Starting phenix.real_space_refine on Sun Dec 29 02:46:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rxc_24728/12_2024/7rxc_24728.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rxc_24728/12_2024/7rxc_24728.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7rxc_24728/12_2024/7rxc_24728.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rxc_24728/12_2024/7rxc_24728.map" model { file = "/net/cci-nas-00/data/ceres_data/7rxc_24728/12_2024/7rxc_24728.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rxc_24728/12_2024/7rxc_24728.cif" } resolution = 3.2 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= 0.006 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 32 5.16 5 C 6056 2.51 5 N 1510 2.21 5 O 1762 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 9360 Number of models: 1 Model: "" Number of chains: 7 Chain: "H" Number of atoms: 1582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1582 Classifications: {'peptide': 207} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 192} Chain breaks: 2 Chain: "L" Number of atoms: 1588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1588 Classifications: {'peptide': 204} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 194} Chain breaks: 2 Chain: "N" Number of atoms: 1008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1008 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 3, 'TRANS': 122} Chain: "B" Number of atoms: 3433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3433 Classifications: {'peptide': 439} Link IDs: {'PTRANS': 24, 'TRANS': 414} Chain breaks: 4 Chain: "K" Number of atoms: 1661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1661 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 3, 'TRANS': 198} Chain: "A" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 23 Unusual residues: {'GLC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "K" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 65 Unusual residues: {'POV': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 143 Unresolved non-hydrogen angles: 179 Unresolved non-hydrogen dihedrals: 123 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'POV:plan-3': 4, 'POV:plan-2': 4} Unresolved non-hydrogen planarities: 23 Time building chain proxies: 6.04, per 1000 atoms: 0.65 Number of scatterers: 9360 At special positions: 0 Unit cell: (128.26, 125.08, 108.12, 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 32 16.00 O 1762 8.00 N 1510 7.00 C 6056 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 150 " - pdb=" SG CYS H 206 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 94 " distance=2.03 Simple disulfide: pdb=" SG CYS L 139 " - pdb=" SG CYS L 199 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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 Links applied ALPHA1-4 " GLC A 1 " - " GLC A 2 " Time building additional restraints: 2.69 Conformation dependent library (CDL) restraints added in 1.2 seconds 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2194 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 19 sheets defined 36.9% alpha, 30.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.35 Creating SS restraints... Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.550A pdb=" N PHE H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'L' and resid 85 through 89 removed outlier: 3.649A pdb=" N LEU L 89 " --> pdb=" O PRO L 86 " (cutoff:3.500A) Processing helix chain 'L' and resid 126 through 132 Processing helix chain 'L' and resid 188 through 194 removed outlier: 3.984A pdb=" N HIS L 194 " --> pdb=" O ASP L 190 " (cutoff:3.500A) Processing helix chain 'N' and resid 87 through 91 Processing helix chain 'B' and resid 17 through 28 Processing helix chain 'B' and resid 43 through 52 Proline residue: B 49 - end of helix Processing helix chain 'B' and resid 65 through 75 removed outlier: 3.631A pdb=" N GLY B 69 " --> pdb=" O HIS B 65 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N GLY B 70 " --> pdb=" O ASP B 66 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N TYR B 71 " --> pdb=" O ARG B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 89 Processing helix chain 'B' and resid 91 through 98 Processing helix chain 'B' and resid 129 through 131 No H-bonds generated for 'chain 'B' and resid 129 through 131' Processing helix chain 'B' and resid 132 through 141 Processing helix chain 'B' and resid 154 through 164 removed outlier: 3.712A pdb=" N THR B 158 " --> pdb=" O GLU B 154 " (cutoff:3.500A) Proline residue: B 160 - end of helix Processing helix chain 'B' and resid 186 through 202 Processing helix chain 'B' and resid 210 through 220 Processing helix chain 'B' and resid 231 through 240 removed outlier: 4.545A pdb=" N ASN B 235 " --> pdb=" O TRP B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 284 Processing helix