Starting phenix.real_space_refine on Sat Dec 28 17:13:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ypx_34017/12_2024/7ypx_34017.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ypx_34017/12_2024/7ypx_34017.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ypx_34017/12_2024/7ypx_34017.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ypx_34017/12_2024/7ypx_34017.map" model { file = "/net/cci-nas-00/data/ceres_data/7ypx_34017/12_2024/7ypx_34017.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ypx_34017/12_2024/7ypx_34017.cif" } resolution = 3.12 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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 12 5.16 5 C 5481 2.51 5 N 1572 2.21 5 O 1743 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 8808 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 1704 Classifications: {'peptide': 250} Link IDs: {'PTRANS': 11, 'TRANS': 238} Chain: "B" Number of atoms: 1704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 1704 Classifications: {'peptide': 250} Link IDs: {'PTRANS': 11, 'TRANS': 238} Chain: "C" Number of atoms: 1704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 1704 Classifications: {'peptide': 250} Link IDs: {'PTRANS': 11, 'TRANS': 238} Chain: "a" Number of atoms: 1232 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1232 Classifications: {'peptide': 162} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 148} Chain: "b" Number of atoms: 1232 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1232 Classifications: {'peptide': 162} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 148} Chain: "c" Number of atoms: 1232 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1232 Classifications: {'peptide': 162} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 148} Time building chain proxies: 5.48, per 1000 atoms: 0.62 Number of scatterers: 8808 At special positions: 0 Unit cell: (92.02, 86.67, 156.22, 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 12 16.00 O 1743 8.00 N 1572 7.00 C 5481 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.31 Conformation dependent library (CDL) restraints added in 1.2 seconds 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2052 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 16 sheets defined 28.4% alpha, 16.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.89 Creating SS restraints... Processing helix chain 'A' and resid 32 through 54 removed outlier: 3.576A pdb=" N ASP A 36 " --> pdb=" O ASP A 32 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ASN A 37 " --> pdb=" O VAL A 33 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N VAL A 50 " --> pdb=" O GLN A 46 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ILE A 51 " --> pdb=" O VAL A 47 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLU A 52 " --> pdb=" O ASP A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 69 Processing helix chain 'A' and resid 69 through 75 Processing helix chain 'B' and resid 32 through 52 removed outlier: 3.508A pdb=" N ASP B 36 " --> pdb=" O ASP B 32 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ASN B 37 " --> pdb=" O VAL B 33 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ASP B 48 " --> pdb=" O THR B 44 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLY B 49 " --> pdb=" O GLY B 45 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N VAL B 50 " --> pdb=" O GLN B 46 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ILE B 51 " --> pdb=" O VAL B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 75 removed outlier: 5.244A pdb=" N GLN B 71 " --> pdb=" O TYR B 67 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N SER B 72 " --> pdb=" O LYS B 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 32 through 52 removed outlier: 3.511A pdb=" N ASP C 36 " --> pdb=" O ASP C 32 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ASN C 37 " --> pdb=" O VAL C 33 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ASP C 48 " --> pdb=" O THR C 44 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLY C 49 " --> pdb=" O GLY C 45 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N VAL C 50 " --> pdb=" O GLN C 46 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ILE C 51 " --> pdb=" O VAL C 47 " (cutoff:3.500A) Processing helix chain 'C' and resid 64 through 75 removed outlier: 5.335A pdb=" N GLN C 71 " --> pdb=" O TYR C 67 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N SER C 72 " --> pdb=" O LYS C 68 " (cutoff:3.500A) Processing helix chain 'a' and resid 25 through 31 Processing helix chain 'a' and resid 63 through 75 Processing helix chain 'a' and resid 76 through 83 removed outlier: 4.337A pdb=" N PHE a 80 " --> pdb=" O SER a 76 " (cutoff:3.500A) Processing helix chain 'a' and resid 84 through 100 Processing helix chain 'a' and resid 107 through 133 Processing helix chain 'a' and resid 152 through 162 Processing helix chain 'b' and resid 25 through 31 Processing helix chain 'b' and resid 63 through 83 removed outlier: 3.711A pdb=" N ARG b 77 " --> pdb=" O ALA b 73 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N