Starting phenix.real_space_refine on Fri Jul 19 15:50:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w88_37348/07_2024/8w88_37348_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w88_37348/07_2024/8w88_37348.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w88_37348/07_2024/8w88_37348.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w88_37348/07_2024/8w88_37348.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w88_37348/07_2024/8w88_37348_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w88_37348/07_2024/8w88_37348_neut.cif" } resolution = 2.6 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= 0.131 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 62 5.16 5 C 5307 2.51 5 N 1419 2.21 5 O 1519 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 20": "OE1" <-> "OE2" Residue "A GLU 313": "OE1" <-> "OE2" Residue "A GLU 326": "OE1" <-> "OE2" Residue "A GLU 343": "OE1" <-> "OE2" Residue "B GLU 151": "OE1" <-> "OE2" Residue "B PHE 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 185": "OE1" <-> "OE2" Residue "G GLU 16": "OE1" <-> "OE2" Residue "G GLU 41": "OE1" <-> "OE2" Residue "N GLU 7": "OE1" <-> "OE2" Residue "N GLU 47": "OE1" <-> "OE2" Residue "R GLU 93": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 8307 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1957 Classifications: {'peptide': 236} Link IDs: {'PTRANS': 6, 'TRANS': 229} Chain breaks: 2 Chain: "B" Number of atoms: 2600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2600 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "G" Number of atoms: 433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 433 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: 2254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2254 Classifications: {'peptide': 281} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 11, 'TRANS': 269} Chain breaks: 1 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "R" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 96 Unusual residues: {'CLR': 3, 'UJL': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 4.89, per 1000 atoms: 0.59 Number of scatterers: 8307 At special positions: 0 Unit cell: (83.224, 99.704, 135.136, 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 62 16.00 O 1519 8.00 N 1419 7.00 C 5307 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=2.28 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: 3.23 Conformation dependent library (CDL) restraints added in 1.6 seconds 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1956 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 10 sheets defined 44.6% alpha, 20.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.89 Creating SS restraints... Processing helix chain 'A' and resid 8 through 37 removed outlier: 3.558A pdb=" N LYS A 31 " --> pdb=" O LYS A 27 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VAL A 35 " --> pdb=" O LYS A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 60 Processing helix chain 'A' and resid 234 through 238 removed outlier: 3.522A pdb=" N ASN A 238 " --> pdb=" O GLN A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 278 removed outlier: 3.815A pdb=" N GLU A 267 " --> pdb=" O ASN A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 302 Processing helix chain 'A' and resid 306 through 311 Processing helix chain 'A' and resid 312 through 317 Processing helix chain 'A' and resid 330 through 351 removed outlier: 3.506A pdb=" N PHE A 344 " --> pdb=" O ILE A 340 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ILE A 347 " --> pdb=" O GLU A 343 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N SER A 351 " --> pdb=" O ILE A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 390 removed outlier: 4.494A pdb=" N ARG A 372 " --> pdb=" O THR A 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 17 through 39 removed outlier: 3.520A pdb=" N ARG B 21 " --> pdb=" O LEU B 17 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 47 Processing helix chain 'B' and resid 48 through 50 No H-bonds generated for 'chain 'B' and resid 48 through 50' Processing helix chain 'G' and resid 5 through 23 Processing helix chain 'G' and resid 28 through 43 Processing helix chain 'N' and resid 29 through 33 Processing helix chain 'N' and resid 75 through 77 No H-bonds generated for 'chain 'N' and resid 75 through 77' Processing helix chain 'N' and resid 88 through 92 Processing helix chain 'R' and resid 20 through 51 Processing helix chain 'R' and resid 52 through 55 Processing helix chain 'R' and resid 56 through 76 Processing helix chain 'R' and resid 76 through 86 Processing helix chain 'R' and resid 92 through 127 removed outlier: 3.685A pdb=" N LYS R 97 " --> pdb=" O GLU R 93 " (cutoff:3.500A) Processing helix chain 'R' and resid 130 through 135 Processing helix chain 'R' and resid 136 through 160 Proline residue: R 151 - end of helix Processing helix chain 'R' and resid 168 through 179 removed outlier: 3.740A pdb=" N HIS R 177 " --> pdb=" O TYR R 173 " (cutoff:3.500A) Processing helix chain 'R' and resid 187 through 199 Processing helix chain 'R' and resid 199 through 229 Processing helix chain 'R' and resid 248 through 277 removed outlier: 3.683A 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 282 through 305 removed outlier: 3.585A pdb=" N ASN R 286 " --> pdb=" O PRO R 282 " (cutoff:3.500A) removed outlier: 3.722A 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 