Starting phenix.real_space_refine on Wed Feb 4 01:56:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ydp_72825/02_2026/9ydp_72825.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ydp_72825/02_2026/9ydp_72825.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ydp_72825/02_2026/9ydp_72825.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ydp_72825/02_2026/9ydp_72825.map" model { file = "/net/cci-nas-00/data/ceres_data/9ydp_72825/02_2026/9ydp_72825.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ydp_72825/02_2026/9ydp_72825.cif" } resolution = 1.95 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.033 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 59 5.16 5 C 5153 2.51 5 N 1406 2.21 5 O 1596 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8214 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 1798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1798 Classifications: {'peptide': 227} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 6, 'TRANS': 220} Chain breaks: 1 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ASP:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "B" Number of atoms: 2586 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2586 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "G" Number of atoms: 434 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 434 Classifications: {'peptide': 58} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 53} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "N" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "R" Number of atoms: 2289 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2289 Classifications: {'peptide': 293} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 280} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "P" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Classifications: {'peptide': 1} Chain: "P" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 20 Classifications: {'peptide': 3} Modifications used: {'PEPT-D': 1} Link IDs: {'TRANS': 2} Chain: "P" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Classifications: {'peptide': 1} Modifications used: {'COO': 1, 'PEPT-D': 1} Chain: "A" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 22 Classifications: {'water': 22} Link IDs: {None: 21} Chain: "B" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 46 Classifications: {'water': 46} Link IDs: {None: 45} Chain: "G" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "N" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 20 Classifications: {'water': 20} Link IDs: {None: 19} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 1.97, per 1000 atoms: 0.24 Number of scatterers: 8214 At special positions: 0 Unit cell: (72.98, 95.94, 129.56, 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 59 16.00 O 1596 8.00 N 1406 7.00 C 5153 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Simple disulfide: pdb=" SG CYS R 121 " - pdb=" SG CYS R 198 " 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 TRANS " DAL P 2 " - " TYR P 1 " Time building additional restraints: 0.64 Conformation dependent library (CDL) restraints added in 311.3 milliseconds 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue name is d-peptide pdb=" CB DAL P 2 " pdb=" CB DLE P 5 " Number of C-beta restraints generated: 1970 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 11 sheets defined 44.2% alpha, 21.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'A' and resid 1 through 27 removed outlier: 3.537A pdb=" N LYS A 5 " --> pdb=" O SER A 1 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 44 removed outlier: 4.318A pdb=" N GLY A 40 " --> pdb=" O ASP A 37 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N LYS A 41 " --> pdb=" O ASN A 38 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N SER A 42 " --> pdb=" O SER A 39 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILE A 44 " --> pdb=" O LYS A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 96 removed outlier: 3.608A pdb=" N ASN A 96 " --> pdb=" O GLN A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 111 No H-bonds generated for 'chain 'A' and resid 109 through 111' Processing helix chain 'A' and resid 112 through 125 Processing helix chain 'A' and resid 140 through 151 Processing helix chain 'A' and resid 154 through 158 Processing helix chain 'A' and resid 159 through 165 Processing helix chain 'A' and resid 178 through 199 removed outlier: 3.876A pdb=" N ILE A 195 " --> pdb=" O GLU A 191 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N SER A 199 " --> pdb=" O ILE A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 238 Processing helix chain 'B' and resid 3 through 26 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 6 through 24 removed outlier: 3.502A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'N' and resid 28 through 32 Processing helix chain 'N' and resid 62 through 65 removed outlier: 3.569A pdb=" N LYS N 65 " --> pdb=" O GLY N 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 62 through 65' Processing helix chain 'N' and resid 87 through 91 Processing helix chain 'R' and resid 43 through 77 Processing helix chain 'R' and resid 82 through 100 Processing helix chain 'R' and resid 101 through 112 Processing helix chain 'R' and resid 116 