Starting phenix.real_space_refine on Fri Dec 8 11:26:12 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w87_37347/12_2023/8w87_37347_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w87_37347/12_2023/8w87_37347.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w87_37347/12_2023/8w87_37347.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w87_37347/12_2023/8w87_37347.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w87_37347/12_2023/8w87_37347_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w87_37347/12_2023/8w87_37347_neut_updated.pdb" } resolution = 2.8 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= 0.001 sd= 0.047 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: 4 Type Number sf(0) Gaussians S 63 5.16 5 C 5235 2.51 5 N 1415 2.21 5 O 1515 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 224": "OD1" <-> "OD2" Residue "A PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 233": "OD1" <-> "OD2" Residue "A GLU 242": "OE1" <-> "OE2" Residue "A GLU 273": "OE1" <-> "OE2" Residue "A PHE 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 296": "OE1" <-> "OE2" Residue "A GLU 318": "OE1" <-> "OE2" Residue "A ASP 352": "OD1" <-> "OD2" Residue "B PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 163": "OD1" <-> "OD2" Residue "B GLU 172": "OE1" <-> "OE2" Residue "B GLU 215": "OE1" <-> "OE2" Residue "B GLU 226": "OE1" <-> "OE2" Residue "B PHE 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 246": "OD1" <-> "OD2" Residue "B TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 267": "OD1" <-> "OD2" Residue "G ASP 36": "OD1" <-> "OD2" Residue "G GLU 42": "OE1" <-> "OE2" Residue "G GLU 47": "OE1" <-> "OE2" Residue "G ASP 48": "OD1" <-> "OD2" Residue "G GLU 58": "OE1" <-> "OE2" Residue "N TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 90": "OD1" <-> "OD2" Residue "R ASP 21": "OD1" <-> "OD2" Residue "R PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 86": "OE1" <-> "OE2" Residue "R TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 8228 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1906 Classifications: {'peptide': 234} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 6, 'TRANS': 227} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "B" Number of atoms: 2593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2593 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "G" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "N" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 967 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 5, 'TRANS': 121} Chain: "R" Number of atoms: 2315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2315 Classifications: {'peptide': 289} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 11, 'TRANS': 277} Chain breaks: 1 Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 31 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 23 Chain: "R" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'B40': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.72, per 1000 atoms: 0.57 Number of scatterers: 8228 At special positions: 0 Unit cell: (82.4, 98.88, 132.664, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 63 16.00 O 1515 8.00 N 1415 7.00 C 5235 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 96 " - pdb=" SG CYS R 182 " distance=2.26 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: 2.84 Conformation dependent library (CDL) restraints added in 1.4 seconds 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input volumes are d-peptide like pdb=" CB B40 R 501 " Number of C-beta restraints generated: 1968 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 27 helices and 10 sheets defined 39.8% alpha, 21.