308 through 316 removed outlier: 3.514A pdb=" N ALA R 314 " --> pdb=" O TRP R 310 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 206 through 213 removed outlier: 6.407A pdb=" N HIS A 40 " --> pdb=" O HIS A 219 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N PHE A 221 " --> pdb=" O HIS A 40 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N LEU A 42 " --> pdb=" O PHE A 221 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N VAL A 223 " --> pdb=" O LEU A 42 " (cutoff:3.500A) removed outlier: 8.564A pdb=" N LEU A 44 " --> pdb=" O VAL A 223 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N ALA A 242 " --> pdb=" O ARG A 41 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N ILE A 243 " --> pdb=" O ILE A 287 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N PHE A 289 " --> pdb=" O ILE A 243 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N PHE A 245 " --> pdb=" O PHE A 289 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ASN A 291 " --> pdb=" O PHE A 245 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N VAL A 247 " --> pdb=" O ASN A 291 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 59 through 64 removed outlier: 6.308A pdb=" N THR B 60 " --> pdb=" O ASN B 353 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N ASN B 353 " --> pdb=" O THR B 60 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N CYS B 330 " --> pdb=" O GLY B 343 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 71 through 76 removed outlier: 3.690A pdb=" N LYS B 91 " --> pdb=" O SER B 87 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N LEU B 92 " --> pdb=" O ALA B 105 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N ALA B 105 " --> pdb=" O LEU B 92 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ILE B 94 " --> pdb=" O VAL B 103 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 113 through 118 removed outlier: 6.657A pdb=" N GLY B 128 " --> pdb=" O MET B 114 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N CYS B 116 " --> pdb=" O ALA B 126 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N ALA B 126 " --> pdb=" O CYS B 116 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N TYR B 118 " --> pdb=" O TYR B 124 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N TYR B 124 " --> pdb=" O TYR B 118 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N ASN B 138 " --> pdb=" O VAL B 148 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N VAL B 148 " --> pdb=" O ASN B 138 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 159 through 164 removed outlier: 3.609A pdb=" N CYS B 161 " --> pdb=" O SER B 173 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE B 170 " --> pdb=" O TRP B 182 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N ASP B 183 " --> pdb=" O GLN B 189 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N GLN B 189 " --> pdb=" O ASP B 183 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 200 through 205 removed outlier: 6.786A pdb=" N GLY B 215 " --> pdb=" O MET B 201 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N LEU B 203 " --> pdb=" O VAL B 213 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N VAL B 213 " --> pdb=" O LEU B 203 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N LEU B 205 " --> pdb=" O LEU B 211 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N LEU B 211 " --> pdb=" O LEU B 205 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ALA B 221 " --> pdb=" O THR B 234 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N THR B 234 " --> pdb=" O ALA B 221 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N LEU B 223 " --> pdb=" O ARG B 232 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 242 through 247 removed outlier: 6.579A pdb=" N CYS B 263 " --> pdb=" O THR B 276 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N THR B 276 " --> pdb=" O CYS B 263 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N LEU B 265 " --> pdb=" O LEU B 274 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLN B 272 " --> pdb=" O ASP B 267 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 286 through 291 removed outlier: 3.713A pdb=" N SER B 288 " --> pdb=" O GLY B 301 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N ASP B 311 " --> pdb=" O ARG B 317 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N ARG B 317 " --> pdb=" O ASP B 311 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 4 through 8 removed outlier: 3.522A pdb=" N THR N 79 " --> pdb=" O ASP N 74 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 11 through 13 removed outlier: 6.004A pdb=" N GLY N 11 " --> pdb=" O THR N 126 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N MET N 35 " --> pdb=" O ASP N 51 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N ASP N 51 " --> pdb=" O MET N 35 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N TRP N 37 " --> pdb=" O VAL N 49 " (cutoff:3.500A) 438 hydrogen bonds defined for protein. 