Starting phenix.real_space_refine on Fri Dec 8 08:13:00 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wuh_21913/12_2023/6wuh_21913.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wuh_21913/12_2023/6wuh_21913.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wuh_21913/12_2023/6wuh_21913.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wuh_21913/12_2023/6wuh_21913.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wuh_21913/12_2023/6wuh_21913.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wuh_21913/12_2023/6wuh_21913.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.011 sd= 0.094 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 16 5.16 5 C 4930 2.51 5 N 1400 2.21 5 O 1444 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 22": "NH1" <-> "NH2" Residue "A ARG 30": "NH1" <-> "NH2" Residue "A GLU 33": "OE1" <-> "OE2" Residue "A PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 146": "OD1" <-> "OD2" Residue "A ARG 152": "NH1" <-> "NH2" Residue "A ASP 188": "OD1" <-> "OD2" Residue "A ARG 255": "NH1" <-> "NH2" Residue "A GLU 258": "OE1" <-> "OE2" Residue "A PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 288": "OE1" <-> "OE2" Residue "A GLU 289": "OE1" <-> "OE2" Residue "A GLU 327": "OE1" <-> "OE2" Residue "A ARG 333": "NH1" <-> "NH2" Residue "B ARG 58": "NH1" <-> "NH2" Residue "B PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 85": "OD1" <-> "OD2" Residue "B ARG 86": "NH1" <-> "NH2" Residue "B PHE 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 145": "OD1" <-> "OD2" Residue "B PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 150": "OE1" <-> "OE2" Residue "B TYR 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 178": "NH1" <-> "NH2" Residue "B TYR 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 205": "NH1" <-> "NH2" Residue "B ASP 234": "OD1" <-> "OD2" Residue "B TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 261": "OD1" <-> "OD2" Residue "B ASP 264": "OD1" <-> "OD2" Residue "B PHE 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 277": "OD1" <-> "OD2" Residue "B ARG 278": "NH1" <-> "NH2" Residue "B ASP 280": "OD1" <-> "OD2" Residue "B TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 345": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 389": "OD1" <-> "OD2" Residue "B PHE 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 413": "OD1" <-> "OD2" Residue "B ASP 436": "OD1" <-> "OD2" Residue "B GLU 441": "OE1" <-> "OE2" Residue "B PHE 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 476": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 482": "NH1" <-> "NH2" Residue "C ASP 57": "OD1" <-> "OD2" Residue "C TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 243": "OE1" <-> "OE2" Residue "C TYR 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 315": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 359": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 7790 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2400 Classifications: {'peptide': 308} Link IDs: {'PTRANS': 24, 'TRANS': 283} Chain breaks: 2 Chain: "B" Number of atoms: 3176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3176 Classifications: {'peptide': 435} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 22, 'TRANS': 412} Chain breaks: 3 Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 3, 'GLU:plan': 4} Unresolved non-hydrogen planarities: 34 Chain: "C" Number of atoms: 2214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2214 Classifications: {'peptide': 294} Link IDs: {'PTRANS': 20, 'TRANS': 273} Chain breaks: 2 Time building chain proxies: 4.68, per 1000 atoms: 0.60 Number of scatterers: 7790 At special positions: 0 Unit cell: (110.24, 89.04, 129.32, 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 16 16.00 O 1444 8.00 N 1400 7.00 C 4930 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 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: 2.93 Conformation dependent library (CDL) restraints added in 1.5 seconds 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1890 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 9 sheets defined 36.0% alpha, 7.