Starting phenix.real_space_refine on Tue Aug 4 22:28:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/22gk_68262/08_2026/22gk_68262.cif Found real_map, /net/cci-nas-00/data/ceres_data/22gk_68262/08_2026/22gk_68262.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/22gk_68262/08_2026/22gk_68262.cif" } default_model = "/net/cci-nas-00/data/ceres_data/22gk_68262/08_2026/22gk_68262.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/22gk_68262/08_2026/22gk_68262.map" default_real_map = "/net/cci-nas-00/data/ceres_data/22gk_68262/08_2026/22gk_68262.map" } resolution = 2.84 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= 0.002 sd= 0.016 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 5 5.49 5 S 39 5.16 5 C 4446 2.51 5 N 1189 2.21 5 O 1286 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6965 Number of models: 1 Model: "" Number of chains: 5 Chain: "C" Number of atoms: 554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 554 Classifications: {'peptide': 74} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 1, 'TRANS': 72} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "R" Number of atoms: 2243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2243 Classifications: {'peptide': 297} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 279} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'TPO:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "H" Number of atoms: 896 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 896 Classifications: {'peptide': 117} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 114} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "L" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 795 Classifications: {'peptide': 105} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 98} Chain breaks: 1 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: "A" Number of atoms: 2477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2477 Classifications: {'peptide': 324} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 302} Chain breaks: 5 Unresolved non-hydrogen bonds: 93 Unresolved non-hydrogen angles: 109 Unresolved non-hydrogen dihedrals: 77 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 6, 'ARG:plan': 4, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 53 Time building chain proxies: 1.21, per 1000 atoms: 0.17 Number of scatterers: 6965 At special positions: 0 Unit cell: (75.33, 95.79, 166.47, 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 39 16.00 P 5 15.00 O 1286 8.00 N 1189 7.00 C 4446 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS C 21 " - pdb=" SG CYS C 47 " distance=2.04 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 54 " distance=2.03 Simple disulfide: pdb=" SG CYS C 34 " - pdb=" SG CYS C 55 " distance=2.04 Simple disulfide: pdb=" SG CYS R 107 " - pdb=" SG CYS R 186 " distance=2.02 Simple disulfide: pdb=" SG CYS R 133 " - pdb=" SG CYS R 219 " distance=2.04 Simple disulfide: pdb=" SG CYS H 25 " - pdb=" SG CYS H 99 " distance=1.82 Simple disulfide: pdb=" SG CYS L 24 " - pdb=" SG CYS L 89 " 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 Time building additional restraints: 0.55 Conformation dependent library (CDL) restraints added in 300.1 milliseconds 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1720 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 13 sheets defined 32.2% alpha, 35.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'C' and resid 4 through 12 Processing helix chain 'C' and resid 17 through 24 Processing helix chain 'C' and resid 34 through 39 removed outlier: 3.640A pdb=" N ALA C 39 " --> pdb=" O GLU C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 44 through 65 removed outlier: 3.518A pdb=" N GLN C 60 " --> pdb=" O VAL C 56 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ILE C 65 " --> pdb=" O LEU C 61 " (cutoff:3.500A) Processing helix chain 'R' and resid 32 through 36 Processing helix chain 'R' and resid 37 through 58 Proline residue: R 51 - end of helix Processing helix chain 'R' and resid 70 through 86 Processing helix chain 'R' and resid 86 through 96 Proline residue: R 93 - end of helix Processing helix chain 'R' and resid 103 through 108 Processing helix chain 'R' and resid 109 through 138 removed outlier: 4.065A pdb=" N LEU R 135 " --> pdb=" O ASP R 131 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N ALA R 136 " --> pdb=" O LEU R 132 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N LEU R 137 " --> pdb=" O CYS R 133 " (cutoff:3.500A) Processing helix chain 'R' and resid 146 through 150 Processing helix chain 'R' and resid 151 through 166 Processing helix chain 'R' and resid 168 through 172 Processing helix chain 'R' and resid 194 through 209 removed outlier: 3.625A pdb=" N PHE R 209 " --> pdb=" O PHE R 205 " (cutoff:3.500A) Processing helix chain 'R' and resid 209 through 227 removed outlier: 3.575A pdb=" N VAL R 214 " --> pdb=" O LEU R 210 " (cutoff:3.500A) Processing helix chain 'R' and resid 231 through 259 removed outlier: 4.043A pdb=" N ALA R 237 " --> pdb=" O PRO R 233 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLY R 241 " --> pdb=" O ALA R 237 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N PHE R 242 " --> pdb=" O ILE R 238 " (cutoff:3.500A) Proline residue: R 248 - end of helix Processing helix chain 'R' and resid 263 through 281 removed outlier: 3.516A pdb=" N ALA R 267 " --> pdb=" O SER R 263 " (cutoff:3.500A) Proline residue: R 274 - end of helix Processing helix chain 'R' and resid 282 through 295 Proline residue: R 288 - end of helix removed outlier: 3.906A pdb=" N TYR R 293 " --> pdb=" O MET R 289 " (cutoff:3.500A) Processing helix chain 'H' and resid 67 through 69 No H-bonds generated for 'chain 'H' and resid 67 through 69' Processing helix chain 'H' and resid 77 through 79 No H-bonds generated for 'chain 'H' and resid 77 through 79' Processing helix chain 'H' and resid 90 through 94 Processing helix chain 'L' and resid 80 through 84 removed outlier: 4.183A pdb=" N PHE L 84 " --> pdb=" O PRO L 