Starting phenix.real_space_refine on Wed Feb 14 14:15:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6osa_20181/02_2024/6osa_20181.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6osa_20181/02_2024/6osa_20181.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6osa_20181/02_2024/6osa_20181.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6osa_20181/02_2024/6osa_20181.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6osa_20181/02_2024/6osa_20181.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6osa_20181/02_2024/6osa_20181.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.011 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2130 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 54 5.16 5 C 4672 2.51 5 N 1256 2.21 5 O 1356 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "R ARG 90": "NH1" <-> "NH2" Residue "R ARG 148": "NH1" <-> "NH2" Residue "R ARG 294": "NH1" <-> "NH2" Residue "R ARG 303": "NH1" <-> "NH2" Residue "R ARG 323": "NH1" <-> "NH2" Residue "A ARG 21": "NH1" <-> "NH2" Residue "A ARG 32": "NH1" <-> "NH2" Residue "A ARG 242": "NH1" <-> "NH2" Residue "B ARG 19": "NH1" <-> "NH2" Residue "B ARG 49": "NH1" <-> "NH2" Residue "B ARG 68": "NH1" <-> "NH2" Residue "B TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 96": "NH1" <-> "NH2" Residue "B ARG 251": "NH1" <-> "NH2" Residue "B ARG 256": "NH1" <-> "NH2" Residue "B PHE 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 304": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 7338 Number of models: 1 Model: "" Number of chains: 5 Chain: "R" Number of atoms: 2532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2532 Classifications: {'peptide': 321} Link IDs: {'PTRANS': 10, 'TRANS': 310} Chain breaks: 1 Chain: "L" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 53 Classifications: {'peptide': 6} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 4} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "A" Number of atoms: 1758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1758 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 215} Chain breaks: 2 Chain: "B" Number of atoms: 2585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2585 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "C" Number of atoms: 410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 410 Classifications: {'peptide': 54} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 49} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Time building chain proxies: 4.27, per 1000 atoms: 0.58 Number of scatterers: 7338 At special positions: 0 Unit cell: (78.44, 114.48, 112.36, 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 54 16.00 O 1356 8.00 N 1256 7.00 C 4672 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS R 141 " - pdb=" SG CYS R 224 " distance=2.03 Simple disulfide: pdb=" SG CYS B 121 " - pdb=" SG CYS B 149 " distance=2.05 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: 2.64 Conformation dependent library (CDL) restraints added in 1.2 seconds 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1772 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 9 sheets defined 48.3% alpha, 18.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.74 Creating SS restraints... Processing helix chain 'R' and resid 59 through 91 Processing helix chain 'R' and resid 97 through 129 removed outlier: 3.987A pdb=" N VAL R 101 " --> pdb=" O LEU R 97 " (cutoff:3.500A) Proline residue: R 121 - end of helix Processing helix chain 'R' and resid 139 through 171 Processing helix chain 'R' and resid 172 through 180 removed outlier: 3.514A pdb=" N ALA R 176 " --> pdb=" O HIS R 172 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LYS R 177 " --> pdb=" O PRO R 173 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N THR R 178 " --> pdb=" O PHE R 174 " (cutoff:3.500A) Processing helix chain 'R' and resid 181 through 200 removed outlier: 3.886A pdb=" N ALA R 200 " --> pdb=" O SER R 196 " (cutoff:3.500A) Processing helix chain 'R' and resid 200 through 206 Processing helix chain 'R' and resid 229 through 273 Proline residue: R 248 - end of helix Processing helix chain 'R' and resid 280 through 329 removed outlier: 4.211A pdb=" N GLN R 296 " --> pdb=" O PRO R 292 " (cutoff:3.500A) Proline residue: R 318 - end of helix removed outlier: 3.803A pdb=" N ILE R 329 " --> pdb=" O MET R 325 " (cutoff:3.500A) Processing helix chain 'R' and resid 335 through 356 removed outlier: 4.025A pdb=" N SER R 356 " --> pdb=" O LEU R 352 " (cutoff:3.500A) Processing helix chain 'R' and resid 358 through 368 removed outlier: 4.141A pdb=" N ILE R 362 " --> pdb=" O THR R 358 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU R 363 " --> pdb=" O ILE R 359 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N TYR R 364 " --> pdb=" O ASN R 360 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N