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.62 Creating SS restraints... Processing helix chain 'A' and resid 13 through 34 removed outlier: 3.820A pdb=" N GLU A 34 " --> pdb=" O ARG A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 62 removed outlier: 3.934A pdb=" N ILE A 62 " --> pdb=" O LYS A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 222 removed outlier: 3.511A pdb=" N PHE A 222 " --> pdb=" O ILE A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 252 removed outlier: 4.795A pdb=" N GLN A 241 " --> pdb=" O ASN A 238 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASN A 252 " --> pdb=" O SER A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 277 Processing helix chain 'A' and resid 282 through 285 No H-bonds generated for 'chain 'A' and resid 282 through 285' Processing helix chain 'A' and resid 287 through 290 Processing helix chain 'A' and resid 306 through 325 removed outlier: 3.749A pdb=" N ILE A 322 " --> pdb=" O GLU A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 364 Processing helix chain 'B' and resid 4 through 24 Processing helix chain 'B' and resid 30 through 34 Processing helix chain 'G' and resid 7 through 23 Processing helix chain 'G' and resid 30 through 47 removed outlier: 4.880A pdb=" N LYS G 46 " --> pdb=" O GLU G 42 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N GLU G 47 " --> pdb=" O ALA G 43 " (cutoff:3.500A) Processing helix chain 'N' and resid 29 through 31 No H-bonds generated for 'chain 'N' and resid 29 through 31' Processing helix chain 'N' and resid 88 through 90 No H-bonds generated for 'chain 'N' and resid 88 through 90' Processing helix chain 'R' and resid 20 through 50 Processing helix chain 'R' and resid 57 through 75 Processing helix chain 'R' and resid 77 through 86 Processing helix chain 'R' and resid 92 through 126 Processing helix chain 'R' and resid 131 through 134 No H-bonds generated for 'chain 'R' and resid 131 through 134' Processing helix chain 'R' and resid 137 through 161 Proline residue: R 151 - end of helix Processing helix chain 'R' and resid 169 through 179 Processing helix chain 'R' and resid 188 through 198 Processing helix chain 'R' and resid 200 through 230 Processing helix chain 'R' and resid 248 through 277 removed outlier: 3.610A pdb=" N PHE R 260 " --> pdb=" O VAL R 256 " (cutoff:3.500A) Proline residue: R 266 - end of helix Proline residue: R 275 - end of helix Processing helix chain 'R' and resid 285 through 304 removed outlier: 3.631A pdb=" N SER R 297 " --> pdb=" O GLY R 293 " (cutoff:3.500A) Proline residue: R 301 - end of helix Processing helix chain 'R' and resid 309 through 319 Processing sheet with id= A, first strand: chain 'A' and resid 333 through 337 removed outlier: 7.240A pdb=" N VAL A 261 " --> pdb=" O TYR A 334 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N HIS A 336 " --> pdb=" O VAL A 261 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N LEU A 263 " --> pdb=" O HIS A 336 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ALA A 227 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ASN A 202 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N LEU A 43 " --> pdb=" O ASN A 202 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N HIS A 204 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N LEU A 45 " --> pdb=" O HIS A 204 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N PHE A 206 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 8.314A pdb=" N GLY A 47 " --> pdb=" O PHE A 206 " (cutoff:3.500A) removed outlier: 8.227A pdb=" N VAL A 208 " --> pdb=" O GLY A 47 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.808A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.743A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.667A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.802A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.638A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.454A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N ASN B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.556A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'N' and resid 3 through 7 Processing sheet with id= J, first strand: chain 'N' and resid 10 through 13 removed outlier: 6.190A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) 411 hydrogen bonds defined for protein. 1155 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: 2.40 Time building geometry restraints manager: 3.