from input model: 0.230 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:11.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6951 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 : 0.019 1.576 8469 Z= 1.552 Angle : 1.004 15.296 11472 Z= 0.538 Chirality : 0.170 5.866 1324 Planarity : 0.007 0.131 1424 Dihedral : 14.176 114.647 3008 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 2.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Rotamer: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -1.38 (0.25), residues: 1033 helix: 1.19 (0.29), residues: 312 sheet: -1.83 (0.30), residues: 239 loop : -1.84 (0.27), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP C 63 HIS 0.011 0.002 HIS B 213 PHE 0.040 0.003 PHE C 151 TYR 0.023 0.003 TYR A 31 ARG 0.011 0.001 ARG C 304 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 173 time to evaluate : 1.013 Fit side-chains REVERT: E 18 ARG cc_start: 0.7798 (tpp80) cc_final: 0.7583 (ttt90) outliers start: 0 outliers final: 0 residues processed: 173 average time/residue: 1.1259 time to fit residues: 208.5935 Evaluate side-chains 148 residues out of total 911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 148 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 87 optimal weight: 2.9990 chunk 78 optimal weight: 0.8980 chunk 43 optimal weight: 0.7980 chunk 26 optimal weight: 6.9990 chunk 53 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 81 optimal weight: 0.8980 chunk 31 optimal weight: 0.6980 chunk 49 optimal weight: 0.7980 chunk 60 optimal weight: 0.9980 chunk 94 optimal weight: 10.0000 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 ASN ** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 220 GLN C 237 ASN C 340 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6953 moved from start: 0.0556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.139 8469 Z= 0.406 Angle : 1.143 24.561 11472 Z= 0.542 Chirality : 0.075 2.123 1324 Planarity : 0.007 0.068 1424 Dihedral : 9.332 107.950 1155 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 2.76 % Allowed : 10.28 % Favored : 86.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -1.31 (0.25), residues: 1033 helix: 1.21 (0.29), residues: 311 sheet: -1.59 (0.30), residues: 249 loop : -1.88 (0.27), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 63 HIS 0.008 0.002 HIS B 213 PHE 0.033 0.002 PHE C 151 TYR 0.016 0.002 TYR E 103 ARG 0.014 0.000 ARG A 320 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 145 time to evaluate : 1.003 Fit side-chains REVERT: A 141 GLU cc_start: 0.7047 (OUTLIER) cc_final: 0.6588 (tm-30) REVERT: E 90 ASP cc_start: 0.6912 (OUTLIER) cc_final: 0.6197 (m-30) REVERT: E 128 MET cc_start: 0.6399 (OUTLIER) cc_final: 0.5377 (mmm) outliers start: 25 outliers final: 17 residues processed: 153 average time/residue: 1.0950 time to fit residues: 179.0920 Evaluate side-chains 161 residues out of total 911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 141 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 141 GLU Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 316 LYS Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain C residue 78 LYS Chi-restraints excluded: chain C residue 229 ILE Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 90 ASP Chi-restraints excluded: chain E residue 128 MET Chi-restraints excluded: chain E residue 149 SER Chi-restraints excluded: chain E residue 183 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 52 optimal weight: 0.4980 chunk 29 optimal weight: 0.9990 chunk 78 optimal weight: 0.0980 chunk 64 optimal weight: 0.0980 chunk 26 optimal weight: 0.4980 chunk 94 optimal weight: 8.9990 chunk 102 optimal weight: 0.9980 chunk 84 optimal weight: 2.9990 chunk 93 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 75 optimal weight: 0.5980 overall best weight: 0.3580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 220 GLN C 340 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6954 moved from start: 0.0589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.139 8469 Z= 0.406 Angle : 1.143 24.555 11472 Z= 0.542 Chirality : 0.075 2.123 1324 Planarity : 0.007 0.068 1424 Dihedral : 9.337 107.944 1155 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 2.32 % Allowed : 11.16 % Favored : 86.