Starting phenix.real_space_refine on Fri Nov 15 10:27:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j7m_36042/11_2024/8j7m_36042_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j7m_36042/11_2024/8j7m_36042.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j7m_36042/11_2024/8j7m_36042.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j7m_36042/11_2024/8j7m_36042.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j7m_36042/11_2024/8j7m_36042_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j7m_36042/11_2024/8j7m_36042_neut.cif" } resolution = 3.1 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= 0.004 sd= 0.128 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: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 44 5.16 5 C 6020 2.51 5 N 1316 2.21 5 O 1422 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 8806 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2096 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2096 Classifications: {'peptide': 257} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain breaks: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "D" Number of atoms: 2096 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2096 Classifications: {'peptide': 257} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain breaks: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "B" Number of atoms: 2096 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2096 Classifications: {'peptide': 257} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain breaks: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "C" Number of atoms: 2096 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2096 Classifications: {'peptide': 257} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain breaks: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "A" Number of atoms: 92 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 92 Unusual residues: {'CLR': 2, 'POV': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 119 Unusual residues: {'CLR': 3, 'POV': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 91 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 91 Unusual residues: {'CLR': 2, 'POV': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 120 Unusual residues: {'CLR': 3, 'POV': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 3 Time building chain proxies: 5.73, per 1000 atoms: 0.65 Number of scatterers: 8806 At special positions: 0 Unit cell: (117.52, 117.52, 71.76, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 44 16.00 P 4 15.00 O 1422 8.00 N 1316 7.00 C 6020 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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 Time building additional restraints: 2.67 Conformation dependent library (CDL) restraints added in 922.7 milliseconds 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1936 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 0 sheets defined 84.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.72 Creating SS restraints... Processing helix chain 'A' and resid 72 through 81 removed outlier: 3.530A pdb=" N ASP A 78 " --> pdb=" O ARG A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 107 Processing helix chain 'A' and resid 114 through 140 Processing helix chain 'A' and resid 148 through 172 Processing helix chain 'A' and resid 176 through 191 removed outlier: 4.259A pdb=" N LEU A 181 " --> pdb=" O SER A 178 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N ARG A 186 " --> pdb=" O ARG A 183 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ALA A 187 " --> pdb=" O ASN A 184 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILE A 190 " --> pdb=" O ALA A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 197 removed outlier: 3.852A pdb=" N ARG A 196 " --> pdb=" O ARG A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 237 removed outlier: 3.779A pdb=" N ILE A 203 " --> pdb=" O SER A 199 " (cutoff:3.500A) Proline residue: A 212 - end of helix removed outlier: 3.764A pdb=" N ASN A 216 " --> pdb=" O PRO A 212 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA A 217 " --> pdb=" O GLY A 213 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N HIS A 237 " --> pdb=" O VAL A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 288 Processing helix chain 'A' and resid 290 through 303 Processing helix chain 'A' and resid 306 through 310 removed outlier: 3.859A pdb=" N GLU A 309 " --> pdb=" O SER A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 318 Processing helix chain 'A' and resid 324 through 337 Processing helix chain 'A' and resid 337 through 356 Processing helix chain 'D' and resid 72 through 81 removed outlier: 3.531A pdb=" N ASP D 78 " --> pdb=" O ARG D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 107 Processing helix chain 'D' and resid 114 through 140 Processing helix chain 'D' and resid 148 through 172 Processing helix chain 'D' and resid 176 through 191 removed