Starting phenix.real_space_refine on Wed Jan 15 23:01:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ypx_34017/01_2025/7ypx_34017.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ypx_34017/01_2025/7ypx_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_34017/01_2025/7ypx_34017.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ypx_34017/01_2025/7ypx_34017.map" model { file = "/net/cci-nas-00/data/ceres_data/7ypx_34017/01_2025/7ypx_34017.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ypx_34017/01_2025/7ypx_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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: 5.35, per 1000 atoms: 0.61 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: 2.02 Conformation dependent library (CDL) restraints added in 1.1 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: 0.96 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: 2.34 Time building geometry restraints manager: 2.39 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: 0.02 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: 1.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 22.200 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.340 ------------------------------------------------------------------------------- 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 : 1.468 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: 0.3587 time to fit residues: 42.5830 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 : 0.939 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.055751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.036003 restraints weight = 40838.757| |-----------------------------------------------------------------------------| r_work (start): 0.2768 rms_B_bonded: 4.35 r_work: 0.2619 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.2619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 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 : 0.900 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: 0.9122 (t0) cc_final: 0.8585 (t0) REVERT: A 62 ASP cc_start: 0.9198 (t0) cc_final: 0.8862 (t0) REVERT: B 48 ASP cc_start: 0.9378 (p0) cc_final: 0.9163 (p0) REVERT: B 52 GLU cc_start: 0.9200 (pm20) cc_final: 0.8994 (pm20) REVERT: B 59 ASP cc_start: 0.9195 (t0) cc_final: 0.8642 (t0) REVERT: B 160 TYR cc_start: 0.8931 (m-80) cc_final: 0.8465 (m-80) REVERT: B 204 GLU cc_start: 0.8786 (mp0) cc_final: 0.8559 (mp0) REVERT: C 40 MET cc_start: 0.9367 (ptp) cc_final: 0.9040 (ptp) REVERT: C 59 ASP cc_start: 0.9121 (t0) cc_final: 0.8557 (t0) REVERT: a 25 ASN cc_start: 0.9192 (t0) cc_final: 0.8803 (t0) REVERT: c 111 ARG cc_start: 0.9626 (mpp80) cc_final: 0.9360 (ptp90) outliers start: 1 outliers final: 0 residues processed: 92 average time/residue: 0.3411 time to fit residues: 39.3977 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 : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 75 optimal weight: 7.9990 chunk 23 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 21 optimal weight: 0.7980 chunk 85 optimal weight: 5.9990 chunk 94 optimal weight: 4.9990 chunk 36 optimal weight: 0.9980 chunk 18 optimal weight: 9.9990 chunk 108 optimal weight: 6.9990 chunk 83 optimal weight: 9.9990 chunk 3 optimal weight: 0.3980 overall best weight: 1.8384 ------------------------------------------------------------------------------- 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 ** b 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.055002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.035253 restraints weight = 41693.003| |-----------------------------------------------------------------------------| r_work (start): 0.2739 rms_B_bonded: 4.34 r_work: 0.2587 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.2587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.1199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9000 Z= 0.262 Angle : 0.583 8.847 12279 Z= 0.301 Chirality : 0.043 0.146 1347 Planarity : 0.003 0.027 1662 Dihedral : 4.085 22.996 1299 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % 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 (0.26), residues: 375 sheet: -0.32 (0.28), residues: 255 loop : -0.18 (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 0.009 