through 152 removed outlier: 4.149A pdb=" N LEU R 120 " --> pdb=" O PHE R 116 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU R 125 " --> pdb=" O CYS R 121 " (cutoff:3.500A) Processing helix chain 'R' and resid 152 through 160 removed outlier: 4.203A pdb=" N ASP R 158 " --> pdb=" O VAL R 154 " (cutoff:3.500A) Processing helix chain 'R' and resid 161 through 176 Processing helix chain 'R' and resid 176 through 186 Proline residue: R 182 - end of helix Processing helix chain 'R' and resid 205 through 222 Processing helix chain 'R' and resid 222 through 241 Processing helix chain 'R' and resid 248 through 287 Proline residue: R 276 - end of helix Processing helix chain 'R' and resid 293 through 319 removed outlier: 4.336A pdb=" N SER R 311 " --> pdb=" O GLY R 307 " (cutoff:3.500A) Proline residue: R 315 - end of helix Processing helix chain 'R' and resid 322 through 334 Processing sheet with id=AA1, first strand: chain 'A' and resid 64 through 71 removed outlier: 6.411A pdb=" N VAL A 29 " --> pdb=" O HIS A 77 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N PHE A 79 " --> pdb=" O VAL A 29 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N LEU A 31 " --> pdb=" O PHE A 79 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N VAL A 81 " --> pdb=" O LEU A 31 " (cutoff:3.500A) removed outlier: 8.457A pdb=" N LEU A 33 " --> pdb=" O VAL A 81 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ALA A 100 " --> pdb=" O LYS A 30 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 52 removed outlier: 3.915A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.531A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.898A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.429A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 4.262A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.479A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.608A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'N' and resid 11 through 12 removed outlier: 6.614A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'R' and resid 187 through 192 472 hydrogen bonds defined for protein. 1341 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.52 Time building geometry restraints manager: 0.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2641 1.34 - 1.46: 1787 1.46 - 1.58: 3768 1.58 - 1.70: 0 1.70 - 1.82: 84 Bond restraints: 8280 Sorted by residual: bond pdb=" C VAL R 181 " pdb=" N PRO R 182 " ideal model delta sigma weight residual 1.335 1.358 -0.024 1.28e-02 6.10e+03 3.45e+00 bond pdb=" C ALA R 275 " pdb=" N PRO R 276 " ideal model delta sigma weight residual 1.335 1.360 -0.024 1.36e-02 5.41e+03 3.19e+00 bond pdb=" C VAL R 224 " pdb=" N PRO R 225 " ideal model delta sigma weight residual 1.335 1.354 -0.019 1.36e-02 5.41e+03 1.91e+00 bond pdb=" CG1 ILE A 132 " pdb=" CD1 ILE A 132 " ideal model delta sigma weight residual 1.513 1.459 0.054 3.90e-02 6.57e+02 1.91e+00 bond pdb=" C LEU R 102 " pdb=" N PRO R 103 " ideal model delta sigma weight residual 1.335 1.351 -0.017 1.28e-02 6.10e+03 1.68e+00 ... (remaining 8275 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.58: 10747 1.58 - 3.16: 413 3.16 - 4.74: 52 4.74 - 6.33: 17 6.33 - 7.91: 6 Bond angle restraints: 11235 Sorted by residual: angle pdb=" CA TRP A 91 " pdb=" CB TRP A 91 " pdb=" CG TRP A 91 " ideal model delta sigma weight residual 113.60 120.41 -6.81 1.90e+00 2.77e-01 1.28e+01 angle pdb=" CA MET B 61 " pdb=" CB MET B 61 " pdb=" CG MET B 61 " ideal model delta sigma weight residual 114.10 120.07 -5.97 2.00e+00 2.50e-01 8.92e+00 angle pdb=" C SER N 52 " pdb=" N GLN N 53 " pdb=" CA GLN N 53 " ideal model delta sigma weight residual 120.54 124.49 -3.95 1.35e+00 5.49e-01 8.58e+00 angle pdb=" C ASP B 163 " pdb=" N THR B 164 " pdb=" CA THR B 164 " ideal model delta sigma weight residual 123.91 128.66 -4.75 1.66e+00 3.63e-01 8.18e+00 angle pdb=" CA TRP B 82 " pdb=" CB TRP B 82 " pdb=" CG TRP B 82 " ideal model delta sigma weight residual 113.60 118.83 -5.23 1.90e+00 2.77e-01 7.58e+00 ... (remaining 11230 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.33: 4563 17.33 - 34.66: 305 34.66 - 52.00: 39 52.00 - 69.33: 19 69.33 - 86.66: 6 Dihedral angle restraints: 4932 sinusoidal: 1886 harmonic: 3046 Sorted by residual: dihedral pdb=" CA PHE B 234 " pdb=" C PHE B 234 " pdb=" N PHE B 235 " pdb=" CA PHE B 235 " ideal model delta harmonic sigma weight residual 180.00 159.05 20.95 0 5.00e+00 4.00e-02 1.76e+01 dihedral pdb=" CA LYS B 78 " pdb=" C LYS B 78 " pdb=" N LEU B 79 " pdb=" CA LEU B 79 " ideal model delta harmonic sigma weight residual 180.00 160.73 19.27 0 5.00e+00 4.00e-02 1.48e+01 dihedral pdb=" CA TRP B 169 " pdb=" C TRP B 169 " pdb=" N ASP B 170 " pdb=" CA ASP B 170 " ideal model delta harmonic sigma weight residual 180.00 161.61 18.39 0 5.00e+00 4.00e-02 1.35e+01 ... (remaining 4929 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 719 0.032 - 0.065: 366 0.065 - 0.097: 132 0.097 - 0.129: 56 0.129 - 0.162: 21 Chirality restraints: 1294 Sorted by residual: chirality pdb=" CB ILE A 64 " pdb=" CA ILE A 64 " pdb=" CG1 ILE A 64 " pdb=" CG2 ILE A 64 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.16 2.00e-01 2.50e+01 6.54e-01 chirality pdb=" CA ILE N 58 " pdb=" N ILE N 58 " pdb=" C ILE N 58 " pdb=" CB ILE N 58 