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1386 1.32 - 1.44: 2303 1.44 - 1.57: 4625 1.57 - 1.69: 0 1.69 - 1.81: 92 Bond restraints: 8406 Sorted by residual: bond pdb=" C THR R 102 " pdb=" N ASP R 103 " ideal model delta sigma weight residual 1.334 1.415 -0.082 1.23e-02 6.61e+03 4.39e+01 bond pdb=" C ASP R 103 " pdb=" N ILE R 104 " ideal model delta sigma weight residual 1.334 1.258 0.076 1.25e-02 6.40e+03 3.74e+01 bond pdb=" C ASP R 103 " pdb=" O ASP R 103 " ideal model delta sigma weight residual 1.236 1.200 0.036 1.15e-02 7.56e+03 9.89e+00 bond pdb=" CB ASP R 103 " pdb=" CG ASP R 103 " ideal model delta sigma weight residual 1.516 1.459 0.057 2.50e-02 1.60e+03 5.29e+00 bond pdb=" CA ASP R 103 " pdb=" CB ASP R 103 " ideal model delta sigma weight residual 1.530 1.557 -0.027 1.57e-02 4.06e+03 3.05e+00 ... (remaining 8401 not shown) Histogram of bond angle deviations from ideal: 100.49 - 107.21: 222 107.21 - 113.94: 4701 113.94 - 120.67: 3468 120.67 - 127.39: 2904 127.39 - 134.12: 89 Bond angle restraints: 11384 Sorted by residual: angle pdb=" C ASP R 103 " pdb=" CA ASP R 103 " pdb=" CB ASP R 103 " ideal model delta sigma weight residual 110.96 105.05 5.91 1.54e+00 4.22e-01 1.47e+01 angle pdb=" CA B40 R 501 " pdb=" N B40 R 501 " pdb=" CM B40 R 501 " ideal model delta sigma weight residual 115.05 104.23 10.82 3.00e+00 1.11e-01 1.30e+01 angle pdb=" N B40 R 501 " pdb=" CA B40 R 501 " pdb=" C B40 R 501 " ideal model delta sigma weight residual 114.49 104.29 10.20 3.00e+00 1.11e-01 1.16e+01 angle pdb=" N VAL R 150 " pdb=" CA VAL R 150 " pdb=" C VAL R 150 " ideal model delta sigma weight residual 112.35 108.63 3.72 1.20e+00 6.94e-01 9.62e+00 angle pdb=" N SER B 331 " pdb=" CA SER B 331 " pdb=" C SER B 331 " ideal model delta sigma weight residual 108.60 112.56 -3.96 1.46e+00 4.69e-01 7.37e+00 ... (remaining 11379 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.64: 4508 19.64 - 39.29: 381 39.29 - 58.93: 79 58.93 - 78.58: 16 78.58 - 98.22: 6 Dihedral angle restraints: 4990 sinusoidal: 1945 harmonic: 3045 Sorted by residual: dihedral pdb=" CA PHE B 292 " pdb=" C PHE B 292 " pdb=" N ASN B 293 " pdb=" CA ASN B 293 " ideal model delta harmonic sigma weight residual 180.00 161.73 18.27 0 5.00e+00 4.00e-02 1.33e+01 dihedral pdb=" CA PHE N 108 " pdb=" C PHE N 108 " pdb=" N ASP N 109 " pdb=" CA ASP N 109 " ideal model delta harmonic sigma weight residual -180.00 -162.49 -17.51 0 5.00e+00 4.00e-02 1.23e+01 dihedral pdb=" CB B40 R 501 " pdb=" N B40 R 501 " pdb=" CA B40 R 501 " pdb=" CM B40 R 501 " ideal model delta sinusoidal sigma weight residual 168.08 -93.70 -98.22 1 3.00e+01 1.11e-03 1.22e+01 ... (remaining 4987 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1106 0.056 - 0.113: 144 0.113 - 0.169: 23 0.169 - 0.226: 1 0.226 - 0.282: 1 Chirality restraints: 1275 Sorted by residual: chirality pdb=" CA B40 R 501 " pdb=" N B40 R 501 " pdb=" C B40 R 501 " pdb=" CB B40 R 501 " both_signs ideal model delta sigma weight residual False -2.42 -2.71 0.28 2.00e-01 2.50e+01 1.99e+00 chirality pdb=" CA ASP R 103 " pdb=" N ASP R 103 " pdb=" C ASP R 103 " pdb=" CB ASP R 103 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.70e-01 chirality pdb=" CA PHE B 292 " pdb=" N PHE B 292 " pdb=" C PHE B 292 " pdb=" CB PHE B 292 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.95e-01 ... (remaining 1272 not shown) Planarity restraints: 1448 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR R 284 " 0.017 2.00e-02 2.50e+03 3.43e-02 1.18e+01 pdb=" C THR R 284 " -0.059 2.00e-02 2.50e+03 pdb=" O THR R 284 " 0.022 2.00e-02 2.50e+03 pdb=" N LEU R 285 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO R 282 " 0.056 5.00e-02 4.00e+02 8.32e-02 1.11e+01 pdb=" N PRO R 283 " -0.144 5.00e-02 4.00e+02 pdb=" CA PRO R 283 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO R 283 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 19 " -0.182 9.50e-02 1.11e+02 8.20e-02 4.90e+00 pdb=" NE ARG B 19 " 0.016 2.00e-02 2.50e+03 pdb=" CZ ARG B 19 " -0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG B 19 " 0.007 2.00e-02 2.50e+03 pdb=" NH2 ARG B 19 " -0.002 2.00e-02 2.50e+03 ... (remaining 1445 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 602 2.73 - 3.28: 8423 3.28 - 3.82: 13984 3.82 - 4.36: 17323 4.36 - 4.90: 30113 Nonbonded interactions: 70445 Sorted by model distance: nonbonded pdb=" O ASP B 195 " pdb=" OG1 THR B 196 " model vdw 2.193 2.440 nonbonded pdb=" O ASN A 188 " pdb=" OG SER A 189 " model vdw 2.226 2.440 nonbonded pdb=" C B40 R 501 " pdb=" CM B40 R 501 " model vdw 2.251 3.104 nonbonded pdb=" OG SER B 147 " pdb=" O VAL B 187 " model vdw 2.314 2.440 nonbonded pdb=" OE2 GLU B 260 " pdb=" OG1 THR B 263 " model vdw 2.319 2.440 ... (remaining 70440 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: 1.430 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: 3.990 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 25.170 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.030 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:13.