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -1.31 (0.25), residues: 1033 helix: 1.21 (0.29), residues: 311 sheet: -1.59 (0.30), residues: 249 loop : -1.88 (0.27), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 63 HIS 0.008 0.002 HIS B 213 PHE 0.033 0.002 PHE C 151 TYR 0.016 0.002 TYR E 103 ARG 0.014 0.000 ARG A 320 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 141 time to evaluate : 0.900 Fit side-chains REVERT: A 141 GLU cc_start: 0.7048 (OUTLIER) cc_final: 0.6588 (tm-30) REVERT: E 90 ASP cc_start: 0.6908 (OUTLIER) cc_final: 0.6197 (m-30) REVERT: E 128 MET cc_start: 0.6400 (OUTLIER) cc_final: 0.5377 (mmm) outliers start: 21 outliers final: 17 residues processed: 150 average time/residue: 1.0829 time to fit residues: 173.6528 Evaluate side-chains 161 residues out of total 911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 141 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 141 GLU Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 316 LYS Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain C residue 78 LYS Chi-restraints excluded: chain C residue 229 ILE Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 90 ASP Chi-restraints excluded: chain E residue 128 MET Chi-restraints excluded: chain E residue 149 SER Chi-restraints excluded: chain E residue 183 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 93 optimal weight: 4.9990 chunk 71 optimal weight: 0.5980 chunk 49 optimal weight: 0.9980 chunk 10 optimal weight: 0.7980 chunk 45 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 chunk 94 optimal weight: 0.0050 chunk 100 optimal weight: 0.7980 chunk 89 optimal weight: 4.9990 chunk 27 optimal weight: 0.9980 chunk 83 optimal weight: 3.9990 overall best weight: 0.6394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 220 GLN C 340 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6954 moved from start: 0.0590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.138 8469 Z= 0.404 Angle : 1.141 24.442 11472 Z= 0.541 Chirality : 0.074 2.119 1324 Planarity : 0.007 0.068 1424 Dihedral : 9.373 107.836 1155 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 2.32 % Allowed : 11.27 % Favored : 86.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -1.31 (0.25), residues: 1033 helix: 1.21 (0.29), residues: 311 sheet: -1.59 (0.30), residues: 249 loop : -1.88 (0.27), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 63 HIS 0.008 0.002 HIS B 213 PHE 0.033 0.002 PHE C 151 TYR 0.016 0.002 TYR E 103 ARG 0.014 0.000 ARG A 320 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 141 time to evaluate : 0.865 Fit side-chains REVERT: A 141 GLU cc_start: 0.7048 (OUTLIER) cc_final: 0.6588 (tm-30) REVERT: E 90 ASP cc_start: 0.6908 (OUTLIER) cc_final: 0.6197 (m-30) REVERT: E 128 MET cc_start: 0.6401 (OUTLIER) cc_final: 0.5377 (mmm) outliers start: 21 outliers final: 17 residues processed: 150 average time/residue: 1.0808 time to fit residues: 173.2420 Evaluate side-chains 161 residues out of total 911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 141 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 141 GLU Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 316 LYS Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain C residue 78 LYS Chi-restraints excluded: chain C residue 229 ILE Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 90 ASP Chi-restraints excluded: chain E residue 128 MET Chi-restraints excluded: chain E residue 149 SER Chi-restraints excluded: chain E residue 183 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 57 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 74 optimal weight: 0.4980 chunk 41 optimal weight: 0.6980 chunk 85 optimal weight: 0.5980 chunk 69 optimal weight: 0.1980 chunk 0 optimal weight: 10.0000 chunk 51 optimal weight: 0.9990 chunk 90 optimal weight: 3.9990 chunk 25 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 overall best weight: 0.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 119 ASN C 220 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6862 moved from start: 0.1270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 8469 Z= 0.212 Angle : 0.680 9.803 11472 Z= 0.350 Chirality : 0.044 0.169 1324 Planarity : 0.005 0.061 1424 Dihedral : 6.655 82.128 1155 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 2.10 % Allowed : 12.71 % Favored : 85.