chain 'B' and resid 287 through 298 removed outlier: 3.868A pdb=" N ASP B 297 " --> pdb=" O ALA B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 313 Processing helix chain 'B' and resid 315 through 328 Processing helix chain 'B' and resid 336 through 353 Processing helix chain 'B' and resid 357 through 370 Processing helix chain 'B' and resid 374 through 388 Processing helix chain 'B' and resid 391 through 406 Processing helix chain 'B' and resid 502 through 517 Processing helix chain 'K' and resid 3 through 27 Processing helix chain 'K' and resid 33 through 48 Processing helix chain 'K' and resid 49 through 52 removed outlier: 4.196A pdb=" N PHE K 52 " --> pdb=" O LEU K 49 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 49 through 52' Processing helix chain 'K' and resid 57 through 80 Processing helix chain 'K' and resid 95 through 110 Proline residue: K 101 - end of helix removed outlier: 3.702A pdb=" N ASN K 110 " --> pdb=" O SER K 106 " (cutoff:3.500A) Processing helix chain 'K' and resid 114 through 129 Processing helix chain 'K' and resid 131 through 142 Processing helix chain 'K' and resid 148 through 173 Processing helix chain 'K' and resid 177 through 202 Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.740A pdb=" N GLY H 33 " --> pdb=" O ARG H 99 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N MET H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N TYR H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALA H 40 " --> pdb=" O GLY H 44 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 11 through 12 removed outlier: 4.344A pdb=" N TYR H 112 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 130 through 134 removed outlier: 3.891A pdb=" N GLY H 149 " --> pdb=" O LEU H 134 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N GLY H 149 " --> pdb=" O VAL H 192 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N VAL H 192 " --> pdb=" O GLY H 149 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N LEU H 151 " --> pdb=" O SER H 190 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N SER H 190 " --> pdb=" O LEU H 151 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N LYS H 153 " --> pdb=" O LEU H 188 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N LEU H 188 " --> pdb=" O LYS H 153 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 130 through 134 removed outlier: 3.891A pdb=" N GLY H 149 " --> pdb=" O LEU H 134 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N GLY H 149 " --> pdb=" O VAL H 192 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N VAL H 192 " --> pdb=" O GLY H 149 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N LEU H 151 " --> pdb=" O SER H 190 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N SER H 190 " --> pdb=" O LEU H 151 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N LYS H 153 " --> pdb=" O LEU H 188 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N LEU H 188 " --> pdb=" O LYS H 153 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N SER H 187 " --> pdb=" O VAL H 179 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 161 through 164 removed outlier: 6.586A pdb=" N LYS B 484 " --> pdb=" O PHE B 532 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N VAL B 534 " --> pdb=" O LYS B 484 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N VAL B 486 " --> pdb=" O VAL B 534 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AA8, first strand: chain 'L' and resid 10 through 14 removed outlier: 6.921A pdb=" N LEU L 11 " --> pdb=" O GLU L 110 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N LYS L 112 " --> pdb=" O LEU L 11 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N VAL L 13 " --> pdb=" O LYS L 112 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA L 90 " --> pdb=" O LEU L 109 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N LEU L 39 " --> pdb=" O TYR L 55 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N TYR L 55 " --> pdb=" O LEU L 39 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N TRP L 41 " --> pdb=" O LEU L 53 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 10 through 14 removed outlier: 6.921A pdb=" N LEU L 11 " --> pdb=" O GLU L 110 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N LYS L 112 " --> pdb=" O LEU L 11 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N VAL L 13 " --> pdb=" O LYS L 112 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA L 90 " --> pdb=" O LEU L 109 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 119 through 123 removed outlier: 5.766A pdb=" N TYR L 178 " --> pdb=" O ASN L 143 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 150 through 154 Processing sheet with id=AB3, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB4, first strand: chain 'N' and resid 11 through 13 removed outlier: 6.719A pdb=" N TRP