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 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 : 0.003 0.082 8406 Z= 0.224 Angle : 0.561 10.817 11384 Z= 0.318 Chirality : 0.041 0.282 1275 Planarity : 0.005 0.083 1448 Dihedral : 15.674 98.222 3019 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 0.45 % Allowed : 16.10 % Favored : 83.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.49 (0.27), residues: 1031 helix: 2.26 (0.25), residues: 416 sheet: 0.46 (0.34), residues: 228 loop : -0.01 (0.32), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 291 HIS 0.004 0.001 HIS B 91 PHE 0.011 0.001 PHE R 70 TYR 0.008 0.001 TYR A 313 ARG 0.015 0.001 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 128 time to evaluate : 0.806 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 130 average time/residue: 1.3291 time to fit residues: 182.7553 Evaluate side-chains 124 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 121 time to evaluate : 0.959 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 1 residues processed: 2 average time/residue: 0.1636 time to fit residues: 1.8857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 85 optimal weight: 0.9990 chunk 76 optimal weight: 10.0000 chunk 42 optimal weight: 3.9990 chunk 26 optimal weight: 5.9990 chunk 51 optimal weight: 3.9990 chunk 40 optimal weight: 0.9990 chunk 79 optimal weight: 5.9990 chunk 30 optimal weight: 3.9990 chunk 48 optimal weight: 0.0870 chunk 58 optimal weight: 7.9990 chunk 91 optimal weight: 0.6980 overall best weight: 1.3564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN B 75 GLN N 123 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.0833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 8406 Z= 0.236 Angle : 0.522 6.931 11384 Z= 0.281 Chirality : 0.043 0.158 1275 Planarity : 0.004 0.059 1448 Dihedral : 5.100 58.686 1144 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.14 % Allowed : 14.98 % Favored : 82.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.37 (0.27), residues: 1031 helix: 2.06 (0.25), residues: 423 sheet: 0.34 (0.34), residues: 226 loop : 0.06 (0.33), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 169 HIS 0.004 0.001 HIS A 336 PHE 0.021 0.002 PHE R 165 TYR 0.030 0.001 TYR R 27 ARG 0.009 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 126 time to evaluate : 0.953 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 4 residues processed: 137 average time/residue: 1.3351 time to fit residues: 193.7226 Evaluate side-chains 128 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 124 time to evaluate : 0.909 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 2 residues processed: 2 average time/residue: 0.1539 time to fit residues: 1.7121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 50 optimal weight: 3.9990 chunk 28 optimal weight: 0.5980 chunk 76 optimal weight: 8.9990 chunk 62 optimal weight: 0.9980 chunk 25 optimal weight: 5.9990 chunk 91 optimal weight: 4.9990 chunk 99 optimal weight: 0.8980 chunk 81 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 chunk 73 optimal weight: 7.9990 chunk 90 optimal weight: 3.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 123 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.1048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8406 Z= 0.173 Angle : 0.474 6.444 11384 Z= 0.255 Chirality : 0.041 0.154 1275 Planarity : 0.004 0.052 1448 Dihedral : 4.474 49.817 1144 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 2.14 % Allowed : 16.22 % Favored : 81.