outlier: 4.258A pdb=" N LEU D 181 " --> pdb=" O SER D 178 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N ARG D 186 " --> pdb=" O ARG D 183 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ALA D 187 " --> pdb=" O ASN D 184 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILE D 190 " --> pdb=" O ALA D 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 192 through 197 removed outlier: 3.851A pdb=" N ARG D 196 " --> pdb=" O ARG D 192 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 237 removed outlier: 3.780A pdb=" N ILE D 203 " --> pdb=" O SER D 199 " (cutoff:3.500A) Proline residue: D 212 - end of helix removed outlier: 3.526A pdb=" N GLU D 234 " --> pdb=" O ILE D 230 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N HIS D 237 " --> pdb=" O VAL D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 282 through 288 Processing helix chain 'D' and resid 290 through 303 Processing helix chain 'D' and resid 312 through 318 Processing helix chain 'D' and resid 324 through 337 Processing helix chain 'D' and resid 339 through 356 Processing helix chain 'B' and resid 72 through 81 removed outlier: 3.530A pdb=" N ASP B 78 " --> pdb=" O ARG B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 107 Processing helix chain 'B' and resid 114 through 140 Processing helix chain 'B' and resid 148 through 172 Processing helix chain 'B' and resid 176 through 191 removed outlier: 4.258A pdb=" N LEU B 181 " --> pdb=" O SER B 178 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N ARG B 186 " --> pdb=" O ARG B 183 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ALA B 187 " --> pdb=" O ASN B 184 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILE B 190 " --> pdb=" O ALA B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 192 through 197 removed outlier: 3.852A pdb=" N ARG B 196 " --> pdb=" O ARG B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 237 removed outlier: 3.779A pdb=" N ILE B 203 " --> pdb=" O SER B 199 " (cutoff:3.500A) Proline residue: B 212 - end of helix removed outlier: 3.768A pdb=" N HIS B 237 " --> pdb=" O VAL B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 288 Processing helix chain 'B' and resid 290 through 303 Processing helix chain 'B' and resid 306 through 310 removed outlier: 3.860A pdb=" N GLU B 309 " --> pdb=" O SER B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 312 through 318 Processing helix chain 'B' and resid 324 through 339 Processing helix chain 'B' and resid 340 through 356 Processing helix chain 'C' and resid 72 through 81 removed outlier: 3.531A pdb=" N ASP C 78 " --> pdb=" O ARG C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 107 Processing helix chain 'C' and resid 114 through 140 Processing helix chain 'C' and resid 148 through 172 Processing helix chain 'C' and resid 176 through 191 removed outlier: 4.258A pdb=" N LEU C 181 " --> pdb=" O SER C 178 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N ARG C 186 " --> pdb=" O ARG C 183 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ALA C 187 " --> pdb=" O ASN C 184 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILE C 190 " --> pdb=" O ALA C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 192 through 197 removed outlier: 3.851A pdb=" N ARG C 196 " --> pdb=" O ARG C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 236 removed outlier: 3.779A pdb=" N ILE C 203 " --> pdb=" O SER C 199 " (cutoff:3.500A) Proline residue: C 212 - end of helix Processing helix chain 'C' and resid 237 through 239 No H-bonds generated for 'chain 'C' and resid 237 through 239' Processing helix chain 'C' and resid 282 through 288 removed outlier: 3.616A pdb=" N GLU C 286 " --> pdb=" O THR C 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 290 through 303 Processing helix chain 'C' and resid 306 through 310 removed outlier: 3.858A pdb=" N GLU C 309 " --> pdb=" O SER C 306 " (cutoff:3.500A) Processing helix chain 'C' and resid 312 through 318 Processing helix chain 'C' and resid 324 through 337 Processing helix chain 'C' and resid 337 through 356 614 hydrogen bonds defined for protein. 1725 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.31 Time building geometry restraints manager: 3.