HIS b 78 " --> pdb=" O GLU b 74 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N ILE b 79 " --> pdb=" O ALA b 75 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N PHE b 80 " --> pdb=" O SER b 76 " (cutoff:3.500A) Processing helix chain 'b' and resid 84 through 100 Processing helix chain 'b' and resid 107 through 133 Processing helix chain 'b' and resid 152 through 162 Processing helix chain 'c' and resid 25 through 31 Processing helix chain 'c' and resid 63 through 75 Processing helix chain 'c' and resid 76 through 83 removed outlier: 4.384A pdb=" N PHE c 80 " --> pdb=" O SER c 76 " (cutoff:3.500A) Processing helix chain 'c' and resid 84 through 100 Processing helix chain 'c' and resid 107 through 133 Processing helix chain 'c' and resid 152 through 162 Processing sheet with id=AA1, first strand: chain 'A' and resid 78 through 83 removed outlier: 3.964A pdb=" N GLN A 273 " --> pdb=" O TRP A 101 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N TRP A 101 " --> pdb=" O GLN A 273 " (cutoff:3.500A) removed outlier: 8.271A pdb=" N PHE A 275 " --> pdb=" O LEU A 99 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N LEU A 99 " --> pdb=" O PHE A 275 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 78 through 83 removed outlier: 3.964A pdb=" N GLN A 273 " --> pdb=" O TRP A 101 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N TRP A 101 " --> pdb=" O GLN A 273 " (cutoff:3.500A) removed outlier: 8.271A pdb=" N PHE A 275 " --> pdb=" O LEU A 99 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N LEU A 99 " --> pdb=" O PHE A 275 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ILE A 205 " --> pdb=" O ASP A 131 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 91 through 92 removed outlier: 3.645A pdb=" N GLY A 140 " --> pdb=" O ILE A 92 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 168 through 170 Processing sheet with id=AA5, first strand: chain 'B' and resid 78 through 83 removed outlier: 3.903A pdb=" N GLN B 273 " --> pdb=" O TRP B 101 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N TRP B 101 " --> pdb=" O GLN B 273 " (cutoff:3.500A) removed outlier: 8.302A pdb=" N PHE B 275 " --> pdb=" O LEU B 99 " (cutoff:3.500A) removed outlier: 8.024A pdb=" N LEU B 99 " --> pdb=" O PHE B 275 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 78 through 83 removed outlier: 3.903A pdb=" N GLN B 273 " --> pdb=" O TRP B 101 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N TRP B 101 " --> pdb=" O GLN B 273 " (cutoff:3.500A) removed outlier: 8.302A pdb=" N PHE B 275 " --> pdb=" O LEU B 99 " (cutoff:3.500A) removed outlier: 8.024A pdb=" N LEU B 99 " --> pdb=" O PHE B 275 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 91 through 92 removed outlier: 3.617A pdb=" N GLY B 140 " --> pdb=" O ILE B 92 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 168 through 170 Processing sheet with id=AA9, first strand: chain 'C' and resid 78 through 83 removed outlier: 3.955A pdb=" N GLN C 273 " --> pdb=" O TRP C 101 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N TRP C 101 " --> pdb=" O GLN C 273 " (cutoff:3.500A) removed outlier: 8.299A pdb=" N PHE C 275 " --> pdb=" O LEU C 99 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N LEU C 99 " --> pdb=" O PHE C 275 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 78 through 83 removed outlier: 3.955A pdb=" N GLN C 273 " --> pdb=" O TRP C 101 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N TRP C 101 " --> pdb=" O GLN C 273 " (cutoff:3.500A) removed outlier: 8.299A pdb=" N PHE C 275 " --> pdb=" O LEU C 99 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N LEU C 99 " --> pdb=" O PHE C 275 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 91 through 92 removed outlier: 3.639A pdb=" N GLY C 140 " --> pdb=" O ILE C 92 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 168 through 170 Processing sheet with id=AB4, first strand: chain 'a' and resid 13 through 21 removed outlier: 6.970A pdb=" N ARG a 8 " --> pdb=" O VAL a 15 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N THR a 17 " --> pdb=" O TYR a 6 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N TYR a 6 " --> pdb=" O THR a 17 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N THR a 19 " --> pdb=" O LYS a 4 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N LYS a 4 " --> pdb=" O THR a 19 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'b' and resid 13 through 21 removed outlier: 6.937A pdb=" N ARG b 8 " --> pdb=" O VAL b 15 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N THR b 17 " --> pdb=" O TYR b 6 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N TYR b 6 " --> pdb=" O THR b 17 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N THR b 19 " --> pdb=" O LYS b 4 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N LYS b 4 " --> pdb=" O THR b 19 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'b' and resid 48 through 50 Processing sheet with id=AB7, first strand: chain 'c' and resid 13 through 21 removed outlier: 6.914A pdb=" N ARG c 8 " --> pdb=" O VAL c 15 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N THR c 17 " --> pdb=" O TYR c 6 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N TYR c 6 " --> pdb=" O THR c 17 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N THR c 19 " --> pdb=" O LYS c 4 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N LYS c 4 " --> pdb=" O THR c 19 " (cutoff:3.500A) 345 hydrogen bonds defined for protein. 