N 32 " --> pdb=" O ARG N 52 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N ARG N 52 " --> pdb=" O TRP N 32 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N MET N 34 " --> pdb=" O ALA N 50 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N ALA N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'N' and resid 11 through 13 Processing sheet with id=AB6, first strand: chain 'B' and resid 37 through 39 removed outlier: 5.931A pdb=" N ILE B 10 " --> pdb=" O GLU B 39 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N VAL B 9 " --> pdb=" O ILE B 60 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N PHE B 62 " --> pdb=" O VAL B 9 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N TRP B 11 " --> pdb=" O PHE B 62 " (cutoff:3.500A) removed outlier: 8.666A pdb=" N ALA B 64 " --> pdb=" O TRP B 11 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N GLY B 261 " --> pdb=" O VAL B 111 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N VAL B 111 " --> pdb=" O GLY B 261 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N LEU B 263 " --> pdb=" O ILE B 109 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 37 through 39 removed outlier: 5.931A pdb=" N ILE B 10 " --> pdb=" O GLU B 39 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N VAL B 9 " --> pdb=" O ILE B 60 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N PHE B 62 " --> pdb=" O VAL B 9 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N TRP B 11 " --> pdb=" O PHE B 62 " (cutoff:3.500A) removed outlier: 8.666A pdb=" N ALA B 64 " --> pdb=" O TRP B 11 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 99 through 100 Processing sheet with id=AB9, first strand: chain 'B' and resid 225 through 228 Processing sheet with id=AC1, first strand: chain 'B' and resid 171 through 173 removed outlier: 4.059A pdb=" N LYS B 171 " --> pdb=" O ASP B 178 " (cutoff:3.500A) 502 hydrogen bonds defined for protein. 1368 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: 3.51 Time building geometry restraints manager: 3.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1509 1.31 - 1.44: 2699 1.44 - 1.56: 5330 1.56 - 1.69: 1 1.69 - 1.81: 51 Bond restraints: 9590 Sorted by residual: bond pdb=" C29 POV K 304 " pdb="C210 POV K 304 " ideal model delta sigma weight residual 1.333 1.528 -0.195 2.00e-02 2.50e+03 9.46e+01 bond pdb=" C29 POV K 302 " pdb="C210 POV K 302 " ideal model delta sigma weight residual 1.333 1.527 -0.194 2.00e-02 2.50e+03 9.42e+01 bond pdb=" C29 POV K 303 " pdb="C210 POV K 303 " ideal model delta sigma weight residual 1.333 1.527 -0.194 2.00e-02 2.50e+03 9.37e+01 bond pdb=" C29 POV K 301 " pdb="C210 POV K 301 " ideal model delta sigma weight residual 1.333 1.526 -0.193 2.00e-02 2.50e+03 9.27e+01 bond pdb=" C21 POV K 302 " pdb=" O21 POV K 302 " ideal model delta sigma weight residual 1.330 1.185 0.145 2.00e-02 2.50e+03 5.24e+01 ... (remaining 9585 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.73: 12946 3.73 - 7.46: 47 7.46 - 11.19: 3 11.19 - 14.92: 1 14.92 - 18.65: 8 Bond angle restraints: 13005 Sorted by residual: angle pdb=" C29 POV K 301 " pdb="C210 POV K 301 " pdb="C211 POV K 301 " ideal model delta sigma weight residual 127.67 109.02 18.65 3.00e+00 1.11e-01 3.86e+01 angle pdb=" C28 POV K 303 " pdb=" C29 POV K 303 " pdb="C210 POV K 303 " ideal model delta sigma weight residual 127.79 109.29 18.50 3.00e+00 1.11e-01 3.80e+01 angle pdb=" C28 POV K 302 " pdb=" C29 POV K 302 " pdb="C210 POV K 302 " ideal model delta sigma weight residual 127.79 109.32 18.47 3.00e+00 1.11e-01 3.79e+01 angle pdb=" C29 POV K 303 " pdb="C210 POV K 303 " pdb="C211 POV K 303 " ideal model delta sigma weight residual 127.67 109.31 18.36 3.00e+00 1.11e-01 3.75e+01 angle pdb=" C28 POV K 301 " pdb=" C29 POV K 301 " pdb="C210 POV K 301 " ideal model delta sigma weight residual 127.79 109.48 18.31 3.00e+00 1.11e-01 3.73e+01 ... (remaining 13000 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 5128 17.95 - 35.91: 428 35.91 - 53.86: 92 53.86 - 71.82: 17 71.82 - 89.77: 10 Dihedral angle restraints: 5675 sinusoidal: 2250 harmonic: 3425 Sorted by residual: dihedral pdb=" CA GLU H 158 " pdb=" C GLU H 158 " pdb=" N PRO H 159 " pdb=" CA PRO H 159 " ideal model delta harmonic sigma weight residual 180.00 148.16 31.84 0 5.00e+00 4.00e-02 4.05e+01 dihedral pdb=" CB CYS N 22 " pdb=" SG CYS N 22 " pdb=" SG CYS N 96 " pdb=" CB CYS N 96 " ideal model delta sinusoidal sigma weight residual 93.00 47.49 45.51 1 1.00e+01 1.00e-02 2.87e+01 dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 96 " pdb=" CB CYS H 96 " ideal model delta sinusoidal sigma weight residual 93.00 58.52 34.48 1 1.00e+01 1.00e-02 1.69e+01 ... (remaining 5672 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 1243 0.059 - 0.118: 181 0.118 - 0.177: 14 0.177 - 0.236: 1 0.236 - 0.294: 1 Chirality