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.44e-01 chirality pdb=" CB ILE B 157 " pdb=" CA ILE B 157 " pdb=" CG1 ILE B 157 " pdb=" CG2 ILE B 157 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.16 2.00e-01 2.50e+01 6.23e-01 ... (remaining 1291 not shown) Planarity restraints: 1431 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG R 244 " -0.218 9.50e-02 1.11e+02 9.87e-02 7.71e+00 pdb=" NE ARG R 244 " 0.021 2.00e-02 2.50e+03 pdb=" CZ ARG R 244 " -0.021 2.00e-02 2.50e+03 pdb=" NH1 ARG R 244 " 0.010 2.00e-02 2.50e+03 pdb=" NH2 ARG R 244 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN R 314 " -0.042 5.00e-02 4.00e+02 6.30e-02 6.35e+00 pdb=" N PRO R 315 " 0.109 5.00e-02 4.00e+02 pdb=" CA PRO R 315 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO R 315 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP R 293 " 0.040 5.00e-02 4.00e+02 6.04e-02 5.84e+00 pdb=" N PRO R 294 " -0.105 5.00e-02 4.00e+02 pdb=" CA PRO R 294 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO R 294 " 0.033 5.00e-02 4.00e+02 ... (remaining 1428 not shown) Histogram of nonbonded interaction distances: 1.33 - 2.04: 1 2.04 - 2.76: 1023 2.76 - 3.47: 11933 3.47 - 4.19: 22677 4.19 - 4.90: 38461 Nonbonded interactions: 74095 Sorted by model distance: nonbonded pdb=" C PHE P 4 " pdb=" N DLE P 5 " model vdw 1.328 3.350 nonbonded pdb=" OD1 ASP N 50 " pdb=" OG SER N 59 " model vdw 2.243 3.040 nonbonded pdb=" O PHE P 4 " pdb=" N DLE P 5 " model vdw 2.253 3.120 nonbonded pdb=" OE2 GLU B 260 " pdb=" OG1 THR B 263 " model vdw 2.274 3.040 nonbonded pdb=" OG SER B 147 " pdb=" O VAL B 187 " model vdw 2.288 3.040 ... (remaining 74090 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=0.30 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: 3.160 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: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.350 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 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:7.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8942 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 : 0.004 0.054 8283 Z= 0.184 Angle : 0.714 7.908 11242 Z= 0.400 Chirality : 0.048 0.162 1294 Planarity : 0.008 0.099 1430 Dihedral : 12.593 86.659 2953 Min Nonbonded Distance : 1.328 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 0.12 % Allowed : 0.92 % Favored : 98.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.09 (0.24), residues: 1033 helix: -0.77 (0.21), residues: 408 sheet: -0.53 (0.32), residues: 217 loop : -0.52 (0.31), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG R 244 TYR 0.020 0.002 TYR A 205 PHE 0.023 0.002 PHE B 199 TRP 0.033 0.003 TRP A 91 HIS 0.013 0.002 HIS A 204 Details of bonding type rmsd covalent geometry : bond 0.00382 ( 8280) covalent geometry : angle 0.71401 (11235) SS BOND : bond 0.00196 ( 2) SS BOND : angle 1.50782 ( 4) hydrogen bonds : bond 0.16346 ( 472) hydrogen bonds : angle 7.73979 ( 1341) link_TRANS : bond 0.00213 ( 1) link_TRANS : angle 0.21327 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 152 time to evaluate : 0.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 GLU cc_start: 0.8920 (pt0) cc_final: 0.8697 (pp20) REVERT: B 15 LYS cc_start: 0.9218 (mttm) cc_final: 0.8977 (mtmm) REVERT: R 93 LEU cc_start: 0.9348 (tp) cc_final: 0.9144 (tt) REVERT: R 166 LYS cc_start: 0.8963 (mttp) cc_final: 0.8251 (mmtt) REVERT: R 252 LYS cc_start: 0.8925 (tttt) cc_final: 0.8484 (ttmm) outliers start: 1 outliers final: 0 residues processed: 152 average time/residue: 0.7499 time to fit residues: 119.3061 Evaluate side-chains 106 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 8.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.4980 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 0.9980 chunk 100 optimal weight: 0.9980 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN N 39 GLN N 82 GLN R 85 ASN R 105 GLN R 169 ASN R 201 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.079059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.056213 restraints weight = 16567.848| |-----------------------------------------------------------------------------| r_work (start): 0.2882 rms_B_bonded: 1.97 r_work: 0.2766 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2661 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2661 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2657 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2657 r_free = 0.2657 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2657 r_free = 0.2657 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.78 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2657 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9127 moved from start: 0.1764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 8283 Z= 0.171 Angle : 0.565 8.335 11242 Z= 0.300 Chirality : 0.042 0.197 1294 Planarity : 0.005 0.042 1430 Dihedral : 5.014 54.057 1143 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 1.50 % Allowed : 8.18 % Favored : 90.