VAL R 367 " --> pdb=" O LEU R 363 " (cutoff:3.500A) Processing helix chain 'R' and resid 368 through 383 removed outlier: 3.593A pdb=" N HIS R 373 " --> pdb=" O ALA R 369 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ILE R 374 " --> pdb=" O ASN R 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 6 through 31 removed outlier: 3.961A pdb=" N ALA A 11 " --> pdb=" O ALA A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 54 Processing helix chain 'A' and resid 207 through 212 removed outlier: 4.169A pdb=" N TRP A 211 " --> pdb=" O GLU A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 216 removed outlier: 3.563A pdb=" N GLU A 216 " --> pdb=" O HIS A 213 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 213 through 216' Processing helix chain 'A' and resid 228 through 231 removed outlier: 3.914A pdb=" N ASP A 231 " --> pdb=" O SER A 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 228 through 231' Processing helix chain 'A' and resid 242 through 255 Processing helix chain 'A' and resid 270 through 281 removed outlier: 4.105A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LYS A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.733A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 311 removed outlier: 3.520A pdb=" N ALA A 299 " --> pdb=" O THR A 295 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ASN A 311 " --> pdb=" O PHE A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 352 Processing helix chain 'B' and resid 4 through 25 Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.800A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 37 No H-bonds generated for 'chain 'B' and resid 35 through 37' Processing helix chain 'C' and resid 9 through 24 removed outlier: 3.644A pdb=" N ASN C 24 " --> pdb=" O LYS C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 44 Processing sheet with id=AA1, first strand: chain 'R' and resid 207 through 211 Processing sheet with id=AA2, first strand: chain 'A' and resid 185 through 190 removed outlier: 6.765A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 8.564A pdb=" N ALA A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 46 through 52 removed outlier: 4.072A pdb=" N ARG B 46 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ASN B 340 " --> pdb=" O ARG B 46 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N SER B 331 " --> pdb=" O PHE B 335 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.732A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.348A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.615A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.857A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.261A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.759A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) 417 hydrogen bonds defined for protein. 1227 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: 2.46 Time building geometry restraints manager: 2.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 2372 1.35 - 1.48: 1912 1.48 - 1.61: 3125 1.61 - 1.74: 0 1.74 - 1.86: 77 Bond restraints: 7486 Sorted by residual: bond pdb=" C LEU R 317 " pdb=" N PRO R 318 " ideal model delta sigma weight residual 1.335 1.388 -0.053 1.28e-02 6.10e+03 1.71e+01 bond pdb=" C MET R 120 " pdb=" N PRO R 121 " ideal model delta sigma weight residual 1.336 1.382 -0.046 1.20e-02 6.94e+03 1.44e+01 bond pdb=" SD MET B 61 " pdb=" CE MET B 61 " ideal model delta sigma weight residual 1.791 1.736 0.055 2.50e-02 1.60e+03 4.78e+00 bond pdb=" CG LEU B 51 " pdb=" CD2 LEU B 51 " ideal model delta sigma weight residual 1.521 1.452 0.069 3.30e-02 9.18e+02 4.37e+00 bond pdb=" CG LEU B 146 " pdb=" CD1 LEU B 146 " ideal model delta sigma weight residual 1.521 1.452 0.069 3.30e-02 9.18e+02 4.36e+00 ... (remaining 7481 not shown) Histogram of bond angle deviations from ideal: 98.82 - 105.87: 118 105.87 - 112.92: 4071 112.92 - 119.98: 2534 119.98 - 127.03: 3322 127.03 - 134.08: 99 Bond angle restraints: 10144 Sorted by residual: angle pdb=" CA LEU R 263 " pdb=" CB LEU R 263 " pdb=" CG LEU R 263 " ideal model delta sigma weight residual 116.30 133.92 -17.62 3.50e+00 8.16e-02 2.54e+01 angle pdb=" C HIS B 142 " pdb=" N THR B 143 " pdb=" CA THR B 143 " ideal model delta sigma weight residual 122.08 128.54 -6.46 1.47e+00 4.63e-01 1.93e+01 angle pdb=" C ASP B 118 " pdb=" N ASN B 119 " pdb=" CA ASN B 119 " ideal model delta sigma weight residual 121.54 129.12 -7.58 1.91e+00 2.74e-01 1.57e+01 angle pdb=" C ASP B 291 " pdb=" N PHE B 292 " pdb=" CA PHE B 292 " ideal model delta sigma weight residual 122.07 127.69 -5.62 1.43e+00 4.89e-01 1.55e+01 angle pdb=" CA LEU B 336 " pdb=" CB LEU B 336 " pdb=" CG LEU B 336 " ideal model delta sigma weight residual 116.30 130.04 -13.74 3.50e+00 8.16e-02 1.54e+01 ... (remaining 10139 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.15: 