Starting phenix.real_space_refine on Fri Feb 14 01:55:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rxc_24728/02_2025/7rxc_24728.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rxc_24728/02_2025/7rxc_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_24728/02_2025/7rxc_24728.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rxc_24728/02_2025/7rxc_24728.map" model { file = "/net/cci-nas-00/data/ceres_data/7rxc_24728/02_2025/7rxc_24728.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rxc_24728/02_2025/7rxc_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-5592/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: 5.60, per 1000 atoms: 0.60 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: 2.50 Conformation dependent library (CDL) restraints added in 1.1 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: 3.16 Time building geometry restraints manager: 2.79 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: 0.970 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: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 24.310 Find NCS groups from input model: 0.120 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:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.580 ------------------------------------------------------------------------------- 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 : 1.017 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: 0.2614 time to fit residues: 51.2043 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 : 1.041 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.172225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.130336 restraints weight = 12386.304| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 2.02 r_work: 0.3266 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3128 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 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 : 0.972 Fit side-chains revert: symmetry clash REVERT: H 153 LYS cc_start: 0.8361 (ttpt) cc_final: 0.7895 (ttmt) REVERT: N 46 GLU cc_start: 0.8246 (pt0) cc_final: 0.8027 (pt0) REVERT: B 39 GLU cc_start: 0.6927 (mp0) cc_final: 0.6412 (pm20) REVERT: B 178 ASP cc_start: 0.7157 (t0) cc_final: 0.6109 (p0) REVERT: B 323 GLU cc_start: 0.8356 (tm-30) cc_final: 0.8098 (tt0) REVERT: K 201 LYS cc_start: 0.7988 (ttmt) cc_final: 0.7591 (ttpt) outliers start: 6 outliers final: 4 residues processed: 135 average time/residue: 0.2412 time to fit residues: 44.5653 Evaluate side-chains 126 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 122 time to evaluate : 0.995 ------------------------------------------------------------------------------- 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 8 optimal weight: 7.9990 chunk 15 optimal weight: 10.0000 chunk 30 optimal weight: 0.9990 chunk 18 optimal weight: 6.9990 chunk 4 optimal weight: 0.8980 chunk 43 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 44 optimal weight: 0.0030 chunk 88 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 85 optimal weight: 5.9990 overall best weight: 0.9594 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.171593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.132917 restraints weight = 12495.530| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 2.07 r_work: 0.3264 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3126 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.1217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 9590 Z= 0.193 Angle : 0.506 5.690 13005 Z= 0.262 Chirality : 0.040 0.156 1440 Planarity : 0.004 0.102 1630 Dihedral : 6.733 55.828 1352 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.20 % Allowed : 8.91 % Favored : 89.89 % 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: 1.46 (0.25), residues: 1152 helix: 2.15 (0.26), residues: 386 sheet: 0.77 (0.28), residues: 312 loop : 0.17 (0.30), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 159 HIS 0.004 0.001 HIS H 35 PHE 0.014 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 : 1.024 Fit side-chains revert: symmetry clash REVERT: H 153 LYS cc_start: 0.8289 (ttpt) cc_final: 0.7973 (ttmt) REVERT: N 46 GLU cc_start: 0.8334 (pt0) cc_final: 0.8101 (pt0) REVERT: B 23 GLU cc_start: 0.7894 (OUTLIER) cc_final: 0.6649 (mp0) REVERT: B 178 ASP cc_start: 0.7123 (t0) cc_final: 0.6068 (p0) REVERT: B 323 GLU cc_start: 0.8386 (tm-30) cc_final: 0.8125 (tt0) REVERT: K 33 SER cc_start: 0.8912 (t) cc_final: 0.8544 (m) REVERT: K 134 GLN cc_start: 0.8702 (tp40) cc_final: 0.8218 (tp-100) outliers start: 12 outliers final: 6 residues processed: 137 average time/residue: 0.2341 time to fit residues: 44.0637 Evaluate side-chains 133 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 126 time to evaluate : 0.966 ------------------------------------------------------------------------------- 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 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 56 optimal weight: 7.9990 chunk 108 optimal weight: 5.9990 chunk 37 optimal weight: 5.9990 chunk 91 optimal weight: 20.0000 chunk 83 optimal weight: 3.9990 chunk 33 optimal weight: 6.9990 chunk 112 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 80 optimal weight: 9.9990 chunk 29 optimal weight: 4.9990 chunk 18 optimal weight: 9.