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 109 Processing helix chain 'A' and resid 159 through 161 No H-bonds generated for 'chain 'A' and resid 159 through 161' Processing helix chain 'A' and resid 278 through 282 Processing sheet with id=AA1, first strand: chain 'C' and resid 67 through 68 removed outlier: 3.614A pdb=" N LYS C 68 " --> pdb=" O VAL R 188 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'R' and resid 327 through 328 removed outlier: 3.630A pdb=" N VAL A 8 " --> pdb=" O TPO R 327 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 6 through 10 Processing sheet with id=AA4, first strand: chain 'H' and resid 13 through 14 removed outlier: 8.598A pdb=" N SER H 35 " --> pdb=" O SER H 55 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N SER H 55 " --> pdb=" O SER H 35 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ILE H 37 " --> pdb=" O SER H 53 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N SER H 53 " --> pdb=" O ILE H 37 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N TRP H 39 " --> pdb=" O VAL H 51 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 13 through 14 Processing sheet with id=AA6, first strand: chain 'L' and resid 5 through 8 Processing sheet with id=AA7, first strand: chain 'L' and resid 11 through 13 removed outlier: 6.368A pdb=" N VAL L 34 " --> pdb=" O TYR L 50 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N TYR L 50 " --> pdb=" O VAL L 34 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 11 through 13 Processing sheet with id=AA9, first strand: chain 'A' and resid 33 through 34 removed outlier: 4.025A pdb=" N TYR A 144 " --> pdb=" O ILE A 168 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N LYS A 170 " --> pdb=" O VAL A 142 " (cutoff:3.500A) removed outlier: 9.463A pdb=" N VAL A 142 " --> pdb=" O LYS A 170 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N VAL A 53 " --> pdb=" O SER A 86 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N PHE A 61 " --> pdb=" O ASP A 78 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N ASP A 78 " --> pdb=" O PHE A 61 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 33 through 34 removed outlier: 4.025A pdb=" N TYR A 144 " --> pdb=" O ILE A 168 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N LYS A 170 " --> pdb=" O VAL A 142 " (cutoff:3.500A) removed outlier: 9.463A pdb=" N VAL A 142 " --> pdb=" O LYS A 170 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 183 through 188 Processing sheet with id=AB3, first strand: chain 'A' and resid 207 through 208 removed outlier: 4.064A pdb=" N TYR A 321 " --> pdb=" O PHE A 349 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N LEU A 351 " --> pdb=" O VAL A 319 " (cutoff:3.500A) removed outlier: 9.334A pdb=" N VAL A 319 " --> pdb=" O LEU A 351 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N ILE A 231 " --> pdb=" O GLU A 257 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N GLU A 257 " --> pdb=" O ILE A 231 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N ILE A 233 " --> pdb=" O MET A 255 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N MET A 255 " --> pdb=" O ILE A 233 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N VAL A 235 " --> pdb=" O VAL A 253 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 207 through 208 removed outlier: 6.959A pdb=" N ILE A 231 " --> pdb=" O GLU A 257 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N GLU A 257 " --> pdb=" O ILE A 231 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N ILE A 233 " --> pdb=" O MET A 255 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N MET A 255 " --> pdb=" O ILE A 233 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N VAL A 235 " --> pdb=" O VAL A 253 " (cutoff:3.500A) 376 hydrogen bonds defined for protein. 1002 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: 0.82 Time building geometry restraints manager: 0.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 1307 1.32 - 1.46: 2370 1.46 - 1.59: 3385 1.59 - 1.73: 10 1.73 - 1.87: 45 Bond restraints: 7117 Sorted by residual: bond pdb=" OG1 TPO R 327 " pdb=" P TPO R 327 " ideal model delta sigma weight residual 1.717 1.609 0.108 2.00e-02 2.50e+03 2.92e+01 bond pdb=" O1P SEP R 323 " pdb=" P SEP R 323 " ideal model delta sigma weight residual 1.610 1.507 0.103 2.00e-02 2.50e+03 2.65e+01 bond pdb=" O2P SEP R 326 " pdb=" P SEP R 326 " ideal model delta sigma weight residual 1.610 1.507 0.103 2.00e-02 2.50e+03 2.64e+01 bond pdb=" O1P SEP R 326 " pdb=" P SEP R 326 " ideal model delta sigma weight residual 1.610 1.508 0.102 2.00e-02 2.50e+03 2.61e+01 bond pdb=" O3P SEP R 326 " pdb=" P SEP R 326 " ideal model delta sigma weight residual 1.610 1.509 0.101 2.00e-02 2.50e+03 2.55e+01 ... (remaining 7112 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.28: 8481 2.28 - 4.55: 1046 4.55 - 6.83: 163 6.83 - 9.10: 10 9.10 - 11.38: 3 Bond angle restraints: 9703 Sorted by residual: angle pdb=" C TYR A 113 " pdb=" N PRO A 114 " pdb=" CA PRO A 114 " ideal model delta sigma weight residual 120.31 125.11 -4.80 9.80e-01 1.04e+00 2.40e+01 angle pdb=" C PRO R 93 " pdb=" N ILE R 94 " pdb=" CA ILE R 94 " ideal model delta sigma weight residual 120.56 114.32 6.24 1.28e+00 6.10e-01 2.38e+01 angle pdb=" C ASP R 32 " pdb=" N PRO R 33 " pdb=" CA PRO R 33 " ideal model delta sigma weight residual 119.47 125.07 -5.60 1.16e+00 7.43e-01 2.33e+01 angle pdb=" C LEU A 104 " pdb=" N ILE A 105 " pdb=" CA ILE A 105 " ideal model delta sigma weight residual 120.46 113.86 6.60 1.37e+00 5.33e-01 2.32e+01 angle pdb=" N VAL R 56 " pdb=" CA VAL R 56 " pdb=" C VAL R 56 " ideal model delta sigma weight residual 110.62 105.75 4.87 1.02e+00 9.61e-01 2.28e+01 ... (remaining 9698 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 4072 17.81 - 35.61: 131 35.61 - 53.42: 28 53.42 - 71.22: 12 71.22 - 89.03: 5 Dihedral angle restraints: 4248 sinusoidal: 1583 harmonic: 2665 Sorted by residual: dihedral pdb=" CB CYS C 21 " pdb=" SG CYS C 21 " pdb=" SG CYS C 47 " pdb=" CB CYS C 47 " ideal model delta sinusoidal sigma weight residual 93.00 