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 79 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.914 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: 0.9068 (t0) cc_final: 0.8515 (t0) REVERT: A 62 ASP cc_start: 0.9211 (t70) cc_final: 0.9008 (t70) REVERT: A 160 TYR cc_start: 0.8298 (m-10) cc_final: 0.8078 (m-80) REVERT: B 48 ASP cc_start: 0.9443 (p0) cc_final: 0.9201 (p0) REVERT: B 59 ASP cc_start: 0.9184 (t0) cc_final: 0.8613 (t0) REVERT: B 238 ASN cc_start: 0.9166 (m110) cc_final: 0.8901 (p0) REVERT: C 40 MET cc_start: 0.9375 (ptp) cc_final: 0.9042 (ptp) REVERT: C 46 GLN cc_start: 0.9612 (mm110) cc_final: 0.9234 (mm-40) REVERT: C 59 ASP cc_start: 0.9107 (t0) cc_final: 0.8527 (t0) REVERT: c 111 ARG cc_start: 0.9624 (mpp80) cc_final: 0.9374 (ptp90) outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.3381 time to fit residues: 33.7751 Evaluate side-chains 68 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 76 optimal weight: 0.3980 chunk 36 optimal weight: 4.9990 chunk 1 optimal weight: 6.9990 chunk 104 optimal weight: 8.9990 chunk 70 optimal weight: 0.6980 chunk 122 optimal weight: 0.6980 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 8.9990 chunk 105 optimal weight: 6.9990 chunk 12 optimal weight: 9.9990 chunk 22 optimal weight: 0.1980 overall best weight: 0.5982 ------------------------------------------------------------------------------- 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 = 0.3503 r_free = 0.3503 target = 0.055918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.036195 restraints weight = 41541.419| |-----------------------------------------------------------------------------| r_work (start): 0.2783 rms_B_bonded: 4.38 r_work: 0.2629 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.2629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.1411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9000 Z= 0.149 Angle : 0.541 6.513 12279 Z= 0.277 Chirality : 0.042 0.143 1347 Planarity : 0.003 0.032 1662 Dihedral : 3.922 21.074 1299 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 0.58 % Allowed : 11.19 % Favored : 88.24 % 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: -0.20 (0.24), residues: 1224 helix: 0.31 (0.27), residues: 375 sheet: -0.27 (0.29), residues: 237 loop : -0.22 (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 b 132 PHE 0.005 0.001 PHE A 133 TYR 0.008 0.001 TYR B 207 ARG 0.005 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 88 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 83 time to evaluate : 0.996 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: 0.9051 (t0) cc_final: 0.8514 (t0) REVERT: A 160 TYR cc_start: 0.8354 (m-10) cc_final: 0.8068 (m-80) REVERT: B 46 GLN cc_start: 0.9466 (mm110) cc_final: 0.9084 (mm-40) REVERT: B 59 ASP cc_start: 0.9195 (t0) cc_final: 0.8616 (t0) REVERT: B 160 TYR cc_start: 0.8695 (m-10) cc_final: 0.8245 (m-80) REVERT: B 238 ASN cc_start: 0.9116 (m110) cc_final: 0.8869 (p0) REVERT: C 40 MET cc_start: 0.9359 (ptp) cc_final: 0.9028 (ptp) REVERT: C 59 ASP cc_start: 0.9116 (t0) cc_final: 0.8508 (t0) REVERT: C 160 TYR cc_start: 0.8571 (m-10) cc_final: 0.8207 (m-80) REVERT: C 214 GLU cc_start: 0.8410 (pp20) cc_final: 0.7755 (pp20) REVERT: c 111 ARG cc_start: 0.9625 (mpp80) cc_final: 0.9387 (ptp90) outliers start: 5 outliers final: 1 residues processed: 87 average time/residue: 0.3016 time to fit residues: 33.7842 Evaluate side-chains 71 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 70 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 108 optimal weight: 0.0370 chunk 18 optimal weight: 9.9990 chunk 102 optimal weight: 5.9990 chunk 78 optimal weight: 0.2980 chunk 116 optimal weight: 5.9990 chunk 106 optimal weight: 4.9990 chunk 51 optimal weight: 8.9990 chunk 56 optimal weight: 7.9990 chunk 50 optimal weight: 0.2980 chunk 52 optimal weight: 0.9990 chunk 75 optimal weight: 8.9990 overall best weight: 1.3262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 ASN ** b 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.055446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.035908 restraints weight = 40940.813| |-----------------------------------------------------------------------------| r_work (start): 0.2772 rms_B_bonded: 4.32 r_work: 0.2620 