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.159563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.104018 restraints weight = 12327.176| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 2.12 r_work: 0.3043 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2902 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.1638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.103 9590 Z= 0.567 Angle : 0.691 6.843 13005 Z= 0.355 Chirality : 0.046 0.190 1440 Planarity : 0.005 0.088 1630 Dihedral : 7.707 58.365 1352 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.60 % Allowed : 11.81 % Favored : 86.59 % 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: 0.92 (0.24), residues: 1152 helix: 1.60 (0.25), residues: 388 sheet: 0.49 (0.29), residues: 305 loop : -0.04 (0.30), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP N 32 HIS 0.006 0.001 HIS H 35 PHE 0.022 0.002 PHE B 259 TYR 0.024 0.002 TYR K 158 ARG 0.005 0.001 ARG N 67 *********************** 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 145 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 129 time to evaluate : 1.095 Fit side-chains revert: symmetry clash REVERT: H 89 GLU cc_start: 0.8062 (mp0) cc_final: 0.7655 (pt0) REVERT: H 153 LYS cc_start: 0.8161 (ttpt) cc_final: 0.7919 (ttpt) REVERT: L 175 ASP cc_start: 0.7860 (t0) cc_final: 0.7469 (t0) REVERT: B 23 GLU cc_start: 0.7812 (OUTLIER) cc_final: 0.6472 (mp0) REVERT: B 178 ASP cc_start: 0.7228 (t0) cc_final: 0.6084 (p0) REVERT: B 323 GLU cc_start: 0.8200 (tm-30) cc_final: 0.7911 (tt0) REVERT: B 366 GLN cc_start: 0.8381 (OUTLIER) cc_final: 0.8142 (mm-40) REVERT: K 33 SER cc_start: 0.8975 (t) cc_final: 0.8526 (m) REVERT: K 42 LEU cc_start: 0.8714 (OUTLIER) cc_final: 0.8476 (tp) REVERT: K 134 GLN cc_start: 0.8755 (tp40) cc_final: 0.7992 (tp-100) outliers start: 16 outliers final: 12 residues processed: 140 average time/residue: 0.2491 time to fit residues: 47.8461 Evaluate side-chains 139 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 124 time to evaluate : 1.007 ------------------------------------------------------------------------------- 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 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 356 GLN Chi-restraints excluded: chain B residue 366 GLN Chi-restraints excluded: chain B residue 519 VAL Chi-restraints excluded: chain B residue 524 THR Chi-restraints excluded: chain K residue 42 LEU 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 23 optimal weight: 0.8980 chunk 48 optimal weight: 0.8980 chunk 79 optimal weight: 0.5980 chunk 67 optimal weight: 2.9990 chunk 60 optimal weight: 5.9990 chunk 12 optimal weight: 0.0050 chunk 89 optimal weight: 0.6980 chunk 84 optimal weight: 4.9990 chunk 113 optimal weight: 0.8980 chunk 85 optimal weight: 0.9980 chunk 53 optimal weight: 0.7980 overall best weight: 0.5994 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.164269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.109641 restraints weight = 12128.416| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 2.13 r_work: 0.3121 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.1548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 9590 Z= 0.172 Angle : 0.516 7.310 13005 Z= 0.268 Chirality : 0.040 0.198 1440 Planarity : 0.004 0.057 1630 Dihedral : 6.872 59.210 1352 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.30 % Allowed : 13.01 % Favored : 85.69 % 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: 1.26 (0.25), residues: 1152 helix: 2.06 (0.26), residues: 384 sheet: 0.52 (0.28), residues: 322 loop : 0.10 (0.30), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 47 HIS 0.006 0.001 HIS L 194 PHE 0.025 0.001 PHE L 144 TYR 0.012 0.001 TYR H 95 ARG 0.006 0.000 ARG B 355 *********************** 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 151 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 138 time to evaluate : 1.025 Fit side-chains revert: symmetry clash REVERT: H 153 LYS cc_start: 0.8036 (ttpt) cc_final: 0.7824 (ttpt) REVERT: B 23 GLU cc_start: 0.7714 (OUTLIER) cc_final: 0.6439 (mp0) REVERT: B 178 ASP cc_start: 0.7099 (t0) cc_final: 0.5916 (p0) REVERT: B 323 GLU cc_start: 0.8187 (tm-30) cc_final: 0.7890 (tt0) REVERT: K 33 SER cc_start: 0.8928 (t) cc_final: 0.8197 (m) REVERT: K 134 GLN cc_start: 0.8699 (tp40) cc_final: 0.8138 (tp-100) outliers start: 13 outliers final: 10 residues processed: 145 average time/residue: 0.2441 time to fit residues: 48.4961 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 : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 8 LEU Chi-restraints excluded: chain B residue 23 GLU Chi-restraints excluded: chain K residue 53 THR Chi-restraints excluded: chain K residue 138 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 29 optimal weight: 4.9990 chunk 8 optimal weight: 5.9990 chunk 78 optimal weight: 8.9990 chunk 76 optimal weight: 0.8980 chunk 9 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 27 optimal weight: 0.5980 chunk 95 optimal weight: 0.5980 chunk 111 optimal weight: 2.9990 chunk 99 optimal weight: 0.7980 chunk 57 optimal weight: 5.