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.39 (0.27), residues: 1031 helix: 2.00 (0.25), residues: 426 sheet: 0.41 (0.34), residues: 224 loop : 0.11 (0.33), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 169 HIS 0.003 0.001 HIS G 44 PHE 0.013 0.001 PHE A 196 TYR 0.010 0.001 TYR R 27 ARG 0.008 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 132 time to evaluate : 0.936 Fit side-chains revert: symmetry clash outliers start: 19 outliers final: 9 residues processed: 143 average time/residue: 1.1804 time to fit residues: 179.7634 Evaluate side-chains 126 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 117 time to evaluate : 0.928 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 7 residues processed: 2 average time/residue: 0.1536 time to fit residues: 1.7119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 69 optimal weight: 5.9990 chunk 47 optimal weight: 4.9990 chunk 10 optimal weight: 6.9990 chunk 43 optimal weight: 5.9990 chunk 61 optimal weight: 9.9990 chunk 92 optimal weight: 0.8980 chunk 97 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 87 optimal weight: 6.9990 chunk 26 optimal weight: 9.9990 chunk 81 optimal weight: 1.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.1239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 8406 Z= 0.355 Angle : 0.551 7.673 11384 Z= 0.294 Chirality : 0.045 0.159 1275 Planarity : 0.004 0.050 1448 Dihedral : 4.863 51.757 1144 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 4.50 % Allowed : 15.65 % Favored : 79.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.01 (0.26), residues: 1031 helix: 1.67 (0.25), residues: 430 sheet: 0.29 (0.34), residues: 225 loop : -0.15 (0.32), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 218 HIS 0.005 0.001 HIS R 63 PHE 0.017 0.002 PHE R 165 TYR 0.011 0.001 TYR A 313 ARG 0.007 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 129 time to evaluate : 0.979 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 40 outliers final: 18 residues processed: 154 average time/residue: 1.1670 time to fit residues: 191.6419 Evaluate side-chains 145 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 127 time to evaluate : 0.995 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 11 residues processed: 7 average time/residue: 0.6303 time to fit residues: 6.2764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 55 optimal weight: 5.9990 chunk 1 optimal weight: 0.9990 chunk 72 optimal weight: 0.6980 chunk 40 optimal weight: 3.9990 chunk 83 optimal weight: 0.9990 chunk 67 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 49 optimal weight: 0.6980 chunk 87 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 overall best weight: 0.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.1350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8406 Z= 0.169 Angle : 0.461 5.505 11384 Z= 0.249 Chirality : 0.041 0.148 1275 Planarity : 0.004 0.050 1448 Dihedral : 4.459 44.467 1144 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 3.15 % Allowed : 17.34 % Favored : 79.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.17 (0.26), residues: 1031 helix: 1.80 (0.26), residues: 431 sheet: 0.41 (0.34), residues: 223 loop : -0.11 (0.32), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 169 HIS 0.003 0.001 HIS B 91 PHE 0.012 0.001 PHE A 196 TYR 0.014 0.001 TYR R 27 ARG 0.008 0.000 ARG A 330 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 133 time to evaluate : 0.952 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 19 residues processed: 153 average time/residue: 1.1975 time to fit residues: 196.0217 Evaluate side-chains 146 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 127 time to evaluate : 1.023 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 15 residues processed: 4 average time/residue: 0.1712 time to fit residues: 2.3135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 87 optimal weight: 0.1980 chunk 19 optimal weight: 0.7980 chunk 57 optimal weight: 7.9990 chunk 24 optimal weight: 4.9990 chunk 97 optimal weight: 10.0000 chunk 81 optimal weight: 0.5980 chunk 45 optimal weight: 6.9990 chunk 8 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 94 optimal weight: 4.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 239 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.1492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8406 Z= 0.199 Angle : 0.478 5.717 11384 Z= 0.257 Chirality : 0.041 0.148 1275 Planarity : 0.004 0.049 1448 Dihedral : 4.399 42.330 1144 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 3.94 % Allowed : 16.89 % Favored : 79.