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1255 1.30 - 1.42: 2666 1.42 - 1.55: 5101 1.55 - 1.68: 10 1.68 - 1.81: 72 Bond restraints: 9104 Sorted by residual: bond pdb=" CA TYR B 114 " pdb=" C TYR B 114 " ideal model delta sigma weight residual 1.524 1.431 0.093 1.38e-02 5.25e+03 4.50e+01 bond pdb=" CA TYR D 114 " pdb=" C TYR D 114 " ideal model delta sigma weight residual 1.524 1.433 0.090 1.38e-02 5.25e+03 4.28e+01 bond pdb=" C21 POV B 901 " pdb=" O21 POV B 901 " ideal model delta sigma weight residual 1.330 1.456 -0.126 2.00e-02 2.50e+03 3.99e+01 bond pdb=" C31 POV A 901 " pdb=" O31 POV A 901 " ideal model delta sigma weight residual 1.327 1.453 -0.126 2.00e-02 2.50e+03 3.97e+01 bond pdb=" C31 POV D 901 " pdb=" O31 POV D 901 " ideal model delta sigma weight residual 1.327 1.451 -0.124 2.00e-02 2.50e+03 3.87e+01 ... (remaining 9099 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.74: 11864 2.74 - 5.48: 440 5.48 - 8.22: 97 8.22 - 10.97: 19 10.97 - 13.71: 6 Bond angle restraints: 12426 Sorted by residual: angle pdb=" N SER D 308 " pdb=" CA SER D 308 " pdb=" C SER D 308 " ideal model delta sigma weight residual 114.12 100.41 13.71 1.39e+00 5.18e-01 9.72e+01 angle pdb=" C ILE C 336 " pdb=" CA ILE C 336 " pdb=" CB ILE C 336 " ideal model delta sigma weight residual 111.97 100.06 11.91 1.28e+00 6.10e-01 8.66e+01 angle pdb=" N ILE C 336 " pdb=" CA ILE C 336 " pdb=" C ILE C 336 " ideal model delta sigma weight residual 110.42 119.28 -8.86 9.60e-01 1.09e+00 8.52e+01 angle pdb=" C ILE B 336 " pdb=" CA ILE B 336 " pdb=" CB ILE B 336 " ideal model delta sigma weight residual 112.14 100.08 12.06 1.35e+00 5.49e-01 7.98e+01 angle pdb=" N ILE B 336 " pdb=" CA ILE B 336 " pdb=" C ILE B 336 " ideal model delta sigma weight residual 110.62 119.23 -8.61 1.02e+00 9.61e-01 7.13e+01 ... (remaining 12421 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.04: 5225 26.04 - 52.09: 338 52.09 - 78.13: 63 78.13 - 104.17: 18 104.17 - 130.22: 4 Dihedral angle restraints: 5648 sinusoidal: 2632 harmonic: 3016 Sorted by residual: dihedral pdb=" C TRP D 307 " pdb=" N TRP D 307 " pdb=" CA TRP D 307 " pdb=" CB TRP D 307 " ideal model delta harmonic sigma weight residual -122.60 -107.20 -15.40 0 2.50e+00 1.60e-01 3.79e+01 dihedral pdb=" C GLU C 285 " pdb=" N GLU C 285 " pdb=" CA GLU C 285 " pdb=" CB GLU C 285 " ideal model delta harmonic sigma weight residual -122.60 -134.79 12.19 0 2.50e+00 1.60e-01 2.38e+01 dihedral pdb=" CA GLU D 305 " pdb=" C GLU D 305 " pdb=" N SER D 306 " pdb=" CA SER D 306 " ideal model delta harmonic sigma weight residual 180.00 158.68 21.32 0 5.00e+00 4.00e-02 1.82e+01 ... (remaining 5645 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 1177 0.093 - 0.185: 134 0.185 - 0.278: 34 0.278 - 0.370: 18 0.370 - 0.463: 9 Chirality restraints: 1372 Sorted by residual: chirality pdb=" CA GLU C 285 " pdb=" N GLU C 285 " pdb=" C GLU C 285 " pdb=" CB GLU C 285 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.35e+00 chirality pdb=" C13 CLR B 902 " pdb=" C12 CLR B 902 " pdb=" C14 CLR B 902 " pdb=" C17 CLR B 902 " both_signs ideal model delta sigma weight residual False -2.93 -2.52 -0.42 2.00e-01 2.50e+01 4.31e+00 chirality pdb=" C13 CLR A 903 " pdb=" C12 CLR A 903 " pdb=" C14 CLR A 903 " pdb=" C17 CLR A 903 " both_signs ideal model delta sigma weight residual False -2.93 -2.52 -0.41 2.00e-01 2.50e+01 4.26e+00 ... (remaining 1369 not shown) Planarity restraints: 1456 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN C 338 " 0.025 2.00e-02 2.50e+03 4.77e-02 2.28e+01 pdb=" C GLN C 338 " -0.083 2.00e-02 2.50e+03 pdb=" O GLN C 338 " 0.030 2.00e-02 2.50e+03 pdb=" N ILE C 339 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 336 " 0.021 2.00e-02 2.50e+03 4.23e-02 1.79e+01 pdb=" C ILE B 336 " -0.073 2.00e-02 2.50e+03 pdb=" O ILE B 336 " 0.027 2.00e-02 2.50e+03 pdb=" N CYS B 337 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE D 144 " 0.014 2.00e-02 2.50e+03 2.85e-02 8.14e+00 pdb=" C PHE D 144 " -0.049 2.00e-02 2.50e+03 pdb=" O PHE D 144 " 0.019 2.00e-02 2.50e+03 pdb=" N TRP D 145 " 0.017 2.00e-02 2.50e+03 ... (remaining 1453 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 223 2.68 - 3.23: 9055 3.23 - 3.79: 13941 3.79 - 4.34: 18996 4.34 - 4.90: 31419 Nonbonded interactions: 73634 Sorted by model distance: nonbonded pdb=" O ILE B 339 " pdb=" ND2 ASN B 343 " model vdw 2.124 3.120 nonbonded pdb=" O CYS D 143 " pdb=" CE3 TRP D 145 " model vdw 2.223 3.340 nonbonded pdb=" O CYS A 143 " pdb=" CE3 TRP A 145 " model vdw 2.244 3.340 nonbonded pdb=" O LEU C 328 " pdb=" OG SER C 332 " model vdw 2.247 3.040 nonbonded pdb=" O LEU D 328 " pdb=" OG SER D 332 " model vdw 2.247 3.040 ... (remaining 73629 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 61 through 356 or (resid 901 and (name C1 or name C2 or na \ me C21 or name C22 or name C23 or name C24 or name C25 or name C26 or name C27 o \ r name C3 or name C31 or name C32 or name C33 or name C34 or name C35 or name C3 \ 6 or name C37 or name C38 or name C39 or name O11 or name O12 or name O13 or nam \ e O14 or name O21 or name O22 or name O31 or name O32 or name P or name C310 or \ name C311 or name C312 or name C313 or name C314 or name C315 or name C316)) or \ resid 902 through 903)) selection = chain 'B' selection = (chain 'C' and (resid 61 through 356 or (resid 901 and (name C1 or name C2 or na \ me C21 or name C22 or name C23 or name C24 or name C25 or name C26 or name C27 o \ r name C3 or name C31 or name C32 or name C33 or name C34 or name C35 or name C3 \ 6 or name C37 or name C38 or name C39 or name O11 or name O12 or name O13 or nam \ e O14 or name O21 or name O22 or name O31 or name O32 