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.163422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.109269 restraints weight = 12165.151| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 2.05 r_work: 0.3120 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2981 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.1675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 9590 Z= 0.219 Angle : 0.523 8.641 13005 Z= 0.268 Chirality : 0.040 0.213 1440 Planarity : 0.004 0.051 1630 Dihedral : 6.534 59.828 1352 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.20 % Allowed : 12.41 % 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: 1.32 (0.25), residues: 1152 helix: 2.18 (0.26), residues: 385 sheet: 0.53 (0.28), residues: 322 loop : 0.07 (0.30), residues: 445 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 0.022 0.001 PHE L 144 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 157 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 135 time to evaluate : 1.010 Fit side-chains revert: symmetry clash REVERT: H 90 ASP cc_start: 0.8199 (m-30) cc_final: 0.7958 (m-30) REVERT: H 153 LYS cc_start: 0.8034 (ttpt) cc_final: 0.7830 (ttpt) REVERT: L 192 GLU cc_start: 0.6628 (mm-30) cc_final: 0.5898 (tm-30) REVERT: B 23 GLU cc_start: 0.7702 (OUTLIER) cc_final: 0.6422 (mp0) REVERT: B 178 ASP cc_start: 0.7017 (t0) cc_final: 0.5771 (p0) REVERT: B 323 GLU cc_start: 0.8184 (tm-30) cc_final: 0.7880 (tt0) REVERT: B 366 GLN cc_start: 0.8099 (OUTLIER) cc_final: 0.7897 (mm-40) REVERT: K 33 SER cc_start: 0.8941 (t) cc_final: 0.8417 (m) REVERT: K 134 GLN cc_start: 0.8686 (tp40) cc_final: 0.7989 (tp-100) outliers start: 22 outliers final: 12 residues processed: 149 average time/residue: 0.2332 time to fit residues: 48.2024 Evaluate side-chains 140 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 126 time to evaluate : 1.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 43 MET 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 181 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain B residue 23 GLU Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 185 ASP Chi-restraints excluded: chain B residue 366 GLN Chi-restraints excluded: chain B residue 519 VAL 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 104 optimal weight: 5.9990 chunk 8 optimal weight: 4.9990 chunk 114 optimal weight: 4.9990 chunk 2 optimal weight: 0.7980 chunk 92 optimal weight: 20.0000 chunk 98 optimal weight: 0.9990 chunk 45 optimal weight: 4.9990 chunk 19 optimal weight: 0.6980 chunk 89 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 82 optimal weight: 0.6980 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 283 ASN B 366 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.163175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.108807 restraints weight = 12324.189| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 2.10 r_work: 0.3110 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.1737 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= 0.242 Angle : 0.534 9.002 13005 Z= 0.273 Chirality : 0.040 0.218 1440 Planarity : 0.004 0.041 1630 Dihedral : 6.416 59.878 1352 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.00 % Allowed : 12.91 % Favored : 85.09 % 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: 1.30 (0.25), residues: 1152 helix: 2.17 (0.26), residues: 386 sheet: 0.53 (0.27), residues: 322 loop : 0.04 (0.30), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 47 HIS 0.005 0.001 HIS L 194 PHE 0.021 0.001 PHE K 97 TYR 0.012 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 149 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 129 time to evaluate : 1.002 Fit side-chains revert: symmetry clash REVERT: L 192 GLU cc_start: 0.6572 (mm-30) cc_final: 0.5822 (tm-30) REVERT: B 23 GLU cc_start: 0.7721 (OUTLIER) cc_final: 0.6426 (mp0) REVERT: B 178 ASP cc_start: 0.7012 (t0) cc_final: 0.5766 (p0) REVERT: B 323 GLU cc_start: 0.8192 (tm-30) cc_final: 0.7885 (tt0) REVERT: K 33 SER cc_start: 0.8947 (t) cc_final: 0.8422 (m) REVERT: K 134 GLN cc_start: 0.8698 (tp40) cc_final: 0.8006 (tp-100) outliers start: 20 outliers final: 