1260 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: 2.23 Time building geometry restraints manager: 3.58 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: 2655 1.34 - 1.46: 1381 1.46 - 1.57: 4369 1.57 - 1.69: 1 1.69 - 1.81: 88 Bond restraints: 8494 Sorted by residual: bond pdb=" C8 UJL R 404 " pdb=" S1 UJL R 404 " ideal model delta sigma weight residual 1.725 1.526 0.199 2.00e-02 2.50e+03 9.94e+01 bond pdb=" C6 UJL R 404 " pdb=" C7 UJL R 404 " ideal model delta sigma weight residual 1.428 1.613 -0.185 2.00e-02 2.50e+03 8.54e+01 bond pdb=" C9 UJL R 404 " pdb=" S1 UJL R 404 " ideal model delta sigma weight residual 1.730 1.564 0.166 2.00e-02 2.50e+03 6.90e+01 bond pdb=" C7 UJL R 404 " pdb=" C8 UJL R 404 " ideal model delta sigma weight residual 1.364 1.428 -0.064 2.00e-02 2.50e+03 1.03e+01 bond pdb=" C3 UJL R 404 " pdb=" C9 UJL R 404 " ideal model delta sigma weight residual 1.503 1.557 -0.054 2.00e-02 2.50e+03 7.31e+00 ... (remaining 8489 not shown) Histogram of bond angle deviations from ideal: 99.46 - 106.39: 191 106.39 - 113.31: 4624 113.31 - 120.24: 3110 120.24 - 127.16: 3499 127.16 - 134.09: 94 Bond angle restraints: 11518 Sorted by residual: angle pdb=" C8 UJL R 404 " pdb=" S1 UJL R 404 " pdb=" C9 UJL R 404 " ideal model delta sigma weight residual 91.70 107.43 -15.73 3.00e+00 1.11e-01 2.75e+01 angle pdb=" N HIS B 238 " pdb=" CA HIS B 238 " pdb=" C HIS B 238 " ideal model delta sigma weight residual 110.43 116.41 -5.98 1.31e+00 5.83e-01 2.08e+01 angle pdb=" CA PRO N 89 " pdb=" N PRO N 89 " pdb=" CD PRO N 89 " ideal model delta sigma weight residual 112.00 107.65 4.35 1.40e+00 5.10e-01 9.67e+00 angle pdb=" C4 UJL R 404 " pdb=" C5 UJL R 404 " pdb=" C6 UJL R 404 " ideal model delta sigma weight residual 109.30 118.13 -8.83 3.00e+00 1.11e-01 8.66e+00 angle pdb=" C3 UJL R 404 " pdb=" C9 UJL R 404 " pdb=" S1 UJL R 404 " ideal model delta sigma weight residual 124.67 133.40 -8.73 3.00e+00 1.11e-01 8.47e+00 ... (remaining 11513 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.21: 4652 17.21 - 34.43: 402 34.43 - 51.64: 100 51.64 - 68.85: 22 68.85 - 86.06: 15 Dihedral angle restraints: 5191 sinusoidal: 2165 harmonic: 3026 Sorted by residual: dihedral pdb=" CA LYS A 306 " pdb=" C LYS A 306 " pdb=" N ILE A 307 " pdb=" CA ILE A 307 " ideal model delta harmonic sigma weight residual -180.00 -161.24 -18.76 0 5.00e+00 4.00e-02 1.41e+01 dihedral pdb=" CA TRP B 95 " pdb=" C TRP B 95 " pdb=" N ASP B 96 " pdb=" CA ASP B 96 " ideal model delta harmonic sigma weight residual 180.00 162.04 17.96 0 5.00e+00 4.00e-02 1.29e+01 dihedral pdb=" CA ILE A 307 " pdb=" C ILE A 307 " pdb=" N GLU A 308 " pdb=" CA GLU A 308 " ideal model delta harmonic sigma weight residual -180.00 -162.53 -17.47 0 5.00e+00 4.00e-02 1.22e+01 ... (remaining 5188 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 966 0.043 - 0.086: 251 0.086 - 0.129: 70 0.129 - 0.172: 6 0.172 - 0.215: 2 Chirality restraints: 1295 Sorted by residual: chirality pdb=" CA ASN R 41 " pdb=" N ASN R 41 " pdb=" C ASN R 41 " pdb=" CB ASN R 41 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.15e+00 chirality pdb=" CA HIS B 238 " pdb=" N HIS B 238 " pdb=" C HIS B 238 " pdb=" CB HIS B 238 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.69e-01 chirality pdb=" CA ILE R 281 " pdb=" N ILE R 281 " pdb=" C ILE R 281 " pdb=" CB ILE R 281 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.24e-01 ... (remaining 1292 not shown) Planarity restraints: 1446 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS N 88 " 0.051 5.00e-02 4.00e+02 7.59e-02 9.21e+00 pdb=" N PRO N 89 " -0.131 5.00e-02 4.00e+02 pdb=" CA PRO N 89 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO N 89 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG N 106 " 0.248 9.50e-02 1.11e+02 1.12e-01 8.65e+00 pdb=" NE ARG N 106 " -0.021 2.00e-02 2.50e+03 pdb=" CZ ARG N 106 " 0.015 2.00e-02 2.50e+03 pdb=" NH1 ARG N 106 " -0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG N 106 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 264 " -0.130 9.50e-02 1.11e+02 5.86e-02 2.20e+00 pdb=" NE ARG A 264 " 0.010 2.00e-02 2.50e+03 pdb=" CZ ARG A 264 " -0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG A 264 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 264 " -0.003 2.00e-02 2.50e+03 ... (remaining 1443 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 202 2.69 - 3.25: 8166 3.25 - 3.80: 13317 3.80 - 4.35: 18534 4.35 - 4.90: 31063 Nonbonded interactions: 71282 Sorted by model distance: nonbonded pdb=" N GLU A 326 " pdb=" OE1 GLU A 326 " model vdw 2.143 2.520 nonbonded pdb=" OG SER B 294 " pdb=" OD2 ASP G 47 " model vdw 2.210 2.440 nonbonded pdb=" OH TYR A 317 " pdb=" OD2 ASP A 342 " model vdw 2.229 2.440 nonbonded pdb=" O PHE R 145 " pdb=" OG SER R 149 " model vdw 2.231 2.440 nonbonded pdb=" O ASP B 208 " pdb=" OG1 THR B 209 " model vdw 2.266 2.440 ... (remaining 71277 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=0.01 max=1.00 mean=0.94 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: 1.740 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: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 25.280 Find NCS groups from input model: 0.080 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:13.