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.2620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.1529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9000 Z= 0.206 Angle : 0.560 7.910 12279 Z= 0.288 Chirality : 0.042 0.198 1347 Planarity : 0.003 0.030 1662 Dihedral : 3.924 20.473 1299 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.04 % Allowed : 12.11 % Favored : 86.85 % 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: -0.22 (0.23), residues: 1224 helix: 0.29 (0.27), residues: 375 sheet: -0.14 (0.29), residues: 228 loop : -0.30 (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 133 TYR 0.009 0.001 TYR C 207 ARG 0.006 0.000 ARG b 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 87 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 78 time to evaluate : 0.962 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: 0.9081 (t0) cc_final: 0.8502 (t0) REVERT: A 62 ASP cc_start: 0.9242 (t70) cc_final: 0.8922 (t0) REVERT: A 160 TYR cc_start: 0.8348 (m-10) cc_final: 0.8007 (m-80) REVERT: B 46 GLN cc_start: 0.9498 (mm110) cc_final: 0.9210 (mm-40) REVERT: B 59 ASP cc_start: 0.9226 (t0) cc_final: 0.8652 (t0) REVERT: B 238 ASN cc_start: 0.9137 (m110) cc_final: 0.8913 (p0) REVERT: C 40 MET cc_start: 0.9370 (ptp) cc_final: 0.9031 (ptp) REVERT: C 46 GLN cc_start: 0.9622 (mm110) cc_final: 0.9219 (mm-40) REVERT: C 59 ASP cc_start: 0.9139 (t0) cc_final: 0.8534 (t0) REVERT: C 160 TYR cc_start: 0.8592 (m-10) cc_final: 0.8202 (m-80) REVERT: C 214 GLU cc_start: 0.8477 (pp20) cc_final: 0.7806 (pp20) outliers start: 9 outliers final: 4 residues processed: 84 average time/residue: 0.3242 time to fit residues: 34.9038 Evaluate side-chains 75 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 71 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 ASP Chi-restraints excluded: chain B residue 204 GLU Chi-restraints excluded: chain C residue 204 GLU Chi-restraints excluded: chain a residue 119 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 91 optimal weight: 0.9980 chunk 103 optimal weight: 6.9990 chunk 19 optimal weight: 0.7980 chunk 73 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 119 optimal weight: 10.0000 chunk 55 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 106 optimal weight: 4.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3491 r_free = 0.3491 target = 0.055533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.035896 restraints weight = 41143.358| |-----------------------------------------------------------------------------| r_work (start): 0.2773 rms_B_bonded: 4.34 r_work: 0.2619 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.2619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.1651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9000 Z= 0.187 Angle : 0.569 8.021 12279 Z= 0.290 Chirality : 0.042 0.143 1347 Planarity : 0.004 0.031 1662 Dihedral : 3.868 21.186 1299 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.38 % Allowed : 12.00 % Favored : 86.62 % 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 (0.24), residues: 1224 helix: 0.24 (0.27), residues: 375 sheet: -0.29 (0.29), residues: 237 loop : -0.20 (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 A 133 TYR 0.007 0.001 TYR C 207 ARG 0.006 0.001 ARG c 111 *********************** 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 86 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 74 time to evaluate : 0.856 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: symmetry clash REVERT: A 59 ASP cc_start: 0.9072 (t0) cc_final: 0.8524 (t0) REVERT: A 62 ASP cc_start: 0.9276 (t70) cc_final: 0.9013 (t0) REVERT: B 59 ASP cc_start: 0.9223 (t0) cc_final: 0.8644 (t0) REVERT: B 238 ASN cc_start: 0.9139 (m110) cc_final: 0.8887 (p0) REVERT: C 46 GLN cc_start: 0.9617 (mm110) cc_final: 0.9229 (mm-40) REVERT: C 59 ASP cc_start: 0.9187 (t0) cc_final: 0.8611 (t0) REVERT: C 160 TYR cc_start: 0.8562 (m-10) cc_final: 0.8165 (m-80) REVERT: C 214 GLU cc_start: 0.8462 (pp20) cc_final: 0.7788 (pp20) REVERT: c 62 ARG cc_start: 0.8833 (mmm-85) cc_final: 0.8386 (tpt90) outliers start: 12 outliers final: 5 residues processed: 84 average time/residue: 0.2935 time to fit residues: 32.1381 Evaluate side-chains 75 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 70 