4167 16.15 - 32.30: 234 32.30 - 48.45: 40 48.45 - 64.60: 3 64.60 - 80.75: 8 Dihedral angle restraints: 4452 sinusoidal: 1719 harmonic: 2733 Sorted by residual: dihedral pdb=" CB CYS B 121 " pdb=" SG CYS B 121 " pdb=" SG CYS B 149 " pdb=" CB CYS B 149 " ideal model delta sinusoidal sigma weight residual 93.00 173.75 -80.75 1 1.00e+01 1.00e-02 8.06e+01 dihedral pdb=" CA PHE B 234 " pdb=" C PHE B 234 " pdb=" N PHE B 235 " pdb=" CA PHE B 235 " ideal model delta harmonic sigma weight residual 180.00 157.93 22.07 0 5.00e+00 4.00e-02 1.95e+01 dihedral pdb=" CA ILE L 12 " pdb=" C ILE L 12 " pdb=" N LEU L 13 " pdb=" CA LEU L 13 " ideal model delta harmonic sigma weight residual 180.00 158.63 21.37 0 5.00e+00 4.00e-02 1.83e+01 ... (remaining 4449 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 826 0.053 - 0.106: 259 0.106 - 0.160: 68 0.160 - 0.213: 14 0.213 - 0.266: 4 Chirality restraints: 1171 Sorted by residual: chirality pdb=" CA ASN B 119 " pdb=" N ASN B 119 " pdb=" C ASN B 119 " pdb=" CB ASN B 119 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.77e+00 chirality pdb=" CB VAL A 201 " pdb=" CA VAL A 201 " pdb=" CG1 VAL A 201 " pdb=" CG2 VAL A 201 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.25 2.00e-01 2.50e+01 1.56e+00 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 2.29 0.22 2.00e-01 2.50e+01 1.22e+00 ... (remaining 1168 not shown) Planarity restraints: 1277 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET R 243 " 0.015 2.00e-02 2.50e+03 3.06e-02 9.39e+00 pdb=" C MET R 243 " -0.053 2.00e-02 2.50e+03 pdb=" O MET R 243 " 0.020 2.00e-02 2.50e+03 pdb=" N SER R 244 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU R 124 " 0.014 2.00e-02 2.50e+03 2.72e-02 7.42e+00 pdb=" C LEU R 124 " -0.047 2.00e-02 2.50e+03 pdb=" O LEU R 124 " 0.018 2.00e-02 2.50e+03 pdb=" N TYR R 125 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP C 48 " 0.043 5.00e-02 4.00e+02 6.50e-02 6.75e+00 pdb=" N PRO C 49 " -0.112 5.00e-02 4.00e+02 pdb=" CA PRO C 49 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO C 49 " 0.036 5.00e-02 4.00e+02 ... (remaining 1274 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1009 2.75 - 3.29: 6844 3.29 - 3.82: 12240 3.82 - 4.36: 13986 4.36 - 4.90: 24939 Nonbonded interactions: 59018 Sorted by model distance: nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.210 2.440 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.309 2.440 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.319 2.440 nonbonded pdb=" O GLY B 182 " pdb=" NZ LYS B 209 " model vdw 2.329 2.520 nonbonded pdb=" O LEU R 94 " pdb=" NE2 GLN R 98 " model vdw 2.335 2.520 ... (remaining 59013 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=0.00 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.010 Extract box with map and model: 3.410 Check model and map are aligned: 0.100 Set scattering table: 0.060 Process input model: 23.200 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:14.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 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 : 0.008 0.093 7486 Z= 0.554 Angle : 1.075 17.625 10144 Z= 0.593 Chirality : 0.058 0.266 1171 Planarity : 0.007 0.065 1277 Dihedral : 11.086 75.182 2674 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % 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: -2.75 (0.23), residues: 921 helix: -1.70 (0.20), residues: 414 sheet: -0.85 (0.39), residues: 169 loop : -2.31 (0.27), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.004 TRP B 99 HIS 0.028 0.004 HIS B 142 PHE 0.042 0.004 PHE B 180 TYR 0.032 0.004 TYR R 354 ARG 0.015 0.001 ARG R 212 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 218 time to evaluate : 0.819 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "LYS L 8 " (corrupted residue). Skipping it. REVERT: R 91 LYS cc_start: 0.7132 (mttt) cc_final: 0.6903 (mmmm) REVERT: R 237 ILE cc_start: 0.8094 (mt) cc_final: 0.7812 (mp) REVERT: R 325 MET cc_start: 0.6473 (mmt) cc_final: 0.5754 (pp-130) REVERT: A 6 SER cc_start: 0.6884 (m) cc_final: 0.6495 (p) REVERT: A 208 ARG cc_start: 0.7982 (ttm-80) cc_final: 0.7707 (ttp-110) REVERT: A 245 GLU cc_start: 0.7920 (tm-30) cc_final: 0.7593 (tm-30) REVERT: A 280 LYS cc_start: 0.8342 (mppt) cc_final: 0.7870 (mtmt) REVERT: B 12 GLU cc_start: 0.8301 (tm-30) cc_final: 0.7360 (tp30) REVERT: B 175 GLN cc_start: 0.8375 (mm110) cc_final: 0.8051 (mm-40) REVERT: B 264 TYR cc_start: 0.8458 (m-80) cc_final: 0.8162 (m-80) REVERT: C 19 LEU cc_start: 0.8978 (mt) cc_final: 0.8771 (mt) REVERT: C 27 ARG cc_start: 0.8186 (mtt90) cc_final: 0.7970 (mtt-85) outliers start: 0 outliers final: 2 residues processed: 218 average time/residue: 1.1628 time to fit residues: 267.3110 Evaluate side-chains 136 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 134 time to evaluate : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 270 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 76 optimal weight: 0.9990 chunk 68 optimal weight: 0.7980 chunk 38 optimal weight: 0.9980 chunk 23 optimal weight: 0.5980 chunk 46 optimal weight: 9.9990 chunk 36 optimal weight: 0.8980 chunk 71 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 chunk 53 optimal weight: 7.9990 chunk 82 optimal weight: 6.