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.74 Creating SS restraints... Processing helix chain 'A' and resid 38 through 42 Processing helix chain 'A' and resid 59 through 64 removed outlier: 4.118A pdb=" N LEU A 63 " --> pdb=" O SER A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 82 removed outlier: 3.702A pdb=" N LYS A 74 " --> pdb=" O PRO A 70 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N TRP A 75 " --> pdb=" O GLY A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 127 Processing helix chain 'A' and resid 150 through 163 removed outlier: 3.536A pdb=" N GLN A 154 " --> pdb=" O PRO A 150 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ALA A 155 " --> pdb=" O PRO A 151 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N TYR A 156 " --> pdb=" O ARG A 152 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N LEU A 159 " --> pdb=" O ALA A 155 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N HIS A 162 " --> pdb=" O ALA A 158 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N SER A 163 " --> pdb=" O LEU A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 173 Processing helix chain 'A' and resid 175 through 177 No H-bonds generated for 'chain 'A' and resid 175 through 177' Processing helix chain 'A' and resid 178 through 186 Processing helix chain 'A' and resid 193 through 213 removed outlier: 4.143A pdb=" N ALA A 199 " --> pdb=" O ALA A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 255 Processing helix chain 'A' and resid 269 through 285 removed outlier: 4.122A pdb=" N TYR A 278 " --> pdb=" O ALA A 274 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N LEU A 281 " --> pdb=" O SER A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 308 Processing helix chain 'A' and resid 311 through 321 removed outlier: 3.611A pdb=" N HIS A 316 " --> pdb=" O GLU A 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 66 removed outlier: 3.886A pdb=" N GLN B 64 " --> pdb=" O SER B 60 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ILE B 65 " --> pdb=" O LEU B 61 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N PHE B 66 " --> pdb=" O LEU B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 94 removed outlier: 3.648A pdb=" N GLY B 88 " --> pdb=" O LEU B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 260 Processing helix chain 'B' and resid 369 through 374 removed outlier: 3.857A pdb=" N ASP B 373 " --> pdb=" O GLY B 369 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL B 374 " --> pdb=" O GLY B 370 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 369 through 374' Processing helix chain 'B' and resid 446 through 462 removed outlier: 3.694A pdb=" N THR B 462 " --> pdb=" O VAL B 458 " (cutoff:3.500A) Processing helix chain 'C' and resid 18 through 32 Processing helix chain 'C' and resid 43 through 47 removed outlier: 3.596A pdb=" N VAL C 47 " --> pdb=" O PRO C 44 " (cutoff:3.500A) Processing helix chain 'C' and resid 66 through 73 removed outlier: 3.581A pdb=" N ILE C 70 " --> pdb=" O GLY C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 106 through 120 removed outlier: 3.642A pdb=" N SER C 120 " --> pdb=" O THR C 116 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 128 removed outlier: 3.519A pdb=" N LEU C 127 " --> pdb=" O ALA C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 141 through 148 Processing helix chain 'C' and resid 153 through 156 removed outlier: 3.626A pdb=" N TRP C 156 " --> pdb=" O PRO C 153 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 153 through 156' Processing helix chain 'C' and resid 157 through 170 Processing helix chain 'C' and resid 239 through 251 removed outlier: 4.612A pdb=" N VAL C 249 " --> pdb=" O ALA C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 284 removed outlier: 3.746A pdb=" N LEU C 274 " --> pdb=" O GLU C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 300 removed outlier: 4.201A pdb=" N ILE C 295 " --> pdb=" O TRP C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 300 through 315 removed outlier: 3.755A pdb=" N CYS C 304 " --> pdb=" O TYR C 300 " (cutoff:3.500A) Processing helix chain 'C' and resid 316 through 320 removed outlier: 3.923A pdb=" N LYS C 320 " --> pdb=" O GLN C 317 " (cutoff:3.500A) Processing helix chain 'C' and resid 329 through 333 removed outlier: 3.829A pdb=" N ALA C 333 " --> pdb=" O GLN C 330 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 352 Processing helix chain 'C' and resid 356 through 377 removed outlier: 4.646A pdb=" N TRP C 360 " --> pdb=" O LEU C 356 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N TRP C 361 " --> pdb=" O VAL C 357 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 30 through 32 Processing sheet with id=AA2, first strand: chain 'A' and resid 87 through 90 Processing sheet with id=AA3, first strand: chain 'B' and resid 139 through 140 removed outlier: 3.566A pdb=" N VAL B 158 " --> pdb=" O VAL B 139 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 179 through 182 removed outlier: 6.000A pdb=" N ALA B 207 " --> pdb=" O ARG B 180 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N HIS B 215 " --> pdb=" O LYS B 210 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 234 through 235 removed outlier: 3.988A pdb=" N THR B 275 " --> pdb=" O THR B 235 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N PHE B 291 " --> pdb=" O ARG B 276 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU B 339 " --> pdb=" O ALA B 316 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N SER B 400 " --> pdb=" O GLY B 338 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLY B 342 " --> pdb=" O PHE B 396 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N PHE B 396 " --> pdb=" O GLY B 342 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 416 through 417 Processing sheet with id=AA7, first strand: chain 'B' and resid 420 through 423 Processing sheet with id=AA8, first strand: chain 'C' and resid 6 through 7 Processing sheet with id=AA9, first strand: chain 'C' and resid 54 through 56 removed outlier: 3.705A pdb=" N ILE C 64 " --> pdb=" O LEU C 55 " (cutoff:3.500A) 260 hydrogen bonds defined for protein. 744 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: 1.80 Time building geometry restraints manager: 3.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2604 1.34 - 1.46: 1569 1.46 - 1.58: 3766 1.58 - 1.69: 0 1.69 - 1.81: 27 Bond restraints: 7966 Sorted by residual: bond pdb=" C ALA B 254 " pdb=" N SER B 255 " ideal model delta sigma weight residual 1.339 1.281 0.058 5.57e-02 3.22e+02 1.08e+00 bond pdb=" C LEU C 154 " pdb=" N PRO C 155 " ideal model delta sigma weight residual 1.334 1.356 -0.022 2.34e-02 1.83e+03 8.86e-01 bond pdb=" C PHE A 27 " pdb=" N PRO A 28 " ideal model delta sigma weight residual 1.334 1.355 -0.021 2.34e-02 1.83e+03 8.41e-01 bond pdb=" C LYS B 67 " pdb=" N PRO B 68 " ideal model delta sigma weight residual 1.334 1.355 -0.021 2.34e-02 1.83e+03 8.09e-01 bond pdb=" CG LEU B 169 " pdb=" CD2 LEU B 169 " ideal model delta sigma weight residual 1.521 1.492 0.029 3.30e-02 9.18e+02 7.87e-01 ... (remaining 7961 not shown) Histogram of bond angle deviations from ideal: 99.91 - 106.74: 326 106.74 - 113.56: 4332 113.56 - 120.38: 2989 120.38 - 127.20: 3082 127.20 - 134.03: 114 Bond angle restraints: 10843 Sorted by residual: angle pdb=" N LEU C 284 " pdb=" CA LEU C 284 " pdb=" C LEU C 284 " ideal model delta sigma weight residual 109.81 117.74 -7.93 2.21e+00 2.05e-01 1.29e+01 angle pdb=" N ILE C 17 " pdb=" CA ILE C 17 " pdb=" C ILE C 17 " ideal model delta sigma weight residual 111.88 108.76 3.12 1.06e+00 8.90e-01 8.67e+00 angle pdb=" N LEU A 101 " pdb=" CA LEU A 101 " pdb=" C LEU A 101 " ideal model delta sigma weight residual 109.81 116.06 -6.25 2.21e+00 2.05e-01 8.00e+00 angle pdb=" C SER A 257 " pdb=" N GLU A 258 " pdb=" CA GLU A 258 " ideal model delta sigma weight residual 125.66 130.44 -4.78 1.85e+00 2.92e-01 6.68e+00 angle pdb=" CA LEU C 52 " pdb=" CB LEU C 52 " pdb=" CG LEU C 52 " ideal model delta sigma weight residual 116.30 107.88 8.42 3.50e+00 8.16e-02 5.79e+00 ... (remaining 10838 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 4267 17.90 - 35.80: 376 35.80 - 53.70: 77 53.70 - 71.60: 15 