restraints: 1440 Sorted by residual: chirality pdb=" C1 GLC A 2 " pdb=" O4 GLC A 1 " pdb=" C2 GLC A 2 " pdb=" O5 GLC A 2 " both_signs ideal model delta sigma weight residual False 2.40 2.33 0.07 2.00e-02 2.50e+03 1.28e+01 chirality pdb=" C1 GLC A 1 " pdb=" C2 GLC A 1 " pdb=" O1 GLC A 1 " pdb=" O5 GLC A 1 " both_signs ideal model delta sigma weight residual False -2.04 -2.33 0.29 2.00e-01 2.50e+01 2.17e+00 chirality pdb=" CA ASN B 283 " pdb=" N ASN B 283 " pdb=" C ASN B 283 " pdb=" CB ASN B 283 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.08e+00 ... (remaining 1437 not shown) Planarity restraints: 1630 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C28 POV K 303 " -0.278 2.00e-02 2.50e+03 2.79e-01 7.76e+02 pdb=" C29 POV K 303 " 0.278 2.00e-02 2.50e+03 pdb="C210 POV K 303 " 0.279 2.00e-02 2.50e+03 pdb="C211 POV K 303 " -0.279 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C28 POV K 304 " 0.172 2.00e-02 2.50e+03 1.72e-01 2.96e+02 pdb=" C29 POV K 304 " -0.173 2.00e-02 2.50e+03 pdb="C210 POV K 304 " -0.171 2.00e-02 2.50e+03 pdb="C211 POV K 304 " 0.172 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C28 POV K 302 " -0.147 2.00e-02 2.50e+03 1.47e-01 2.16e+02 pdb=" C29 POV K 302 " 0.146 2.00e-02 2.50e+03 pdb="C210 POV K 302 " 0.148 2.00e-02 2.50e+03 pdb="C211 POV K 302 " -0.147 2.00e-02 2.50e+03 ... (remaining 1627 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 111 2.65 - 3.21: 8507 3.21 - 3.78: 14725 3.78 - 4.34: 20837 4.34 - 4.90: 34383 Nonbonded interactions: 78563 Sorted by model distance: nonbonded pdb=" OD1 ASP K 9 " pdb=" OH TYR K 162 " model vdw 2.089 3.040 nonbonded pdb=" OH TYR N 106 " pdb=" OD2 ASP K 9 " model vdw 2.126 3.040 nonbonded pdb=" OG1 THR K 45 " pdb=" OH TYR K 72 " model vdw 2.157 3.040 nonbonded pdb=" O ASN B 235 " pdb=" OG1 THR B 238 " model vdw 2.173 3.040 nonbonded pdb=" O PRO H 129 " pdb=" OH TYR B 513 " model vdw 2.182 3.040 ... (remaining 78558 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 0.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.380 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 25.630 Find NCS groups from input model: 0.130 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: 0.010 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.195 9590 Z= 0.328 Angle : 0.777 18.648 13005 Z= 0.348 Chirality : 0.042 0.294 1440 Planarity : 0.011 0.279 1630 Dihedral : 14.270 89.769 3466 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % Cis-general : 0.00 % Twisted Proline : 1.92 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.24), residues: 1152 helix: 1.83 (0.26), residues: 381 sheet: 0.63 (0.28), residues: 305 loop : 0.12 (0.30), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP N 107 HIS 0.004 0.001 HIS L 95 PHE 0.030 0.001 PHE B 259 TYR 0.048 0.001 TYR K 162 ARG 0.005 0.000 ARG B 99 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 147 time to evaluate : 1.037 Fit side-chains REVERT: N 46 GLU cc_start: 0.7803 (pt0) cc_final: 0.7590 (pt0) REVERT: K 201 LYS cc_start: 0.7742 (ttmt) cc_final: 0.7519 (ttpt) outliers start: 0 outliers final: 0 residues processed: 147 average time/residue: 0.2568 time to fit residues: 50.6712 Evaluate side-chains 118 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 118 time to evaluate : 1.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 97 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 chunk 48 optimal weight: 0.8980 chunk 29 optimal weight: 0.8980 chunk 58 optimal weight: 4.9990 chunk 46 optimal weight: 0.3980 chunk 90 optimal weight: 5.9990 chunk 34 optimal weight: 6.9990 chunk 54 optimal weight: 0.0170 chunk 67 optimal weight: 3.9990 chunk 104 optimal weight: 5.9990 overall best weight: 1.0420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 84 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.0990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9590 Z= 0.215 Angle : 0.537 7.496 13005 Z= 0.279 Chirality : 0.040 0.149 1440 Planarity : 0.005 0.123 1630 Dihedral : 7.172 69.181 1352 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 0.60 % Allowed : 6.71 % Favored : 92.