43.88 49.12 1 1.00e+01 1.00e-02 3.32e+01 dihedral pdb=" CB CYS R 133 " pdb=" SG CYS R 133 " pdb=" SG CYS R 219 " pdb=" CB CYS R 219 " ideal model delta sinusoidal sigma weight residual -86.00 -129.93 43.93 1 1.00e+01 1.00e-02 2.69e+01 dihedral pdb=" CA PHE R 180 " pdb=" C PHE R 180 " pdb=" N PRO R 181 " pdb=" CA PRO R 181 " ideal model delta harmonic sigma weight residual 0.00 -24.50 24.50 0 5.00e+00 4.00e-02 2.40e+01 ... (remaining 4245 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 883 0.093 - 0.187: 217 0.187 - 0.280: 26 0.280 - 0.374: 5 0.374 - 0.467: 1 Chirality restraints: 1132 Sorted by residual: chirality pdb=" CB VAL H 5 " pdb=" CA VAL H 5 " pdb=" CG1 VAL H 5 " pdb=" CG2 VAL H 5 " both_signs ideal model delta sigma weight residual False -2.63 -3.10 0.47 2.00e-01 2.50e+01 5.45e+00 chirality pdb=" CA ASN A 225 " pdb=" N ASN A 225 " pdb=" C ASN A 225 " pdb=" CB ASN A 225 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.41e+00 chirality pdb=" CA GLU R 273 " pdb=" N GLU R 273 " pdb=" C GLU R 273 " pdb=" CB GLU R 273 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.28e+00 ... (remaining 1129 not shown) Planarity restraints: 1221 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR L 92 " -0.052 2.00e-02 2.50e+03 2.63e-02 1.39e+01 pdb=" CG TYR L 92 " 0.028 2.00e-02 2.50e+03 pdb=" CD1 TYR L 92 " 0.022 2.00e-02 2.50e+03 pdb=" CD2 TYR L 92 " 0.021 2.00e-02 2.50e+03 pdb=" CE1 TYR L 92 " 0.008 2.00e-02 2.50e+03 pdb=" CE2 TYR L 92 " 0.009 2.00e-02 2.50e+03 pdb=" CZ TYR L 92 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR L 92 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 13 " -0.045 2.00e-02 2.50e+03 2.31e-02 1.07e+01 pdb=" CG TYR C 13 " 0.021 2.00e-02 2.50e+03 pdb=" CD1 TYR C 13 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 TYR C 13 " 0.019 2.00e-02 2.50e+03 pdb=" CE1 TYR C 13 " 0.008 2.00e-02 2.50e+03 pdb=" CE2 TYR C 13 " 0.010 2.00e-02 2.50e+03 pdb=" CZ TYR C 13 " -0.005 2.00e-02 2.50e+03 pdb=" OH TYR C 13 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 249 " 0.040 2.00e-02 2.50e+03 2.07e-02 8.56e+00 pdb=" CG TYR A 249 " -0.021 2.00e-02 2.50e+03 pdb=" CD1 TYR A 249 " -0.024 2.00e-02 2.50e+03 pdb=" CD2 TYR A 249 " -0.016 2.00e-02 2.50e+03 pdb=" CE1 TYR A 249 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR A 249 " -0.007 2.00e-02 2.50e+03 pdb=" CZ TYR A 249 " 0.011 2.00e-02 2.50e+03 pdb=" OH TYR A 249 " 0.019 2.00e-02 2.50e+03 ... (remaining 1218 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 2215 2.81 - 3.33: 6614 3.33 - 3.86: 11881 3.86 - 4.38: 13994 4.38 - 4.90: 23113 Nonbonded interactions: 57817 Sorted by model distance: nonbonded pdb=" O ASP R 25 " pdb=" OD1 ASP R 25 " model vdw 2.288 3.040 nonbonded pdb=" O THR C 33 " pdb=" N ARG C 37 " model vdw 2.344 3.120 nonbonded pdb=" OD2 ASP H 76 " pdb=" NZ LYS H 79 " model vdw 2.374 3.120 nonbonded pdb=" O PRO R 111 " pdb=" CG2 ILE R 114 " model vdw 2.388 3.460 nonbonded pdb=" O ARG C 37 " pdb=" N ARG C 40 " model vdw 2.431 3.120 ... (remaining 57812 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.370 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: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 6.270 Find NCS groups from input model: 0.030 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: 0.000 Load rotamer database and sin/cos tables:5.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 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 : 0.018 0.208 7124 Z= 0.975 Angle : 1.547 11.381 9717 Z= 1.011 Chirality : 0.080 0.467 1132 Planarity : 0.007 0.045 1221 Dihedral : 10.366 89.025 2507 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 15.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.80 % Favored : 93.20 % Rotamer: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: -0.91 (0.27), residues: 882 helix: -1.41 (0.30), residues: 248 sheet: 0.96 (0.33), residues: 250 loop : -1.02 (0.30), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG R 204 TYR 0.052 0.006 TYR L 92 PHE 0.022 0.003 PHE R 291 TRP 0.030 0.005 TRP L 36 HIS 0.006 0.001 HIS A 210 Details of bonding type rmsd/Z covalent geometry : bond 0.01802 / 0.97 ( 7117) covalent geometry : angle 1.54625 / 1.01 ( 9703) SS BOND : bond 0.07869 / 4.91 ( 7) SS BOND : angle 1.83505 / 0.91 ( 14) hydrogen bonds : bond 0.19229 / 13.73 ( 348) hydrogen bonds : angle 8.22018 / 5.69 ( 1002) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 187 time to evaluate : 0.181 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 3 GLN cc_start: 0.7355 (mm-40) cc_final: 0.7095 (mm-40) REVERT: R 296 ARG cc_start: 0.7723 (ptt180) cc_final: 0.6116 (tmt170) REVERT: L 94 TYR cc_start: 0.8804 (m-80) cc_final: 0.8597 (m-80) REVERT: A 244 PHE cc_start: 0.6114 (m-80) cc_final: 0.5910 (m-80) outliers start: 0 outliers final: 0 residues processed: 187 average time/residue: 0.3700 time to fit residues: 73.5093 Evaluate side-chains 115 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 49 optimal weight: 4.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 0.6980 chunk 45 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 36 GLN C 71 GLN R 287 ASN R 317 GLN A 223 ASN ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.106966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.090999 restraints weight = 17753.286| |-----------------------------------------------------------------------------| r_work (start): 0.3643 rms_B_bonded: 2.72 r_work: 0.3538 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.3236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.092 7124 Z= 0.223 Angle : 0.767 9.493 9717 Z= 0.399 Chirality : 0.046 0.164 1132 Planarity : 0.006 0.053 1221 Dihedral : 6.522 82.330 1004 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 3.70 % Allowed : 12.74 % Favored : 83.