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.25), residues: 1033 helix: 1.56 (0.24), residues: 408 sheet: -0.51 (0.33), residues: 195 loop : -0.20 (0.31), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG R 292 TYR 0.014 0.001 TYR A 205 PHE 0.012 0.001 PHE A 69 TRP 0.017 0.002 TRP A 91 HIS 0.008 0.001 HIS A 204 Details of bonding type rmsd covalent geometry : bond 0.00353 ( 8280) covalent geometry : angle 0.56533 (11235) SS BOND : bond 0.00177 ( 2) SS BOND : angle 0.32917 ( 4) hydrogen bonds : bond 0.04271 ( 472) hydrogen bonds : angle 5.22147 ( 1341) link_TRANS : bond 0.00005 ( 1) link_TRANS : angle 0.06597 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 111 time to evaluate : 0.235 Fit side-chains revert: symmetry clash REVERT: B 12 GLU cc_start: 0.8282 (pp20) cc_final: 0.8012 (pp20) REVERT: B 59 TYR cc_start: 0.9178 (OUTLIER) cc_final: 0.8549 (t80) REVERT: B 172 GLU cc_start: 0.8866 (tp30) cc_final: 0.8531 (tp30) REVERT: B 197 ARG cc_start: 0.8756 (mmm-85) cc_final: 0.8503 (mmm160) REVERT: B 267 ASP cc_start: 0.8947 (m-30) cc_final: 0.8670 (m-30) REVERT: G 22 GLU cc_start: 0.8275 (mt-10) cc_final: 0.8028 (mt-10) REVERT: R 79 LYS cc_start: 0.8097 (mmmt) cc_final: 0.7696 (mmmm) REVERT: R 90 ASN cc_start: 0.8988 (m-40) cc_final: 0.8731 (m-40) REVERT: R 166 LYS cc_start: 0.9155 (mttp) cc_final: 0.8338 (mmtt) REVERT: R 199 MET cc_start: 0.8735 (OUTLIER) cc_final: 0.8503 (ppp) REVERT: R 252 LYS cc_start: 0.8664 (tttt) cc_final: 0.8423 (ttmm) outliers start: 13 outliers final: 2 residues processed: 116 average time/residue: 0.5796 time to fit residues: 70.6930 Evaluate side-chains 102 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 98 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain R residue 199 MET Chi-restraints excluded: chain R residue 219 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 15 optimal weight: 0.6980 chunk 26 optimal weight: 0.9980 chunk 28 optimal weight: 0.9990 chunk 19 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 61 optimal weight: 0.4980 chunk 39 optimal weight: 0.9980 chunk 57 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN B 132 ASN ** R 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 310 ASN R 324 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.078677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.055505 restraints weight = 16093.443| |-----------------------------------------------------------------------------| r_work (start): 0.2876 rms_B_bonded: 1.96 r_work: 0.2759 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2653 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2653 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2635 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2635 r_free = 0.2635 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.78 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2635 r_free = 0.2635 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2635 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9137 moved from start: 0.2011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8283 Z= 0.168 Angle : 0.549 8.589 11242 Z= 0.288 Chirality : 0.041 0.141 1294 Planarity : 0.004 0.038 1430 Dihedral : 4.816 48.428 1143 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.50 % Allowed : 10.48 % Favored : 88.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.14 (0.26), residues: 1033 helix: 2.36 (0.24), residues: 408 sheet: -0.63 (0.33), residues: 201 loop : -0.05 (0.31), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG N 105 TYR 0.012 0.001 TYR A 205 PHE 0.013 0.001 PHE A 95 TRP 0.015 0.002 TRP A 91 HIS 0.006 0.001 HIS A 204 Details of bonding type rmsd covalent geometry : bond 0.00349 ( 8280) covalent geometry : angle 0.54868 (11235) SS BOND : bond 0.00176 ( 2) SS BOND : angle 0.37020 ( 4) hydrogen bonds : bond 0.04156 ( 472) hydrogen bonds : angle 4.98675 ( 1341) link_TRANS : bond 0.00079 ( 1) link_TRANS : angle 0.05745 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 107 time to evaluate : 0.200 Fit side-chains revert: symmetry clash REVERT: B 12 GLU cc_start: 0.8324 (pp20) cc_final: 0.8046 (pp20) REVERT: B 59 TYR cc_start: 0.9212 (OUTLIER) cc_final: 0.8499 (t80) REVERT: B 172 GLU cc_start: 0.8901 (tp30) cc_final: 0.8598 (tp30) REVERT: B 197 ARG cc_start: 0.8797 (mmm-85) cc_final: 0.8450 (mmm160) REVERT: B 267 ASP cc_start: 0.8945 (m-30) cc_final: 0.8678 (m-30) REVERT: G 22 GLU cc_start: 0.8301 (mt-10) cc_final: 0.8047 (mt-10) REVERT: R 90 ASN cc_start: 0.9080 (m-40) cc_final: 0.8815 (m-40) REVERT: R 199 MET cc_start: 0.8727 (OUTLIER) cc_final: 0.8509 (ppp) outliers start: 13 outliers final: 4 residues processed: 113 average time/residue: 0.6326 time to fit residues: 75.1180 Evaluate side-chains 111 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 105 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain R residue 199 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 86 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 54 optimal weight: 0.0010 chunk 39 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 56 optimal weight: 0.0970 chunk 64 optimal weight: 4.9990 chunk 70 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 overall best weight: 0.