71.60 - 89.50: 7 Dihedral angle restraints: 4742 sinusoidal: 1798 harmonic: 2944 Sorted by residual: dihedral pdb=" CA TRP A 261 " pdb=" C TRP A 261 " pdb=" N PHE A 262 " pdb=" CA PHE A 262 " ideal model delta harmonic sigma weight residual 180.00 -156.23 -23.77 0 5.00e+00 4.00e-02 2.26e+01 dihedral pdb=" CA ALA B 213 " pdb=" C ALA B 213 " pdb=" N SER B 214 " pdb=" CA SER B 214 " ideal model delta harmonic sigma weight residual -180.00 -156.74 -23.26 0 5.00e+00 4.00e-02 2.16e+01 dihedral pdb=" CA HIS C 51 " pdb=" C HIS C 51 " pdb=" N LEU C 52 " pdb=" CA LEU C 52 " ideal model delta harmonic sigma weight residual -180.00 -157.50 -22.50 0 5.00e+00 4.00e-02 2.03e+01 ... (remaining 4739 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 732 0.032 - 0.063: 320 0.063 - 0.095: 106 0.095 - 0.126: 57 0.126 - 0.158: 9 Chirality restraints: 1224 Sorted by residual: chirality pdb=" CB VAL C 287 " pdb=" CA VAL C 287 " pdb=" CG1 VAL C 287 " pdb=" CG2 VAL C 287 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.21e-01 chirality pdb=" CA LEU C 52 " pdb=" N LEU C 52 " pdb=" C LEU C 52 " pdb=" CB LEU C 52 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.20e-01 chirality pdb=" CA LEU C 284 " pdb=" N LEU C 284 " pdb=" C LEU C 284 " pdb=" CB LEU C 284 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.47e-01 ... (remaining 1221 not shown) Planarity restraints: 1412 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS B 478 " -0.036 5.00e-02 4.00e+02 5.49e-02 4.82e+00 pdb=" N PRO B 479 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO B 479 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 479 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO C 159 " 0.033 5.00e-02 4.00e+02 4.93e-02 3.89e+00 pdb=" N PRO C 160 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO C 160 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO C 160 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 18 " 0.030 5.00e-02 4.00e+02 4.55e-02 3.31e+00 pdb=" N PRO A 19 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO A 19 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 19 " 0.025 5.00e-02 4.00e+02 ... (remaining 1409 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 256 2.68 - 3.24: 7543 3.24 - 3.79: 11225 3.79 - 4.35: 14611 4.35 - 4.90: 24770 Nonbonded interactions: 58405 Sorted by model distance: nonbonded pdb=" O LEU A 159 " pdb=" OG SER A 163 " model vdw 2.129 2.440 nonbonded pdb=" OG SER B 268 " pdb=" O ASN B 304 " model vdw 2.137 2.440 nonbonded pdb=" O GLY C 328 " pdb=" OG SER C 332 " model vdw 2.218 2.440 nonbonded pdb=" OH TYR C 132 " pdb=" OH TYR C 146 " model vdw 2.218 2.440 nonbonded pdb=" OD1 ASN B 148 " pdb=" ND2 ASN B 372 " model vdw 2.226 2.520 ... (remaining 58400 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.330 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: 1.830 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 23.650 Find NCS groups from input model: 0.230 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:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 7966 Z= 0.227 Angle : 0.668 8.419 10843 Z= 0.364 Chirality : 0.043 0.158 1224 Planarity : 0.005 0.055 1412 Dihedral : 14.686 89.502 2852 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.49 % Favored : 87.51 % Rotamer: Outliers : 5.42 % Allowed : 14.38 % 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: -5.07 (0.22), residues: 1017 helix: -1.63 (0.25), residues: 340 sheet: -4.48 (0.27), residues: 193 loop : -4.23 (0.22), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 258 HIS 0.005 0.001 HIS C 6 PHE 0.015 0.001 PHE A 68 TYR 0.010 0.001 TYR B 240 ARG 0.003 0.000 ARG A 108 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 122 time to evaluate : 0.879 Fit side-chains outliers start: 43 outliers final: 27 residues processed: 161 average time/residue: 0.2168 time to fit residues: 46.3157 Evaluate side-chains 118 residues out of total 807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 91 time to evaluate : 0.851 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 0 residues processed: 27 average time/residue: 0.0857 time to fit residues: 5.1955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 86 optimal weight: 5.9990 chunk 77 optimal weight: 0.7980 chunk 42 optimal weight: 3.9990 chunk 26 optimal weight: 7.9990 chunk 52 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 30 optimal weight: 9.9990 chunk 48 optimal weight: 2.9990 chunk 59 optimal weight: 0.0010 chunk 92 optimal weight: 0.7980 overall best weight: 0.