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 0.00 (0.28), residues: 882 helix: 0.11 (0.31), residues: 253 sheet: 0.85 (0.32), residues: 271 loop : -0.65 (0.33), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG R 229 TYR 0.026 0.002 TYR C 23 PHE 0.022 0.002 PHE R 205 TRP 0.015 0.002 TRP R 141 HIS 0.005 0.001 HIS A 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00503 / 0.22 ( 7117) covalent geometry : angle 0.75939 / 0.40 ( 9703) SS BOND : bond 0.00998 / 0.52 ( 7) SS BOND : angle 2.97474 / 1.54 ( 14) hydrogen bonds : bond 0.05682 / 4.04 ( 348) hydrogen bonds : angle 5.61007 / 3.90 ( 1002) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 146 time to evaluate : 0.204 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 47 CYS cc_start: 0.6271 (OUTLIER) cc_final: 0.5859 (m) REVERT: R 161 LEU cc_start: 0.7814 (OUTLIER) cc_final: 0.7575 (tm) REVERT: R 171 ILE cc_start: 0.8304 (mt) cc_final: 0.8004 (tp) REVERT: R 187 VAL cc_start: 0.7408 (m) cc_final: 0.6949 (m) REVERT: R 189 ASP cc_start: 0.7330 (t0) cc_final: 0.7127 (t0) REVERT: R 190 TYR cc_start: 0.5953 (m-80) cc_final: 0.5732 (m-10) REVERT: R 231 CYS cc_start: 0.7929 (t) cc_final: 0.7649 (t) REVERT: R 296 ARG cc_start: 0.7936 (ptt180) cc_final: 0.5917 (tmt170) REVERT: L 5 MET cc_start: 0.8808 (mtp) cc_final: 0.8434 (mtt) REVERT: A 226 LYS cc_start: 0.7352 (tptt) cc_final: 0.6708 (ttmt) REVERT: A 244 PHE cc_start: 0.6569 (m-80) cc_final: 0.6325 (m-80) REVERT: A 269 CYS cc_start: 0.8158 (m) cc_final: 0.7832 (t) outliers start: 27 outliers final: 8 residues processed: 159 average time/residue: 0.3652 time to fit residues: 62.1446 Evaluate side-chains 129 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 119 time to evaluate : 0.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 47 CYS Chi-restraints excluded: chain R residue 85 LEU Chi-restraints excluded: chain R residue 147 ARG Chi-restraints excluded: chain R residue 161 LEU Chi-restraints excluded: chain R residue 265 LEU Chi-restraints excluded: chain R residue 277 VAL Chi-restraints excluded: chain H residue 32 VAL Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain L residue 103 THR Chi-restraints excluded: chain A residue 145 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 14 optimal weight: 0.9980 chunk 80 optimal weight: 0.9990 chunk 83 optimal weight: 0.5980 chunk 11 optimal weight: 0.8980 chunk 36 optimal weight: 3.9990 chunk 32 optimal weight: 0.6980 chunk 59 optimal weight: 0.6980 chunk 7 optimal weight: 0.9980 chunk 13 optimal weight: 3.9990 chunk 54 optimal weight: 0.1980 chunk 29 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 30 ASN R 317 GLN ** R 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 80 ASN H 104 GLN H 115 GLN L 101 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.106005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.089831 restraints weight = 17677.757| |-----------------------------------------------------------------------------| r_work (start): 0.3639 rms_B_bonded: 2.71 r_work: 0.3538 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.4083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 7124 Z= 0.167 Angle : 0.682 10.065 9717 Z= 0.352 Chirality : 0.043 0.147 1132 Planarity : 0.005 0.052 1221 Dihedral : 6.246 79.807 1004 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 3.97 % Allowed : 15.21 % Favored : 80.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 0.15 (0.28), residues: 882 helix: 0.41 (0.31), residues: 261 sheet: 0.82 (0.32), residues: 277 loop : -0.65 (0.33), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 165 TYR 0.027 0.002 TYR C 23 PHE 0.011 0.002 PHE R 291 TRP 0.012 0.001 TRP R 141 HIS 0.003 0.001 HIS A 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.17 ( 7117) covalent geometry : angle 0.66870 / 0.35 ( 9703) SS BOND : bond 0.00783 / 0.45 ( 7) SS BOND : angle 3.53966 / 1.88 ( 14) hydrogen bonds : bond 0.04564 / 3.18 ( 348) hydrogen bonds : angle 5.04426 / 3.49 ( 1002) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 133 time to evaluate : 0.251 Fit side-chains revert: symmetry clash REVERT: R 161 LEU cc_start: 0.7832 (OUTLIER) cc_final: 0.7535 (tm) REVERT: R 171 ILE cc_start: 0.8298 (mt) cc_final: 0.8093 (tp) REVERT: R 189 ASP cc_start: 0.7628 (t0) cc_final: 0.7327 (t0) REVERT: R 194 SER cc_start: 0.7510 (t) cc_final: 0.6990 (p) REVERT: R 205 PHE cc_start: 0.6470 (t80) cc_final: 0.6232 (t80) REVERT: R 231 CYS cc_start: 0.8117 (t) cc_final: 0.7750 (t) REVERT: R 286 LEU cc_start: 0.7327 (OUTLIER) cc_final: 0.7124 (mm) REVERT: H 20 SER cc_start: 0.9139 (p) cc_final: 0.8781 (m) REVERT: L 5 MET cc_start: 0.8749 (mtt) cc_final: 0.8317 (mtt) REVERT: A 153 ASN cc_start: 0.7802 (t0) cc_final: 0.6983 (p0) REVERT: A 226 LYS cc_start: 0.7342 (tptt) cc_final: 0.6467 (ttmm) REVERT: A 269 CYS cc_start: 0.8104 (m) cc_final: 0.7785 (t) REVERT: A 290 ASP cc_start: 0.8740 (OUTLIER) cc_final: 0.8433 (m-30) outliers start: 29 outliers final: 10 residues processed: 151 average time/residue: 0.3957 time to fit residues: 64.1281 Evaluate side-chains 129 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 116 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 53 ASN Chi-restraints excluded: chain R residue 85 LEU Chi-restraints excluded: chain R residue 137 LEU Chi-restraints excluded: chain R residue 142 TRP Chi-restraints excluded: chain R residue 147 ARG Chi-restraints excluded: chain R residue 161 LEU Chi-restraints excluded: chain R residue 265 LEU Chi-restraints excluded: chain R residue 266 LEU Chi-restraints excluded: chain R residue 286 LEU Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain L residue 103 THR Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain A residue 343 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 76 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 78 optimal weight: 2.9990 chunk 87 optimal weight: 0.6980 chunk 25 optimal weight: 3.9990 chunk 2 optimal weight: 0.4980 chunk 64 optimal weight: 1.9990 chunk 33 optimal weight: 0.0870 chunk 35 optimal weight: 2.9990 overall best weight: 0.8160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 80 ASN H 115 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.104749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.088787 restraints weight = 17827.934| |-----------------------------------------------------------------------------| r_work (start): 0.3608 rms_B_bonded: 2.72 r_work: 0.3509 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.4442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 7124 Z= 0.186 Angle : 0.678 9.451 9717 Z= 0.350 Chirality : 0.043 0.147 1132 Planarity : 0.005 0.050 1221 Dihedral : 6.161 78.643 1004 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 4.25 % Allowed : 17.26 % Favored : 78.