Starting phenix.real_space_refine on Wed Feb 14 06:42:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ypx_34017/02_2024/7ypx_34017.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ypx_34017/02_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ypx_34017/02_2024/7ypx_34017.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ypx_34017/02_2024/7ypx_34017.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ypx_34017/02_2024/7ypx_34017.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ypx_34017/02_2024/7ypx_34017.pdb" } 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 Residue "A TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 48": "OD1" <-> "OD2" Residue "B TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 48": "OD1" <-> "OD2" Residue "C ASP 95": "OD1" <-> "OD2" Residue "C PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 4.78, per 1000 atoms: 0.54 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 - 3.50 Amino acid : False - 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: 3.57 Conformation dependent library (CDL) restraints added in 1.8 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: 2.65 Time building geometry restraints manager: 3.87 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: 100.58 - 107.26: 396 107.26 - 113.94: 4987 113.94 - 120.62: 3354 120.62 - 127.30: 3413 127.30 - 133.98: 129 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 2.520 nonbonded pdb=" OG SER B 119 " pdb=" O ASN B 185 " model vdw 2.154 2.440 nonbonded pdb=" OG SER A 119 " pdb=" O ASN A 185 " model vdw 2.162 2.440 nonbonded pdb=" OG SER C 119 " pdb=" O ASN C 185 " model vdw 2.221 2.440 nonbonded pdb=" NH1 ARG A 231 " pdb=" O GLY A 252 " model vdw 2.228 2.520 ... (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 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: 1.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 3.930 Check model and map are aligned: 0.140 Set scattering table: 0.080 Process input model: 27.020 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.060 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:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.280 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 0 poor density : 95 time to evaluate : 1.015 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: 0.3471 time to fit residues: 41.0566 Evaluate side-chains 72 residues out of total 867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 72 time to evaluate : 0.999 ------------------------------------------------------------------------------- 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: 0.9990 chunk 93 optimal weight: 0.1980 chunk 51 optimal weight: 0.7980 chunk 31 optimal weight: 0.0060 chunk 62 optimal weight: 9.9990 chunk 49 optimal weight: 0.9990 chunk 96 optimal weight: 0.0570 chunk 37 optimal weight: 5.9990 chunk 58 optimal weight: 9.9990 chunk 71 optimal weight: 0.6980 chunk 111 optimal weight: 4.9990 overall best weight: 0.3514 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 230 GLN ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 230 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.0933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 9000 Z= 0.146 Angle : 0.548 9.342 12279 Z= 0.278 Chirality : 0.042 0.141 1347 Planarity : 0.004 0.056 1662 Dihedral : 3.969 24.922 1299 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 0.23 % Allowed : 7.04 % Favored : 92.73 % 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: -0.15 (0.24), residues: 1224 helix: 0.31 (0.27), residues: 375 sheet: -0.14 (0.29), residues: 237 loop : -0.20 (0.26), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP c 148 HIS 0.010 0.001 HIS b 132 PHE 0.008 0.001 PHE A 133 TYR 0.009 0.001 TYR B 207 ARG 0.006 0.000 ARG b 62 *********************** 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 fitting. rotamer outliers: 2 poor