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 ASP Chi-restraints excluded: chain C residue 204 GLU Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain a residue 119 GLU Chi-restraints excluded: chain b residue 119 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 96 optimal weight: 0.0370 chunk 22 optimal weight: 8.9990 chunk 36 optimal weight: 0.6980 chunk 29 optimal weight: 3.9990 chunk 106 optimal weight: 0.9980 chunk 92 optimal weight: 0.7980 chunk 112 optimal weight: 0.9990 chunk 85 optimal weight: 8.9990 chunk 47 optimal weight: 5.9990 chunk 42 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 overall best weight: 0.7060 ------------------------------------------------------------------------------- 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 = 0.3510 r_free = 0.3510 target = 0.055867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.035804 restraints weight = 41981.039| |-----------------------------------------------------------------------------| r_work (start): 0.2780 rms_B_bonded: 4.42 r_work: 0.2632 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.2632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.1766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 9000 Z= 0.159 Angle : 0.584 7.997 12279 Z= 0.294 Chirality : 0.042 0.142 1347 Planarity : 0.003 0.031 1662 Dihedral : 3.792 22.717 1299 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 1.38 % Allowed : 12.69 % Favored : 85.93 % 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: -0.17 (0.23), residues: 1224 helix: 0.31 (0.27), residues: 354 sheet: -0.29 (0.29), residues: 237 loop : -0.16 (0.25), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 101 HIS 0.002 0.001 HIS a 78 PHE 0.005 0.001 PHE a 162 TYR 0.006 0.001 TYR B 207 ARG 0.007 0.001 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 93 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 81 time to evaluate : 0.931 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: 0.9075 (t0) cc_final: 0.8522 (t0) REVERT: A 62 ASP cc_start: 0.9298 (t70) cc_final: 0.9053 (t0) REVERT: B 59 ASP cc_start: 0.9241 (t0) cc_final: 0.8616 (t0) REVERT: B 62 ASP cc_start: 0.9089 (t0) cc_final: 0.8873 (t0) REVERT: B 160 TYR cc_start: 0.8635 (m-10) cc_final: 0.8364 (m-80) REVERT: B 214 GLU cc_start: 0.7990 (pp20) cc_final: 0.7781 (pp20) REVERT: B 238 ASN cc_start: 0.9128 (m110) cc_final: 0.8870 (p0) REVERT: C 40 MET cc_start: 0.9371 (ptp) cc_final: 0.9036 (ptp) REVERT: C 46 GLN cc_start: 0.9631 (mm110) cc_final: 0.9249 (mm-40) REVERT: C 59 ASP cc_start: 0.9200 (t0) cc_final: 0.8608 (t0) REVERT: C 160 TYR cc_start: 0.8592 (m-10) cc_final: 0.8178 (m-80) REVERT: C 214 GLU cc_start: 0.8454 (pp20) cc_final: 0.7777 (pp20) REVERT: b 62 ARG cc_start: 0.8507 (tpt90) cc_final: 0.8217 (tpm170) REVERT: c 62 ARG cc_start: 0.8874 (mmm-85) cc_final: 0.8434 (tpt90) outliers start: 12 outliers final: 7 residues processed: 90 average time/residue: 0.3144 time to fit residues: 36.5253 Evaluate side-chains 81 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 74 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 ASP 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 Chi-restraints excluded: chain a residue 119 GLU Chi-restraints excluded: chain b residue 119 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 72 optimal weight: 7.9990 chunk 73 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 chunk 34 optimal weight: 7.9990 chunk 30 optimal weight: 3.9990 chunk 63 optimal weight: 6.9990 chunk 14 optimal weight: 5.9990 chunk 90 optimal weight: 0.9990 chunk 22 optimal weight: 10.0000 chunk 82 optimal weight: 8.9990 chunk 89 optimal weight: 5.