960 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.40 Time building geometry restraints manager: 2.65 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: 3065 1.34 - 1.46: 1546 1.46 - 1.57: 4365 1.57 - 1.69: 0 1.69 - 1.80: 24 Bond restraints: 9000 Sorted by residual: bond pdb=" CB LYS A 68 " pdb=" CG LYS A 68 " ideal model delta sigma weight residual 1.520 1.487 0.033 3.00e-02 1.11e+03 1.22e+00 bond pdb=" CD LYS A 68 " pdb=" CE LYS A 68 " ideal model delta sigma weight residual 1.520 1.492 0.028 3.00e-02 1.11e+03 8.58e-01 bond pdb=" CA ILE A 170 " pdb=" CB ILE A 170 " ideal model delta sigma weight residual 1.548 1.538 0.010 1.13e-02 7.83e+03 8.11e-01 bond pdb=" CB ILE C 205 " pdb=" CG2 ILE C 205 " ideal model delta sigma weight residual 1.521 1.492 0.029 3.30e-02 9.18e+02 7.82e-01 bond pdb=" CD LYS C 68 " pdb=" CE LYS C 68 " ideal model delta sigma weight residual 1.520 1.494 0.026 3.00e-02 1.11e+03 7.62e-01 ... (remaining 8995 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.18: 11732 1.18 - 2.36: 406 2.36 - 3.54: 117 3.54 - 4.71: 15 4.71 - 5.89: 9 Bond angle restraints: 12279 Sorted by residual: angle pdb=" N SER A 97 " pdb=" CA SER A 97 " pdb=" C SER A 97 " ideal model delta sigma weight residual 114.56 110.53 4.03 1.27e+00 6.20e-01 1.01e+01 angle pdb=" N GLU c 119 " pdb=" CA GLU c 119 " pdb=" CB GLU c 119 " ideal model delta sigma weight residual 110.28 115.11 -4.83 1.55e+00 4.16e-01 9.71e+00 angle pdb=" C ASN A 186 " pdb=" N ASN A 187 " pdb=" CA ASN A 187 " ideal model delta sigma weight residual 121.54 127.16 -5.62 1.91e+00 2.74e-01 8.66e+00 angle pdb=" CA LYS b 53 " pdb=" CB LYS b 53 " pdb=" CG LYS b 53 " ideal model delta sigma weight residual 114.10 119.49 -5.39 2.00e+00 2.50e-01 7.27e+00 angle pdb=" C VAL A 47 " pdb=" N ASP A 48 " pdb=" CA ASP A 48 " ideal model delta sigma weight residual 122.06 117.06 5.00 1.86e+00 2.89e-01 7.22e+00 ... (remaining 12274 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.46: 4857 17.46 - 34.92: 272 34.92 - 52.38: 15 52.38 - 69.84: 1 69.84 - 87.30: 6 Dihedral angle restraints: 5151 sinusoidal: 1851 harmonic: 3300 Sorted by residual: dihedral pdb=" CA ILE C 216 " pdb=" C ILE C 216 " pdb=" N VAL C 217 " pdb=" CA VAL C 217 " ideal model delta harmonic sigma weight residual 180.00 163.63 16.37 0 5.00e+00 4.00e-02 1.07e+01 dihedral pdb=" CA MET a 1 " pdb=" C MET a 1 " pdb=" N THR a 2 " pdb=" CA THR a 2 " ideal model delta harmonic sigma weight residual -180.00 -165.19 -14.81 0 5.00e+00 4.00e-02 8.78e+00 dihedral pdb=" CA ILE B 216 " pdb=" C ILE B 216 " pdb=" N VAL B 217 " pdb=" CA VAL B 217 " ideal model delta harmonic sigma weight residual 180.00 165.29 14.71 0 5.00e+00 4.00e-02 8.65e+00 ... (remaining 5148 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 789 0.029 - 0.057: 323 0.057 - 0.086: 147 0.086 - 0.115: 70 0.115 - 0.143: 18 Chirality restraints: 1347 Sorted by residual: chirality pdb=" CA ASN A 187 " pdb=" N ASN A 187 " pdb=" C ASN A 187 " pdb=" CB ASN A 187 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.12e-01 chirality pdb=" CA VAL B 143 " pdb=" N VAL B 143 " pdb=" C VAL B 143 " pdb=" CB VAL B 143 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.93e-01 chirality pdb=" CA VAL A 143 " pdb=" N VAL A 143 " pdb=" C VAL A 143 " pdb=" CB VAL A 143 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.56e-01 ... (remaining 1344 not shown) Planarity restraints: 1662 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA b 52 " 0.006 2.00e-02 2.50e+03 1.14e-02 1.30e+00 pdb=" C ALA b 52 " -0.020 2.00e-02 2.50e+03 pdb=" O ALA b 52 " 0.008 2.00e-02 2.50e+03 pdb=" N LYS b 53 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN B 260 " 0.017 5.00e-02 4.00e+02 2.54e-02 1.04e+00 pdb=" N PRO B 261 " -0.044 5.00e-02 4.00e+02 pdb=" CA PRO B 261 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO B 261 " 0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB HIS b 132 " -0.008 2.00e-02 2.50e+03 8.24e-03 1.02e+00 pdb=" CG HIS b 132 " 0.018 2.00e-02 2.50e+03 pdb=" ND1 HIS b 132 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 HIS b 132 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 HIS b 132 " -0.003 2.00e-02 2.50e+03 pdb=" NE2 HIS b 132 " 0.000 2.00e-02 2.50e+03 ... (remaining 1659 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 161 2.65 - 3.21: 9150 3.21 - 3.78: 14695 3.78 - 4.34: 19188 4.34 - 4.90: 30696 Nonbonded interactions: 73890 Sorted by model distance: nonbonded pdb=" NZ LYS b 49 " pdb=" O GLY b 51 " model vdw 2.092 3.120 nonbonded pdb=" OG SER B 119 " pdb=" O ASN B 185 " model vdw 2.154 3.040 nonbonded pdb=" OG SER A 119 " pdb=" O ASN A 185 " model vdw 2.162 3.040 nonbonded