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 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 : 0.006 0.199 8494 Z= 0.402 Angle : 0.638 15.729 11518 Z= 0.342 Chirality : 0.042 0.215 1295 Planarity : 0.005 0.112 1446 Dihedral : 14.725 86.062 3232 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 0.34 % Allowed : 14.77 % Favored : 84.90 % 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: 1.00 (0.26), residues: 1023 helix: 2.06 (0.26), residues: 409 sheet: 0.04 (0.34), residues: 216 loop : -0.39 (0.30), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP R 291 HIS 0.004 0.001 HIS B 67 PHE 0.014 0.002 PHE R 160 TYR 0.013 0.001 TYR R 304 ARG 0.018 0.001 ARG N 106 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 128 time to evaluate : 0.940 Fit side-chains revert: symmetry clash REVERT: A 326 GLU cc_start: 0.6524 (mp0) cc_final: 0.6294 (tp30) REVERT: B 72 TYR cc_start: 0.9043 (OUTLIER) cc_final: 0.7863 (m-80) REVERT: N 47 GLU cc_start: 0.8111 (tt0) cc_final: 0.7891 (tt0) outliers start: 3 outliers final: 2 residues processed: 130 average time/residue: 1.3165 time to fit residues: 181.2007 Evaluate side-chains 117 residues out of total 899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 114 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 72 TYR Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 287 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 85 optimal weight: 1.9990 chunk 76 optimal weight: 0.5980 chunk 42 optimal weight: 0.8980 chunk 26 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 79 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 chunk 58 optimal weight: 7.9990 chunk 91 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 ASN A 34 GLN B 189 GLN B 238 HIS B 272 GLN N 4 GLN N 6 GLN R 175 HIS R 296 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.1067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8494 Z= 0.194 Angle : 0.524 6.209 11518 Z= 0.282 Chirality : 0.043 0.156 1295 Planarity : 0.004 0.052 1446 Dihedral : 5.186 58.179 1344 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.68 % Allowed : 14.21 % Favored : 83.11 % 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: 1.23 (0.26), residues: 1023 helix: 2.25 (0.25), residues: 413 sheet: 0.05 (0.34), residues: 228 loop : -0.22 (0.31), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP R 291 HIS 0.003 0.001 HIS R 63 PHE 0.013 0.001 PHE R 160 TYR 0.015 0.001 TYR R 79 ARG 0.005 0.000 ARG A 19 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 127 time to evaluate : 0.962 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 295 LEU cc_start: 0.8282 (mp) cc_final: 0.8034 (tp) REVERT: A 316 ARG cc_start: 0.7301 (OUTLIER) cc_final: 0.6954 (ptt90) REVERT: B 83 LEU cc_start: 0.8855 (OUTLIER) cc_final: 0.8611 (pp) outliers start: 24 outliers final: 11 residues processed: 144 average time/residue: 1.2239 time to fit residues: 187.3804 Evaluate side-chains 129 residues out of total 899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 116 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 ARG Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 72 TYR Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 111 SER Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 247 PHE Chi-restraints excluded: chain B residue 275 MET Chi-restraints excluded: chain B residue 287 THR Chi-restraints excluded: chain N residue 105 THR Chi-restraints excluded: chain N residue 115 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 50 optimal weight: 4.9990 chunk 28 optimal weight: 0.0770 chunk 76 optimal weight: 3.9990 chunk 62 optimal weight: 6.9990 chunk 25 optimal weight: 7.9990 chunk 91 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 73 optimal weight: 10.0000 chunk 90 optimal weight: 0.7980 overall best weight: 1.5744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 GLN ** A 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 272 GLN N 4 GLN N 6 GLN N 32 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.1365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 8494 Z= 0.267 Angle : 0.544 6.811 11518 Z= 0.291 Chirality : 0.044 0.153 1295 Planarity : 0.004 0.052 1446 Dihedral : 5.341 57.461 1344 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 3.47 % Allowed : 15.21 % Favored : 81.32 % 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: 1023 helix: 2.28 (0.25), residues: 413 sheet: 0.01 (0.34), residues: 228 loop : -0.21 (0.31), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP R 291 HIS 0.004 0.001 HIS R 63 PHE 0.017 0.002 PHE R 160 TYR 0.017 0.001 TYR R 79 ARG 0.006 0.000 ARG A 19 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 109 time to evaluate : 1.204 Fit side-chains revert: symmetry clash REVERT: A 212 GLN cc_start: 0.8975 (OUTLIER) cc_final: 0.8624 (tt0) REVERT: A 316 ARG cc_start: 0.7319 (OUTLIER) cc_final: 0.6946 (ptt90) REVERT: B 83 LEU cc_start: 0.8869 (OUTLIER) cc_final: 0.8655 (pp) REVERT: B 247 PHE cc_start: 0.9168 (OUTLIER) cc_final: 0.8211 (t80) outliers start: 31 outliers final: 16 residues processed: 131 average time/residue: 1.2517 time to fit residues: 174.4308 Evaluate side-chains 128 residues out of total 899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 108 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 GLN Chi-restraints excluded: chain A residue 316 ARG Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 72 TYR Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 111 SER Chi-restraints excluded: chain B residue 114 MET Chi-restraints excluded: chain B residue 116 CYS Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 247 PHE Chi-restraints excluded: chain B residue 287 THR Chi-restraints excluded: chain N residue 60 SER Chi-restraints excluded: chain N residue 105 THR Chi-restraints excluded: chain N residue 109 PHE Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain N residue 115 THR Chi-restraints excluded: chain R residue 183 SER Chi-restraints excluded: chain R residue 209 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 69 optimal weight: 0.9980 chunk 47 optimal