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % Cis-general : 0.00 % Twisted Proline : 1.92 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.25), residues: 1152 helix: 1.95 (0.25), residues: 387 sheet: 0.75 (0.29), residues: 305 loop : 0.12 (0.30), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 523 HIS 0.003 0.001 HIS L 95 PHE 0.019 0.001 PHE B 259 TYR 0.031 0.001 TYR K 162 ARG 0.003 0.000 ARG B 99 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 133 time to evaluate : 0.964 Fit side-chains revert: symmetry clash REVERT: H 153 LYS cc_start: 0.8318 (ttpt) cc_final: 0.7873 (ttmt) REVERT: N 46 GLU cc_start: 0.7785 (pt0) cc_final: 0.7564 (pt0) REVERT: B 178 ASP cc_start: 0.6634 (t0) cc_final: 0.6211 (p0) REVERT: K 201 LYS cc_start: 0.7781 (ttmt) cc_final: 0.7482 (ttpt) outliers start: 6 outliers final: 4 residues processed: 135 average time/residue: 0.2460 time to fit residues: 45.4819 Evaluate side-chains 125 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 121 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 131 VAL Chi-restraints excluded: chain L residue 21 MET Chi-restraints excluded: chain L residue 181 SER Chi-restraints excluded: chain K residue 53 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 58 optimal weight: 0.1980 chunk 32 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 chunk 71 optimal weight: 9.9990 chunk 28 optimal weight: 0.9990 chunk 104 optimal weight: 0.5980 chunk 113 optimal weight: 4.9990 chunk 93 optimal weight: 9.9990 chunk 103 optimal weight: 7.9990 chunk 35 optimal weight: 10.0000 chunk 83 optimal weight: 0.0470 overall best weight: 0.7682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 356 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.1216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9590 Z= 0.175 Angle : 0.502 6.083 13005 Z= 0.260 Chirality : 0.040 0.165 1440 Planarity : 0.004 0.103 1630 Dihedral : 6.713 56.617 1352 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.20 % Allowed : 8.61 % Favored : 90.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % Cis-general : 0.00 % Twisted Proline : 1.92 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.25), residues: 1152 helix: 2.18 (0.26), residues: 386 sheet: 0.78 (0.28), residues: 312 loop : 0.17 (0.30), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 159 HIS 0.003 0.001 HIS L 194 PHE 0.012 0.001 PHE B 259 TYR 0.018 0.001 TYR K 162 ARG 0.002 0.000 ARG H 19 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 131 time to evaluate : 1.066 Fit side-chains revert: symmetry clash REVERT: N 46 GLU cc_start: 0.7828 (pt0) cc_final: 0.7597 (pt0) REVERT: B 23 GLU cc_start: 0.7728 (OUTLIER) cc_final: 0.6586 (mp0) REVERT: B 178 ASP cc_start: 0.6581 (t0) cc_final: 0.6163 (p0) outliers start: 12 outliers final: 7 residues processed: 137 average time/residue: 0.2310 time to fit residues: 44.0099 Evaluate side-chains 131 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 123 time to evaluate : 1.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 131 VAL Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain L residue 21 MET Chi-restraints excluded: chain L residue 181 SER Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 23 GLU Chi-restraints excluded: chain B residue 487 ILE Chi-restraints excluded: chain K residue 53 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 103 optimal weight: 7.9990 chunk 78 optimal weight: 10.0000 chunk 54 optimal weight: 0.9990 chunk 11 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 chunk 70 optimal weight: 0.9980 chunk 104 optimal weight: 5.9990 chunk 111 optimal weight: 2.9990 chunk 99 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 92 optimal weight: 20.0000 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 194 HIS B 356 GLN B 366 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.1393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 9590 Z= 0.291 Angle : 0.547 6.433 13005 Z= 0.282 Chirality : 0.041 0.184 1440 Planarity : 0.004 0.087 1630 Dihedral : 6.752 55.025 1352 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.60 % Allowed : 10.21 % Favored : 88.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.25), residues: 1152 helix: 2.11 (0.26), residues: 386 sheet: 0.70 (0.28), residues: 320 loop : 0.14 (0.30), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 47 HIS 0.005 0.001 HIS H 35 PHE 0.014 0.001 PHE B 259 TYR 0.016 0.001 TYR K 158 ARG 0.003 0.000 ARG B 99 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 131 time to evaluate : 1.076 Fit side-chains revert: symmetry clash REVERT: L 193 LYS cc_start: 0.7473 (pptt) cc_final: 0.6691 (pptt) REVERT: N 46 GLU cc_start: 0.7811 (pt0) cc_final: 0.7571 (pt0) REVERT: B 23 GLU cc_start: 0.7678 (OUTLIER) cc_final: 0.6466 (mp0) REVERT: B 178 ASP cc_start: 0.6502 (t0) cc_final: 0.6192 (p0) REVERT: B 366 GLN cc_start: 0.8400 (OUTLIER) cc_final: 0.8175 (mm-40) outliers start: 16 outliers final: 9 residues processed: 141 average time/residue: 0.2395 time to fit residues: 46.1094 Evaluate side-chains 138 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 127 time to evaluate : 1.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 131 VAL Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain L residue 21 MET Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 181 SER Chi-restraints excluded: chain B residue 23 GLU Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 366 GLN Chi-restraints excluded: chain B residue 524 THR Chi-restraints excluded: chain K residue 53 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 63 optimal weight: 8.9990 chunk 1 optimal weight: 5.9990 chunk 82 optimal weight: 10.0000 chunk 45 optimal weight: 2.9990 chunk 94 optimal weight: 0.7980 chunk 76 optimal weight: 0.8980 chunk 0 optimal weight: 6.9990 chunk 56 optimal weight: 2.9990 chunk 99 optimal weight: 0.8980 chunk 28 optimal weight: 0.3980 chunk 37 optimal weight: 5.