pdb=" OG SER C 119 " pdb=" O ASN C 185 " model vdw 2.221 3.040 nonbonded pdb=" NH1 ARG A 231 " pdb=" O GLY A 252 " model vdw 2.228 3.120 ... (remaining 73885 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'a' selection = chain 'b' selection = chain 'c' } 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: 1.560 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: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 22.870 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 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 0.033 9000 Z= 0.260 Angle : 0.567 5.893 12279 Z= 0.302 Chirality : 0.043 0.143 1347 Planarity : 0.004 0.034 1662 Dihedral : 10.613 87.301 3099 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.23), residues: 1224 helix: 0.64 (0.27), residues: 348 sheet: -0.31 (0.27), residues: 276 loop : -0.45 (0.26), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 259 HIS 0.009 0.002 HIS b 132 PHE 0.006 0.001 PHE b 54 TYR 0.013 0.001 TYR A 207 ARG 0.002 0.000 ARG b 48 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 0.877 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 ASP cc_start: 0.9311 (p0) cc_final: 0.9027 (p0) REVERT: A 59 ASP cc_start: 0.9161 (t0) cc_final: 0.8747 (t0) REVERT: A 131 ASP cc_start: 0.8716 (p0) cc_final: 0.8323 (p0) REVERT: B 52 GLU cc_start: 0.9226 (pm20) cc_final: 0.9021 (pm20) REVERT: B 59 ASP cc_start: 0.9256 (t0) cc_final: 0.8743 (t0) REVERT: B 62 ASP cc_start: 0.9164 (t70) cc_final: 0.8953 (t0) REVERT: B 160 TYR cc_start: 0.8901 (m-80) cc_final: 0.8538 (m-80) REVERT: B 204 GLU cc_start: 0.8702 (mp0) cc_final: 0.8437 (mp0) REVERT: C 40 MET cc_start: 0.9143 (ptp) cc_final: 0.8727 (ptp) REVERT: C 59 ASP cc_start: 0.9207 (t0) cc_final: 0.8693 (t0) REVERT: C 62 ASP cc_start: 0.9237 (t70) cc_final: 0.9020 (t0) REVERT: c 111 ARG cc_start: 0.9608 (mpp80) cc_final: 0.9276 (ptp90) outliers start: 0 outliers final: 0 residues processed: 95 average time/residue: 0.3476 time to fit residues: 41.1548 Evaluate side-chains 72 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 0.7980 chunk 93 optimal weight: 0.5980 chunk 51 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 chunk 62 optimal weight: 9.9990 chunk 49 optimal weight: 0.9990 chunk 96 optimal weight: 4.9990 chunk 37 optimal weight: 8.9990 chunk 58 optimal weight: 7.9990 chunk 71 optimal weight: 0.9990 chunk 111 optimal weight: 4.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 227 GLN A 230 GLN B 113 ASN ** C 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 113 ASN ** C 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 230 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.1008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9000 Z= 0.184 Angle : 0.575 9.122 12279 Z= 0.298 Chirality : 0.043 0.145 1347 Planarity : 0.004 0.060 1662 Dihedral : 4.060 24.594 1299 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 0.12 % Allowed : 6.57 % Favored : 93.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.24), residues: 1224 helix: 0.25 (0.27), residues: 375 sheet: -0.35 (0.28), residues: 258 loop : -0.10 (0.26), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP c 148 HIS 0.008 0.001 HIS b 132 PHE 0.007 0.001 PHE A 133 TYR 0.008 0.001 TYR B 207 ARG 0.006 0.001 ARG b 48 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 92 time to evaluate : 0.944 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 ASP cc_start: 0.9142 (t0) cc_final: 0.8610 (t0) REVERT: A 62 ASP cc_start: 0.9188 (t0) cc_final: 0.8845 (t0) REVERT: B 48 ASP cc_start: 0.9246 (p0) cc_final: 0.8992 (p0) REVERT: B 59 ASP cc_start: 0.9210 (t0) cc_final: 0.8652 (t0) REVERT: B 160 TYR cc_start: 0.8908 (m-80) cc_final: 0.8398 (m-80) REVERT: B 204 GLU cc_start: 0.8416 (mp0) cc_final: 0.8170 (mp0) REVERT: C 40 MET cc_start: 0.9186 (ptp) cc_final: 0.8797 (ptp) REVERT: C 59 ASP cc_start: 0.9150 (t0) cc_final: 0.8581 (t0) REVERT: a 25 ASN cc_start: 0.9060 (t0) cc_final: 0.8677 (t0) REVERT: c 111 ARG cc_start: 0.9591 (mpp80) cc_final: 0.9305 (ptp90) outliers start: 1 outliers final: 0 residues processed: 92 average time/residue: 0.3457 time to fit residues: 40.0311 Evaluate side-chains 70 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 62 optimal weight: 9.9990 chunk 34 optimal weight: 7.9990 chunk 92 optimal weight: 0.9990 chunk 76 optimal weight: 0.9990 chunk 30 optimal weight: 5.9990 chunk 111 optimal weight: 4.9990 chunk 120 optimal weight: 4.9990 chunk 99 optimal weight: 6.9990 chunk 110 optimal weight: 5.9990 chunk 38 optimal weight: 8.9990 chunk 89 optimal weight: 0.0270 overall best weight: 2.4046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 GLN ** C 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.1189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 9000 Z= 0.320 Angle : 0.596 8.629 12279 Z= 0.309 Chirality : 0.043 0.148 1347 Planarity : 0.003 0.026 1662 Dihedral : 4.145 22.782 1299 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 0.00 % Allowed : 10.73 % Favored : 89.