weight: 0.9980 chunk 10 optimal weight: 8.9990 chunk 43 optimal weight: 2.9990 chunk 61 optimal weight: 6.9990 chunk 92 optimal weight: 0.7980 chunk 97 optimal weight: 3.9990 chunk 48 optimal weight: 0.9980 chunk 87 optimal weight: 8.9990 chunk 26 optimal weight: 4.9990 chunk 81 optimal weight: 3.9990 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 GLN ** A 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 233 GLN B 272 GLN N 4 GLN N 6 GLN N 78 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.1525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8494 Z= 0.236 Angle : 0.513 5.622 11518 Z= 0.276 Chirality : 0.043 0.163 1295 Planarity : 0.004 0.054 1446 Dihedral : 5.129 57.570 1344 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 3.36 % Allowed : 15.44 % Favored : 81.21 % 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: 1.21 (0.26), residues: 1023 helix: 2.32 (0.25), residues: 413 sheet: -0.12 (0.34), residues: 225 loop : -0.23 (0.31), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP R 291 HIS 0.004 0.001 HIS R 63 PHE 0.014 0.001 PHE R 160 TYR 0.014 0.001 TYR R 79 ARG 0.006 0.000 ARG A 19 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 112 time to evaluate : 0.892 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 212 GLN cc_start: 0.8927 (OUTLIER) cc_final: 0.8652 (tt0) REVERT: A 316 ARG cc_start: 0.7313 (OUTLIER) cc_final: 0.6919 (ptt90) REVERT: B 83 LEU cc_start: 0.8865 (OUTLIER) cc_final: 0.8635 (pp) REVERT: B 247 PHE cc_start: 0.9155 (OUTLIER) cc_final: 0.8235 (t80) REVERT: N 61 TYR cc_start: 0.9009 (m-80) cc_final: 0.8791 (m-80) outliers start: 30 outliers final: 16 residues processed: 133 average time/residue: 1.3361 time to fit residues: 188.8327 Evaluate side-chains 128 residues out of total 899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 108 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 GLN Chi-restraints excluded: chain A residue 299 LYS Chi-restraints excluded: chain A residue 316 ARG Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 72 TYR Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 111 SER Chi-restraints excluded: chain B residue 114 MET Chi-restraints excluded: chain B residue 116 CYS Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 247 PHE Chi-restraints excluded: chain N residue 60 SER Chi-restraints excluded: chain N residue 105 THR Chi-restraints excluded: chain N residue 109 PHE Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain N residue 115 THR Chi-restraints excluded: chain R residue 209 VAL 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: 1.9990 chunk 72 optimal weight: 6.9990 chunk 40 optimal weight: 0.4980 chunk 83 optimal weight: 0.7980 chunk 67 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 49 optimal weight: 0.0040 chunk 87 optimal weight: 6.9990 chunk 24 optimal weight: 9.9990 chunk 32 optimal weight: 1.9990 overall best weight: 1.0596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 GLN ** A 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 233 GLN N 4 GLN N 6 GLN N 78 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.1680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8494 Z= 0.199 Angle : 0.499 9.222 11518 Z= 0.265 Chirality : 0.042 0.143 1295 Planarity : 0.004 0.053 1446 Dihedral : 4.888 58.078 1343 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 3.47 % Allowed : 15.77 % Favored : 80.76 % 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: 1.29 (0.26), residues: 1023 helix: 2.41 (0.25), residues: 413 sheet: -0.14 (0.33), residues: 225 loop : -0.19 (0.31), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP R 291 HIS 0.003 0.001 HIS R 63 PHE 0.012 0.001 PHE B 164 TYR 0.015 0.001 TYR R 79 ARG 0.006 0.000 ARG A 19 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 111 time to evaluate : 0.913 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 212 GLN cc_start: 0.8891 (OUTLIER) cc_final: 0.8612 (tt0) REVERT: A 316 ARG cc_start: 0.7330 (OUTLIER) cc_final: 0.6923 (ptt90) REVERT: B 83 LEU cc_start: 0.8850 (OUTLIER) cc_final: 0.8615 (pp) REVERT: B 247 PHE cc_start: 0.9139 (OUTLIER) cc_final: 0.8236 (t80) REVERT: N 61 TYR cc_start: 0.9004 (m-80) cc_final: 0.8790 (m-80) REVERT: R 53 GLN cc_start: 0.7423 (OUTLIER) cc_final: 0.6969 (pm20) REVERT: R 193 LEU cc_start: 0.8594 (OUTLIER) cc_final: 0.8270 (mm) outliers start: 31 outliers final: 17 residues processed: 133 average time/residue: 1.1483 time to fit residues: 162.7550 Evaluate side-chains 130 residues out of total 899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 107 time to evaluate : 1.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 GLN Chi-restraints excluded: chain A residue 299 LYS Chi-restraints excluded: chain A residue 316 ARG Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 72 TYR Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 111 SER Chi-restraints excluded: chain B residue 114 MET Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 247 PHE Chi-restraints excluded: chain B residue 330 CYS Chi-restraints excluded: chain N residue 60 SER Chi-restraints excluded: chain N residue 105 THR Chi-restraints excluded: chain N residue 109 PHE Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain N residue 115 THR Chi-restraints excluded: chain R residue 53 GLN Chi-restraints excluded: chain R residue 193 LEU Chi-restraints excluded: chain R residue 209 VAL Chi-restraints excluded: chain R residue 229 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 87 optimal weight: 8.9990 chunk 19 optimal weight: 0.6980 chunk 57 optimal weight: 9.9990 chunk 24 optimal weight: 6.9990 chunk 97 optimal weight: 4.9990 chunk 81 optimal weight: 5.9990 chunk 45 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 chunk 32 optimal weight: 0.9990 chunk 51 optimal weight: 0.7980 chunk 94 optimal weight: 2.