density : 91 time to evaluate : 0.902 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 ASP cc_start: 0.9172 (t0) cc_final: 0.8700 (t0) REVERT: A 62 ASP cc_start: 0.9151 (t70) cc_final: 0.8826 (t0) REVERT: B 59 ASP cc_start: 0.9256 (t0) cc_final: 0.8676 (t0) REVERT: B 62 ASP cc_start: 0.9178 (t70) cc_final: 0.8948 (t0) REVERT: B 204 GLU cc_start: 0.8398 (mp0) cc_final: 0.8174 (mp0) REVERT: C 40 MET cc_start: 0.9176 (ptp) cc_final: 0.8728 (ptp) REVERT: C 59 ASP cc_start: 0.9196 (t0) cc_final: 0.8665 (t0) REVERT: a 25 ASN cc_start: 0.8906 (t0) cc_final: 0.8491 (t0) REVERT: a 158 MET cc_start: 0.9335 (ptt) cc_final: 0.9095 (ptt) REVERT: c 62 ARG cc_start: 0.8765 (mmm-85) cc_final: 0.8428 (tpt90) REVERT: c 111 ARG cc_start: 0.9588 (mpp80) cc_final: 0.9301 (ptp90) outliers start: 2 outliers final: 1 residues processed: 91 average time/residue: 0.3272 time to fit residues: 37.5629 Evaluate side-chains 70 residues out of total 867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 69 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 62 optimal weight: 8.9990 chunk 34 optimal weight: 4.9990 chunk 92 optimal weight: 0.9990 chunk 76 optimal weight: 3.9990 chunk 30 optimal weight: 0.0570 chunk 111 optimal weight: 0.0370 chunk 120 optimal weight: 5.9990 chunk 99 optimal weight: 9.9990 chunk 110 optimal weight: 3.9990 chunk 38 optimal weight: 9.9990 chunk 89 optimal weight: 0.6980 overall best weight: 1.1580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 78 HIS b 78 HIS ** 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: 0.8348 moved from start: 0.1138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9000 Z= 0.188 Angle : 0.529 8.688 12279 Z= 0.271 Chirality : 0.042 0.140 1347 Planarity : 0.003 0.028 1662 Dihedral : 3.920 24.140 1299 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 0.58 % Allowed : 11.42 % Favored : 88.00 % 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: 0.31 (0.27), residues: 372 sheet: -0.16 (0.29), residues: 237 loop : -0.29 (0.26), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP b 148 HIS 0.009 0.001 HIS b 132 PHE 0.007 0.001 PHE a 162 TYR 0.008 0.001 TYR B 207 ARG 0.005 0.000 ARG a 62 *********************** 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 86 residues out of total 867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 81 time to evaluate : 0.909 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 ASP cc_start: 0.9155 (t0) cc_final: 0.8655 (t0) REVERT: A 62 ASP cc_start: 0.9177 (t70) cc_final: 0.8960 (t0) REVERT: B 59 ASP cc_start: 0.9290 (t0) cc_final: 0.8715 (t0) REVERT: B 62 ASP cc_start: 0.9201 (t70) cc_final: 0.8952 (t0) REVERT: B 238 ASN cc_start: 0.8989 (m110) cc_final: 0.8771 (p0) REVERT: C 40 MET cc_start: 0.9207 (ptp) cc_final: 0.8799 (ptp) REVERT: C 59 ASP cc_start: 0.9232 (t0) cc_final: 0.8678 (t0) REVERT: a 25 ASN cc_start: 0.8964 (t0) cc_final: 0.8569 (t0) REVERT: c 111 ARG cc_start: 0.9584 (mpp80) cc_final: 0.9346 (ptp90) outliers start: 5 outliers final: 2 residues processed: 82 average time/residue: 0.3358 time to fit residues: 35.0198 Evaluate side-chains 72 residues out of total 867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 70 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 131 ASP Chi-restraints excluded: chain C residue 131 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 110 optimal weight: 4.9990 chunk 84 optimal weight: 9.9990 chunk 58 optimal weight: 8.9990 chunk 12 optimal weight: 9.9990 chunk 53 optimal weight: 5.9990 chunk 75 optimal weight: 7.9990 chunk 112 optimal weight: 7.9990 chunk 118 optimal weight: 0.9980 chunk 106 optimal weight: 4.9990 chunk 32 optimal weight: 4.9990 chunk 99 optimal weight: 4.