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -0.73 (0.25), residues: 1033 helix: 1.52 (0.29), residues: 312 sheet: -0.74 (0.30), residues: 262 loop : -1.77 (0.27), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 82 HIS 0.007 0.001 HIS E 35 PHE 0.016 0.002 PHE C 199 TYR 0.014 0.001 TYR A 81 ARG 0.008 0.000 ARG A 320 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 158 time to evaluate : 1.023 Fit side-chains REVERT: A 141 GLU cc_start: 0.6716 (OUTLIER) cc_final: 0.6303 (tm-30) REVERT: C 340 ASN cc_start: 0.7535 (OUTLIER) cc_final: 0.7317 (p0) REVERT: E 90 ASP cc_start: 0.6987 (OUTLIER) cc_final: 0.6429 (m-30) outliers start: 19 outliers final: 7 residues processed: 165 average time/residue: 1.0376 time to fit residues: 183.9407 Evaluate side-chains 157 residues out of total 911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 147 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 141 GLU Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 340 ASN Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 90 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 90 optimal weight: 0.9990 chunk 19 optimal weight: 4.9990 chunk 59 optimal weight: 0.5980 chunk 24 optimal weight: 0.8980 chunk 100 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 chunk 46 optimal weight: 3.9990 chunk 8 optimal weight: 5.9990 chunk 33 optimal weight: 0.2980 chunk 52 optimal weight: 2.9990 chunk 97 optimal weight: 0.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 220 GLN D 18 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6869 moved from start: 0.1484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 8469 Z= 0.204 Angle : 0.643 10.336 11472 Z= 0.333 Chirality : 0.043 0.175 1324 Planarity : 0.005 0.058 1424 Dihedral : 6.276 81.335 1155 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.21 % Allowed : 14.81 % Favored : 82.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -0.48 (0.26), residues: 1033 helix: 1.76 (0.29), residues: 313 sheet: -0.35 (0.31), residues: 247 loop : -1.79 (0.27), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 82 HIS 0.006 0.001 HIS E 35 PHE 0.018 0.002 PHE C 151 TYR 0.012 0.002 TYR E 95 ARG 0.006 0.000 ARG A 320 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 148 time to evaluate : 0.972 Fit side-chains REVERT: A 141 GLU cc_start: 0.6750 (OUTLIER) cc_final: 0.6270 (tm-30) REVERT: B 209 LYS cc_start: 0.5245 (ptpt) cc_final: 0.4703 (mmtp) REVERT: C 230 ASN cc_start: 0.7149 (OUTLIER) cc_final: 0.6897 (p0) REVERT: E 90 ASP cc_start: 0.6946 (OUTLIER) cc_final: 0.6302 (m-30) outliers start: 20 outliers final: 12 residues processed: 156 average time/residue: 1.0772 time to fit residues: 180.3546 Evaluate side-chains 156 residues out of total 911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 141 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 141 GLU Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain C residue 78 LYS Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 230 ASN Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 90 ASP Chi-restraints excluded: chain E residue 126 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 11 optimal weight: 0.9990 chunk 57 optimal weight: 0.5980 chunk 73 optimal weight: 0.5980 chunk 56 optimal weight: 2.9990 chunk 84 optimal weight: 0.7980 chunk 100 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 chunk 61 optimal weight: 0.5980 chunk 46 optimal weight: 1.9990 chunk 40 optimal weight: 0.0470 chunk 59 optimal weight: 0.8980 overall best weight: 0.5278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 220 GLN C 237 ASN C 239 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6836 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 0.074 8469 Z= 0.180 Angle : 0.616 11.142 11472 Z= 0.315 Chirality : 0.042 0.176 1324 Planarity : 0.005 0.055 1424 Dihedral : 6.079 82.823 1155 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.10 % Allowed : 15.91 % Favored : 81.