or name P or name C310 or \ name C311 or name C312 or name C313 or name C314 or name C315 or name C316)) or \ resid 902 through 903)) selection = (chain 'D' and (resid 61 through 356 or resid 901 through 903)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.45 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: 0.680 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: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 22.620 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 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 : 0.011 0.126 9104 Z= 0.685 Angle : 1.237 13.707 12426 Z= 0.685 Chirality : 0.082 0.463 1372 Planarity : 0.006 0.048 1456 Dihedral : 18.144 130.218 3712 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 16.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.30 % Favored : 91.70 % Rotamer: Outliers : 1.27 % Allowed : 15.05 % Favored : 83.68 % Cbeta Deviations : 0.62 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.26 (0.24), residues: 1012 helix: -0.93 (0.17), residues: 732 sheet: None (None), residues: 0 loop : -2.73 (0.37), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 149 HIS 0.004 0.001 HIS C 237 PHE 0.022 0.002 PHE C 144 TYR 0.014 0.003 TYR B 114 ARG 0.002 0.000 ARG B 293 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 192 time to evaluate : 0.923 Fit side-chains revert: symmetry clash REVERT: A 142 PHE cc_start: 0.8284 (m-80) cc_final: 0.8074 (m-80) REVERT: A 185 LEU cc_start: 0.8595 (mt) cc_final: 0.8218 (tt) REVERT: A 209 LYS cc_start: 0.7860 (mmpt) cc_final: 0.7621 (mttm) REVERT: A 286 GLU cc_start: 0.7924 (tt0) cc_final: 0.7723 (tt0) REVERT: A 288 TYR cc_start: 0.8550 (m-80) cc_final: 0.8202 (m-80) REVERT: A 328 LEU cc_start: 0.8459 (mt) cc_final: 0.8227 (mt) REVERT: D 185 LEU cc_start: 0.8587 (mt) cc_final: 0.8224 (tt) REVERT: D 288 TYR cc_start: 0.8591 (m-80) cc_final: 0.8240 (m-80) REVERT: D 328 LEU cc_start: 0.8464 (mt) cc_final: 0.8233 (mt) REVERT: B 123 PHE cc_start: 0.7560 (t80) cc_final: 0.7271 (t80) REVERT: B 142 PHE cc_start: 0.8124 (m-80) cc_final: 0.7837 (m-10) REVERT: B 209 LYS cc_start: 0.7850 (mmpt) cc_final: 0.7649 (mttm) REVERT: B 288 TYR cc_start: 0.8465 (m-80) cc_final: 0.8113 (m-80) REVERT: B 328 LEU cc_start: 0.8473 (mt) cc_final: 0.8239 (mt) REVERT: C 288 TYR cc_start: 0.8579 (m-80) cc_final: 0.8221 (m-80) REVERT: C 328 LEU cc_start: 0.8536 (mt) cc_final: 0.8328 (mt) outliers start: 11 outliers final: 7 residues processed: 203 average time/residue: 0.2060 time to fit residues: 57.8180 Evaluate side-chains 175 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 168 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain D residue 311 VAL Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain C residue 211 ILE Chi-restraints excluded: chain C residue 311 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 84 optimal weight: 0.7980 chunk 75 optimal weight: 8.9990 chunk 42 optimal weight: 0.5980 chunk 25 optimal weight: 8.9990 chunk 51 optimal weight: 0.3980 chunk 40 optimal weight: 0.0370 chunk 78 optimal weight: 0.8980 chunk 30 optimal weight: 0.8980 chunk 47 optimal weight: 0.0570 chunk 58 optimal weight: 3.9990 chunk 90 optimal weight: 2.9990 overall best weight: 0.3776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 HIS ** A 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 126 ASN D 72 HIS D 126 ASN B 72 HIS ** B 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 126 ASN ** B 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 72 HIS ** C 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 126 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.1372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9104 Z= 0.187 Angle : 0.610 6.789 12426 Z= 0.308 Chirality : 0.043 0.169 1372 Planarity : 0.005 0.060 1456 Dihedral : 12.335 117.311 1902 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 0.58 % Allowed : 17.71 % Favored : 81.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.26), residues: 1012 helix: 0.21 (0.18), residues: 732 sheet: None (None), residues: 0 loop : -2.28 (0.39), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP D 145 HIS 0.001 0.001 HIS C 237 PHE 0.019 0.001 PHE D 218 TYR 0.012 0.002 TYR C 283 ARG 0.003 0.000 ARG D 313 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 171 time to evaluate : 0.925 Fit side-chains revert: symmetry clash REVERT: A 145 TRP cc_start: 0.8309 (p90) cc_final: 0.7980 (p90) REVERT: A 209 LYS cc_start: 0.7826 (mmpt) cc_final: 0.7463 (mtpp) REVERT: A 328 LEU cc_start: 0.8319 (mt) cc_final: 0.8096 (mt) REVERT: D 145 TRP cc_start: 0.8224 (p90) cc_final: 0.7956 (p90) REVERT: D 209 LYS cc_start: 0.7761 (mmpt) cc_final: 0.7558 (mmtt) REVERT: D 328 LEU cc_start: 0.8417 (mt) cc_final: 0.8167 (mt) REVERT: B 123 PHE cc_start: 0.7611 (t80) cc_final: 0.7341 (t80) REVERT: B 145 TRP cc_start: 0.8303 (p90) cc_final: 0.7859 (p90) REVERT: B 209 LYS cc_start: 0.7828 (mmpt) cc_final: 