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 0.19 (0.28), residues: 882 helix: 0.52 (0.32), residues: 257 sheet: 0.94 (0.32), residues: 273 loop : -0.76 (0.33), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 165 TYR 0.022 0.002 TYR C 23 PHE 0.010 0.002 PHE H 105 TRP 0.034 0.002 TRP R 141 HIS 0.003 0.001 HIS A 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00426 / 0.19 ( 7117) covalent geometry : angle 0.66612 / 0.34 ( 9703) SS BOND : bond 0.00672 / 0.34 ( 7) SS BOND : angle 3.38327 / 1.75 ( 14) hydrogen bonds : bond 0.04362 / 3.07 ( 348) hydrogen bonds : angle 5.13770 / 3.52 ( 1002) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 129 time to evaluate : 0.231 Fit side-chains revert: symmetry clash REVERT: R 161 LEU cc_start: 0.7891 (OUTLIER) cc_final: 0.7555 (tm) REVERT: R 194 SER cc_start: 0.7050 (t) cc_final: 0.6815 (m) REVERT: R 231 CYS cc_start: 0.8164 (t) cc_final: 0.7771 (t) REVERT: H 20 SER cc_start: 0.9141 (p) cc_final: 0.8822 (m) REVERT: H 86 MET cc_start: 0.8907 (mtp) cc_final: 0.8627 (mtt) REVERT: A 81 VAL cc_start: 0.8706 (t) cc_final: 0.8488 (m) REVERT: A 153 ASN cc_start: 0.7795 (t0) cc_final: 0.6903 (p0) REVERT: A 160 LYS cc_start: 0.8342 (mmpt) cc_final: 0.7326 (mttp) REVERT: A 226 LYS cc_start: 0.7430 (tptt) cc_final: 0.6527 (ttmm) REVERT: A 269 CYS cc_start: 0.8140 (m) cc_final: 0.7779 (t) REVERT: A 290 ASP cc_start: 0.8749 (OUTLIER) cc_final: 0.8474 (m-30) outliers start: 31 outliers final: 16 residues processed: 148 average time/residue: 0.3662 time to fit residues: 58.0792 Evaluate side-chains 134 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 116 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 53 ASN Chi-restraints excluded: chain R residue 55 MET Chi-restraints excluded: chain R residue 85 LEU Chi-restraints excluded: chain R residue 105 VAL Chi-restraints excluded: chain R residue 142 TRP Chi-restraints excluded: chain R residue 147 ARG Chi-restraints excluded: chain R residue 161 LEU Chi-restraints excluded: chain R residue 209 PHE Chi-restraints excluded: chain R residue 218 SER Chi-restraints excluded: chain R residue 265 LEU Chi-restraints excluded: chain R residue 286 LEU Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 103 THR Chi-restraints excluded: chain L residue 107 ILE Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain A residue 343 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 23 optimal weight: 0.2980 chunk 83 optimal weight: 0.5980 chunk 88 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 chunk 34 optimal weight: 0.9980 chunk 40 optimal weight: 3.9990 chunk 16 optimal weight: 0.9980 chunk 8 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 250 HIS ** R 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 80 ASN H 115 GLN L 101 GLN A 248 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.103377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.087788 restraints weight = 18169.981| |-----------------------------------------------------------------------------| r_work (start): 0.3602 rms_B_bonded: 2.72 r_work: 0.3503 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.4782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 7124 Z= 0.172 Angle : 0.678 9.564 9717 Z= 0.346 Chirality : 0.044 0.246 1132 Planarity : 0.005 0.049 1221 Dihedral : 6.025 77.802 1004 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 4.52 % Allowed : 19.59 % Favored : 75.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 0.15 (0.29), residues: 882 helix: 0.36 (0.32), residues: 265 sheet: 0.96 (0.32), residues: 267 loop : -0.71 (0.34), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 165 TYR 0.026 0.002 TYR C 23 PHE 0.012 0.002 PHE R 291 TRP 0.016 0.002 TRP R 141 HIS 0.003 0.001 HIS A 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.17 ( 7117) covalent geometry : angle 0.66906 / 0.34 ( 9703) SS BOND : bond 0.00640 / 0.36 ( 7) SS BOND : angle 2.98765 / 1.54 ( 14) hydrogen bonds : bond 0.04193 / 2.90 ( 348) hydrogen bonds : angle 5.04049 / 3.44 ( 1002) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 119 time to evaluate : 0.300 Fit side-chains REVERT: R 161 LEU cc_start: 0.7958 (OUTLIER) cc_final: 0.7639 (tm) REVERT: R 194 SER cc_start: 0.7141 (t) cc_final: 0.6761 (m) REVERT: R 231 CYS cc_start: 0.8153 (t) cc_final: 0.7790 (t) REVERT: H 20 SER cc_start: 0.9118 (p) cc_final: 0.8820 (m) REVERT: H 86 MET cc_start: 0.8910 (mtp) cc_final: 0.8652 (mtm) REVERT: L 5 MET cc_start: 0.8740 (mtt) cc_final: 0.8385 (mtt) REVERT: A 81 VAL cc_start: 0.8803 (t) cc_final: 0.8583 (m) REVERT: A 153 ASN cc_start: 0.7766 (t0) cc_final: 0.6813 (p0) REVERT: A 226 LYS cc_start: 0.7441 (tptt) cc_final: 0.6525 (ttmm) REVERT: A 269 CYS cc_start: 0.8197 (m) cc_final: 0.7800 (t) REVERT: A 290 ASP cc_start: 0.8729 (OUTLIER) cc_final: 0.8448 (m-30) outliers start: 33 outliers final: 15 residues processed: 138 average time/residue: 0.3632 time to fit residues: 54.0878 Evaluate side-chains 134 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 117 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 85 LEU Chi-restraints excluded: chain R residue 105 VAL Chi-restraints excluded: chain R residue 141 TRP Chi-restraints excluded: chain R residue 142 TRP Chi-restraints excluded: chain R residue 161 LEU Chi-restraints excluded: chain R residue 209 PHE Chi-restraints excluded: chain R residue 258 VAL Chi-restraints excluded: chain R residue 265 LEU Chi-restraints excluded: chain R residue 266 LEU Chi-restraints excluded: chain R residue 286 LEU Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 103 THR Chi-restraints