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 366 GLN K 134 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.1485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 9590 Z= 0.219 Angle : 0.513 7.276 13005 Z= 0.265 Chirality : 0.040 0.198 1440 Planarity : 0.004 0.061 1630 Dihedral : 6.556 56.121 1352 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.10 % Allowed : 11.71 % Favored : 87.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.25), residues: 1152 helix: 2.20 (0.26), residues: 386 sheet: 0.67 (0.28), residues: 324 loop : 0.17 (0.31), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 47 HIS 0.006 0.001 HIS L 194 PHE 0.011 0.001 PHE B 259 TYR 0.013 0.001 TYR H 95 ARG 0.003 0.000 ARG B 99 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 129 time to evaluate : 1.060 Fit side-chains revert: symmetry clash REVERT: L 193 LYS cc_start: 0.7613 (pptt) cc_final: 0.6925 (pptt) REVERT: N 46 GLU cc_start: 0.7842 (pt0) cc_final: 0.7604 (pt0) REVERT: B 23 GLU cc_start: 0.7629 (OUTLIER) cc_final: 0.6377 (mp0) REVERT: B 178 ASP cc_start: 0.6517 (t0) cc_final: 0.6132 (p0) outliers start: 11 outliers final: 8 residues processed: 136 average time/residue: 0.2451 time to fit residues: 45.6983 Evaluate side-chains 134 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 125 time to evaluate : 1.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 131 VAL Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain L residue 21 MET Chi-restraints excluded: chain L residue 181 SER Chi-restraints excluded: chain B residue 12 ILE Chi-restraints excluded: chain B residue 23 GLU Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 519 VAL Chi-restraints excluded: chain K residue 53 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 100 optimal weight: 0.0170 chunk 21 optimal weight: 0.9980 chunk 65 optimal weight: 0.8980 chunk 27 optimal weight: 5.9990 chunk 111 optimal weight: 2.9990 chunk 92 optimal weight: 20.0000 chunk 51 optimal weight: 3.9990 chunk 9 optimal weight: 5.9990 chunk 36 optimal weight: 0.4980 chunk 58 optimal weight: 8.9990 chunk 107 optimal weight: 3.9990 overall best weight: 1.0820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 356 GLN B 366 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.1601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 9590 Z= 0.203 Angle : 0.503 8.697 13005 Z= 0.259 Chirality : 0.040 0.193 1440 Planarity : 0.004 0.054 1630 Dihedral : 6.273 58.856 1352 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.60 % Allowed : 12.11 % Favored : 86.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.25), residues: 1152 helix: 2.33 (0.26), residues: 386 sheet: 0.68 (0.28), residues: 324 loop : 0.16 (0.31), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 47 HIS 0.004 0.001 HIS L 194 PHE 0.011 0.001 PHE B 259 TYR 0.012 0.001 TYR H 95 ARG 0.003 0.000 ARG B 99 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 131 time to evaluate : 0.951 Fit side-chains revert: symmetry clash REVERT: L 193 LYS cc_start: 0.7705 (pptt) cc_final: 0.7469 (pptt) REVERT: B 23 GLU cc_start: 0.7613 (OUTLIER) cc_final: 0.6378 (mp0) REVERT: B 178 ASP cc_start: 0.6571 (t0) cc_final: 0.6155 (p0) outliers start: 16 outliers final: 11 residues processed: 143 average time/residue: 0.2482 time to fit residues: 48.4005 Evaluate side-chains 135 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 123 time to evaluate : 1.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 43 MET Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 131 VAL Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain L residue 21 MET Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 181 SER Chi-restraints excluded: chain B residue 23 GLU Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain K residue 53 THR Chi-restraints excluded: chain K residue 138 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 12 optimal weight: 9.9990 chunk 63 optimal weight: 0.0870 chunk 81 optimal weight: 0.0970 chunk 62 optimal weight: 0.0570 chunk 93 optimal weight: 10.0000 chunk 110 optimal weight: 4.9990 chunk 69 optimal weight: 1.9990 chunk 67 optimal weight: 0.5980 chunk 51 optimal weight: 2.9990 chunk 68 optimal weight: 6.9990 chunk 44 optimal weight: 0.7980 overall best weight: 0.3274 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 356 GLN B 366 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.1774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 9590 Z= 0.136 Angle : 0.491 9.281 13005 Z= 0.251 Chirality : 0.039 0.190 1440 Planarity : 0.003 0.040 1630 Dihedral : 5.870 58.799 1352 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.10 % Allowed : 13.51 % Favored : 85.