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN R 105 GLN R 169 ASN ** R 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 310 ASN R 324 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.078575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.055462 restraints weight = 16576.625| |-----------------------------------------------------------------------------| r_work (start): 0.2861 rms_B_bonded: 1.98 r_work: 0.2744 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2637 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9139 moved from start: 0.2190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8283 Z= 0.161 Angle : 0.533 7.151 11242 Z= 0.281 Chirality : 0.041 0.152 1294 Planarity : 0.004 0.036 1430 Dihedral : 4.599 24.893 1143 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 2.07 % Allowed : 9.68 % Favored : 88.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.32 (0.26), residues: 1033 helix: 2.64 (0.24), residues: 408 sheet: -0.69 (0.33), residues: 194 loop : -0.03 (0.31), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG N 105 TYR 0.011 0.001 TYR A 205 PHE 0.013 0.001 PHE A 95 TRP 0.014 0.002 TRP A 91 HIS 0.005 0.001 HIS A 204 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 8280) covalent geometry : angle 0.53331 (11235) SS BOND : bond 0.00172 ( 2) SS BOND : angle 0.40110 ( 4) hydrogen bonds : bond 0.04009 ( 472) hydrogen bonds : angle 4.86389 ( 1341) link_TRANS : bond 0.00028 ( 1) link_TRANS : angle 0.06344 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 115 time to evaluate : 0.266 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 12 GLU cc_start: 0.8274 (OUTLIER) cc_final: 0.8015 (pp20) REVERT: B 59 TYR cc_start: 0.9252 (OUTLIER) cc_final: 0.8511 (t80) REVERT: B 172 GLU cc_start: 0.8926 (tp30) cc_final: 0.8616 (tp30) REVERT: B 197 ARG cc_start: 0.8818 (mmm-85) cc_final: 0.8543 (mmm160) REVERT: B 267 ASP cc_start: 0.8942 (m-30) cc_final: 0.8686 (m-30) REVERT: G 22 GLU cc_start: 0.8302 (mt-10) cc_final: 0.8080 (mt-10) REVERT: R 79 LYS cc_start: 0.8106 (mmmt) cc_final: 0.7573 (mmmm) REVERT: R 166 LYS cc_start: 0.9131 (mttp) cc_final: 0.8393 (mmtt) REVERT: R 252 LYS cc_start: 0.8698 (tttt) cc_final: 0.8469 (ttmm) outliers start: 18 outliers final: 5 residues processed: 121 average time/residue: 0.6685 time to fit residues: 84.6561 Evaluate side-chains 112 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 105 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 GLU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 65 LYS Chi-restraints excluded: chain R residue 219 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 20 optimal weight: 0.9980 chunk 55 optimal weight: 4.9990 chunk 43 optimal weight: 0.5980 chunk 63 optimal weight: 0.5980 chunk 9 optimal weight: 0.9980 chunk 88 optimal weight: 0.0470 chunk 92 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 58 optimal weight: 0.7980 chunk 10 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 105 GLN ** R 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 310 ASN R 324 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.079115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.056182 restraints weight = 16317.977| |-----------------------------------------------------------------------------| r_work (start): 0.2881 rms_B_bonded: 1.96 r_work: 0.2765 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2660 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9123 moved from start: 0.2244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8283 Z= 0.140 Angle : 0.527 6.969 11242 Z= 0.276 Chirality : 0.041 0.158 1294 Planarity : 0.004 0.035 1430 Dihedral : 4.506 28.004 1143 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 1.15 % Allowed : 11.52 % Favored : 87.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.44 (0.27), residues: 1033 helix: 2.79 (0.24), residues: 409 sheet: -0.65 (0.33), residues: 199 loop : 0.01 (0.32), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG N 105 TYR 0.011 0.001 TYR N 95 PHE 0.011 0.001 PHE A 69 TRP 0.014 0.001 TRP A 91 HIS 0.004 0.001 HIS A 204 Details of bonding type rmsd covalent geometry : bond 0.00293 ( 8280) covalent geometry : angle 0.52716 (11235) SS BOND : bond 0.00093 ( 2) SS BOND : angle 0.39272 ( 4) hydrogen bonds : bond 0.03828 ( 472) hydrogen bonds : angle 4.78396 ( 1341) link_TRANS : bond 0.00049 ( 1) link_TRANS : angle 0.05469 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 110 time to evaluate : 0.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 237 ASP cc_start: 0.9028 (t70) cc_final: 0.8672 (t0) REVERT: B 12 GLU cc_start: 0.8287 (OUTLIER) cc_final: 0.8025 (pp20) REVERT: B 59 TYR cc_start: 0.9246 (OUTLIER) cc_final: 0.8601 (t80) REVERT: B 172 GLU cc_start: 0.8955 (tp30) cc_final: 0.8623 (tp30) REVERT: B 197 ARG cc_start: 0.8830 (mmm-85) cc_final: 0.8588 (mmm160) REVERT: B 267 ASP cc_start: 0.8945 (m-30) cc_final: 0.8689 (m-30) REVERT: G 22 GLU cc_start: 0.8220 (mt-10) cc_final: 0.8003 (mt-10) REVERT: N 114 THR cc_start: 0.9084 (OUTLIER) cc_final: 0.8849 (p) REVERT: R 90 ASN cc_start: 0.8956 (m-40) cc_final: 0.8750 (m-40) outliers start: 10 outliers final: 4 residues processed: 113 average time/residue: 0.6843 time to fit residues: 81.1120 Evaluate side-chains 114 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 107 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 GLU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain R residue 219 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 96 optimal weight: 3.9990 chunk 72 optimal weight: 10.0000 chunk 63 optimal weight: 0.5980 chunk 25 optimal weight: 0.0980 