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 ASN ** A 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 178 HIS B 64 GLN ** B 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 172 ASN B 367 GLN ** B 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 419 GLN B 463 ASN ** B 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 4 GLN C 6 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.1262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7966 Z= 0.195 Angle : 0.639 9.459 10843 Z= 0.316 Chirality : 0.043 0.159 1224 Planarity : 0.006 0.054 1412 Dihedral : 5.095 23.162 1130 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.98 % Favored : 87.02 % Rotamer: Outliers : 3.66 % Allowed : 19.04 % Favored : 77.30 % 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: -3.91 (0.25), residues: 1017 helix: -0.36 (0.29), residues: 340 sheet: -3.92 (0.32), residues: 183 loop : -3.79 (0.25), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 8 HIS 0.003 0.001 HIS C 172 PHE 0.012 0.001 PHE A 68 TYR 0.010 0.001 TYR C 300 ARG 0.005 0.000 ARG C 169 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 106 time to evaluate : 1.009 Fit side-chains outliers start: 29 outliers final: 16 residues processed: 128 average time/residue: 0.1631 time to fit residues: 30.6997 Evaluate side-chains 110 residues out of total 807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 94 time to evaluate : 0.841 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.0748 time to fit residues: 3.3799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 51 optimal weight: 4.9990 chunk 28 optimal weight: 5.9990 chunk 77 optimal weight: 6.9990 chunk 63 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 92 optimal weight: 0.9990 chunk 100 optimal weight: 2.9990 chunk 82 optimal weight: 4.9990 chunk 31 optimal weight: 0.8980 chunk 74 optimal weight: 0.0980 chunk 91 optimal weight: 0.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 504 GLN C 50 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.1562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7966 Z= 0.186 Angle : 0.626 9.602 10843 Z= 0.307 Chirality : 0.042 0.154 1224 Planarity : 0.005 0.053 1412 Dihedral : 4.922 22.802 1130 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.70 % Favored : 88.30 % Rotamer: Outliers : 3.66 % Allowed : 20.05 % Favored : 76.29 % 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: -3.42 (0.26), residues: 1017 helix: 0.11 (0.30), residues: 342 sheet: -3.70 (0.33), residues: 179 loop : -3.54 (0.26), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 258 HIS 0.004 0.001 HIS C 172 PHE 0.017 0.001 PHE A 68 TYR 0.012 0.001 TYR A 240 ARG 0.006 0.000 ARG A 303 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 102 time to evaluate : 0.844 Fit side-chains outliers start: 29 outliers final: 11 residues processed: 125 average time/residue: 0.1537 time to fit residues: 28.3126 Evaluate side-chains 109 residues out of total 807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 98 time to evaluate : 0.764 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.0703 time to fit residues: 2.5138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 69 optimal weight: 3.9990 chunk 48 optimal weight: 0.0170 chunk 10 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 62 optimal weight: 6.9990 chunk 93 optimal weight: 1.9990 chunk 98 optimal weight: 0.8980 chunk 88 optimal weight: 1.9990 chunk 26 optimal weight: 8.9990 chunk 82 optimal weight: 5.9990 chunk 55 optimal weight: 0.7980 overall best weight: 1.1422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.1721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 7966 Z= 0.213 Angle : 0.635 