excluded: chain L residue 107 ILE Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain A residue 343 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 9 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 48 optimal weight: 0.0040 chunk 2 optimal weight: 0.7980 chunk 54 optimal weight: 0.5980 chunk 75 optimal weight: 0.9980 chunk 63 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 7 optimal weight: 7.9990 chunk 36 optimal weight: 3.9990 chunk 28 optimal weight: 0.8980 overall best weight: 0.6392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 80 ASN H 115 GLN A 248 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.103843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.087796 restraints weight = 17852.587| |-----------------------------------------------------------------------------| r_work (start): 0.3604 rms_B_bonded: 2.77 r_work: 0.3502 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.5058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 7124 Z= 0.156 Angle : 0.655 8.766 9717 Z= 0.334 Chirality : 0.043 0.147 1132 Planarity : 0.005 0.048 1221 Dihedral : 5.874 76.474 1004 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 4.66 % Allowed : 19.32 % Favored : 76.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 0.27 (0.29), residues: 882 helix: 0.56 (0.32), residues: 265 sheet: 0.95 (0.32), residues: 268 loop : -0.65 (0.34), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 165 TYR 0.023 0.002 TYR C 23 PHE 0.010 0.001 PHE R 291 TRP 0.016 0.002 TRP R 100 HIS 0.002 0.001 HIS A 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.16 ( 7117) covalent geometry : angle 0.64706 / 0.33 ( 9703) SS BOND : bond 0.00649 / 0.36 ( 7) SS BOND : angle 2.73527 / 1.41 ( 14) hydrogen bonds : bond 0.03935 / 2.73 ( 348) hydrogen bonds : angle 4.91505 / 3.36 ( 1002) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 125 time to evaluate : 0.213 Fit side-chains REVERT: R 161 LEU cc_start: 0.7972 (OUTLIER) cc_final: 0.7693 (tm) REVERT: R 183 ARG cc_start: 0.7845 (ptm160) cc_final: 0.7638 (ptm160) REVERT: R 194 SER cc_start: 0.7135 (t) cc_final: 0.6742 (m) REVERT: R 201 THR cc_start: 0.8219 (t) cc_final: 0.7843 (m) REVERT: R 231 CYS cc_start: 0.8171 (t) cc_final: 0.7781 (t) REVERT: H 20 SER cc_start: 0.9084 (p) cc_final: 0.8812 (m) REVERT: H 86 MET cc_start: 0.8880 (mtp) cc_final: 0.8634 (mtt) REVERT: L 5 MET cc_start: 0.8722 (mtt) cc_final: 0.8429 (mtt) REVERT: L 84 PHE cc_start: 0.7505 (m-80) cc_final: 0.7185 (m-80) REVERT: A 8 VAL cc_start: 0.8759 (t) cc_final: 0.8469 (m) REVERT: A 160 LYS cc_start: 0.8297 (mmpt) cc_final: 0.7346 (mttm) REVERT: A 226 LYS cc_start: 0.7388 (tptt) cc_final: 0.6501 (ttmm) REVERT: A 269 CYS cc_start: 0.8120 (m) cc_final: 0.7759 (t) REVERT: A 290 ASP cc_start: 0.8750 (OUTLIER) cc_final: 0.8480 (m-30) outliers start: 34 outliers final: 13 residues processed: 145 average time/residue: 0.3930 time to fit residues: 61.2279 Evaluate side-chains 130 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 115 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 85 LEU Chi-restraints excluded: chain R residue 141 TRP Chi-restraints excluded: chain R residue 142 TRP Chi-restraints excluded: chain R residue 161 LEU Chi-restraints excluded: chain R residue 209 PHE Chi-restraints excluded: chain R residue 258 VAL Chi-restraints excluded: chain R residue 266 LEU Chi-restraints excluded: chain R residue 286 LEU Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 103 THR Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain A residue 343 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 36 optimal weight: 4.9990 chunk 14 optimal weight: 0.0970 chunk 72 optimal weight: 0.1980 chunk 26 optimal weight: 0.8980 chunk 44 optimal weight: 0.8980 chunk 68 optimal weight: 0.2980 chunk 39 optimal weight: 3.9990 chunk 15 optimal weight: 0.6980 chunk 79 optimal weight: 2.9990 chunk 54 optimal weight: 0.9980 chunk 88 optimal weight: 0.8980 overall best weight: 0.4378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 317 GLN ** R 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 80 ASN H 115 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.104293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.088803 restraints weight = 18172.873| |-----------------------------------------------------------------------------| r_work (start): 0.3624 rms_B_bonded: 2.69 r_work: 0.3525 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.5182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 7124 Z= 0.139 Angle : 0.645 8.448 9717 Z= 0.328 Chirality : 0.043 0.146 1132 Planarity : 0.005 0.047 1221 Dihedral : 5.703 75.205 1004 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 3.56 % Allowed : 21.10 % Favored : 75.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 0.36 (0.29), residues: 882 helix: 0.79 (0.32), residues: 259 sheet: 0.98 (0.32), residues: 268 loop : -0.69 (0.34), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 165 TYR 0.023 0.001 TYR C 23 PHE 0.010 0.001 PHE R 291 TRP 0.028 0.002 TRP R 100 HIS 0.002 0.001 HIS C 67 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 ( 7117) covalent geometry : angle 0.63778 / 0.32 ( 9703) SS BOND : bond 0.00610 / 0.34 ( 7) SS BOND : angle 2.62204 / 1.35 ( 14) hydrogen bonds : bond 0.03739 / 2.59 ( 348) hydrogen bonds : angle 4.84004 / 3.31 ( 1002) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 124 time to evaluate : 0.193 Fit side-chains REVERT: R 85 LEU cc_start: 0.8319 (OUTLIER) cc_final: 0.8105 (mm) REVERT: R 161 LEU cc_start: 0.8031 (OUTLIER) cc_final: 0.7760 (tm) REVERT: R 194 SER cc_start: 0.7025 (t) cc_final: 0.6727 (m) REVERT: R 231 CYS cc_start: 0.8177 (t) cc_final: 0.7790 (t) REVERT: H 20 SER cc_start: 0.9070 (p) cc_final: 0.8795 (m) REVERT: H 86 MET cc_start: 0.8868 (mtp) cc_final: 0.8647 (mtt) REVERT: L 5 MET cc_start: 0.8715 (mtt) cc_final: 0.8477 (mtt) REVERT: A 147 LYS cc_start: 0.8702 (ttmm) cc_final: 0.8448 (tttm) REVERT: A 160 LYS cc_start: 0.8328 (mmpt) cc_final: 0.7260 (mttp) REVERT: A 226 LYS cc_start: 0.7432 (tptt) cc_final: 0.6525 (ttmm) REVERT: A 269 CYS cc_start: 0.8115 (m) cc_final: 0.7736 (t) REVERT: A 290 ASP cc_start: 0.8734 (OUTLIER) cc_final: 0.8483 (m-30) outliers start: 26 outliers final: 12 residues processed: 141 average time/residue: 0.3443 time to fit residues: 52.2042 Evaluate side-chains 134 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 119 time to evaluate : 0.