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- 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 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 260 GLN ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 260 GLN ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 260 GLN ** b 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.053371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2777 r_free = 0.2777 target = 0.033536 restraints weight = 42510.364| |-----------------------------------------------------------------------------| r_work (start): 0.2667 rms_B_bonded: 4.31 r_work: 0.2507 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.2507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.1871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.058 9000 Z= 0.484 Angle : 0.693 9.708 12279 Z= 0.358 Chirality : 0.044 0.160 1347 Planarity : 0.004 0.036 1662 Dihedral : 4.270 22.641 1299 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 1.27 % Allowed : 13.61 % Favored : 85.12 % 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: -0.59 (0.23), residues: 1224 helix: -0.14 (0.26), residues: 375 sheet: -0.47 (0.27), residues: 273 loop : -0.35 (0.27), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP c 36 HIS 0.007 0.002 HIS a 78 PHE 0.007 0.002 PHE C 133 TYR 0.011 0.002 TYR A 207 ARG 0.006 0.001 ARG c 111 *********************** 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 80 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 69 time to evaluate : 0.913 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: 0.9015 (t0) cc_final: 0.8455 (t0) REVERT: A 62 ASP cc_start: 0.9280 (t70) cc_final: 0.9064 (t70) REVERT: B 59 ASP cc_start: 0.9224 (t0) cc_final: 0.8670 (t0) REVERT: B 238 ASN cc_start: 0.9204 (m110) cc_final: 0.8943 (p0) REVERT: C 46 GLN cc_start: 0.9610 (mm110) cc_final: 0.9124 (mm-40) REVERT: C 59 ASP cc_start: 0.9151 (t0) cc_final: 0.8590 (t0) REVERT: C 214 GLU cc_start: 0.8564 (pp20) cc_final: 0.7869 (pp20) outliers start: 11 outliers final: 7 residues processed: 76 average time/residue: 0.3039 time to fit residues: 30.3840 Evaluate side-chains 73 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 66 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 ASP Chi-restraints excluded: chain B residue 52 GLU Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain b residue 83 ILE Chi-restraints excluded: chain b residue 141 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 67.666 > 50: distance: 69 - 71: 20.019 distance: 71 - 72: 28.737 distance: 72 - 73: 32.588 distance: 72 - 75: 52.782 distance: 73 - 74: 37.276 distance: 73 - 78: 46.755 distance: 75 - 76: 49.434 distance: 75 - 77: 39.054 distance: 78 - 79: 6.764 distance: 79 - 80: 21.752 distance: 79 - 82: 45.191 distance: 80 - 81: 8.455 distance: 80 - 85: 43.792 distance: 82 - 83: 29.274 distance: 82 - 84: 41.108 distance: 85 - 86: 11.668 distance: 85 - 91: 41.313 distance: 86 - 87: 50.556 distance: 86 - 89: 38.920 distance: 87 - 88: 19.280 distance: 87 - 92: 28.103 distance: 89 - 90: 44.589 distance: 90 - 91: 19.056 distance: 92 - 93: 21.025 distance: 93 - 94: 7.421 distance: 93 - 96: 29.031 distance: 94 - 95: 11.315 distance: 94 - 101: 5.588 distance: 96 - 97: 26.694 distance: 97 - 98: 28.825 distance: 98 - 99: 50.785 distance: 99 - 100: 24.651 distance: 101 - 102: 51.218 distance: 102 - 103: 18.138 distance: 103 - 104: 56.146 distance: 103 - 105: 28.509 distance: 105 - 106: 10.236 distance: 106 - 107: 18.847 distance: 106 - 109: 19.158 distance: 107 - 108: 8.937 distance: 107 - 114: 27.988 distance: 109 - 110: 23.236 distance: 110 - 111: 20.846 distance: 111 - 112: 3.988 distance: 111 - 113: 17.212 distance: 114 - 115: 18.570 distance: 115 - 116: 11.608 distance: 115 - 118: 9.312 distance: 116 - 117: 15.212 distance: 116 - 122: 16.872 distance: 118 - 119: 16.157 distance: 119 - 120: 18.851 distance: 119 - 121: 22.329 distance: 122 - 123: 13.544 distance: 123 - 124: 33.726 distance: 123 - 126: 20.229 distance: 124 - 125: 27.729 distance: 124 - 133: 28.988 distance: 126 - 127: 29.212 distance: 127 - 128: 8.949 distance: 128 - 129: 18.341 distance: 129 - 130: 18.332 distance: 130 - 131: 7.758 distance: 130 - 132: 4.798 distance: 133 - 134: 7.702 distance: 134 - 135: 23.210 distance: 134 - 137: 21.534 distance: 135 - 136: 6.976 distance: 135 - 147: 43.239 distance: 137 - 138: 13.416 distance: 138 - 139: 9.788 distance: 138 - 140: 12.877 distance: 139 - 141: 27.990 distance: 140 - 142: 16.394 distance: 140 - 143: 7.919 distance: 141 - 142: 17.681 distance: 142 - 144: 28.155 distance: 143 - 145: 25.192 distance: 144 - 146: 23.042 distance: 145 - 146: 23.840 distance: 147 - 148: 35.304 distance: 147 - 153: 20.908 distance: 148 - 149: 41.760 distance: 148 - 151: 18.171 distance: 149 - 150: 32.668 distance: 149 - 154: 28.084 distance: 151 - 152: 56.858 distance: 152 - 153: 5.952