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.24), residues: 1224 helix: 0.22 (0.27), residues: 375 sheet: -0.31 (0.28), residues: 255 loop : -0.19 (0.27), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 101 HIS 0.005 0.001 HIS a 78 PHE 0.007 0.001 PHE b 162 TYR 0.010 0.001 TYR A 207 ARG 0.004 0.000 ARG b 48 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.862 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 ASP cc_start: 0.9097 (t0) cc_final: 0.8551 (t0) REVERT: A 62 ASP cc_start: 0.9210 (t70) cc_final: 0.9002 (t0) REVERT: A 160 TYR cc_start: 0.8327 (m-10) cc_final: 0.8104 (m-80) REVERT: B 59 ASP cc_start: 0.9225 (t0) cc_final: 0.8662 (t0) REVERT: B 238 ASN cc_start: 0.9034 (m110) cc_final: 0.8822 (p0) REVERT: C 40 MET cc_start: 0.9191 (ptp) cc_final: 0.8809 (ptp) REVERT: C 46 GLN cc_start: 0.9570 (mm110) cc_final: 0.9186 (mm-40) REVERT: C 59 ASP cc_start: 0.9148 (t0) cc_final: 0.8568 (t0) REVERT: a 158 MET cc_start: 0.9381 (ptt) cc_final: 0.9175 (ptt) REVERT: c 111 ARG cc_start: 0.9582 (mpp80) cc_final: 0.9310 (ptp90) outliers start: 0 outliers final: 0 residues processed: 76 average time/residue: 0.3370 time to fit residues: 32.6037 Evaluate side-chains 66 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 110 optimal weight: 0.0470 chunk 84 optimal weight: 9.9990 chunk 58 optimal weight: 9.9990 chunk 12 optimal weight: 9.9990 chunk 53 optimal weight: 5.9990 chunk 75 optimal weight: 6.9990 chunk 112 optimal weight: 6.9990 chunk 118 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 99 optimal weight: 5.9990 overall best weight: 2.8086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 113 ASN ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 260 GLN ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 227 GLN C 260 GLN ** b 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.1507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 9000 Z= 0.367 Angle : 0.600 7.453 12279 Z= 0.313 Chirality : 0.043 0.148 1347 Planarity : 0.004 0.027 1662 Dihedral : 4.294 19.698 1299 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 1.15 % Allowed : 11.07 % Favored : 87.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.24), residues: 1224 helix: 0.23 (0.27), residues: 375 sheet: -0.47 (0.27), residues: 279 loop : -0.29 (0.27), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 101 HIS 0.006 0.001 HIS a 78 PHE 0.006 0.001 PHE a 24 TYR 0.013 0.002 TYR C 207 ARG 0.004 0.000 ARG a 62 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 76 time to evaluate : 0.896 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 ASP cc_start: 0.9058 (t0) cc_final: 0.8526 (t0) REVERT: A 160 TYR cc_start: 0.8427 (m-10) cc_final: 0.8134 (m-80) REVERT: B 40 MET cc_start: 0.9198 (ptp) cc_final: 0.8958 (ptp) REVERT: B 46 GLN cc_start: 0.9352 (mm110) cc_final: 0.8959 (mm-40) REVERT: B 48 ASP cc_start: 0.9281 (p0) cc_final: 0.9005 (p0) REVERT: B 59 ASP cc_start: 0.9234 (t0) cc_final: 0.8683 (t0) REVERT: B 238 ASN cc_start: 0.9038 (m110) cc_final: 0.8822 (p0) REVERT: C 40 MET cc_start: 0.9193 (ptp) cc_final: 0.8803 (ptp) REVERT: C 46 GLN cc_start: 0.9581 (mm110) cc_final: 0.9159 (mm-40) REVERT: C 59 ASP cc_start: 0.9151 (t0) cc_final: 0.8556 (t0) REVERT: C 214 GLU cc_start: 0.8384 (pp20) cc_final: 0.7762 (pp20) REVERT: c 111 ARG cc_start: 0.9582 (mpp80) cc_final: 0.9372 (ptp90) outliers start: 10 outliers final: 3 residues processed: 85 average time/residue: 0.3003 time to fit residues: 32.9691 Evaluate side-chains 68 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 65 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 ASP Chi-restraints excluded: chain b residue 141 THR Chi-restraints excluded: chain c residue 141 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 67 optimal weight: 0.9990 chunk 1 optimal weight: 6.9990 chunk 88 optimal weight: 0.9990 chunk 49 optimal weight: 0.5980 chunk 101 optimal weight: 5.9990 chunk 82 optimal weight: 7.9990 chunk 0 optimal weight: 8.9990 chunk 60 optimal weight: 0.9980 chunk 106 optimal weight: 0.9980 chunk 30 optimal weight: 0.9980 chunk 40 optimal weight: 9.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 ASN A 260 GLN C 260 GLN ** b 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.1594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9000 Z= 0.178 Angle : 0.592 8.497 12279 Z= 0.298 Chirality : 0.043 0.209 1347 Planarity : 0.003 0.030 1662 Dihedral : 4.116 21.511 1299 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.61 % Allowed : 11.65 % Favored : 86.