10.215 10843 Z= 0.308 Chirality : 0.042 0.152 1224 Planarity : 0.005 0.055 1412 Dihedral : 4.918 22.591 1130 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.39 % Favored : 87.61 % Rotamer: Outliers : 2.52 % Allowed : 21.44 % Favored : 76.04 % 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: -3.20 (0.27), residues: 1017 helix: 0.42 (0.31), residues: 339 sheet: -3.62 (0.33), residues: 190 loop : -3.47 (0.26), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 8 HIS 0.004 0.001 HIS C 172 PHE 0.016 0.001 PHE A 68 TYR 0.013 0.001 TYR A 240 ARG 0.004 0.000 ARG B 500 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 107 time to evaluate : 0.850 Fit side-chains outliers start: 20 outliers final: 9 residues processed: 120 average time/residue: 0.1659 time to fit residues: 28.9312 Evaluate side-chains 110 residues out of total 807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 101 time to evaluate : 0.900 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0722 time to fit residues: 2.3773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 1 optimal weight: 4.9990 chunk 73 optimal weight: 0.7980 chunk 40 optimal weight: 6.9990 chunk 84 optimal weight: 5.9990 chunk 68 optimal weight: 1.9990 chunk 0 optimal weight: 40.0000 chunk 50 optimal weight: 8.9990 chunk 88 optimal weight: 0.9980 chunk 24 optimal weight: 4.9990 chunk 33 optimal weight: 7.9990 chunk 19 optimal weight: 9.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 75 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.1743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.090 7966 Z= 0.384 Angle : 0.728 11.727 10843 Z= 0.352 Chirality : 0.046 0.171 1224 Planarity : 0.006 0.058 1412 Dihedral : 5.357 25.900 1130 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.34 % Favored : 84.66 % Rotamer: Outliers : 2.14 % Allowed : 23.83 % Favored : 74.02 % 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: -3.30 (0.27), residues: 1017 helix: 0.36 (0.31), residues: 338 sheet: -3.68 (0.33), residues: 190 loop : -3.53 (0.26), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 8 HIS 0.006 0.001 HIS C 75 PHE 0.021 0.002 PHE A 68 TYR 0.015 0.002 TYR A 240 ARG 0.007 0.000 ARG C 247 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 96 time to evaluate : 0.928 Fit side-chains outliers start: 17 outliers final: 10 residues processed: 104 average time/residue: 0.1698 time to fit residues: 25.8387 Evaluate side-chains 95 residues out of total 807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 85 time to evaluate : 0.876 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0742 time to fit residues: 2.5908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 57 optimal weight: 0.0000 chunk 24 optimal weight: 0.5980 chunk 98 optimal weight: 0.9980 chunk 81 optimal weight: 0.2980 chunk 45 optimal weight: 0.5980 chunk 8 optimal weight: 0.8980 chunk 32 optimal weight: 9.9990 chunk 51 optimal weight: 3.9990 chunk 95 optimal weight: 0.9980 chunk 11 optimal weight: 0.8980 chunk 56 optimal weight: 2.9990 overall best weight: 0.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 56 ASN B 82 GLN ** B 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 75 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.1983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7966 Z= 0.169 Angle : 0.627 11.277 10843 Z= 0.301 Chirality : 0.041 0.152 1224 Planarity : 0.005 0.058 1412 Dihedral : 4.838 22.358 1130 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.21 % Favored : 88.79 % Rotamer: Outliers : 1.13 % Allowed : 25.73 % Favored : 73.14 % 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: -2.96 (0.27), residues: 1017 helix: 0.67 (0.31), residues: 340 sheet: -3.42 (0.34), residues: 186 loop : -3.41 (0.26), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 244 HIS 0.006 0.001 HIS C 75 PHE 0.011 0.001 PHE A 68 TYR 0.015 0.001 TYR A 240 ARG 0.005 0.000 ARG C 169 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 107 time to evaluate : 0.878 Fit side-chains outliers start: 9 outliers final: 4 residues processed: 112 average time/residue: 0.1698 time to fit