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.17 (0.26), residues: 1031 helix: 1.82 (0.26), residues: 430 sheet: 0.43 (0.34), residues: 222 loop : -0.14 (0.32), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 218 HIS 0.003 0.001 HIS B 91 PHE 0.015 0.001 PHE R 165 TYR 0.009 0.001 TYR A 313 ARG 0.012 0.000 ARG A 330 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 132 time to evaluate : 0.993 Fit side-chains revert: symmetry clash outliers start: 35 outliers final: 23 residues processed: 157 average time/residue: 1.0731 time to fit residues: 180.5922 Evaluate side-chains 154 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 131 time to evaluate : 0.930 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 18 residues processed: 5 average time/residue: 0.1715 time to fit residues: 2.4709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 11 optimal weight: 0.5980 chunk 55 optimal weight: 7.9990 chunk 71 optimal weight: 0.0670 chunk 82 optimal weight: 1.9990 chunk 54 optimal weight: 0.8980 chunk 97 optimal weight: 1.9990 chunk 60 optimal weight: 7.9990 chunk 59 optimal weight: 2.9990 chunk 44 optimal weight: 0.0030 chunk 38 optimal weight: 0.8980 chunk 58 optimal weight: 7.9990 overall best weight: 0.4928 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.1637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 8406 Z= 0.136 Angle : 0.452 6.635 11384 Z= 0.242 Chirality : 0.040 0.149 1275 Planarity : 0.004 0.055 1448 Dihedral : 4.132 35.246 1144 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 3.15 % Allowed : 17.91 % Favored : 78.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.30 (0.26), residues: 1031 helix: 1.94 (0.26), residues: 430 sheet: 0.60 (0.34), residues: 220 loop : -0.15 (0.32), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP R 291 HIS 0.003 0.001 HIS B 91 PHE 0.012 0.001 PHE R 154 TYR 0.012 0.001 TYR N 60 ARG 0.015 0.001 ARG A 330 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 147 time to evaluate : 0.917 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 17 residues processed: 168 average time/residue: 1.1095 time to fit residues: 199.7512 Evaluate side-chains 153 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 136 time to evaluate : 0.952 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 14 residues processed: 3 average time/residue: 0.1340 time to fit residues: 1.8943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 29 optimal weight: 3.9990 chunk 19 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 61 optimal weight: 9.9990 chunk 66 optimal weight: 0.7980 chunk 48 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 chunk 88 optimal weight: 8.9990 chunk 93 optimal weight: 1.9990 chunk 85 optimal weight: 0.8980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 259 GLN R 296 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.1688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8406 Z= 0.230 Angle : 0.499 6.759 11384 Z= 0.266 Chirality : 0.042 0.149 1275 Planarity : 0.004 0.071 1448 Dihedral : 4.312 39.422 1144 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 3.27 % Allowed : 18.24 % Favored : 78.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.19 (0.26), residues: 1031 helix: 1.82 (0.26), residues: 431 sheet: 0.49 (0.34), residues: 222 loop : -0.15 (0.31), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 218 HIS 0.003 0.001 HIS R 63 PHE 0.013 0.001 PHE A 196 TYR 0.013 0.001 TYR R 27 ARG 0.019 0.001 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 135 time to evaluate : 1.002 Fit side-chains revert: symmetry clash outliers start: 29 outliers final: 18 residues processed: 154 average time/residue: 1.1664 time to fit residues: 191.8423 Evaluate side-chains 148 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 130 time to evaluate : 0.959 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 14 residues processed: 4 average time/residue: 0.4446 time to fit residues: 3.3325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 90 optimal weight: 6.9990 chunk 93 optimal weight: 2.9990 chunk 54 optimal weight: 0.7980 chunk 39 optimal weight: 4.9990 chunk 71 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 81 optimal weight: 0.5980 chunk 85 optimal weight: 0.8980 chunk 59 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 chunk 58 optimal weight: 5.