0.7507 (mtpp) REVERT: B 221 MET cc_start: 0.8023 (ttm) cc_final: 0.7766 (ttp) REVERT: B 328 LEU cc_start: 0.8394 (mt) cc_final: 0.8143 (mt) REVERT: C 145 TRP cc_start: 0.8213 (p90) cc_final: 0.7936 (p90) REVERT: C 328 LEU cc_start: 0.8412 (mt) cc_final: 0.8210 (mt) outliers start: 5 outliers final: 4 residues processed: 174 average time/residue: 0.2096 time to fit residues: 50.5334 Evaluate side-chains 167 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 163 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 211 ILE Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 211 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 50 optimal weight: 10.0000 chunk 28 optimal weight: 1.9990 chunk 75 optimal weight: 10.0000 chunk 61 optimal weight: 0.2980 chunk 25 optimal weight: 10.0000 chunk 90 optimal weight: 0.8980 chunk 98 optimal weight: 0.7980 chunk 81 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 chunk 72 optimal weight: 3.9990 chunk 89 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 184 ASN ** C 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 184 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.1798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9104 Z= 0.218 Angle : 0.562 5.322 12426 Z= 0.285 Chirality : 0.044 0.188 1372 Planarity : 0.005 0.037 1456 Dihedral : 11.021 106.729 1896 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 1.85 % Allowed : 18.29 % Favored : 79.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.27), residues: 1012 helix: 0.69 (0.19), residues: 744 sheet: None (None), residues: 0 loop : -1.91 (0.42), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 145 HIS 0.003 0.001 HIS B 72 PHE 0.019 0.001 PHE A 144 TYR 0.015 0.002 TYR D 283 ARG 0.003 0.000 ARG C 183 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 163 time to evaluate : 0.908 Fit side-chains REVERT: A 145 TRP cc_start: 0.8349 (p90) cc_final: 0.7998 (p90) REVERT: A 286 GLU cc_start: 0.8006 (tt0) cc_final: 0.7754 (tm-30) REVERT: A 328 LEU cc_start: 0.8419 (mt) cc_final: 0.8182 (mt) REVERT: D 145 TRP cc_start: 0.8231 (p90) cc_final: 0.7965 (p90) REVERT: D 286 GLU cc_start: 0.7923 (tt0) cc_final: 0.7719 (tt0) REVERT: D 328 LEU cc_start: 0.8378 (mt) cc_final: 0.8125 (mt) REVERT: B 145 TRP cc_start: 0.8382 (p90) cc_final: 0.7982 (p90) REVERT: C 145 TRP cc_start: 0.8280 (p90) cc_final: 0.8000 (p90) REVERT: C 209 LYS cc_start: 0.7835 (mmpt) cc_final: 0.7558 (mmtt) REVERT: C 286 GLU cc_start: 0.7959 (tt0) cc_final: 0.7712 (tt0) outliers start: 16 outliers final: 11 residues processed: 176 average time/residue: 0.2238 time to fit residues: 53.4071 Evaluate side-chains 167 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 156 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain D residue 164 LEU Chi-restraints excluded: chain D residue 211 ILE Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 211 ILE Chi-restraints excluded: chain C residue 219 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 68 optimal weight: 3.9990 chunk 47 optimal weight: 0.5980 chunk 10 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 91 optimal weight: 0.5980 chunk 96 optimal weight: 0.7980 chunk 86 optimal weight: 0.0670 chunk 26 optimal weight: 0.7980 chunk 80 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 184 ASN ** B 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.2119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 9104 Z= 0.177 Angle : 0.534 5.107 12426 Z= 0.272 Chirality : 0.042 0.158 1372 Planarity : 0.004 0.031 1456 Dihedral : 10.332 97.867 1896 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 1.50 % Allowed : 17.01 % Favored : 81.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.27), residues: 1012 helix: 0.90 (0.19), residues: 744 sheet: None (None), residues: 0 loop : -1.59 (0.44), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 145 HIS 0.002 0.001 HIS D 237 PHE 0.017 0.001 PHE C 144 TYR 0.012 0.001 TYR A 138 ARG 0.007 0.000 ARG C 192 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 162 time to evaluate : 0.886 Fit side-chains REVERT: A 145 TRP cc_start: 0.8324 (p90) cc_final: 0.8121 (p90) REVERT: D 328 LEU cc_start: 0.8379 (mt) cc_final: 0.8129 (mt) REVERT: B 145 TRP cc_start: 0.8383 (p90) cc_final: 0.8013 (p90) REVERT: B 328 LEU cc_start: 0.8422 (mt) cc_final: 0.8157 (mt) REVERT: C 145 TRP cc_start: 0.8208 (p90) cc_final: 0.7969 (p90) outliers start: 13 outliers final: 9 residues processed: 173 average time/residue: 0.2283 time to fit residues: 53.2581 Evaluate side-chains 169 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 160 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain D residue 211 ILE Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 219 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 1 optimal weight: 5.9990 chunk 71 optimal weight: 0.9980 chunk 39 optimal weight: 0.8980 chunk 82 optimal weight: 4.9990 chunk 66 optimal weight: 0.5980 chunk 0 optimal weight: 7.9990 chunk 49 optimal weight: 0.6980 chunk 86 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 32 optimal weight: 4.9990 chunk 87 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.2286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9104 Z= 0.208 Angle : 0.541 5.867 12426 Z= 0.274 Chirality : 0.043 0.164 1372 Planarity : 0.004 0.053 1456 Dihedral : 10.083 91.338 1892 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 1.39 % Allowed : 17.82 % Favored : 80.