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- 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 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 37 ASN ** C 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 187 ASN ** C 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.8396 moved from start: 0.1582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.065 9000 Z= 0.544 Angle : 0.687 9.041 12279 Z= 0.356 Chirality : 0.044 0.138 1347 Planarity : 0.004 0.037 1662 Dihedral : 4.526 19.059 1299 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 21.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 2.08 % Allowed : 11.42 % Favored : 86.51 % 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: -0.50 (0.24), residues: 1224 helix: 0.19 (0.27), residues: 372 sheet: -0.52 (0.27), residues: 279 loop : -0.45 (0.27), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP b 148 HIS 0.012 0.002 HIS b 78 PHE 0.010 0.002 PHE C 133 TYR 0.015 0.002 TYR A 207 ARG 0.010 0.001 ARG b 147 *********************** 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 93 residues out of total 867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 75 time to evaluate : 1.083 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: 0.9117 (t0) cc_final: 0.8676 (t0) REVERT: A 62 ASP cc_start: 0.9168 (t70) cc_final: 0.8947 (t0) REVERT: B 59 ASP cc_start: 0.9328 (t0) cc_final: 0.8833 (t0) REVERT: B 62 ASP cc_start: 0.9218 (t70) cc_final: 0.8971 (t0) REVERT: C 59 ASP cc_start: 0.9233 (t0) cc_final: 0.8708 (t0) REVERT: a 1 MET cc_start: 0.7860 (tmm) cc_final: 0.7539 (tmm) REVERT: a 53 LYS cc_start: 0.9506 (tppp) cc_final: 0.9171 (tptt) outliers start: 18 outliers final: 8 residues processed: 87 average time/residue: 0.3001 time to fit residues: 33.8849 Evaluate side-chains 72 residues out of total 867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 64 time to evaluate : 1.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 ASP Chi-restraints excluded: chain A residue 100 ASN Chi-restraints excluded: chain B residue 131 ASP Chi-restraints excluded: chain C residue 239 ASN Chi-restraints excluded: chain a residue 82 THR Chi-restraints excluded: chain a residue 141 THR 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: 0.8980 chunk 1 optimal weight: 5.9990 chunk 88 optimal weight: 5.9990 chunk 49 optimal weight: 0.7980 chunk 101 optimal weight: 2.9990 chunk 82 optimal weight: 7.9990 chunk 0 optimal weight: 9.9990 chunk 60 optimal weight: 0.7980 chunk 106 optimal weight: 5.9990 chunk 30 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 GLN C 37 ASN ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.1541 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= 0.204 Angle : 0.578 8.805 12279 Z= 0.294 Chirality : 0.043 0.139 1347 Planarity : 0.003 0.027 1662 Dihedral : 4.132 22.621 1299 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 15.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 2.19 % Allowed : 12.69 % 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: -0.35 (0.24), residues: 1224 helix: 0.22 (0.27), residues: 372 sheet: -0.33 (0.27), residues: 276 loop : -0.34 (0.27), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP b 148 HIS 0.005 0.001 HIS b 132 PHE 0.006 0.001 PHE A 133 TYR 0.009 0.001 TYR B 207 ARG 0.006 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 95 residues out of total 867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 76 time to evaluate : 1.023 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 ASP cc_start: 0.9104 (t0) cc_final: 0.8591 (t0) REVERT: A 62 ASP cc_start: 0.9213 (t70) cc_final: 0.8978 (t0) REVERT: B 46 GLN cc_start: 0.9313 (mm110) cc_final: 0.9033 (mm110) REVERT: B 59 ASP cc_start: 0.9334 (t0) cc_final: 0.8807 (t0) REVERT: B 62 ASP cc_start: 0.9235 (t70) cc_final: 0.8993 (t0) REVERT: B 238 ASN cc_start: 0.8922 (m-40) cc_final: 0.8577 (p0) REVERT: C 40 MET cc_start: 0.9233 (ptp) cc_final: 0.8846 (ptp) REVERT: C 46 GLN cc_start: 0.9534 (mm110) cc_final: 0.9124 (mm-40) REVERT: C 59 ASP cc_start: 0.9231 (t0) cc_final: 0.8721 (t0) REVERT: C 214 GLU cc_start: 0.8388 (pp20) cc_final: 0.7814 (pp20) REVERT: a 25 ASN cc_start: 0.8909 (t0) cc_final: 0.8496 (t0) REVERT: c 111 ARG cc_start: 0.9746 (mpp80) cc_final: 0.9545 (ptp90) outliers start: 19 outliers final: 10 residues processed: 89 average time/residue: 0.2810 time to fit residues: 32.7564 Evaluate side-chains 83 residues out of total 867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 73 time to evaluate : 1.