residues: 27.7677 Evaluate side-chains 104 residues out of total 807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 100 time to evaluate : 0.932 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0663 time to fit residues: 1.7026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 72 optimal weight: 0.0030 chunk 55 optimal weight: 0.0060 chunk 83 optimal weight: 3.9990 chunk 98 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 59 optimal weight: 4.9990 chunk 45 optimal weight: 0.3980 chunk 60 optimal weight: 0.9980 chunk 39 optimal weight: 4.9990 chunk 58 optimal weight: 1.9990 chunk 29 optimal weight: 5.9990 overall best weight: 0.4806 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 75 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.2193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 7966 Z= 0.164 Angle : 0.629 10.962 10843 Z= 0.298 Chirality : 0.041 0.148 1224 Planarity : 0.005 0.057 1412 Dihedral : 4.641 20.851 1130 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.91 % Favored : 89.09 % Rotamer: Outliers : 1.39 % Allowed : 25.98 % Favored : 72.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.76 (0.27), residues: 1017 helix: 0.81 (0.30), residues: 341 sheet: -3.39 (0.33), residues: 191 loop : -3.22 (0.26), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 258 HIS 0.006 0.001 HIS C 75 PHE 0.014 0.001 PHE A 24 TYR 0.013 0.001 TYR A 240 ARG 0.006 0.000 ARG B 500 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 108 time to evaluate : 1.013 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 9 residues processed: 114 average time/residue: 0.2297 time to fit residues: 38.6222 Evaluate side-chains 111 residues out of total 807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 102 time to evaluate : 0.896 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0945 time to fit residues: 2.8098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 19 optimal weight: 7.9990 chunk 62 optimal weight: 0.0870 chunk 66 optimal weight: 8.9990 chunk 48 optimal weight: 0.0050 chunk 9 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 chunk 89 optimal weight: 0.1980 chunk 94 optimal weight: 9.9990 chunk 85 optimal weight: 0.0050 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 6.9990 overall best weight: 0.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.2480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 7966 Z= 0.150 Angle : 0.611 11.543 10843 Z= 0.294 Chirality : 0.041 0.149 1224 Planarity : 0.005 0.058 1412 Dihedral : 4.479 19.898 1130 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.54 % Favored : 90.46 % Rotamer: Outliers : 0.38 % Allowed : 26.36 % Favored : 73.27 % 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: -2.53 (0.27), residues: 1017 helix: 0.98 (0.30), residues: 341 sheet: -3.13 (0.35), residues: 179 loop : -3.15 (0.26), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 258 HIS 0.005 0.001 HIS C 122 PHE 0.009 0.001 PHE A 68 TYR 0.010 0.001 TYR A 240 ARG 0.009 0.000 ARG C 169 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 111 time to evaluate : 0.805 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 113 average time/residue: 0.1886 time to fit residues: 29.8788 Evaluate side-chains 99 residues out of total 807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 97 time to evaluate : 0.794 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0754 time to fit residues: 1.4878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 39 optimal weight: 0.8980 chunk 71 optimal weight: 6.9990 chunk 28 optimal weight: 2.9990 chunk 82 optimal weight: 0.6980 chunk 86 optimal weight: 0.9980 chunk 91 optimal weight: 6.9990 chunk 60 optimal weight: 3.9990 chunk 96 optimal weight: 0.8980 chunk 59 optimal weight: 0.7980 chunk 45 optimal weight: 5.9990 chunk 67 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 51 HIS C 75 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.2511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 7966 Z= 0.192 Angle : 0.640 10.746 10843 Z= 0.304 Chirality : 0.042 0.139 1224 Planarity : 0.006 0.058 1412 Dihedral : 4.541 20.624 1130 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.52 % Favored : 89.48 % Rotamer: Outliers : 0.25 % Allowed : 27.11 % Favored : 72.