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 85 LEU Chi-restraints excluded: chain R residue 141 TRP Chi-restraints excluded: chain R residue 142 TRP Chi-restraints excluded: chain R residue 161 LEU Chi-restraints excluded: chain R residue 209 PHE Chi-restraints excluded: chain R residue 258 VAL Chi-restraints excluded: chain R residue 265 LEU Chi-restraints excluded: chain R residue 266 LEU Chi-restraints excluded: chain R residue 286 LEU Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 103 THR Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 290 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 53 optimal weight: 0.6980 chunk 65 optimal weight: 0.4980 chunk 44 optimal weight: 1.9990 chunk 85 optimal weight: 0.8980 chunk 51 optimal weight: 0.0970 chunk 32 optimal weight: 0.9990 chunk 18 optimal weight: 0.7980 chunk 17 optimal weight: 0.5980 chunk 31 optimal weight: 0.7980 chunk 70 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 80 ASN H 115 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.104007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.088429 restraints weight = 17824.219| |-----------------------------------------------------------------------------| r_work (start): 0.3641 rms_B_bonded: 2.70 r_work: 0.3541 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.5359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 7124 Z= 0.147 Angle : 0.681 16.026 9717 Z= 0.337 Chirality : 0.043 0.188 1132 Planarity : 0.005 0.050 1221 Dihedral : 5.652 74.236 1004 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 3.29 % Allowed : 22.19 % Favored : 74.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 0.36 (0.29), residues: 882 helix: 0.74 (0.33), residues: 259 sheet: 1.11 (0.31), residues: 263 loop : -0.77 (0.33), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 165 TYR 0.025 0.001 TYR R 190 PHE 0.009 0.001 PHE H 105 TRP 0.027 0.002 TRP R 100 HIS 0.002 0.001 HIS A 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 ( 7117) covalent geometry : angle 0.67421 / 0.33 ( 9703) SS BOND : bond 0.00615 / 0.34 ( 7) SS BOND : angle 2.59618 / 1.35 ( 14) hydrogen bonds : bond 0.03740 / 2.60 ( 348) hydrogen bonds : angle 4.85383 / 3.33 ( 1002) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 125 time to evaluate : 0.272 Fit side-chains REVERT: R 161 LEU cc_start: 0.7962 (OUTLIER) cc_final: 0.7700 (tm) REVERT: R 194 SER cc_start: 0.6999 (t) cc_final: 0.6741 (m) REVERT: R 231 CYS cc_start: 0.8199 (t) cc_final: 0.7831 (t) REVERT: H 20 SER cc_start: 0.9026 (p) cc_final: 0.8803 (m) REVERT: L 5 MET cc_start: 0.8748 (mtt) cc_final: 0.8503 (mtt) REVERT: A 8 VAL cc_start: 0.8760 (t) cc_final: 0.8472 (m) REVERT: A 81 VAL cc_start: 0.8165 (t) cc_final: 0.7964 (m) REVERT: A 147 LYS cc_start: 0.8687 (ttmm) cc_final: 0.8475 (tttm) REVERT: A 160 LYS cc_start: 0.8294 (mmpt) cc_final: 0.7308 (mttp) REVERT: A 226 LYS cc_start: 0.7451 (tptt) cc_final: 0.6677 (ttmm) REVERT: A 269 CYS cc_start: 0.8052 (m) cc_final: 0.7704 (t) REVERT: A 290 ASP cc_start: 0.8765 (OUTLIER) cc_final: 0.8510 (m-30) outliers start: 24 outliers final: 12 residues processed: 137 average time/residue: 0.4091 time to fit residues: 60.0392 Evaluate side-chains 128 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 114 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 141 TRP Chi-restraints excluded: chain R residue 142 TRP Chi-restraints excluded: chain R residue 161 LEU Chi-restraints excluded: chain R residue 197 GLU Chi-restraints excluded: chain R residue 209 PHE Chi-restraints excluded: chain R residue 258 VAL Chi-restraints excluded: chain R residue 265 LEU Chi-restraints excluded: chain R residue 286 LEU Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 103 THR Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 290 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 40 optimal weight: 3.9990 chunk 48 optimal weight: 5.9990 chunk 67 optimal weight: 0.3980 chunk 31 optimal weight: 0.0980 chunk 29 optimal weight: 0.5980 chunk 21 optimal weight: 0.7980 chunk 11 optimal weight: 0.3980 chunk 8 optimal weight: 0.0980 chunk 43 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 overall best weight: 0.3180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 115 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.104871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.089374 restraints weight = 18000.515| |-----------------------------------------------------------------------------| r_work (start): 0.3649 rms_B_bonded: 2.69 r_work: 0.3552 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.5519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 7124 Z= 0.134 Angle : 0.712 18.384 9717 Z= 0.345 Chirality : 0.043 0.201 1132 Planarity : 0.005 0.050 1221 Dihedral : 5.550 73.352 1004 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 2.60 % Allowed : 23.70 % Favored : 73.