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.27), residues: 1012 helix: 1.00 (0.19), residues: 744 sheet: None (None), residues: 0 loop : -1.48 (0.44), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP D 145 HIS 0.002 0.001 HIS D 237 PHE 0.017 0.001 PHE C 144 TYR 0.011 0.002 TYR A 138 ARG 0.002 0.000 ARG A 192 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 170 time to evaluate : 0.921 Fit side-chains REVERT: A 328 LEU cc_start: 0.8435 (mt) cc_final: 0.8182 (mt) REVERT: D 145 TRP cc_start: 0.8133 (p90) cc_final: 0.7872 (p90) REVERT: D 328 LEU cc_start: 0.8402 (mt) cc_final: 0.8141 (mt) REVERT: B 145 TRP cc_start: 0.8413 (p90) cc_final: 0.8079 (p90) REVERT: B 328 LEU cc_start: 0.8441 (mt) cc_final: 0.8175 (mt) outliers start: 12 outliers final: 12 residues processed: 179 average time/residue: 0.2206 time to fit residues: 53.7103 Evaluate side-chains 183 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 171 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain D residue 211 ILE Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 211 ILE Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 352 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 19 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 23 optimal weight: 0.9990 chunk 96 optimal weight: 0.3980 chunk 80 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 32 optimal weight: 5.9990 chunk 50 optimal weight: 10.0000 chunk 93 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 overall best weight: 0.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.2404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9104 Z= 0.213 Angle : 0.542 5.916 12426 Z= 0.274 Chirality : 0.042 0.158 1372 Planarity : 0.004 0.034 1456 Dihedral : 9.985 84.325 1892 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 1.74 % Allowed : 18.29 % Favored : 79.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.27), residues: 1012 helix: 1.06 (0.19), residues: 744 sheet: None (None), residues: 0 loop : -1.40 (0.44), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP C 145 HIS 0.002 0.001 HIS D 237 PHE 0.017 0.001 PHE D 144 TYR 0.012 0.001 TYR A 236 ARG 0.002 0.000 ARG B 192 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 172 time to evaluate : 1.017 Fit side-chains REVERT: A 145 TRP cc_start: 0.8236 (p90) cc_final: 0.7936 (p90) REVERT: A 185 LEU cc_start: 0.8723 (OUTLIER) cc_final: 0.8352 (tt) REVERT: A 328 LEU cc_start: 0.8443 (mt) cc_final: 0.8176 (mt) REVERT: D 145 TRP cc_start: 0.8216 (p90) cc_final: 0.7878 (p90) REVERT: D 185 LEU cc_start: 0.8698 (OUTLIER) cc_final: 0.8316 (tt) REVERT: D 328 LEU cc_start: 0.8409 (mt) cc_final: 0.8146 (mt) REVERT: B 145 TRP cc_start: 0.8347 (p90) cc_final: 0.7980 (p90) REVERT: B 286 GLU cc_start: 0.7942 (tt0) cc_final: 0.7699 (tt0) REVERT: B 328 LEU cc_start: 0.8436 (mt) cc_final: 0.8175 (mt) REVERT: C 145 TRP cc_start: 0.8212 (p90) cc_final: 0.7958 (p90) REVERT: C 286 GLU cc_start: 0.7934 (tt0) cc_final: 0.7709 (tt0) outliers start: 15 outliers final: 12 residues processed: 181 average time/residue: 0.2186 time to fit residues: 54.1101 Evaluate side-chains 181 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 167 time to evaluate : 1.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 211 ILE Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain B residue 128 MET Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 211 ILE Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 352 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 55 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 chunk 96 optimal weight: 2.9990 chunk 60 optimal weight: 8.9990 chunk 58 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 chunk 38 optimal weight: 0.7980 chunk 57 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.2399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 9104 Z= 0.327 Angle : 0.617 8.148 12426 Z= 0.307 Chirality : 0.046 0.189 1372 Planarity : 0.004 0.030 1456 Dihedral : 10.115 79.503 1892 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 2.20 % Allowed : 18.98 % Favored : 78.