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -0.32 (0.26), residues: 1033 helix: 1.94 (0.29), residues: 313 sheet: -0.27 (0.31), residues: 252 loop : -1.74 (0.27), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 82 HIS 0.005 0.001 HIS E 35 PHE 0.015 0.001 PHE C 199 TYR 0.012 0.001 TYR A 295 ARG 0.009 0.000 ARG A 320 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 146 time to evaluate : 1.011 Fit side-chains revert: symmetry clash REVERT: B 209 LYS cc_start: 0.5060 (OUTLIER) cc_final: 0.4566 (mmtp) REVERT: C 340 ASN cc_start: 0.7383 (p0) cc_final: 0.7136 (p0) REVERT: E 90 ASP cc_start: 0.6895 (OUTLIER) cc_final: 0.6283 (m-30) outliers start: 19 outliers final: 16 residues processed: 154 average time/residue: 1.0178 time to fit residues: 168.3620 Evaluate side-chains 161 residues out of total 911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 143 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 141 GLU Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 209 LYS Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain C residue 78 LYS Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 237 ASN Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 90 ASP Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 126 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 30 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 63 optimal weight: 0.9990 chunk 68 optimal weight: 0.8980 chunk 49 optimal weight: 0.1980 chunk 9 optimal weight: 6.9990 chunk 78 optimal weight: 0.4980 chunk 91 optimal weight: 0.4980 chunk 96 optimal weight: 0.0670 chunk 87 optimal weight: 4.9990 chunk 93 optimal weight: 3.9990 overall best weight: 0.4318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 220 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6836 moved from start: 0.1734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.118 8469 Z= 0.213 Angle : 0.676 18.173 11472 Z= 0.368 Chirality : 0.042 0.165 1324 Planarity : 0.006 0.103 1424 Dihedral : 6.085 82.835 1155 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 2.10 % Allowed : 16.80 % Favored : 81.10 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 4.00 % 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: -0.30 (0.26), residues: 1033 helix: 1.96 (0.29), residues: 313 sheet: -0.22 (0.31), residues: 252 loop : -1.76 (0.27), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 82 HIS 0.005 0.001 HIS E 35 PHE 0.015 0.001 PHE C 199 TYR 0.012 0.001 TYR A 295 ARG 0.009 0.000 ARG A 320 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 145 time to evaluate : 1.072 Fit side-chains REVERT: B 209 LYS cc_start: 0.5058 (OUTLIER) cc_final: 0.4562 (mmtp) REVERT: C 340 ASN cc_start: 0.7376 (p0) cc_final: 0.7128 (p0) REVERT: E 90 ASP cc_start: 0.6898 (OUTLIER) cc_final: 0.6277 (m-30) outliers start: 19 outliers final: 15 residues processed: 151 average time/residue: 1.0602 time to fit residues: 171.6586 Evaluate side-chains 160 residues out of total 911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 143 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 141 GLU Chi-restraints excluded: chain A residue 316 LYS Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 209 LYS Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain C residue 78 LYS Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 90 ASP Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 126 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 96 optimal weight: 0.5980 chunk 56 optimal weight: 0.8980 chunk 40 optimal weight: 4.9990 chunk 73 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 chunk 61 optimal weight: 0.5980 chunk 98 optimal weight: 0.8980 chunk 60 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 220 GLN C 237 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6837 moved from start: 0.1739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.118 8469 Z= 0.213 Angle : 0.676 18.168 11472 Z= 0.368 Chirality : 0.042 0.165 1324 Planarity : 0.006 0.103 1424 Dihedral : 6.085 82.835 1155 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 1.88 % Allowed : 17.13 % Favored : 80.99 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 4.00 % 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: -0.30 (0.26), residues: 1033 helix: 1.96 (0.29), residues: 313 sheet: -0.22 (0.31), residues: 252 loop : -1.76 (0.27), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 82 HIS 0.005 0.001 HIS E 35 PHE 0.015 0.001 PHE C 199 TYR 0.012 0.001 TYR A 295 ARG 0.009 0.000 ARG A 320 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 143 time to evaluate : 0.966 Fit side-chains REVERT: B 209 LYS cc_start: 0.5056 (OUTLIER) cc_final: 0.4562 (mmtp) REVERT: C 340 ASN cc_start: 0.7377 (p0) cc_final: 0.7129 (p0) REVERT: E 90 ASP cc_start: 0.6900 (OUTLIER) cc_final: 0.6277 (m-30) outliers start: 17 outliers final: 15 residues processed: 149 average time/residue: 1.0858 time to fit residues: 173.2105 Evaluate side-chains 160 residues out of total 911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 143 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 141 GLU Chi-restraints excluded: chain A residue 316 LYS Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 209 LYS Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain C residue 78 LYS Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 90 ASP Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 126 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 46 optimal weight: 4.9990 chunk 68 optimal weight: 0.6980 chunk 103 optimal weight: 0.9990 chunk 95 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 63 optimal weight: 0.5980 chunk 50 optimal weight: 0.0970 chunk 65 optimal weight: 0.8980 chunk 87 optimal weight: 1.9990 chunk 25 optimal weight: 5.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 220 GLN ** C 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6837 moved from start: 0.1739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.116 8469 Z= 0.213 Angle : 0.675 17.981 11472 Z= 0.367 Chirality : 0.042 0.164 1324 Planarity : 0.006 0.102 1424 Dihedral : 6.081 82.835 1155 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 1.88 % Allowed : 17.13 % Favored : 80.99 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 4.00 % 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: -0.30 (0.26), residues: 1033 helix: 1.96 (0.29), residues: 313 sheet: -0.22 (0.31), residues: 252 loop : -1.76 (0.27), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 82 HIS 0.005 0.001 HIS E 35 PHE 0.015 0.001 PHE C 199 TYR 0.012 0.001 TYR A 295 ARG 0.008 0.000 ARG A 320 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 143 time to evaluate : 0.958 Fit side-chains REVERT: B 209 LYS cc_start: 0.5056 (OUTLIER) cc_final: 0.4562 (mmtp) REVERT: C 340 ASN cc_start: 0.7377 (p0) cc_final: 0.7129 (p0) REVERT: E 90 ASP cc_start: 0.6900 (OUTLIER) cc_final: 0.6277 (m-30) outliers start: 17 outliers final: 15 residues processed: 149 average time/residue: 1.0612 time to fit residues: 169.3910 Evaluate side-chains 160 residues out of total 911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 143 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 141 GLU Chi-restraints excluded: chain A residue 316 LYS Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 209 LYS Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain C residue 78 LYS Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 90 ASP Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 126 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 76 optimal weight: 9.9990 chunk 12 optimal weight: 0.8980 chunk 22 optimal weight: 0.9980 chunk 82 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 10 optimal weight: 0.3980 chunk 15 optimal weight: 5.9990 chunk 72 optimal weight: 0.0010 chunk 4 optimal weight: 5.9990 chunk 59 optimal weight: 0.6980 overall best weight: 0.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 220 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.228998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.194152 restraints weight = 16021.783| |-----------------------------------------------------------------------------| r_work (start): 0.4059 rms_B_bonded: 2.58 r_work: 0.3725 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 moved from start: 0.1742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 8469 Z= 0.197 Angle : 0.643 11.483 11472 Z= 0.337 Chirality : 0.042 0.184 1324 Planarity : 0.005 0.087 1424 Dihedral : 6.068 82.886 1155 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 2.10 % Allowed : 16.80 % Favored : 81.10 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 4.00 % 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: -0.30 (0.26), residues: 1033 helix: 1.92 (0.29), residues: 313 sheet: -0.20 (0.31), residues: 252 loop : -1.74 (0.27), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 82 HIS 0.005 0.001 HIS E 35 PHE 0.015 0.001 PHE C 199 TYR 0.011 0.001 TYR A 295 ARG 0.007 0.000 ARG A 320 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3409.72 seconds wall clock time: 61 minutes 31.08 seconds (3691.08 seconds total)