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 233 GLN N 4 GLN N 6 GLN N 78 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.1813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8494 Z= 0.176 Angle : 0.480 8.499 11518 Z= 0.256 Chirality : 0.041 0.141 1295 Planarity : 0.004 0.053 1446 Dihedral : 4.754 58.760 1343 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 3.02 % Allowed : 16.89 % Favored : 80.09 % 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: 1.35 (0.27), residues: 1023 helix: 2.50 (0.25), residues: 413 sheet: -0.17 (0.33), residues: 223 loop : -0.16 (0.32), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP R 291 HIS 0.003 0.001 HIS R 63 PHE 0.011 0.001 PHE R 95 TYR 0.013 0.001 TYR R 79 ARG 0.006 0.000 ARG A 19 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 116 time to evaluate : 0.962 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 GLN cc_start: 0.7729 (mm110) cc_final: 0.6825 (tm-30) REVERT: A 212 GLN cc_start: 0.8844 (OUTLIER) cc_final: 0.8558 (tt0) REVERT: A 316 ARG cc_start: 0.7291 (OUTLIER) cc_final: 0.6878 (ptt90) REVERT: B 83 LEU cc_start: 0.8833 (OUTLIER) cc_final: 0.8584 (pp) REVERT: B 247 PHE cc_start: 0.9131 (OUTLIER) cc_final: 0.8320 (t80) REVERT: R 53 GLN cc_start: 0.7366 (OUTLIER) cc_final: 0.6935 (pm20) REVERT: R 193 LEU cc_start: 0.8607 (OUTLIER) cc_final: 0.8275 (mm) outliers start: 27 outliers final: 17 residues processed: 135 average time/residue: 1.1349 time to fit residues: 163.6026 Evaluate side-chains 134 residues out of total 899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 111 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 GLN Chi-restraints excluded: chain A residue 299 LYS Chi-restraints excluded: chain A residue 316 ARG Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 72 TYR Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 111 SER Chi-restraints excluded: chain B residue 114 MET Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 247 PHE Chi-restraints excluded: chain B residue 330 CYS Chi-restraints excluded: chain N residue 60 SER Chi-restraints excluded: chain N residue 105 THR Chi-restraints excluded: chain N residue 109 PHE Chi-restraints excluded: chain N residue 115 THR Chi-restraints excluded: chain R residue 32 LEU Chi-restraints excluded: chain R residue 53 GLN Chi-restraints excluded: chain R residue 193 LEU Chi-restraints excluded: chain R residue 209 VAL Chi-restraints excluded: chain R residue 229 GLN Chi-restraints excluded: chain R residue 280 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 11 optimal weight: 6.9990 chunk 55 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 82 optimal weight: 0.9980 chunk 54 optimal weight: 0.9980 chunk 97 optimal weight: 7.9990 chunk 60 optimal weight: 0.1980 chunk 59 optimal weight: 2.9990 chunk 44 optimal weight: 6.9990 chunk 38 optimal weight: 0.8980 chunk 58 optimal weight: 5.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 233 GLN N 4 GLN N 6 GLN N 78 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.1881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8494 Z= 0.192 Angle : 0.485 8.052 11518 Z= 0.258 Chirality : 0.041 0.130 1295 Planarity : 0.004 0.054 1446 Dihedral : 4.672 58.788 1341 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 3.24 % Allowed : 16.89 % Favored : 79.87 % 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: 1.38 (0.27), residues: 1023 helix: 2.54 (0.25), residues: 413 sheet: -0.16 (0.33), residues: 225 loop : -0.16 (0.32), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP R 291 HIS 0.004 0.001 HIS R 63 PHE 0.012 0.001 PHE R 95 TYR 0.015 0.001 TYR R 79 ARG 0.006 0.000 ARG A 264 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 114 time to evaluate : 0.886 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 GLN cc_start: 0.7729 (mm110) cc_final: 0.6866 (tm-30) REVERT: A 212 GLN cc_start: 0.8850 (OUTLIER) cc_final: 0.8576 (tt0) REVERT: A 316 ARG cc_start: 0.7215 (OUTLIER) cc_final: 0.6811 (ptt90) REVERT: B 83 LEU cc_start: 0.8846 (OUTLIER) cc_final: 0.8601 (pp) REVERT: B 247 PHE cc_start: 0.9130 (OUTLIER) cc_final: 0.8323 (t80) REVERT: R 53 GLN cc_start: 0.7370 (OUTLIER) cc_final: 0.6940 (pm20) REVERT: R 193 LEU cc_start: 0.8602 (OUTLIER) cc_final: 0.8272 (mm) outliers start: 29 outliers final: 20 residues processed: 134 average time/residue: 1.1731 time to fit residues: 167.9642 Evaluate side-chains 137 residues out of total 899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 111 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 GLN Chi-restraints excluded: chain A residue 299 LYS Chi-restraints excluded: chain A residue 316 ARG Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 72 TYR Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 111 SER Chi-restraints excluded: chain B residue 114 MET Chi-restraints excluded: chain B residue 116 CYS Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 247 PHE Chi-restraints excluded: chain B residue 330 CYS Chi-restraints excluded: chain N residue 105 