chunk 14 optimal weight: 0.8980 chunk 78 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 chunk 97 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 chunk 46 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN R 105 GLN R 169 ASN ** R 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 310 ASN R 324 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.078735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.055735 restraints weight = 16195.029| |-----------------------------------------------------------------------------| r_work (start): 0.2868 rms_B_bonded: 1.95 r_work: 0.2752 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2648 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9130 moved from start: 0.2330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8283 Z= 0.155 Angle : 0.532 7.018 11242 Z= 0.279 Chirality : 0.041 0.168 1294 Planarity : 0.004 0.035 1430 Dihedral : 4.526 27.908 1143 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 1.73 % Allowed : 11.06 % Favored : 87.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.51 (0.27), residues: 1033 helix: 2.87 (0.24), residues: 409 sheet: -0.63 (0.34), residues: 198 loop : 0.02 (0.32), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG N 105 TYR 0.011 0.001 TYR N 95 PHE 0.012 0.001 PHE A 95 TRP 0.014 0.001 TRP A 91 HIS 0.004 0.001 HIS A 204 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 8280) covalent geometry : angle 0.53178 (11235) SS BOND : bond 0.00202 ( 2) SS BOND : angle 0.38618 ( 4) hydrogen bonds : bond 0.03876 ( 472) hydrogen bonds : angle 4.77364 ( 1341) link_TRANS : bond 0.00064 ( 1) link_TRANS : angle 0.05806 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 118 time to evaluate : 1.783 Fit side-chains revert: symmetry clash REVERT: B 12 GLU cc_start: 0.8299 (OUTLIER) cc_final: 0.8015 (pp20) REVERT: B 59 TYR cc_start: 0.9258 (OUTLIER) cc_final: 0.8561 (t80) REVERT: B 172 GLU cc_start: 0.8950 (tp30) cc_final: 0.8628 (tp30) REVERT: B 197 ARG cc_start: 0.8833 (mmm-85) cc_final: 0.8612 (mmm160) REVERT: B 267 ASP cc_start: 0.8957 (m-30) cc_final: 0.8711 (m-30) REVERT: G 22 GLU cc_start: 0.8200 (mt-10) cc_final: 0.7945 (mt-10) REVERT: N 114 THR cc_start: 0.9111 (OUTLIER) cc_final: 0.8886 (p) REVERT: R 79 LYS cc_start: 0.8205 (mmmt) cc_final: 0.7692 (mmmm) REVERT: R 166 LYS cc_start: 0.9084 (mttp) cc_final: 0.8366 (mmtt) REVERT: R 252 LYS cc_start: 0.8764 (tttt) cc_final: 0.8551 (ttmm) outliers start: 15 outliers final: 3 residues processed: 125 average time/residue: 0.6588 time to fit residues: 86.2683 Evaluate side-chains 107 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 101 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 GLU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain R residue 219 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 83 optimal weight: 0.9990 chunk 95 optimal weight: 0.6980 chunk 56 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 91 optimal weight: 0.8980 chunk 63 optimal weight: 0.5980 chunk 73 optimal weight: 3.9990 chunk 30 optimal weight: 0.9980 chunk 11 optimal weight: 3.9990 chunk 57 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 105 GLN ** R 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 310 ASN R 324 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.078543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.054712 restraints weight = 16434.093| |-----------------------------------------------------------------------------| r_work (start): 0.2810 rms_B_bonded: 2.02 r_work: 0.2690 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2579 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9120 moved from start: 0.2390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8283 Z= 0.173 Angle : 0.564 7.909 11242 Z= 0.295 Chirality : 0.041 0.184 1294 Planarity : 0.004 0.035 1430 Dihedral : 4.588 27.979 1143 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.15 % Allowed : 12.56 % Favored : 86.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.53 (0.27), residues: 1033 helix: 2.86 (0.24), residues: 409 sheet: -0.63 (0.34), residues: 198 loop : 0.06 (0.32), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG N 105 TYR 0.012 0.001 TYR A 158 PHE 0.012 0.001 PHE A 95 TRP 0.014 0.001 TRP B 82 HIS 0.005 0.001 HIS A 204 Details of bonding type rmsd covalent geometry : bond 0.00367 ( 8280) covalent geometry : angle 0.56426 (11235) SS BOND : bond 0.00235 ( 2) SS BOND : angle 0.39859 ( 4) hydrogen bonds : bond 0.03959 ( 472) hydrogen bonds : angle 4.80519 ( 1341) link_TRANS : bond 0.00069 ( 1) link_TRANS : angle 0.04417 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 111 time to evaluate : 0.273 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 237 ASP cc_start: 0.9023 (t70) cc_final: 0.8642 (t0) REVERT: B 12 GLU cc_start: 0.8260 (OUTLIER) cc_final: 0.8000 (pp20) REVERT: B 59 TYR cc_start: 0.9294 (OUTLIER) cc_final: 0.8620 (t80) REVERT: B 172 GLU cc_start: 0.8981 (tp30) cc_final: 0.8654 (tp30) REVERT: B 197 ARG cc_start: 0.8877 (mmm-85) cc_final: 0.8622 (mmm160) REVERT: B 267 ASP cc_start: 0.9014 (m-30) cc_final: 0.8764 (m-30) REVERT: G 20 LYS cc_start: 0.8831 (mttp) cc_final: 0.8511 (mttm) REVERT: G 22 GLU cc_start: 0.8200 (mt-10) cc_final: 0.7943 (mt-10) REVERT: N 114 THR cc_start: 0.9175 (OUTLIER) cc_final: 0.8954 (p) outliers start: 10 outliers final: 4 residues processed: 116 average time/residue: 0.6626 time to fit residues: 80.8990 Evaluate side-chains 113 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 106 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 GLU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 65 LYS Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain R residue 219 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 59 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 78 optimal weight: 0.7980 chunk 73 optimal weight: 0.8980 chunk 75 optimal weight: 4.9990 chunk 55 optimal weight: 5.9990 chunk 80 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 GLN R 105 GLN ** R 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 310 ASN R 324 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.076142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2786 r_free = 0.2786 target = 0.051685 restraints weight = 16446.195| |-----------------------------------------------------------------------------| r_work (start): 0.2741 rms_B_bonded: 2.02 r_work: 0.2617 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2506 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9169 moved from start: 0.2624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.048 8283 Z= 0.314 Angle : 0.643 8.215 11242 Z= 0.339 Chirality : 0.044 0.205 1294 Planarity : 0.004 0.050 1430 Dihedral : 5.012 28.540 1143 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 1.61 % Allowed : 12.21 % Favored : 86.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.41 (0.26), residues: 1033 helix: 2.73 (0.24), residues: 410 sheet: -0.58 (0.33), residues: 201 loop : -0.03 (0.32), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG R 254 TYR 0.014 0.002 TYR N 117 PHE 0.017 0.002 PHE A 95 TRP 0.016 0.002 TRP B 82 HIS 0.006 0.002 HIS A 204 Details of bonding type rmsd covalent geometry : bond 0.00666 ( 8280) covalent geometry : angle 0.64337 (11235) SS BOND : bond 0.00430 ( 2) SS BOND : angle 0.61312 ( 4) hydrogen bonds : bond 0.04674 ( 472) hydrogen bonds : angle 5.05465 ( 1341) link_TRANS : bond 0.00208 ( 1) link_TRANS : angle 0.11302 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 101 time to evaluate : 0.295 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 12 GLU cc_start: 0.8287 (OUTLIER) cc_final: 0.8013 (pp20) REVERT: B 59 TYR cc_start: 0.9369 (OUTLIER) cc_final: 0.8466 (t80) REVERT: B 172 GLU cc_start: 0.9011 (tp30) cc_final: 0.8770 (tp30) REVERT: B 197 ARG cc_start: 0.8977 (mmm-85) cc_final: 0.8667 (mmm160) REVERT: N 73 ASP cc_start: 0.9178 (t0) cc_final: 0.8965 (t0) REVERT: R 125 LEU cc_start: 0.8754 (OUTLIER) cc_final: 0.8501 (mt) outliers start: 14 outliers final: 7 residues processed: 108 average time/residue: 0.6608 time to fit residues: 74.9304 Evaluate side-chains 111 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 101 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 GLU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain N residue 43 LYS Chi-restraints excluded: chain N residue 65 LYS Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain R residue 125 LEU Chi-restraints excluded: chain R residue 219 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 63 optimal weight: 0.5980 chunk 10 optimal weight: 0.7980 chunk 17 optimal weight: 0.5980 chunk 41 optimal weight: 0.9980 chunk 72 optimal weight: 10.0000 chunk 80 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 100 optimal weight: 0.9980 chunk 73 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 GLN R 105 GLN ** R 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 310 ASN R 324 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.077857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.054546 restraints weight = 16462.102| |-----------------------------------------------------------------------------| r_work (start): 0.2801 rms_B_bonded: 1.98 r_work: 0.2680 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2570 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9120 moved from start: 0.2529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8283 Z= 0.168 Angle : 0.583 7.389 11242 Z= 0.305 Chirality : 0.042 0.219 1294 Planarity : 0.004 0.037 1430 Dihedral : 4.731 28.277 1143 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.27 % Allowed : 12.56 % Favored : 86.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.51 (0.26), residues: 1033 helix: 2.82 (0.24), residues: 412 sheet: -0.68 (0.34), residues: 193 loop : 0.07 (0.31), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG R 254 TYR 0.012 0.001 TYR R 318 PHE 0.013 0.001 PHE A 95 TRP 0.013 0.002 TRP B 82 HIS 0.006 0.001 HIS A 204 Details of bonding type rmsd covalent geometry : bond 0.00359 ( 8280) covalent geometry : angle 0.58353 (11235) SS BOND : bond 0.00238 ( 2) SS BOND : angle 0.37361 ( 4) hydrogen bonds : bond 0.04002 ( 472) hydrogen bonds : angle 4.88454 ( 1341) link_TRANS : bond 0.00090 ( 1) link_TRANS : angle 0.02244 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 106 time to evaluate : 0.272 Fit side-chains revert: symmetry clash REVERT: B 12 GLU cc_start: 0.8292 (OUTLIER) cc_final: 0.8039 (pp20) REVERT: B 59 TYR cc_start: 0.9301 (OUTLIER) cc_final: 0.8580 (t80) REVERT: B 172 GLU