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.24), residues: 1224 helix: 0.25 (0.27), residues: 375 sheet: -0.34 (0.27), residues: 276 loop : -0.25 (0.27), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 101 HIS 0.003 0.001 HIS a 78 PHE 0.008 0.001 PHE A 133 TYR 0.008 0.001 TYR B 207 ARG 0.005 0.000 ARG a 62 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 82 time to evaluate : 0.933 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 ASP cc_start: 0.9072 (t0) cc_final: 0.8497 (t0) REVERT: A 62 ASP cc_start: 0.9250 (t0) cc_final: 0.8882 (t0) REVERT: B 46 GLN cc_start: 0.9411 (mm110) cc_final: 0.9177 (mm-40) REVERT: B 59 ASP cc_start: 0.9238 (t0) cc_final: 0.8676 (t0) REVERT: B 214 GLU cc_start: 0.8043 (pp20) cc_final: 0.7551 (pp20) REVERT: B 238 ASN cc_start: 0.8968 (m110) cc_final: 0.8760 (p0) REVERT: C 40 MET cc_start: 0.9201 (ptp) cc_final: 0.8831 (ptp) REVERT: C 46 GLN cc_start: 0.9584 (mm110) cc_final: 0.9147 (mm-40) REVERT: C 59 ASP cc_start: 0.9151 (t0) cc_final: 0.8541 (t0) REVERT: C 62 ASP cc_start: 0.9104 (t0) cc_final: 0.8900 (t0) REVERT: C 214 GLU cc_start: 0.8333 (pp20) cc_final: 0.7773 (pp20) REVERT: b 62 ARG cc_start: 0.8985 (mmm-85) cc_final: 0.8486 (tpm170) REVERT: c 62 ARG cc_start: 0.8806 (mmm-85) cc_final: 0.8405 (tpt90) REVERT: c 111 ARG cc_start: 0.9584 (mpp80) cc_final: 0.9363 (ptp90) outliers start: 14 outliers final: 4 residues processed: 92 average time/residue: 0.2977 time to fit residues: 35.4793 Evaluate side-chains 77 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 73 time to evaluate : 1.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 ASP Chi-restraints excluded: chain B residue 204 GLU Chi-restraints excluded: chain B residue 239 ASN Chi-restraints excluded: chain C residue 217 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 107 optimal weight: 0.8980 chunk 23 optimal weight: 3.9990 chunk 69 optimal weight: 0.1980 chunk 29 optimal weight: 2.9990 chunk 119 optimal weight: 3.9990 chunk 98 optimal weight: 0.9990 chunk 55 optimal weight: 7.9990 chunk 9 optimal weight: 10.0000 chunk 39 optimal weight: 7.9990 chunk 62 optimal weight: 9.9990 chunk 114 optimal weight: 3.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 ASN C 260 GLN ** b 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.1691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9000 Z= 0.264 Angle : 0.613 7.515 12279 Z= 0.311 Chirality : 0.043 0.146 1347 Planarity : 0.003 0.030 1662 Dihedral : 4.087 21.978 1299 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 1.27 % Allowed : 13.03 % Favored : 85.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.24), residues: 1224 helix: 0.17 (0.27), residues: 375 sheet: -0.45 (0.27), residues: 279 loop : -0.23 (0.27), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 101 HIS 0.004 0.001 HIS a 78 PHE 0.007 0.001 PHE b 162 TYR 0.012 0.001 TYR C 207 ARG 0.006 0.000 ARG a 62 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 76 time to evaluate : 0.955 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 ASP cc_start: 0.9071 (t0) cc_final: 0.8505 (t0) REVERT: A 62 ASP cc_start: 0.9278 (t0) cc_final: 0.8988 (t0) REVERT: B 48 ASP cc_start: 0.9256 (p0) cc_final: 0.9044 (p0) REVERT: B 59 ASP cc_start: 0.9253 (t0) cc_final: 0.8692 (t0) REVERT: B 214 GLU cc_start: 0.8123 (pp20) cc_final: 0.7596 (pp20) REVERT: B 238 ASN cc_start: 0.9008 (m110) cc_final: 0.8769 (p0) REVERT: C 40 MET cc_start: 0.9196 (ptp) cc_final: 0.8809 (ptp) REVERT: C 46 GLN cc_start: 0.9589 (mm110) cc_final: 0.9172 (mm-40) REVERT: C 59 ASP cc_start: 0.9199 (t0) cc_final: 0.8621 (t0) REVERT: C 214 GLU cc_start: 0.8375 (pp20) cc_final: 0.7799 (pp20) REVERT: b 62 ARG cc_start: 0.9005 (mmm-85) cc_final: 0.8443 (tpm170) REVERT: c 62 ARG cc_start: 0.8856 (mmm-85) cc_final: 0.8375 (tpt90) REVERT: c 111 ARG cc_start: 0.9585 (mpp80) cc_final: 0.9357 (ptp-110) outliers start: 11 outliers final: 6 residues processed: 83 average time/residue: 0.3355 time to fit residues: 36.4734 Evaluate side-chains 78 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 72 time to evaluate : 1.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 ASP Chi-restraints excluded: chain B residue 239 ASN Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 204 GLU Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain a residue 119 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 13 optimal weight: 9.9990 chunk 67 optimal weight: 0.7980 chunk 86 optimal weight: 0.9980 chunk 100 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 118 optimal weight: 0.8980 chunk 74 optimal weight: 0.8980 chunk 72 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 47 optimal weight: 7.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 260 GLN ** b 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.1779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9000 Z= 0.194 Angle : 0.598 8.013 12279 Z= 0.303 Chirality : 0.043 0.144 1347 Planarity : 0.003 0.030 1662 Dihedral : 3.981 23.775 1299 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 1.15 % Allowed : 13.61 % Favored : 85.