THR Chi-restraints excluded: chain N residue 109 PHE Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain N residue 115 THR Chi-restraints excluded: chain R residue 32 LEU Chi-restraints excluded: chain R residue 53 GLN Chi-restraints excluded: chain R residue 80 SER Chi-restraints excluded: chain R residue 193 LEU Chi-restraints excluded: chain R residue 209 VAL Chi-restraints excluded: chain R residue 229 GLN Chi-restraints excluded: chain R residue 280 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 29 optimal weight: 0.6980 chunk 19 optimal weight: 3.9990 chunk 18 optimal weight: 0.9990 chunk 61 optimal weight: 3.9990 chunk 66 optimal weight: 4.9990 chunk 48 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 76 optimal weight: 0.9980 chunk 88 optimal weight: 5.9990 chunk 93 optimal weight: 0.7980 chunk 85 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 233 GLN N 4 GLN N 6 GLN N 78 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.1958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8494 Z= 0.170 Angle : 0.475 7.758 11518 Z= 0.254 Chirality : 0.041 0.138 1295 Planarity : 0.004 0.054 1446 Dihedral : 4.590 59.293 1341 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 3.13 % Allowed : 17.00 % Favored : 79.87 % 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: 1.41 (0.27), residues: 1023 helix: 2.56 (0.25), residues: 413 sheet: -0.16 (0.33), residues: 225 loop : -0.13 (0.32), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP R 291 HIS 0.003 0.001 HIS R 63 PHE 0.011 0.001 PHE R 95 TYR 0.014 0.001 TYR R 79 ARG 0.005 0.000 ARG A 19 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 113 time to evaluate : 0.960 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 GLN cc_start: 0.7724 (mm110) cc_final: 0.6842 (tm-30) REVERT: A 212 GLN cc_start: 0.8836 (OUTLIER) cc_final: 0.8565 (tt0) REVERT: A 316 ARG cc_start: 0.7193 (OUTLIER) cc_final: 0.6785 (ptt90) REVERT: B 83 LEU cc_start: 0.8836 (OUTLIER) cc_final: 0.8582 (pp) REVERT: B 247 PHE cc_start: 0.9119 (OUTLIER) cc_final: 0.8324 (t80) REVERT: R 53 GLN cc_start: 0.7307 (OUTLIER) cc_final: 0.6893 (pm20) REVERT: R 193 LEU cc_start: 0.8609 (OUTLIER) cc_final: 0.8278 (mm) outliers start: 28 outliers final: 19 residues processed: 133 average time/residue: 1.1469 time to fit residues: 162.9350 Evaluate side-chains 138 residues out of total 899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 113 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 GLN Chi-restraints excluded: chain A residue 299 LYS Chi-restraints excluded: chain A residue 316 ARG Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 72 TYR Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 111 SER Chi-restraints excluded: chain B residue 114 MET Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 247 PHE Chi-restraints excluded: chain B residue 330 CYS Chi-restraints excluded: chain N residue 105 THR Chi-restraints excluded: chain N residue 109 PHE Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain N residue 115 THR Chi-restraints excluded: chain R residue 32 LEU Chi-restraints excluded: chain R residue 53 GLN Chi-restraints excluded: chain R residue 80 SER Chi-restraints excluded: chain R residue 193 LEU Chi-restraints excluded: chain R residue 209 VAL Chi-restraints excluded: chain R residue 229 GLN Chi-restraints excluded: chain R residue 280 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 90 optimal weight: 4.9990 chunk 93 optimal weight: 2.9990 chunk 54 optimal weight: 0.6980 chunk 39 optimal weight: 0.7980 chunk 71 optimal weight: 0.9980 chunk 27 optimal weight: 5.9990 chunk 81 optimal weight: 6.9990 chunk 85 optimal weight: 3.9990 chunk 59 optimal weight: 0.9990 chunk 95 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 4 GLN N 6 GLN N 78 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.1969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8494 Z= 0.201 Angle : 0.495 7.502 11518 Z= 0.264 Chirality : 0.042 0.186 1295 Planarity : 0.004 0.054 1446 Dihedral : 4.678 58.715 1341 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 3.24 % Allowed : 16.55 % Favored : 80.20 % 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: 1.41 (0.27), residues: 1023 helix: 2.59 (0.25), residues: 413 sheet: -0.17 (0.33), residues: 225 loop : -0.14 (0.32), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP R 291 HIS 0.004 0.001 HIS R 63 PHE 0.012 0.001 PHE R 95 TYR 0.014 0.001 TYR R 79 ARG 0.005 0.000 ARG B 147 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 114 time to evaluate : 0.916 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 212 GLN cc_start: 0.8846 (OUTLIER) cc_final: 0.8573 (tt0) REVERT: A 316 ARG cc_start: 0.7196 (OUTLIER) cc_final: 0.6801 (ptt90) REVERT: B 83 LEU cc_start: 0.8854 (OUTLIER) cc_final: 0.8617 (pp) REVERT: B 247 PHE cc_start: 0.9122 (OUTLIER) cc_final: 0.8308 (t80) REVERT: R 53 GLN cc_start: 0.7350 (OUTLIER) cc_final: 0.6863 (pm20) outliers start: 29 outliers final: 21 residues processed: 135 average time/residue: 1.1350 time to fit residues: 163.7656 Evaluate side-chains 138 residues out of total 899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 112 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 GLN Chi-restraints excluded: chain A residue 299 LYS Chi-restraints excluded: chain A residue 316 ARG Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 72 TYR Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 