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.72 (0.25), residues: 1152 helix: 2.51 (0.26), residues: 386 sheet: 0.81 (0.28), residues: 323 loop : 0.24 (0.31), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 113 HIS 0.003 0.000 HIS L 194 PHE 0.011 0.001 PHE N 104 TYR 0.008 0.001 TYR H 95 ARG 0.003 0.000 ARG B 99 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 131 time to evaluate : 1.073 Fit side-chains revert: symmetry clash REVERT: N 46 GLU cc_start: 0.7806 (pt0) cc_final: 0.7583 (pt0) REVERT: B 23 GLU cc_start: 0.7615 (OUTLIER) cc_final: 0.6471 (mp0) REVERT: B 178 ASP cc_start: 0.6455 (t0) cc_final: 0.6072 (p0) outliers start: 11 outliers final: 6 residues processed: 137 average time/residue: 0.2284 time to fit residues: 43.4374 Evaluate side-chains 130 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 123 time to evaluate : 1.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 43 MET Chi-restraints excluded: chain H residue 131 VAL Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain L residue 21 MET Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain B residue 23 GLU Chi-restraints excluded: chain K residue 138 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 66 optimal weight: 6.9990 chunk 33 optimal weight: 8.9990 chunk 21 optimal weight: 1.9990 chunk 70 optimal weight: 9.9990 chunk 75 optimal weight: 0.6980 chunk 54 optimal weight: 0.4980 chunk 10 optimal weight: 0.8980 chunk 87 optimal weight: 0.9980 chunk 100 optimal weight: 5.9990 chunk 106 optimal weight: 2.9990 chunk 96 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 194 HIS B 366 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.1813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9590 Z= 0.170 Angle : 0.506 9.109 13005 Z= 0.258 Chirality : 0.039 0.176 1440 Planarity : 0.003 0.042 1630 Dihedral : 5.829 56.440 1352 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.50 % Allowed : 13.81 % Favored : 84.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.71 (0.25), residues: 1152 helix: 2.50 (0.26), residues: 386 sheet: 0.83 (0.28), residues: 323 loop : 0.23 (0.31), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 159 HIS 0.003 0.001 HIS L 95 PHE 0.008 0.001 PHE N 104 TYR 0.011 0.001 TYR H 95 ARG 0.003 0.000 ARG B 99 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 130 time to evaluate : 1.021 Fit side-chains revert: symmetry clash REVERT: L 192 GLU cc_start: 0.6392 (mm-30) cc_final: 0.6052 (pp20) REVERT: N 46 GLU cc_start: 0.7825 (pt0) cc_final: 0.7598 (pt0) REVERT: B 23 GLU cc_start: 0.7628 (OUTLIER) cc_final: 0.6454 (mp0) REVERT: B 178 ASP cc_start: 0.6407 (t0) cc_final: 0.6036 (p0) outliers start: 15 outliers final: 10 residues processed: 140 average time/residue: 0.2241 time to fit residues: 43.4988 Evaluate side-chains 134 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 123 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 43 MET Chi-restraints excluded: chain H residue 131 VAL Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain L residue 21 MET Chi-restraints excluded: chain L residue 181 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain B residue 23 GLU Chi-restraints excluded: chain B residue 107 TYR Chi-restraints excluded: chain B residue 185 ASP Chi-restraints excluded: chain K residue 42 LEU Chi-restraints excluded: chain K residue 138 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 103 optimal weight: 0.0770 chunk 106 optimal weight: 0.7980 chunk 62 optimal weight: 0.0770 chunk 44 optimal weight: 3.9990 chunk 81 optimal weight: 6.9990 chunk 31 optimal weight: 7.9990 chunk 93 optimal weight: 9.9990 chunk 97 optimal weight: 1.9990 chunk 102 optimal weight: 4.9990 chunk 67 optimal weight: 6.9990 chunk 109 optimal weight: 6.9990 overall best weight: 1.3900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 194 HIS B 366 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.1830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 9590 Z= 0.239 Angle : 0.535 10.175 13005 Z= 0.271 Chirality : 0.040 0.153 1440 Planarity : 0.003 0.041 1630 Dihedral : 6.050 58.665 1352 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.90 % Allowed : 13.21 % Favored : 84.