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.45 (0.27), residues: 1017 helix: 1.02 (0.30), residues: 341 sheet: -3.12 (0.35), residues: 184 loop : -3.05 (0.26), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP C 258 HIS 0.006 0.001 HIS C 75 PHE 0.013 0.001 PHE A 68 TYR 0.014 0.001 TYR B 240 ARG 0.008 0.000 ARG C 169 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 102 time to evaluate : 0.849 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 103 average time/residue: 0.1759 time to fit residues: 26.1707 Evaluate side-chains 98 residues out of total 807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 97 time to evaluate : 0.798 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0747 time to fit residues: 1.2943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 101 optimal weight: 0.0980 chunk 93 optimal weight: 5.9990 chunk 80 optimal weight: 10.0000 chunk 8 optimal weight: 0.6980 chunk 62 optimal weight: 8.9990 chunk 49 optimal weight: 0.0060 chunk 64 optimal weight: 0.9990 chunk 86 optimal weight: 3.9990 chunk 24 optimal weight: 0.8980 chunk 74 optimal weight: 2.9990 chunk 11 optimal weight: 0.0670 overall best weight: 0.3534 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 75 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.2723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 7966 Z= 0.163 Angle : 0.643 16.399 10843 Z= 0.303 Chirality : 0.041 0.149 1224 Planarity : 0.005 0.059 1412 Dihedral : 4.396 19.248 1130 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.14 % Favored : 90.86 % Rotamer: Outliers : 0.25 % Allowed : 27.74 % Favored : 72.01 % 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: -2.34 (0.27), residues: 1017 helix: 0.99 (0.30), residues: 341 sheet: -2.85 (0.37), residues: 175 loop : -3.00 (0.26), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 258 HIS 0.007 0.001 HIS C 75 PHE 0.008 0.001 PHE A 68 TYR 0.017 0.001 TYR B 240 ARG 0.007 0.000 ARG B 500 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 103 time to evaluate : 0.845 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 104 average time/residue: 0.1989 time to fit residues: 28.9421 Evaluate side-chains 94 residues out of total 807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 94 time to evaluate : 0.857 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 22 optimal weight: 0.7980 chunk 81 optimal weight: 0.8980 chunk 33 optimal weight: 20.0000 chunk 83 optimal weight: 0.7980 chunk 10 optimal weight: 0.0270 chunk 14 optimal weight: 3.9990 chunk 71 optimal weight: 0.2980 chunk 4 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 92 optimal weight: 0.9980 chunk 54 optimal weight: 6.9990 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 215 HIS B 286 GLN C 75 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.176281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.139715 restraints weight = 9640.028| |-----------------------------------------------------------------------------| r_work (start): 0.3618 rms_B_bonded: 2.52 r_work: 0.3462 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3331 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.2816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7966 Z= 0.170 Angle : 0.651 14.931 10843 Z= 0.307 Chirality : 0.041 0.140 1224 Planarity : 0.005 0.059 1412 Dihedral : 4.378 19.073 1130 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.34 % Favored : 90.66 % Rotamer: Outliers : 0.25 % Allowed : 28.12 % Favored : 71.63 % 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: -2.23 (0.27), residues: 1017 helix: 1.10 (0.31), residues: 342 sheet: -2.80 (0.36), residues: 180 loop : -2.94 (0.26), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP C 258 HIS 0.007 0.001 HIS C 75 PHE 0.008 0.001 PHE A 68 TYR 0.015 0.001 TYR B 240 ARG 0.007 0.000 ARG B 500 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1890.64 seconds wall clock time: 35 minutes 1.47 seconds (2101.47 seconds total)