111 SER Chi-restraints excluded: chain B residue 114 MET Chi-restraints excluded: chain B residue 116 CYS Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 247 PHE Chi-restraints excluded: chain B residue 330 CYS Chi-restraints excluded: chain N residue 6 GLN Chi-restraints excluded: chain N residue 105 THR Chi-restraints excluded: chain N residue 109 PHE Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain N residue 115 THR Chi-restraints excluded: chain R residue 32 LEU Chi-restraints excluded: chain R residue 53 GLN Chi-restraints excluded: chain R residue 80 SER Chi-restraints excluded: chain R residue 209 VAL Chi-restraints excluded: chain R residue 229 GLN Chi-restraints excluded: chain R residue 280 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 45 optimal weight: 3.9990 chunk 66 optimal weight: 6.9990 chunk 100 optimal weight: 0.5980 chunk 92 optimal weight: 0.9980 chunk 80 optimal weight: 0.2980 chunk 8 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 63 optimal weight: 0.7980 chunk 85 optimal weight: 0.8980 chunk 24 optimal weight: 9.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 4 GLN N 6 GLN N 78 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.2054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8494 Z= 0.160 Angle : 0.477 7.470 11518 Z= 0.255 Chirality : 0.041 0.174 1295 Planarity : 0.004 0.053 1446 Dihedral : 4.588 59.464 1341 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 3.02 % Allowed : 17.23 % Favored : 79.75 % 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: 1.43 (0.27), residues: 1023 helix: 2.62 (0.25), residues: 413 sheet: -0.22 (0.33), residues: 223 loop : -0.12 (0.32), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP R 291 HIS 0.003 0.001 HIS R 63 PHE 0.012 0.001 PHE R 95 TYR 0.013 0.001 TYR R 79 ARG 0.004 0.000 ARG A 19 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 118 time to evaluate : 1.026 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 GLN cc_start: 0.7738 (mm110) cc_final: 0.6867 (tm-30) REVERT: A 212 GLN cc_start: 0.8832 (OUTLIER) cc_final: 0.8568 (tt0) REVERT: A 316 ARG cc_start: 0.7178 (OUTLIER) cc_final: 0.6785 (ptt90) REVERT: B 83 LEU cc_start: 0.8836 (OUTLIER) cc_final: 0.8582 (pp) REVERT: B 247 PHE cc_start: 0.9119 (OUTLIER) cc_final: 0.8321 (t80) REVERT: R 53 GLN cc_start: 0.7304 (OUTLIER) cc_final: 0.6895 (pm20) outliers start: 27 outliers final: 18 residues processed: 138 average time/residue: 1.1494 time to fit residues: 169.1919 Evaluate side-chains 136 residues out of total 899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 113 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 GLN Chi-restraints excluded: chain A residue 299 LYS Chi-restraints excluded: chain A residue 316 ARG Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 72 TYR Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 114 MET Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 247 PHE Chi-restraints excluded: chain B residue 330 CYS Chi-restraints excluded: chain N residue 105 THR Chi-restraints excluded: chain N residue 109 PHE Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain N residue 115 THR Chi-restraints excluded: chain R residue 32 LEU Chi-restraints excluded: chain R residue 53 GLN Chi-restraints excluded: chain R residue 80 SER Chi-restraints excluded: chain R residue 209 VAL Chi-restraints excluded: chain R residue 229 GLN Chi-restraints excluded: chain R residue 280 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 73 optimal weight: 10.0000 chunk 11 optimal weight: 0.7980 chunk 22 optimal weight: 0.9980 chunk 80 optimal weight: 4.9990 chunk 33 optimal weight: 0.5980 chunk 82 optimal weight: 0.8980 chunk 10 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 chunk 70 optimal weight: 7.9990 chunk 4 optimal weight: 2.9990 chunk 57 optimal weight: 8.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 4 GLN N 78 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.154503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.119273 restraints weight = 9492.627| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 1.84 r_work: 0.3441 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3341 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3349 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3349 r_free = 0.3349 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 47 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3301 r_free = 0.3301 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 82 | |-----------------------------------------------------------------------------| r_final: 0.3301 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.2049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8494 Z= 0.196 Angle : 0.497 7.329 11518 Z= 0.263 Chirality : 0.042 0.178 1295 Planarity : 0.004 0.053 1446 Dihedral : 4.666 58.906 1341 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.91 % Allowed : 17.56 % Favored : 79.53 % 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: 1.42 (0.27), residues: 1023 helix: 2.59 (0.25), residues: 413 sheet: -0.15 (0.33), residues: 223 loop : -0.14 (0.32), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP R 291 HIS 0.004 0.001 HIS R 63 PHE 0.012 0.001 PHE R 95 TYR 0.016 0.001 TYR N 96 ARG 0.004 0.000 ARG A 19 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3539.67 seconds wall clock time: 62 minutes 57.68 seconds (3777.68 seconds total)