17 residues processed: 142 average time/residue: 0.2427 time to fit residues: 47.7504 Evaluate side-chains 143 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 125 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 43 MET 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 61 ILE Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 185 ASP Chi-restraints excluded: chain B residue 519 VAL Chi-restraints excluded: chain K residue 53 THR 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 88 optimal weight: 0.0060 chunk 44 optimal weight: 0.7980 chunk 96 optimal weight: 0.6980 chunk 62 optimal weight: 7.9990 chunk 114 optimal weight: 4.9990 chunk 95 optimal weight: 0.1980 chunk 94 optimal weight: 20.0000 chunk 47 optimal weight: 0.5980 chunk 87 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 overall best weight: 0.4596 ------------------------------------------------------------------------------- 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 366 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.165804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.112514 restraints weight = 12323.560| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 2.09 r_work: 0.3152 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.1850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 9590 Z= 0.147 Angle : 0.503 10.907 13005 Z= 0.256 Chirality : 0.039 0.207 1440 Planarity : 0.003 0.041 1630 Dihedral : 5.884 58.203 1352 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.30 % Allowed : 14.61 % Favored : 84.08 % 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: 1.50 (0.25), residues: 1152 helix: 2.38 (0.26), residues: 386 sheet: 0.66 (0.28), residues: 323 loop : 0.09 (0.30), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 47 HIS 0.004 0.001 HIS L 194 PHE 0.024 0.001 PHE K 97 TYR 0.013 0.001 TYR B 525 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 146 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 133 time to evaluate : 1.121 Fit side-chains revert: symmetry clash REVERT: H 90 ASP cc_start: 0.8159 (m-30) cc_final: 0.7955 (m-30) REVERT: L 192 GLU cc_start: 0.6575 (mm-30) cc_final: 0.5834 (pp20) REVERT: N 7 SER cc_start: 0.8468 (m) cc_final: 0.8221 (p) REVERT: B 23 GLU cc_start: 0.7740 (OUTLIER) cc_final: 0.6476 (mp0) REVERT: B 39 GLU cc_start: 0.7006 (mp0) cc_final: 0.6409 (pm20) REVERT: B 178 ASP cc_start: 0.6978 (t0) cc_final: 0.5728 (p0) REVERT: B 284 TYR cc_start: 0.7290 (m-80) cc_final: 0.7002 (m-80) REVERT: B 312 LEU cc_start: 0.6973 (tp) cc_final: 0.6599 (pp) REVERT: B 323 GLU cc_start: 0.8150 (tm-30) cc_final: 0.7840 (tt0) REVERT: K 33 SER cc_start: 0.8931 (t) cc_final: 0.8376 (m) REVERT: K 127 GLU cc_start: 0.8618 (tt0) cc_final: 0.8392 (tt0) REVERT: K 134 GLN cc_start: 0.8712 (tp40) cc_final: 0.8094 (tp-100) outliers start: 13 outliers final: 10 residues processed: 140 average time/residue: 0.2308 time to fit residues: 44.7707 Evaluate side-chains 136 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 125 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 43 MET 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 K residue 138 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 86 optimal weight: 0.6980 chunk 92 optimal weight: 10.0000 chunk 101 optimal weight: 4.9990 chunk 78 optimal weight: 7.9990 chunk 95 optimal weight: 0.0170 chunk 81 optimal weight: 8.9990 chunk 1 optimal weight: 5.9990 chunk 91 optimal weight: 10.0000 chunk 97 optimal weight: 4.9990 chunk 8 optimal weight: 7.9990 chunk 98 optimal weight: 1.9990 overall best weight: 2.5424 ------------------------------------------------------------------------------- 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 = 0.3881 r_free = 0.3881 target = 0.161366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.107366 restraints weight = 12305.271| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 2.14 r_work: 0.3059 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2919 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.1881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 9590 Z= 0.376 Angle : 0.599 10.018 13005 Z= 0.305 Chirality : 0.042 0.192 1440 Planarity : 0.004 0.040 1630 Dihedral : 6.391 57.888 1352 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.70 % Allowed : 14.71 % Favored : 83.58 % 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: 1.28 (0.25), residues: 1152 helix: 2.18 (0.26), residues: 385 sheet: 0.46 (0.27), residues: 324 loop : 0.05 (0.31), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP N 32 HIS 0.006 0.001 HIS L 95 PHE 0.025 0.002 PHE K 97 TYR 0.017 0.002 TYR K 158 ARG 0.004 0.001 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 146 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 129 time to evaluate : 1.094 Fit side-chains revert: symmetry clash REVERT: L 172 ASP cc_start: 