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 0.39 (0.29), residues: 882 helix: 0.78 (0.33), residues: 257 sheet: 1.22 (0.32), residues: 257 loop : -0.79 (0.33), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 165 TYR 0.024 0.001 TYR R 190 PHE 0.007 0.001 PHE C 51 TRP 0.036 0.002 TRP R 100 HIS 0.002 0.001 HIS A 295 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.13 ( 7117) covalent geometry : angle 0.70695 / 0.34 ( 9703) SS BOND : bond 0.00558 / 0.31 ( 7) SS BOND : angle 2.37535 / 1.22 ( 14) hydrogen bonds : bond 0.03597 / 2.49 ( 348) hydrogen bonds : angle 4.88079 / 3.36 ( 1002) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 123 time to evaluate : 0.284 Fit side-chains REVERT: R 161 LEU cc_start: 0.7989 (OUTLIER) cc_final: 0.7732 (tm) REVERT: R 194 SER cc_start: 0.6776 (t) cc_final: 0.6544 (m) REVERT: R 231 CYS cc_start: 0.8196 (t) cc_final: 0.7824 (t) REVERT: R 263 SER cc_start: 0.6688 (t) cc_final: 0.6460 (p) REVERT: H 20 SER cc_start: 0.9056 (p) cc_final: 0.8777 (m) REVERT: L 5 MET cc_start: 0.8728 (mtt) cc_final: 0.8451 (mtt) REVERT: A 8 VAL cc_start: 0.8711 (t) cc_final: 0.8419 (m) REVERT: A 81 VAL cc_start: 0.8151 (t) cc_final: 0.7936 (m) REVERT: A 147 LYS cc_start: 0.8718 (ttmm) cc_final: 0.8445 (ttmm) REVERT: A 160 LYS cc_start: 0.8354 (mmpt) cc_final: 0.7338 (mttp) REVERT: A 226 LYS cc_start: 0.7433 (tptt) cc_final: 0.6565 (ttmm) REVERT: A 269 CYS cc_start: 0.8091 (m) cc_final: 0.7735 (t) REVERT: A 290 ASP cc_start: 0.8740 (OUTLIER) cc_final: 0.8494 (m-30) outliers start: 19 outliers final: 10 residues processed: 131 average time/residue: 0.4093 time to fit residues: 57.4380 Evaluate side-chains 128 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 116 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 142 TRP Chi-restraints excluded: chain R residue 161 LEU Chi-restraints excluded: chain R residue 209 PHE Chi-restraints excluded: chain R residue 286 LEU Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 103 THR Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 290 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 74 optimal weight: 4.9990 chunk 45 optimal weight: 0.8980 chunk 53 optimal weight: 0.8980 chunk 51 optimal weight: 4.9990 chunk 68 optimal weight: 1.9990 chunk 29 optimal weight: 0.5980 chunk 71 optimal weight: 0.5980 chunk 42 optimal weight: 0.9980 chunk 59 optimal weight: 0.8980 chunk 52 optimal weight: 0.7980 chunk 79 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 80 ASN H 115 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.103817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.088260 restraints weight = 17630.822| |-----------------------------------------------------------------------------| r_work (start): 0.3611 rms_B_bonded: 2.68 r_work: 0.3512 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.5589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.115 7124 Z= 0.184 Angle : 0.766 18.669 9717 Z= 0.373 Chirality : 0.045 0.293 1132 Planarity : 0.005 0.055 1221 Dihedral : 5.745 72.894 1004 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 2.33 % Allowed : 24.52 % Favored : 73.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: 0.33 (0.29), residues: 882 helix: 0.66 (0.33), residues: 258 sheet: 1.12 (0.31), residues: 263 loop : -0.74 (0.34), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 165 TYR 0.022 0.002 TYR R 190 PHE 0.012 0.002 PHE H 105 TRP 0.040 0.002 TRP R 100 HIS 0.003 0.001 HIS R 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00444 / 0.18 ( 7117) covalent geometry : angle 0.75455 / 0.37 ( 9703) SS BOND : bond 0.00619 / 0.35 ( 7) SS BOND : angle 3.56782 / 1.91 ( 14) hydrogen bonds : bond 0.04135 / 2.87 ( 348) hydrogen bonds : angle 5.11916 / 3.51 ( 1002) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 121 time to evaluate : 0.229 Fit side-chains REVERT: R 161 LEU cc_start: 0.8020 (OUTLIER) cc_final: 0.7788 (tm) REVERT: R 194 SER cc_start: 0.6754 (t) cc_final: 0.6493 (m) REVERT: R 231 CYS cc_start: 0.8223 (t) cc_final: 0.7885 (t) REVERT: H 20 SER cc_start: 0.9031 (p) cc_final: 0.8783 (m) REVERT: A 8 VAL cc_start: 0.8748 (t) cc_final: 0.8449 (m) REVERT: A 147 LYS cc_start: 0.8689 (ttmm) cc_final: 0.8483 (ttmm) REVERT: A 226 LYS cc_start: 0.7474 (tptt) cc_final: 0.6681 (ttmm) REVERT: A 269 CYS cc_start: 0.8020 (m) cc_final: 0.7680 (t) REVERT: A 290 ASP cc_start: 0.8753 (OUTLIER) cc_final: 0.8513 (m-30) outliers start: 17 outliers final: 10 residues processed: 131 average time/residue: 0.4196 time to fit residues: 58.8634 Evaluate side-chains 124 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 112 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 142 TRP Chi-restraints excluded: chain R residue 161 LEU Chi-restraints excluded: chain R residue 209 PHE Chi-restraints excluded: chain R residue 266 LEU Chi-restraints excluded: chain R residue 286 LEU Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 103 THR Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 290 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 17 optimal weight: 0.8980 chunk 5 optimal weight: 0.9980 chunk 16 optimal weight: 0.0060 chunk 58 optimal weight: 0.7980 chunk 83 optimal weight: 0.3980 chunk 33 optimal weight: 0.7980 chunk 60 optimal weight: 0.6980 chunk 39 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 48 optimal weight: 5.9990 chunk 69 optimal weight: 0.0010 overall best weight: 0.3802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 115 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.105314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.090063 restraints weight = 18268.539| |-----------------------------------------------------------------------------| r_work (start): 0.3655 rms_B_bonded: 2.72 r_work: 0.3556 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.5805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 7124 Z= 0.149 Angle : 0.742 17.969 9717 Z= 0.360 Chirality : 0.043 0.227 1132 Planarity : 0.005 0.060 1221 Dihedral : 5.628 73.487 1004 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 2.33 % Allowed : 24.79 % Favored : 72.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: 0.38 (0.29), residues: 882 helix: 0.73 (0.33), residues: 258 sheet: 1.16 (0.32), residues: 257 loop : -0.72 (0.34), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 165 TYR 0.022 0.001 TYR C 23 PHE 0.008 0.001 PHE H 71 TRP 0.049 0.002 TRP R 100 HIS 0.002 0.001 HIS R 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.15 ( 7117) covalent geometry : angle 0.73427 / 0.36 ( 9703) SS BOND : bond 0.00646 / 0.37 ( 7) SS BOND : angle 2.99553 / 1.63 ( 14) hydrogen bonds : bond 0.03738 / 2.59 ( 348) hydrogen bonds : angle 5.03103 / 3.46 ( 1002) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2521.16 seconds wall clock time: 43 minutes 42.52 seconds (2622.52 seconds total)