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 259 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.1682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8406 Z= 0.193 Angle : 0.481 5.668 11384 Z= 0.257 Chirality : 0.041 0.154 1275 Planarity : 0.004 0.052 1448 Dihedral : 4.287 38.923 1144 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.82 % Allowed : 18.47 % Favored : 78.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.18 (0.26), residues: 1031 helix: 1.80 (0.25), residues: 431 sheet: 0.48 (0.34), residues: 226 loop : -0.14 (0.32), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 218 HIS 0.003 0.001 HIS A 331 PHE 0.013 0.001 PHE A 196 TYR 0.011 0.001 TYR R 279 ARG 0.015 0.001 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 128 time to evaluate : 0.954 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 20 residues processed: 148 average time/residue: 1.1929 time to fit residues: 188.2824 Evaluate side-chains 147 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 127 time to evaluate : 0.926 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 17 residues processed: 3 average time/residue: 0.5931 time to fit residues: 3.2691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 45 optimal weight: 0.5980 chunk 66 optimal weight: 0.8980 chunk 100 optimal weight: 0.8980 chunk 92 optimal weight: 0.8980 chunk 80 optimal weight: 9.9990 chunk 8 optimal weight: 1.9990 chunk 61 optimal weight: 6.9990 chunk 49 optimal weight: 0.7980 chunk 63 optimal weight: 0.7980 chunk 85 optimal weight: 0.7980 chunk 24 optimal weight: 4.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 239 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.1778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 8406 Z= 0.164 Angle : 0.470 7.643 11384 Z= 0.251 Chirality : 0.041 0.161 1275 Planarity : 0.004 0.080 1448 Dihedral : 4.184 36.468 1144 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 2.36 % Allowed : 19.14 % Favored : 78.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.24 (0.26), residues: 1031 helix: 1.85 (0.26), residues: 431 sheet: 0.54 (0.34), residues: 225 loop : -0.13 (0.32), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP R 291 HIS 0.003 0.001 HIS B 91 PHE 0.012 0.001 PHE A 196 TYR 0.017 0.001 TYR N 60 ARG 0.021 0.001 ARG B 19 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 129 time to evaluate : 0.982 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 17 residues processed: 149 average time/residue: 1.1749 time to fit residues: 186.6277 Evaluate side-chains 143 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 126 time to evaluate : 0.908 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 17 residues processed: 0 time to fit residues: 1.2578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 73 optimal weight: 5.9990 chunk 11 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 chunk 80 optimal weight: 7.9990 chunk 33 optimal weight: 0.5980 chunk 82 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 70 optimal weight: 7.9990 chunk 4 optimal weight: 0.6980 chunk 57 optimal weight: 0.5980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 239 ASN B 259 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.150689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.105960 restraints weight = 9315.418| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 2.31 r_work: 0.3177 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3051 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.1819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8406 Z= 0.185 Angle : 0.481 6.115 11384 Z= 0.257 Chirality : 0.041 0.160 1275 Planarity : 0.004 0.068 1448 Dihedral : 4.201 36.889 1144 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 2.36 % Allowed : 19.14 % Favored : 78.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.18 (0.26), residues: 1031 helix: 1.82 (0.25), residues: 431 sheet: 0.44 (0.34), residues: 227 loop : -0.13 (0.32), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 291 HIS 0.003 0.001 HIS A 331 PHE 0.015 0.001 PHE R 154 TYR 0.016 0.001 TYR N 60 ARG 0.013 0.001 ARG A 330 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3573.28 seconds wall clock time: 64 minutes 16.05 seconds (3856.05 seconds total)