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.24), residues: 1224 helix: 0.15 (0.27), residues: 375 sheet: -0.28 (0.29), residues: 237 loop : -0.18 (0.26), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 101 HIS 0.003 0.001 HIS a 78 PHE 0.005 0.001 PHE a 162 TYR 0.009 0.001 TYR C 207 ARG 0.006 0.000 ARG a 62 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 75 time to evaluate : 0.903 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 ASP cc_start: 0.9057 (t0) cc_final: 0.8497 (t0) REVERT: B 59 ASP cc_start: 0.9260 (t0) cc_final: 0.8695 (t0) REVERT: B 160 TYR cc_start: 0.8554 (m-10) cc_final: 0.8270 (m-80) REVERT: B 214 GLU cc_start: 0.8084 (pp20) cc_final: 0.7639 (pp20) REVERT: B 238 ASN cc_start: 0.8978 (m110) cc_final: 0.8730 (p0) REVERT: C 40 MET cc_start: 0.9190 (ptp) cc_final: 0.8808 (ptp) REVERT: C 46 GLN cc_start: 0.9568 (mm110) cc_final: 0.9149 (mm-40) REVERT: C 59 ASP cc_start: 0.9219 (t0) cc_final: 0.8636 (t0) REVERT: C 214 GLU cc_start: 0.8339 (pp20) cc_final: 0.7768 (pp20) REVERT: b 62 ARG cc_start: 0.8990 (mmm-85) cc_final: 0.8542 (tpm170) REVERT: c 62 ARG cc_start: 0.8846 (mmm-85) cc_final: 0.8357 (tpt90) REVERT: c 111 ARG cc_start: 0.9588 (mpp80) cc_final: 0.9357 (ptp-110) outliers start: 10 outliers final: 7 residues processed: 81 average time/residue: 0.2974 time to fit residues: 31.0481 Evaluate side-chains 79 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 72 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 ASP Chi-restraints excluded: chain B residue 204 GLU Chi-restraints excluded: chain B residue 239 ASN Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 204 GLU Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain a residue 119 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 70 optimal weight: 3.9990 chunk 35 optimal weight: 0.9990 chunk 23 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 75 optimal weight: 6.9990 chunk 80 optimal weight: 0.7980 chunk 58 optimal weight: 10.0000 chunk 11 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 chunk 107 optimal weight: 0.8980 chunk 113 optimal weight: 30.0000 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.1841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 9000 Z= 0.249 Angle : 0.609 9.062 12279 Z= 0.312 Chirality : 0.043 0.145 1347 Planarity : 0.003 0.030 1662 Dihedral : 4.005 24.261 1299 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 1.50 % Allowed : 13.61 % Favored : 84.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.23), residues: 1224 helix: 0.15 (0.27), residues: 375 sheet: -0.15 (0.30), residues: 228 loop : -0.26 (0.26), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 101 HIS 0.004 0.001 HIS a 78 PHE 0.005 0.001 PHE a 24 TYR 0.008 0.001 TYR C 207 ARG 0.004 0.000 ARG a 77 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 74 time to evaluate : 0.880 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 ASP cc_start: 0.9087 (t0) cc_final: 0.8529 (t0) REVERT: B 59 ASP cc_start: 0.9269 (t0) cc_final: 0.8707 (t0) REVERT: B 160 TYR cc_start: 0.8530 (m-10) cc_final: 0.8217 (m-80) REVERT: B 214 GLU cc_start: 0.8167 (pp20) cc_final: 0.7731 (pp20) REVERT: B 238 ASN cc_start: 0.8999 (m110) cc_final: 0.8760 (p0) REVERT: C 40 MET cc_start: 0.9199 (ptp) cc_final: 0.8816 (ptp) REVERT: C 46 GLN cc_start: 0.9563 (mm110) cc_final: 0.9147 (mm-40) REVERT: C 59 ASP cc_start: 0.9221 (t0) cc_final: 0.8639 (t0) REVERT: C 214 GLU cc_start: 0.8371 (pp20) cc_final: 0.7798 (pp20) REVERT: b 62 ARG cc_start: 0.9004 (mmm-85) cc_final: 0.8645 (tpm170) REVERT: c 111 ARG cc_start: 0.9584 (mpp80) cc_final: 0.9354 (ptp-110) outliers start: 13 outliers final: 8 residues processed: 84 average time/residue: 0.2772 time to fit residues: 30.7251 Evaluate side-chains 80 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 72 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 254 ASP Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 204 GLU Chi-restraints excluded: chain B residue 239 ASN Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 204 GLU Chi-restraints excluded: chain C residue 217 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 2.9990 chunk 110 optimal weight: 0.6980 chunk 113 optimal weight: 30.0000 chunk 66 optimal weight: 4.9990 chunk 48 optimal weight: 0.6980 chunk 86 optimal weight: 0.9980 chunk 33 optimal weight: 8.9990 chunk 99 optimal weight: 7.9990 chunk 104 optimal weight: 0.9990 chunk 72 optimal weight: 4.9990 chunk 116 optimal weight: 3.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.1927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9000 Z= 0.212 Angle : 0.627 11.031 12279 Z= 0.321 Chirality : 0.043 0.144 1347 Planarity : 0.003 0.030 1662 Dihedral : 3.992 25.271 1299 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.15 % Allowed : 13.96 % Favored : 84.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.23), residues: 1224 helix: 0.04 (0.27), residues: 375 sheet: -0.29 (0.30), residues: 237 loop : -0.17 (0.26), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 101 HIS 0.003 0.001 HIS a 78 PHE 0.004 0.001 PHE c 162 TYR 0.011 0.001 TYR A 67 ARG 0.004 0.000 ARG a 77 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 75 time to evaluate : 0.939 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 MET cc_start: 0.9472 (ptp) cc_final: 0.9229 (ptp) REVERT: A 52 GLU cc_start: 0.9275 (pm20) cc_final: 0.9065 (pm20) REVERT: A 59 ASP cc_start: 0.9095 (t0) cc_final: 0.8548 (t0) REVERT: B 59 ASP cc_start: 0.9278 (t0) cc_final: 0.8716 (t0) REVERT: B 160 TYR cc_start: 0.8473 (m-10) cc_final: 0.8157 (m-80) REVERT: B 214 GLU cc_start: 0.8216 (pp20) cc_final: 0.7782 (pp20) REVERT: B 238 ASN cc_start: 0.9011 (m110) cc_final: 0.8762 (p0) REVERT: C 40 MET cc_start: 0.9192 (ptp) cc_final: 0.8814 (ptp) REVERT: C 46 GLN cc_start: 0.9563 (mm110) cc_final: 0.9165 (mm-40) REVERT: C 59 ASP cc_start: 0.9219 (t0) cc_final: 0.8632 (t0) REVERT: C 214 GLU cc_start: 0.8358 (pp20) cc_final: 0.7804 (pp20) REVERT: c 111 ARG cc_start: 0.9591 (mpp80) cc_final: 0.9351 (ptp-110) outliers start: 10 outliers final: 7 residues processed: 82 average time/residue: 0.3019 time to fit residues: 32.2503 Evaluate side-chains 80 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 73 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 ASP Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 204 GLU Chi-restraints excluded: chain B residue 239 ASN Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 204 GLU Chi-restraints excluded: chain C residue 217 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 71 optimal weight: 7.9990 chunk 55 optimal weight: 0.8980 chunk 81 optimal weight: 0.0020 chunk 122 optimal weight: 7.9990 chunk 112 optimal weight: 5.9990 chunk 97 optimal weight: 0.0670 chunk 10 optimal weight: 0.6980 chunk 75 optimal weight: 5.9990 chunk 59 optimal weight: 4.9990 chunk 77 optimal weight: 0.8980 chunk 103 optimal weight: 0.9990 overall best weight: 0.5126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.2049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 9000 Z= 0.158 Angle : 0.632 11.221 12279 Z= 0.320 Chirality : 0.043 0.146 1347 Planarity : 0.003 0.031 1662 Dihedral : 3.860 25.961 1299 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 0.92 % Allowed : 14.07 % Favored : 85.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.24), residues: 1224 helix: 0.19 (0.27), residues: 354 sheet: -0.57 (0.28), residues: 273 loop : 0.05 (0.26), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP a 123 HIS 0.003 0.001 HIS a 78 PHE 0.007 0.001 PHE a 162 TYR 0.007 0.001 TYR B 207 ARG 0.005 0.001 ARG a 62 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 79 time to evaluate : 0.937 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 MET cc_start: 0.9454 (ptp) cc_final: 0.9205 (ptp) REVERT: A 52 GLU cc_start: 0.9278 (pm20) cc_final: 0.9044 (pm20) REVERT: A 59 ASP cc_start: 0.9112 (t0) cc_final: 0.8285 (t0) REVERT: A 62 ASP cc_start: 0.9340 (t70) cc_final: 0.9011 (p0) REVERT: B 59 ASP cc_start: 0.9274 (t0) cc_final: 0.8664 (t0) REVERT: B 160 TYR cc_start: 0.8432 (m-10) cc_final: 0.8106 (m-80) REVERT: B 214 GLU cc_start: 0.8214 (pp20) cc_final: 0.7797 (pp20) REVERT: C 40 MET cc_start: 0.9220 (ptp) cc_final: 0.8835 (ptp) REVERT: C 46 GLN cc_start: 0.9544 (mm110) cc_final: 0.9182 (mm-40) REVERT: C 59 ASP cc_start: 0.9226 (t0) cc_final: 0.8662 (t0) REVERT: C 160 TYR cc_start: 0.8497 (m-10) cc_final: 0.8031 (m-80) REVERT: C 214 GLU cc_start: 0.8325 (pp20) cc_final: 0.7762 (pp20) REVERT: a 77 ARG cc_start: 0.7064 (pmt-80) cc_final: 0.6826 (pmt-80) REVERT: b 62 ARG cc_start: 0.8892 (mmm-85) cc_final: 0.8690 (tpm170) REVERT: c 62 ARG cc_start: 0.8777 (mmm-85) cc_final: 0.8405 (tpt90) REVERT: c 111 ARG cc_start: 0.9595 (mpp80) cc_final: 0.9304 (ptp90) outliers start: 8 outliers final: 7 residues processed: 85 average time/residue: 0.2973 time to fit residues: 32.5768 Evaluate side-chains 79 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 72 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 254 ASP Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 204 GLU Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 204 GLU Chi-restraints excluded: chain C residue 217 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 29 optimal weight: 0.4980 chunk 89 optimal weight: 0.2980 chunk 14 optimal weight: 7.9990 chunk 27 optimal weight: 5.9990 chunk 97 optimal weight: 0.0070 chunk 40 optimal weight: 3.9990 chunk 100 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 18 optimal weight: 6.9990 chunk 85 optimal weight: 6.9990 chunk 5 optimal weight: 2.9990 overall best weight: 1.1602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.055293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.035346 restraints weight = 41762.277| |-----------------------------------------------------------------------------| r_work (start): 0.2746 rms_B_bonded: 4.37 r_work: 0.2598 rms_B_bonded: 4.57 restraints_weight: 0.5000 r_work (final): 0.2598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.2086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9000 Z= 0.209 Angle : 0.648 10.832 12279 Z= 0.333 Chirality : 0.043 0.144 1347 Planarity : 0.004 0.050 1662 Dihedral : 3.915 25.225 1299 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.04 % Allowed : 13.61 % Favored : 85.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.24), residues: 1224 helix: -0.02 (0.27), residues: 375 sheet: -0.46 (0.28), residues: 264 loop : -0.07 (0.27), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 101 HIS 0.003 0.001 HIS a 78 PHE 0.005 0.001 PHE A 255 TYR 0.010 0.001 TYR A 67 ARG 0.011 0.001 ARG b 111 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2017.81 seconds wall clock time: 37 minutes 32.26 seconds (2252.26 seconds total)