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 172 HIS ** R 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 229 HIS R 238 GLN ** R 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 261 ASN R 320 HIS R 365 ASN ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 204 GLN B 110 ASN B 259 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.2489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7486 Z= 0.216 Angle : 0.638 10.137 10144 Z= 0.335 Chirality : 0.043 0.154 1171 Planarity : 0.005 0.039 1277 Dihedral : 5.493 48.307 1013 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 4.89 % Allowed : 14.91 % 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: -0.79 (0.25), residues: 921 helix: 0.50 (0.24), residues: 429 sheet: -0.29 (0.39), residues: 153 loop : -1.93 (0.29), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 82 HIS 0.008 0.001 HIS B 142 PHE 0.012 0.001 PHE R 345 TYR 0.023 0.002 TYR A 290 ARG 0.007 0.001 ARG B 49 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 140 time to evaluate : 0.841 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS L 8 " (corrupted residue). Skipping it. REVERT: R 246 ILE cc_start: 0.8198 (mm) cc_final: 0.7953 (mm) REVERT: R 325 MET cc_start: 0.6371 (mmt) cc_final: 0.5864 (pp-130) REVERT: A 52 GLN cc_start: 0.7491 (mt0) cc_final: 0.7162 (mp10) REVERT: A 208 ARG cc_start: 0.7911 (ttm-80) cc_final: 0.7445 (ttp-110) REVERT: A 269 ASN cc_start: 0.8968 (m110) cc_final: 0.8725 (m110) REVERT: A 276 GLU cc_start: 0.7815 (mp0) cc_final: 0.7570 (mp0) REVERT: A 280 LYS cc_start: 0.8210 (mppt) cc_final: 0.7721 (mtmm) REVERT: A 281 SER cc_start: 0.8649 (OUTLIER) cc_final: 0.8217 (p) REVERT: A 310 LEU cc_start: 0.8767 (OUTLIER) cc_final: 0.8452 (tt) REVERT: B 12 GLU cc_start: 0.7935 (tm-30) cc_final: 0.7517 (tp30) REVERT: B 175 GLN cc_start: 0.8330 (mm110) cc_final: 0.8020 (mm-40) REVERT: B 217 MET cc_start: 0.7858 (pmm) cc_final: 0.7629 (pmm) outliers start: 39 outliers final: 14 residues processed: 164 average time/residue: 1.0966 time to fit residues: 190.7440 Evaluate side-chains 126 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 110 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 66 VAL Chi-restraints excluded: chain R residue 131 HIS Chi-restraints excluded: chain R residue 201 VAL Chi-restraints excluded: chain R residue 258 ILE Chi-restraints excluded: chain R residue 358 THR Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 270 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 45 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 56 optimal weight: 5.9990 chunk 22 optimal weight: 5.9990 chunk 82 optimal weight: 4.9990 chunk 89 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 66 optimal weight: 0.9990 chunk 81 optimal weight: 0.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 238 GLN ** R 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 204 GLN A 304 GLN B 259 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.2902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7486 Z= 0.277 Angle : 0.634 10.000 10144 Z= 0.330 Chirality : 0.043 0.157 1171 Planarity : 0.004 0.054 1277 Dihedral : 5.215 47.354 1013 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 5.14 % Allowed : 16.79 % Favored : 78.07 % 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: -0.18 (0.27), residues: 921 helix: 1.16 (0.25), residues: 432 sheet: -0.47 (0.38), residues: 163 loop : -1.66 (0.31), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 82 HIS 0.011 0.002 HIS B 142 PHE 0.014 0.002 PHE R 345 TYR 0.019 0.002 TYR R 339 ARG 0.013 0.001 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 115 time to evaluate : 0.803 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS L 8 " (corrupted residue). Skipping it. REVERT: R 246 ILE cc_start: 0.8169 (mm) cc_final: 0.7900 (mm) REVERT: R 325 MET cc_start: 0.6368 (mmt) cc_final: 0.5968 (pp-130) REVERT: A 52 GLN cc_start: 0.7516 (mt0) cc_final: 0.7203 (mp10) REVERT: A 205 ARG cc_start: 0.7089 (OUTLIER) cc_final: 0.6841 (tmt-80) REVERT: A 269 ASN cc_start: 0.8942 (m110) cc_final: 0.8734 (m110) REVERT: A 276 GLU cc_start: 0.7938 (OUTLIER) cc_final: 0.7617 (mp0) REVERT: A 280 LYS cc_start: 0.8245 (mppt) cc_final: 0.7784 (mppt) REVERT: A 281 SER cc_start: 0.8616 (OUTLIER) cc_final: 0.8195 (p) REVERT: B 12 GLU cc_start: 0.8008 (tm-30) cc_final: 0.7516 (tp30) REVERT: B 23 LYS cc_start: 0.7747 (tppp) cc_final: 0.7350 (tptp) REVERT: B 175 GLN