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.27), residues: 1012 helix: 0.48 (0.18), residues: 796 sheet: None (None), residues: 0 loop : -3.39 (0.40), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 145 HIS 0.004 0.001 HIS A 237 PHE 0.020 0.002 PHE D 329 TYR 0.013 0.002 TYR A 236 ARG 0.001 0.000 ARG C 293 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 185 time to evaluate : 0.964 Fit side-chains REVERT: A 145 TRP cc_start: 0.8348 (p90) cc_final: 0.7974 (p90) REVERT: A 185 LEU cc_start: 0.8774 (OUTLIER) cc_final: 0.8355 (tt) REVERT: D 145 TRP cc_start: 0.8292 (p90) cc_final: 0.7984 (p90) REVERT: D 185 LEU cc_start: 0.8780 (OUTLIER) cc_final: 0.8352 (tt) REVERT: B 145 TRP cc_start: 0.8364 (p90) cc_final: 0.8020 (p90) REVERT: B 286 GLU cc_start: 0.7998 (tt0) cc_final: 0.7762 (tt0) REVERT: C 145 TRP cc_start: 0.8305 (p90) cc_final: 0.7983 (p90) outliers start: 19 outliers final: 15 residues processed: 195 average time/residue: 0.1989 time to fit residues: 54.8591 Evaluate side-chains 198 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 181 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 211 ILE Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain B residue 128 MET Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 211 ILE Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 352 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 29 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 61 optimal weight: 10.0000 chunk 65 optimal weight: 0.7980 chunk 47 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 chunk 75 optimal weight: 10.0000 chunk 87 optimal weight: 0.8980 chunk 92 optimal weight: 0.6980 chunk 84 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.2553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9104 Z= 0.209 Angle : 0.548 7.099 12426 Z= 0.274 Chirality : 0.042 0.158 1372 Planarity : 0.004 0.030 1456 Dihedral : 9.699 68.569 1892 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 2.08 % Allowed : 19.79 % Favored : 78.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.27), residues: 1012 helix: 1.05 (0.19), residues: 740 sheet: None (None), residues: 0 loop : -1.48 (0.43), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 145 HIS 0.002 0.001 HIS D 237 PHE 0.018 0.001 PHE C 144 TYR 0.014 0.001 TYR A 236 ARG 0.004 0.000 ARG C 192 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 176 time to evaluate : 0.881 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 145 TRP cc_start: 0.8322 (p90) cc_final: 0.8036 (p90) REVERT: A 185 LEU cc_start: 0.8655 (OUTLIER) cc_final: 0.8270 (tt) REVERT: D 145 TRP cc_start: 0.8271 (p90) cc_final: 0.8063 (p90) REVERT: D 185 LEU cc_start: 0.8700 (OUTLIER) cc_final: 0.8284 (tt) REVERT: D 328 LEU cc_start: 0.8459 (mt) cc_final: 0.8209 (mt) REVERT: B 123 PHE cc_start: 0.7801 (t80) cc_final: 0.7511 (t80) REVERT: B 286 GLU cc_start: 0.7979 (tt0) cc_final: 0.7739 (tt0) REVERT: B 328 LEU cc_start: 0.8450 (mt) cc_final: 0.8198 (mt) REVERT: C 145 TRP cc_start: 0.8276 (p90) cc_final: 0.8035 (p90) outliers start: 18 outliers final: 12 residues processed: 188 average time/residue: 0.1970 time to fit residues: 52.0116 Evaluate side-chains 190 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 176 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 211 ILE Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain B residue 128 MET Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 211 ILE Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 352 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 92 optimal weight: 0.0870 chunk 54 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 70 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 chunk 84 optimal weight: 5.9990 chunk 89 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 94 optimal weight: 0.5980 chunk 57 optimal weight: 3.9990 overall best weight: 1.1362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.2592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9104 Z= 0.257 Angle : 0.573 7.326 12426 Z= 0.287 Chirality : 0.044 0.167 1372 Planarity : 0.004 0.030 1456 Dihedral : 9.654 69.054 1892 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 2.08 % Allowed : 20.02 % Favored : 77.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.27), residues: 1012 helix: 0.61 (0.18), residues: 796 sheet: None (None), residues: 0 loop : -3.28 (0.40), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP B 145 HIS 0.003 0.001 HIS D 237 PHE 0.018 0.001 PHE C 144 TYR 0.013 0.002 TYR D 236 ARG 0.003 0.000 ARG C 192 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 179 time to evaluate : 0.970 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 145 TRP cc_start: 0.8316 (p90) cc_final: 0.8050 (p90) REVERT: A 185 LEU cc_start: 0.8703 (OUTLIER) cc_final: 0.8288 (tt) REVERT: D 92 LEU cc_start: 0.8316 (OUTLIER) cc_final: 0.8027 (mp) REVERT: D 145 TRP cc_start: 0.8299 (p90) cc_final: 0.8070 (p90) REVERT: D 185 LEU cc_start: 0.8674 (OUTLIER) cc_final: 0.8233 (tt) REVERT: D 328 LEU cc_start: 0.8475 (mt) cc_final: 0.8218 (mt) REVERT: B 123 PHE cc_start: 0.7811 (t80) cc_final: 0.7516 (t80) REVERT: B 145 TRP cc_start: 0.8270 (p90) cc_final: 0.8010 (p90) REVERT: B 209 LYS cc_start: 0.7796 (mtmm) cc_final: 0.7518 (pttt) REVERT: B 286 GLU cc_start: 0.7987 (tt0) cc_final: 0.7735 (tt0) REVERT: C 123 PHE cc_start: 0.7875 (t80) cc_final: 0.7603 (t80) REVERT: C 145 TRP cc_start: 0.8320 (p90) cc_final: 0.8059 (p90) outliers start: 18 outliers final: 14 residues processed: 189 average time/residue: 0.1993 time to fit residues: 52.8176 Evaluate side-chains 195 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 178 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 211 ILE Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain B residue 128 MET Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 211 ILE Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 352 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 45 optimal weight: 0.6980 chunk 66 optimal weight: 0.5980 chunk 99 optimal weight: 0.8980 chunk 91 optimal weight: 0.8980 chunk 79 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 61 optimal weight: 5.9990 chunk 48 optimal weight: 0.8980 chunk 63 optimal weight: 1.9990 chunk 84 optimal weight: 4.9990 chunk 24 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 184 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.2719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9104 Z= 0.194 Angle : 0.536 6.992 12426 Z= 0.269 Chirality : 0.042 0.159 1372 Planarity : 0.004 0.030 1456 Dihedral : 9.359 65.911 1892 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 1.74 % Allowed : 20.60 % Favored : 77.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.27), residues: 1012 helix: 1.15 (0.19), residues: 740 sheet: None (None), residues: 0 loop : -1.41 (0.43), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP B 145 HIS 0.002 0.001 HIS B 72 PHE 0.018 0.001 PHE B 144 TYR 0.013 0.001 TYR A 236 ARG 0.004 0.000 ARG C 192 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 179 time to evaluate : 0.888 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 145 TRP cc_start: 0.8294 (p90) cc_final: 0.8021 (p90) REVERT: A 185 LEU cc_start: 0.8707 (OUTLIER) cc_final: 0.8304 (tt) REVERT: D 92 LEU cc_start: 0.8290 (OUTLIER) cc_final: 0.7999 (mp) REVERT: D 185 LEU cc_start: 0.8655 (OUTLIER) cc_final: 0.8238 (tt) REVERT: D 328 LEU cc_start: 0.8455 (mt) cc_final: 0.8200 (mt) REVERT: B 123 PHE cc_start: 0.7803 (t80) cc_final: 0.7514 (t80) REVERT: B 145 TRP cc_start: 0.8279 (p90) cc_final: 0.8046 (p90) REVERT: B 209 LYS cc_start: 0.7811 (mtmm) cc_final: 0.7498 (pttt) REVERT: B 286 GLU cc_start: 0.7959 (tt0) cc_final: 0.7709 (tt0) REVERT: B 328 LEU cc_start: 0.8447 (mt) cc_final: 0.8200 (mt) REVERT: C 123 PHE cc_start: 0.7873 (t80) cc_final: 0.7597 (t80) REVERT: C 145 TRP cc_start: 0.8266 (p90) cc_final: 0.8056 (p90) outliers start: 15 outliers final: 12 residues processed: 190 average time/residue: 0.2029 time to fit residues: 54.2058 Evaluate side-chains 191 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 176 time to evaluate : 1.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 211 ILE Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain B residue 128 MET Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 211 ILE Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 352 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 73 optimal weight: 1.9990 chunk 11 optimal weight: 7.9990 chunk 22 optimal weight: 0.4980 chunk 79 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 81 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 chunk 69 optimal weight: 0.1980 chunk 4 optimal weight: 0.9980 chunk 57 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 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 = 0.4106 r_free = 0.4106 target = 0.184821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.148147 restraints weight = 8597.201| |-----------------------------------------------------------------------------| r_work (start): 0.3747 rms_B_bonded: 1.76 r_work: 0.3508 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3365 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3306 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3306 r_free = 0.3306 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3306 r_free = 0.3306 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3306 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.2816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9104 Z= 0.189 Angle : 0.543 6.966 12426 Z= 0.272 Chirality : 0.041 0.158 1372 Planarity : 0.004 0.031 1456 Dihedral : 9.230 64.596 1892 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 1.62 % Allowed : 20.95 % Favored : 77.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.27), residues: 1012 helix: 1.16 (0.19), residues: 740 sheet: None (None), residues: 0 loop : -1.40 (0.43), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.001 TRP D 145 HIS 0.002 0.001 HIS B 72 PHE 0.018 0.001 PHE B 144 TYR 0.012 0.001 TYR D 236 ARG 0.004 0.000 ARG C 192 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2123.01 seconds wall clock time: 39 minutes 22.56 seconds (2362.56 seconds total)