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.63 (0.25), residues: 1152 helix: 2.43 (0.26), residues: 385 sheet: 0.74 (0.28), residues: 323 loop : 0.23 (0.31), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 47 HIS 0.005 0.001 HIS L 95 PHE 0.010 0.001 PHE N 68 TYR 0.013 0.001 TYR H 95 ARG 0.003 0.000 ARG B 99 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 126 time to evaluate : 1.082 Fit side-chains revert: symmetry clash REVERT: L 192 GLU cc_start: 0.6187 (mm-30) cc_final: 0.5794 (tm-30) REVERT: B 23 GLU cc_start: 0.7608 (OUTLIER) cc_final: 0.6350 (mp0) REVERT: B 178 ASP cc_start: 0.6465 (t0) cc_final: 0.6101 (p0) outliers start: 19 outliers final: 16 residues processed: 138 average time/residue: 0.2300 time to fit residues: 44.3794 Evaluate side-chains 142 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 125 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 43 MET Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 108 TYR Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain H residue 131 VAL Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain L residue 21 MET Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 181 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain B residue 23 GLU Chi-restraints excluded: chain B residue 107 TYR Chi-restraints excluded: chain B residue 185 ASP Chi-restraints excluded: chain K residue 42 LEU Chi-restraints excluded: chain K residue 53 THR Chi-restraints excluded: chain K residue 138 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 66 optimal weight: 7.9990 chunk 51 optimal weight: 0.7980 chunk 75 optimal weight: 4.9990 chunk 114 optimal weight: 3.9990 chunk 105 optimal weight: 2.9990 chunk 91 optimal weight: 9.9990 chunk 9 optimal weight: 4.9990 chunk 70 optimal weight: 10.0000 chunk 55 optimal weight: 4.9990 chunk 72 optimal weight: 0.6980 chunk 97 optimal weight: 5.9990 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.1910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.085 9590 Z= 0.392 Angle : 0.623 10.352 13005 Z= 0.318 Chirality : 0.043 0.176 1440 Planarity : 0.004 0.041 1630 Dihedral : 6.622 59.337 1352 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.70 % Allowed : 13.71 % Favored : 84.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.25), residues: 1152 helix: 2.10 (0.25), residues: 385 sheet: 0.50 (0.27), residues: 321 loop : 0.11 (0.30), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP N 32 HIS 0.005 0.001 HIS L 194 PHE 0.021 0.002 PHE K 97 TYR 0.019 0.002 TYR K 158 ARG 0.006 0.001 ARG B 99 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 129 time to evaluate : 1.060 Fit side-chains revert: symmetry clash REVERT: H 214 ASN cc_start: 0.8515 (t0) cc_final: 0.7950 (m-40) REVERT: L 192 GLU cc_start: 0.6110 (mm-30) cc_final: 0.5781 (tm-30) REVERT: B 23 GLU cc_start: 0.7670 (OUTLIER) cc_final: 0.6372 (mp0) REVERT: B 178 ASP cc_start: 0.6637 (t0) cc_final: 0.6291 (p0) outliers start: 17 outliers final: 15 residues processed: 139 average time/residue: 0.2352 time to fit residues: 45.3760 Evaluate side-chains 142 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 126 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 108 TYR Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain H residue 131 VAL Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain L residue 21 MET Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 181 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain B residue 23 GLU Chi-restraints excluded: chain B residue 107 TYR Chi-restraints excluded: chain B residue 185 ASP Chi-restraints excluded: chain K residue 42 LEU Chi-restraints excluded: chain K residue 53 THR Chi-restraints excluded: chain K residue 138 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 27 optimal weight: 3.9990 chunk 84 optimal weight: 3.9990 chunk 13 optimal weight: 4.9990 chunk 25 optimal weight: 0.0470 chunk 91 optimal weight: 4.9990 chunk 38 optimal weight: 8.9990 chunk 93 optimal weight: 7.9990 chunk 11 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 80 optimal weight: 7.9990 chunk 5 optimal weight: 0.7980 overall best weight: 1.5482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.162865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.108236 restraints weight = 12120.958| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 2.14 r_work: 0.3091 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2952 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.1922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 9590 Z= 0.261 Angle : 0.558 10.487 13005 Z= 0.285 Chirality : 0.041 0.160 1440 Planarity : 0.004 0.057 1630 Dihedral : 6.291 58.470 1352 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.50 % Allowed : 14.11 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.25), residues: 1152 helix: 2.24 (0.25), residues: 384 sheet: 0.45 (0.27), residues: 319 loop : 0.09 (0.30), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 47 HIS 0.004 0.001 HIS H 35 PHE 0.019 0.001 PHE K 97 TYR 0.015 0.001 TYR K 196 ARG 0.013 0.001 ARG B 99 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2206.47 seconds wall clock time: 41 minutes 13.14 seconds (2473.14 seconds total)