cc_start: 0.8988 (tp30) cc_final: 0.8728 (tp30) REVERT: B 197 ARG cc_start: 0.8890 (mmm-85) cc_final: 0.8673 (mmm160) REVERT: B 267 ASP cc_start: 0.9039 (m-30) cc_final: 0.8783 (m-30) REVERT: G 20 LYS cc_start: 0.8800 (mttp) cc_final: 0.8482 (mttm) outliers start: 11 outliers final: 5 residues processed: 112 average time/residue: 0.6197 time to fit residues: 72.9790 Evaluate side-chains 106 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 99 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 GLU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 65 LYS Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain R residue 219 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 11 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 78 optimal weight: 0.6980 chunk 96 optimal weight: 4.9990 chunk 4 optimal weight: 0.3980 chunk 10 optimal weight: 0.9980 chunk 47 optimal weight: 0.8980 chunk 92 optimal weight: 0.9990 chunk 45 optimal weight: 0.5980 chunk 2 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN B 44 GLN R 85 ASN R 105 GLN ** R 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 310 ASN R 324 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.078376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.054916 restraints weight = 16417.398| |-----------------------------------------------------------------------------| r_work (start): 0.2815 rms_B_bonded: 2.00 r_work: 0.2694 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2585 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9114 moved from start: 0.2546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8283 Z= 0.160 Angle : 0.589 7.994 11242 Z= 0.306 Chirality : 0.042 0.217 1294 Planarity : 0.004 0.037 1430 Dihedral : 4.651 27.874 1143 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 1.15 % Allowed : 13.13 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.51 (0.26), residues: 1033 helix: 2.82 (0.24), residues: 413 sheet: -0.72 (0.34), residues: 192 loop : 0.09 (0.31), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG R 254 TYR 0.014 0.001 TYR A 158 PHE 0.012 0.001 PHE A 95 TRP 0.014 0.002 TRP A 91 HIS 0.006 0.001 HIS A 204 Details of bonding type rmsd covalent geometry : bond 0.00344 ( 8280) covalent geometry : angle 0.58913 (11235) SS BOND : bond 0.00204 ( 2) SS BOND : angle 0.42574 ( 4) hydrogen bonds : bond 0.03910 ( 472) hydrogen bonds : angle 4.85009 ( 1341) link_TRANS : bond 0.00073 ( 1) link_TRANS : angle 0.04538 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 106 time to evaluate : 0.368 Fit side-chains revert: symmetry clash REVERT: A 237 ASP cc_start: 0.8923 (t70) cc_final: 0.8532 (t0) REVERT: B 12 GLU cc_start: 0.8287 (OUTLIER) cc_final: 0.8021 (pp20) REVERT: B 59 TYR cc_start: 0.9301 (OUTLIER) cc_final: 0.8654 (t80) REVERT: B 172 GLU cc_start: 0.8993 (tp30) cc_final: 0.8730 (tp30) REVERT: B 267 ASP cc_start: 0.9022 (m-30) cc_final: 0.8773 (m-30) REVERT: N 114 THR cc_start: 0.9181 (OUTLIER) cc_final: 0.8955 (p) outliers start: 10 outliers final: 3 residues processed: 110 average time/residue: 0.6829 time to fit residues: 78.7730 Evaluate side-chains 105 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 99 time to evaluate : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 GLU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain R residue 219 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 83 optimal weight: 0.9990 chunk 15 optimal weight: 0.0870 chunk 21 optimal weight: 0.6980 chunk 73 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 chunk 94 optimal weight: 1.9990 chunk 85 optimal weight: 6.9990 chunk 17 optimal weight: 0.5980 overall best weight: 0.6160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 GLN R 105 GLN ** R 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 310 ASN R 324 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.078862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.055301 restraints weight = 16505.408| |-----------------------------------------------------------------------------| r_work (start): 0.2828 rms_B_bonded: 2.02 r_work: 0.2708 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2599 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9110 moved from start: 0.2584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8283 Z= 0.153 Angle : 0.590 8.812 11242 Z= 0.304 Chirality : 0.042 0.216 1294 Planarity : 0.004 0.037 1430 Dihedral : 4.591 27.855 1143 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 0.92 % Allowed : 13.48 % Favored : 85.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.55 (0.27), residues: 1033 helix: 2.86 (0.24), residues: 414 sheet: -0.70 (0.35), residues: 192 loop : 0.09 (0.31), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG R 254 TYR 0.014 0.001 TYR A 158 PHE 0.015 0.001 PHE R 202 TRP 0.013 0.001 TRP A 91 HIS 0.005 0.001 HIS A 204 Details of bonding type rmsd covalent geometry : bond 0.00330 ( 8280) covalent geometry : angle 0.59042 (11235) SS BOND : bond 0.00240 ( 2) SS BOND : angle 0.41991 ( 4) hydrogen bonds : bond 0.03837 ( 472) hydrogen bonds : angle 4.82493 ( 1341) link_TRANS : bond 0.00064 ( 1) link_TRANS : angle 0.05610 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4510.52 seconds wall clock time: 77 minutes 14.86 seconds (4634.86 seconds total)