cc_start: 0.8312 (mm110) cc_final: 0.7981 (mm-40) outliers start: 41 outliers final: 17 residues processed: 137 average time/residue: 1.1728 time to fit residues: 169.9434 Evaluate side-chains 123 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 103 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 66 VAL Chi-restraints excluded: chain R residue 101 VAL Chi-restraints excluded: chain R residue 131 HIS Chi-restraints excluded: chain R residue 177 LYS Chi-restraints excluded: chain R residue 201 VAL Chi-restraints excluded: chain R residue 258 ILE Chi-restraints excluded: chain R residue 310 ILE Chi-restraints excluded: chain R residue 355 VAL Chi-restraints excluded: chain A residue 205 ARG Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 270 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 62 optimal weight: 0.0570 chunk 42 optimal weight: 10.0000 chunk 9 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 chunk 83 optimal weight: 5.9990 chunk 87 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 78 optimal weight: 0.9980 chunk 23 optimal weight: 0.9990 chunk 73 optimal weight: 3.9990 overall best weight: 0.8104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 365 ASN A 204 GLN A 304 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.3249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7486 Z= 0.197 Angle : 0.592 10.322 10144 Z= 0.306 Chirality : 0.041 0.159 1171 Planarity : 0.004 0.059 1277 Dihedral : 4.877 45.203 1011 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 4.89 % Allowed : 19.05 % Favored : 76.07 % 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: 0.24 (0.27), residues: 921 helix: 1.66 (0.25), residues: 426 sheet: -0.09 (0.39), residues: 151 loop : -1.69 (0.30), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 82 HIS 0.005 0.001 HIS B 142 PHE 0.014 0.001 PHE R 375 TYR 0.016 0.002 TYR R 339 ARG 0.014 0.001 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 113 time to evaluate : 0.964 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS L 8 " (corrupted residue). Skipping it. REVERT: R 246 ILE cc_start: 0.8014 (mm) cc_final: 0.7770 (mm) REVERT: R 325 MET cc_start: 0.6247 (mmt) cc_final: 0.5991 (pp-130) REVERT: A 52 GLN cc_start: 0.7469 (mt0) cc_final: 0.7178 (mp10) REVERT: A 280 LYS cc_start: 0.8189 (mppt) cc_final: 0.7913 (mppt) REVERT: A 281 SER cc_start: 0.8577 (OUTLIER) cc_final: 0.8163 (p) REVERT: B 12 GLU cc_start: 0.7986 (tm-30) cc_final: 0.7460 (tp30) REVERT: B 175 GLN cc_start: 0.8291 (mm110) cc_final: 0.7998 (mm110) REVERT: B 234 PHE cc_start: 0.9266 (OUTLIER) cc_final: 0.9037 (m-80) outliers start: 39 outliers final: 19 residues processed: 138 average time/residue: 1.2031 time to fit residues: 175.8777 Evaluate side-chains 119 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 98 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 66 VAL Chi-restraints excluded: chain R residue 131 HIS Chi-restraints excluded: chain R residue 201 VAL Chi-restraints excluded: chain R residue 258 ILE Chi-restraints excluded: chain R residue 332 GLU Chi-restraints excluded: chain R residue 355 VAL Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 49 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 65 optimal weight: 0.2980 chunk 36 optimal weight: 0.0970 chunk 75 optimal weight: 4.9990 chunk 60 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 44 optimal weight: 0.0370 chunk 78 optimal weight: 2.9990 chunk 22 optimal weight: 10.0000 chunk 29 optimal weight: 0.7980 overall best weight: 0.4456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 365 ASN A 204 GLN A 269 ASN A 304 GLN B 75 GLN B 142 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.3527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7486 Z= 0.162 Angle : 0.556 8.595 10144 Z= 0.290 Chirality : 0.040 0.155 1171 Planarity : 0.004 0.062 1277 Dihedral : 4.634 44.016 1011 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 4.64 % Allowed : 20.05 % Favored : 75.31 % 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: 0.55 (0.27), residues: 921 helix: 2.13 (0.25), residues: 413 sheet: 0.05 (0.39), residues: 150 loop : -1.70 (0.30), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 82 HIS 0.003 0.001 HIS R 343 PHE 0.014 0.001 PHE R 375 TYR 0.016 0.002 TYR R 339 ARG 0.016 0.001 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 121 time to evaluate : 0.845 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS L 8 " (corrupted residue). Skipping it. REVERT: A 280 LYS cc_start: 0.8273 (mppt) cc_final: 0.7885 (mppt) REVERT: A 281 SER cc_start: 0.8509 (OUTLIER) cc_final: 0.8151 (p) REVERT: B 12 GLU cc_start: 0.8009 (tm-30) cc_final: 0.7615 (tp30) REVERT: B 124 TYR cc_start: 0.8487 (m-80) cc_final: 0.8067 (m-80) REVERT: B 175 GLN cc_start: 0.8265 (mm110) cc_final: 0.7971 (mm110) REVERT: B 234 PHE cc_start: 