0.6756 (p0) cc_final: 0.6507 (p0) REVERT: L 192 GLU cc_start: 0.6430 (mm-30) cc_final: 0.5661 (tm-30) REVERT: B 23 GLU cc_start: 0.7715 (OUTLIER) cc_final: 0.6423 (mp0) REVERT: B 39 GLU cc_start: 0.7089 (mp0) cc_final: 0.6539 (pm20) REVERT: B 178 ASP cc_start: 0.7032 (t0) cc_final: 0.5876 (p0) REVERT: B 284 TYR cc_start: 0.7263 (m-80) cc_final: 0.6951 (m-80) REVERT: B 323 GLU cc_start: 0.8162 (tm-30) cc_final: 0.7862 (tt0) REVERT: K 33 SER cc_start: 0.8947 (t) cc_final: 0.8510 (m) REVERT: K 134 GLN cc_start: 0.8724 (tp40) cc_final: 0.8273 (tp-100) outliers start: 17 outliers final: 14 residues processed: 140 average time/residue: 0.2283 time to fit residues: 44.7329 Evaluate side-chains 141 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 126 time to evaluate : 1.206 ------------------------------------------------------------------------------- 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 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 74 SER Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 152 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 112 optimal weight: 0.0980 chunk 109 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 43 optimal weight: 4.9990 chunk 91 optimal weight: 0.9980 chunk 0 optimal weight: 7.9990 chunk 2 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 46 optimal weight: 0.7980 chunk 86 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 = 0.3913 r_free = 0.3913 target = 0.164419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.110664 restraints weight = 12320.120| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 2.10 r_work: 0.3134 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.1898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 9590 Z= 0.175 Angle : 0.526 10.728 13005 Z= 0.267 Chirality : 0.040 0.178 1440 Planarity : 0.003 0.041 1630 Dihedral : 5.916 58.066 1352 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.30 % Allowed : 15.22 % Favored : 83.48 % 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: 2.36 (0.26), residues: 385 sheet: 0.58 (0.27), residues: 323 loop : 0.10 (0.31), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 47 HIS 0.004 0.001 HIS L 95 PHE 0.031 0.001 PHE K 97 TYR 0.013 0.001 TYR B 525 ARG 0.004 0.000 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 143 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 130 time to evaluate : 0.981 Fit side-chains revert: symmetry clash REVERT: H 214 ASN cc_start: 0.8379 (t0) cc_final: 0.7412 (m-40) REVERT: L 192 GLU cc_start: 0.6363 (mm-30) cc_final: 0.5698 (pp20) REVERT: B 23 GLU cc_start: 0.7721 (OUTLIER) cc_final: 0.6431 (mp0) REVERT: B 39 GLU cc_start: 0.6984 (mp0) cc_final: 0.6399 (pm20) REVERT: B 178 ASP cc_start: 0.6985 (t0) cc_final: 0.5733 (p0) REVERT: B 284 TYR cc_start: 0.7324 (m-80) cc_final: 0.7001 (m-80) REVERT: B 312 LEU cc_start: 0.7043 (tp) cc_final: 0.6656 (pp) REVERT: B 323 GLU cc_start: 0.8153 (tm-30) cc_final: 0.7848 (tt0) REVERT: K 33 SER cc_start: 0.8917 (t) cc_final: 0.8379 (m) REVERT: K 134 GLN cc_start: 0.8709 (tp40) cc_final: 0.8052 (tp-100) outliers start: 13 outliers final: 11 residues processed: 138 average time/residue: 0.2114 time to fit residues: 40.8037 Evaluate side-chains 138 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 126 time to evaluate : 1.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 43 MET Chi-restraints excluded: chain H residue 120 THR 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 122 LEU 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 94 optimal weight: 10.0000 chunk 27 optimal weight: 0.9980 chunk 23 optimal weight: 0.3980 chunk 78 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 90 optimal weight: 9.9990 chunk 68 optimal weight: 9.9990 chunk 89 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- 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 = 0.3907 r_free = 0.3907 target = 0.163657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.109592 restraints weight = 12248.920| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 2.03 r_work: 0.3122 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.1935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 9590 Z= 0.224 Angle : 0.543 10.497 13005 Z= 0.275 Chirality : 0.040 0.167 1440 Planarity : 0.004 0.042 1630 Dihedral : 5.884 53.634 1352 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.30 % Allowed : 15.22 % Favored : 83.48 % 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: 2.35 (0.26), residues: 385 sheet: 0.58 (0.27), residues: 323 loop : 0.10 (0.31), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 47 HIS 0.004 0.001 HIS L 95 PHE 0.033 0.001 PHE K 97 TYR 0.020 0.001 TYR K 76 ARG 0.006 0.000 ARG B 99 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6237.22 seconds wall clock time: 111 minutes 7.54 seconds (6667.54 seconds total)