0.9283 (OUTLIER) cc_final: 0.9042 (OUTLIER) REVERT: B 270 ILE cc_start: 0.8474 (OUTLIER) cc_final: 0.8272 (pp) outliers start: 37 outliers final: 14 residues processed: 146 average time/residue: 1.0339 time to fit residues: 160.6845 Evaluate side-chains 125 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 109 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 101 VAL Chi-restraints excluded: chain R residue 131 HIS Chi-restraints excluded: chain R residue 201 VAL Chi-restraints excluded: chain R residue 258 ILE Chi-restraints excluded: chain R residue 332 GLU Chi-restraints excluded: chain R residue 355 VAL Chi-restraints excluded: chain A residue 44 SER Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 79 optimal weight: 0.3980 chunk 17 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 88 optimal weight: 3.9990 chunk 73 optimal weight: 0.6980 chunk 40 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 46 optimal weight: 10.0000 chunk 84 optimal weight: 0.7980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 365 ASN A 204 GLN A 304 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.3583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7486 Z= 0.216 Angle : 0.619 12.869 10144 Z= 0.310 Chirality : 0.041 0.158 1171 Planarity : 0.004 0.065 1277 Dihedral : 4.640 44.207 1011 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 5.26 % Allowed : 20.80 % Favored : 73.93 % 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: 0.58 (0.27), residues: 921 helix: 2.00 (0.25), residues: 426 sheet: -0.15 (0.37), residues: 162 loop : -1.53 (0.31), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 82 HIS 0.005 0.001 HIS R 102 PHE 0.011 0.001 PHE R 375 TYR 0.018 0.002 TYR R 339 ARG 0.015 0.001 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 114 time to evaluate : 0.866 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS L 8 " (corrupted residue). Skipping it. REVERT: R 325 MET cc_start: 0.7538 (OUTLIER) cc_final: 0.7337 (ppp) REVERT: A 48 THR cc_start: 0.8663 (m) cc_final: 0.8375 (t) REVERT: A 280 LYS cc_start: 0.8320 (mppt) cc_final: 0.7938 (mppt) REVERT: A 281 SER cc_start: 0.8574 (OUTLIER) cc_final: 0.8219 (p) REVERT: B 12 GLU cc_start: 0.7963 (tm-30) cc_final: 0.7439 (tp30) REVERT: B 175 GLN cc_start: 0.8271 (mm110) cc_final: 0.7938 (mm-40) REVERT: B 234 PHE cc_start: 0.9302 (OUTLIER) cc_final: 0.9022 (OUTLIER) outliers start: 42 outliers final: 22 residues processed: 142 average time/residue: 1.0667 time to fit residues: 160.9090 Evaluate side-chains 130 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 106 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 101 VAL Chi-restraints excluded: chain R residue 131 HIS Chi-restraints excluded: chain R residue 201 VAL Chi-restraints excluded: chain R residue 258 ILE Chi-restraints excluded: chain R residue 310 ILE Chi-restraints excluded: chain R residue 321 VAL Chi-restraints excluded: chain R residue 325 MET Chi-restraints excluded: chain R residue 332 GLU Chi-restraints excluded: chain R residue 355 VAL Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 44 SER Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 9 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 64 optimal weight: 0.6980 chunk 49 optimal weight: 3.9990 chunk 74 optimal weight: 0.0670 chunk 87 optimal weight: 4.9990 chunk 54 optimal weight: 1.9990 chunk 53 optimal weight: 7.9990 chunk 40 optimal weight: 3.9990 chunk 35 optimal weight: 0.5980 chunk 52 optimal weight: 0.5980 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 240 ASN ** R 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 365 ASN A 204 GLN A 304 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.3816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7486 Z= 0.173 Angle : 0.582 11.629 10144 Z= 0.298 Chirality : 0.040 0.160 1171 Planarity : 0.004 0.069 1277 Dihedral : 4.394 43.252 1009 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 4.01 % Allowed : 22.06 % Favored : 73.93 % 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: 0.78 (0.28), residues: 921 helix: 2.22 (0.25), residues: 419 sheet: -0.10 (0.38), residues: 162 loop : -1.39 (0.32), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.004 0.001 HIS R 102 PHE 0.009 0.001 PHE R 375 TYR 0.017 0.002 TYR R 339 ARG 0.017 0.001 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 116 time to evaluate : 0.817 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS L 8 " (corrupted residue). Skipping it. REVERT: R 128 ILE cc_start: 0.7702 (mm) cc_final: 0.7370 (mm) REVERT: A 52 GLN cc_start: 0.7209 (mp10) cc_final: 0.6956 (mp10) REVERT: A 280 LYS cc_start: 0.8314 (mppt) cc_final: 0.7927 (mppt) REVERT: A 281 SER cc_start: 0.8684 (OUTLIER) cc_final: 0.8307 (p) REVERT: B 12 GLU cc_start: 0.7949 (tm-30) cc_final: 0.7550 (tp30) REVERT: B 124 TYR cc_start: 0.8501 (m-80) cc_final: 0.8128 (m-80) REVERT: B 175 GLN cc_start: 0.8261 (mm110) cc_final: 0.7963 (mm110) REVERT: B 234 PHE cc_start: 0.9286 (OUTLIER) cc_final: 0.8949 (m-80) outliers start: 32 outliers final: 17 residues processed: 137 average time/residue: 1.1478 time to fit residues: 168.2936 Evaluate side-chains 129 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 110 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 101 VAL Chi-restraints excluded: chain R residue 131 HIS Chi-restraints excluded: chain R residue 201 VAL Chi-restraints excluded: chain R residue 310 ILE Chi-restraints excluded: chain R residue 355 VAL Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain C residue 20 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 26 optimal weight: 5.9990 chunk 17 optimal weight: 0.8980 chunk 16 optimal weight: 4.9990 chunk 55 optimal weight: 8.9990 chunk 59 optimal weight: 0.8980 chunk 43 optimal weight: 0.8980 chunk 8 optimal weight: 0.6980 chunk 68 optimal weight: 5.9990 chunk 79 optimal weight: 0.9990 chunk 84 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 204 GLN B 237 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.3844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7486 Z= 0.207 Angle : 0.627 13.132 10144 Z= 0.313 Chirality : 0.041 0.161 1171 Planarity : 0.004 0.076 1277 Dihedral : 4.423 43.602 1009 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 4.14 % Allowed : 22.93 % Favored : 72.93 % 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: 0.72 (0.28), residues: 921 helix: 2.13 (0.25), residues: 426 sheet: -0.24 (0.37), residues: 168 loop : -1.39 (0.33), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 82 HIS 0.004 0.001 HIS R 343 PHE 0.009 0.001 PHE A 189 TYR 0.029 0.002 TYR A 290 ARG 0.017 0.001 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 117 time to evaluate : 0.934 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS L 8 " (corrupted residue). Skipping it. REVERT: R 128 ILE cc_start: 0.7683 (mm) cc_final: 0.7374 (mm) REVERT: A 48 THR cc_start: 0.8641 (m) cc_final: 0.8400 (t) REVERT: A 52 GLN cc_start: 0.7243 (mp10) cc_final: 0.6961 (mp10) REVERT: A 280 LYS cc_start: 0.8330 (mppt) cc_final: 0.7936 (mppt) REVERT: A 281 SER cc_start: 0.8688 (OUTLIER) cc_final: 0.8336 (p) REVERT: B 12 GLU cc_start: 0.7932 (tm-30) cc_final: 0.7446 (tp30) REVERT: B 124 TYR cc_start: 0.8536 (m-80) cc_final: 0.8172 (m-80) REVERT: B 175 GLN cc_start: 0.8278 (mm110) cc_final: 0.7979 (mm110) REVERT: B 234 PHE cc_start: 0.9290 (OUTLIER) cc_final: 0.8953 (m-80) REVERT: C 21 MET cc_start: 0.8189 (tmt) cc_final: 0.7883 (tmt) outliers start: 33 outliers final: 23 residues processed: 142 average time/residue: 1.0422 time to fit residues: 157.4645 Evaluate side-chains 138 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 113 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 101 VAL Chi-restraints excluded: chain R residue 131 HIS Chi-restraints excluded: chain R residue 201 VAL Chi-restraints excluded: chain R residue 258 ILE Chi-restraints excluded: chain R residue 310 ILE Chi-restraints excluded: chain R residue 321 VAL Chi-restraints excluded: chain R residue 355 VAL Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 44 SER Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain C residue 20 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 81 optimal weight: 3.9990 chunk 84 optimal weight: 0.9980 chunk 49 optimal weight: 0.2980 chunk 35 optimal weight: 0.7980 chunk 64 optimal weight: 9.9990 chunk 25 optimal weight: 0.9990 chunk 73 optimal weight: 0.9980 chunk 77 optimal weight: 3.9990 chunk 53 optimal weight: 8.9990 chunk 86 optimal weight: 0.9990 chunk 52 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 204 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.3902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7486 Z= 0.201 Angle : 0.622 11.938 10144 Z= 0.312 Chirality : 0.041 0.168 1171 Planarity : 0.005 0.081 1277 Dihedral : 4.417 43.087 1009 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 3.63 % Allowed : 22.68 % Favored : 73.68 % 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: 0.78 (0.28), residues: 921 helix: 2.13 (0.25), residues: 430 sheet: -0.24 (0.37), residues: 168 loop : -1.33 (0.33), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 82 HIS 0.003 0.001 HIS R 343 PHE 0.009 0.001 PHE A 189 TYR 0.018 0.002 TYR R 339 ARG 0.018 0.001 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 115 time to evaluate : 0.853 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS L 8 " (corrupted residue). Skipping it. REVERT: R 128 ILE cc_start: 0.7719 (mm) cc_final: 0.7414 (mm) REVERT: A 280 LYS cc_start: 0.8343 (mppt) cc_final: 0.7950 (mppt) REVERT: A 281 SER cc_start: 0.8676 (OUTLIER) cc_final: 0.8326 (p) REVERT: B 12 GLU cc_start: 0.7926 (tm-30) cc_final: 0.7539 (tp30) REVERT: B 154 ASP cc_start: 0.8399 (OUTLIER) cc_final: 0.8187 (t0) REVERT: B 175 GLN cc_start: 0.8263 (mm110) cc_final: 0.7966 (mm110) REVERT: B 234 PHE cc_start: 0.9293 (OUTLIER) cc_final: 0.9031 (m-80) outliers start: 29 outliers final: 20 residues processed: 134 average time/residue: 1.1095 time to fit residues: 157.7591 Evaluate side-chains 136 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 113 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 69 VAL Chi-restraints excluded: chain R residue 101 VAL Chi-restraints excluded: chain R residue 131 HIS Chi-restraints excluded: chain R residue 201 VAL Chi-restraints excluded: chain R residue 310 ILE Chi-restraints excluded: chain R residue 355 VAL Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 44 SER Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain C residue 20 LYS Chi-restraints excluded: chain C residue 38 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 41 optimal weight: 0.9990 chunk 60 optimal weight: 0.7980 chunk 90 optimal weight: 3.9990 chunk 83 optimal weight: 0.2980 chunk 72 optimal weight: 3.9990 chunk 7 optimal weight: 0.9980 chunk 55 optimal weight: 8.9990 chunk 44 optimal weight: 0.0370 chunk 57 optimal weight: 2.9990 chunk 76 optimal weight: 0.0570 chunk 22 optimal weight: 10.0000 overall best weight: 0.4376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 269 GLN R 365 ASN A 204 GLN A 304 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.4058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7486 Z= 0.168 Angle : 0.624 11.489 10144 Z= 0.311 Chirality : 0.041 0.173 1171 Planarity : 0.005 0.081 1277 Dihedral : 4.319 41.664 1009 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.88 % Allowed : 23.56 % Favored : 73.56 % 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: 0.80 (0.28), residues: 921 helix: 2.28 (0.25), residues: 422 sheet: -0.16 (0.38), residues: 167 loop : -1.47 (0.32), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.004 0.001 HIS R 102 PHE 0.009 0.001 PHE A 189 TYR 0.034 0.002 TYR A 290 ARG 0.019 0.001 ARG B 96 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 118 time to evaluate : 0.848 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS L 8 " (corrupted residue). Skipping it. REVERT: L 11 TYR cc_start: 0.8418 (p90) cc_final: 0.8202 (p90) REVERT: A 280 LYS cc_start: 0.8327 (mppt) cc_final: 0.7932 (mppt) REVERT: A 281 SER cc_start: 0.8658 (OUTLIER) cc_final: 0.8334 (p) REVERT: B 12 GLU cc_start: 0.7911 (tm-30) cc_final: 0.7525 (tp30) REVERT: B 175 GLN cc_start: 0.8253 (mm110) cc_final: 0.7917 (mm-40) REVERT: B 234 PHE cc_start: 0.9256 (OUTLIER) cc_final: 0.8962 (m-80) REVERT: C 21 MET cc_start: 0.8192 (tmt) cc_final: 0.7864 (tmt) outliers start: 23 outliers final: 16 residues processed: 136 average time/residue: 1.0640 time to fit residues: 153.8814 Evaluate side-chains 128 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 110 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 131 HIS Chi-restraints excluded: chain R residue 201 VAL Chi-restraints excluded: chain R residue 310 ILE Chi-restraints excluded: chain R residue 355 VAL Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain C residue 20 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 66 optimal weight: 4.9990 chunk 10 optimal weight: 0.9990 chunk 20 optimal weight: 0.5980 chunk 72 optimal weight: 0.9990 chunk 30 optimal weight: 3.9990 chunk 74 optimal weight: 0.0170 chunk 9 optimal weight: 1.9990 chunk 13 optimal weight: 5.9990 chunk 63 optimal weight: 4.9990 chunk 4 optimal weight: 10.0000 chunk 52 optimal weight: 1.9990 overall best weight: 0.9224 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 365 ASN A 204 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.140679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.117041 restraints weight = 10574.181| |-----------------------------------------------------------------------------| r_work (start): 0.3619 rms_B_bonded: 2.45 r_work: 0.3497 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3369 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.4044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7486 Z= 0.214 Angle : 0.640 11.988 10144 Z= 0.322 Chirality : 0.042 0.203 1171 Planarity : 0.005 0.085 1277 Dihedral : 4.377 42.926 1009 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 3.13 % Allowed : 24.19 % Favored : 72.68 % 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: 0.80 (0.28), residues: 921 helix: 2.25 (0.25), residues: 423 sheet: -0.30 (0.38), residues: 171 loop : -1.35 (0.33), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 82 HIS 0.004 0.001 HIS B 183 PHE 0.009 0.001 PHE A 189 TYR 0.019 0.002 TYR R 339 ARG 0.019 0.001 ARG B 96 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3294.03 seconds wall clock time: 59 minutes 13.15 seconds (3553.15 seconds total)