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 ASP Chi-restraints excluded: chain A residue 100 ASN Chi-restraints excluded: chain B residue 131 ASP Chi-restraints excluded: chain B residue 239 ASN Chi-restraints excluded: chain C residue 131 ASP Chi-restraints excluded: chain C residue 204 GLU Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain C residue 239 ASN Chi-restraints excluded: chain a residue 82 THR 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 107 optimal weight: 0.9980 chunk 23 optimal weight: 0.8980 chunk 69 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 119 optimal weight: 6.9990 chunk 98 optimal weight: 4.9990 chunk 55 optimal weight: 6.9990 chunk 9 optimal weight: 3.9990 chunk 39 optimal weight: 7.9990 chunk 62 optimal weight: 9.9990 chunk 114 optimal weight: 2.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 227 GLN ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.1634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9000 Z= 0.236 Angle : 0.571 8.766 12279 Z= 0.288 Chirality : 0.042 0.142 1347 Planarity : 0.003 0.027 1662 Dihedral : 4.070 22.957 1299 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 15.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 1.50 % Allowed : 14.30 % Favored : 84.20 % 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: -0.39 (0.23), residues: 1224 helix: 0.16 (0.27), residues: 372 sheet: -0.36 (0.27), residues: 276 loop : -0.33 (0.27), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP b 148 HIS 0.004 0.001 HIS b 132 PHE 0.004 0.001 PHE a 24 TYR 0.007 0.001 TYR A 207 ARG 0.005 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 90 residues out of total 867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 77 time to evaluate : 1.079 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: 0.9109 (t0) cc_final: 0.8598 (t0) REVERT: A 62 ASP cc_start: 0.9223 (t70) cc_final: 0.8992 (t0) REVERT: B 46 GLN cc_start: 0.9335 (mm110) cc_final: 0.9088 (mm110) REVERT: B 59 ASP cc_start: 0.9349 (t0) cc_final: 0.8830 (t0) REVERT: B 62 ASP cc_start: 0.9213 (t70) cc_final: 0.8948 (t0) REVERT: B 238 ASN cc_start: 0.8923 (OUTLIER) cc_final: 0.8613 (p0) REVERT: C 40 MET cc_start: 0.9241 (ptp) cc_final: 0.8857 (ptp) REVERT: C 46 GLN cc_start: 0.9486 (mm110) cc_final: 0.9033 (mm-40) REVERT: C 59 ASP cc_start: 0.9231 (t0) cc_final: 0.8679 (t0) REVERT: C 214 GLU cc_start: 0.8414 (pp20) cc_final: 0.7828 (pp20) REVERT: c 62 ARG cc_start: 0.8774 (mmm-85) cc_final: 0.8364 (tpt90) REVERT: c 111 ARG cc_start: 0.9759 (mpp80) cc_final: 0.9513 (ptp90) outliers start: 13 outliers final: 9 residues processed: 86 average time/residue: 0.3015 time to fit residues: 33.5317 Evaluate side-chains 80 residues out of total 867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 70 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 ASP Chi-restraints excluded: chain A residue 100 ASN Chi-restraints excluded: chain B residue 131 ASP Chi-restraints excluded: chain B residue 238 ASN Chi-restraints excluded: chain B residue 239 ASN Chi-restraints excluded: chain C residue 204 GLU Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain C residue 239 ASN Chi-restraints excluded: chain a residue 82 THR 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: 7.9990 chunk 67 optimal weight: 2.9990 chunk 86 optimal weight: 3.9990 chunk 100 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 118 optimal weight: 8.9990 chunk 74 optimal weight: 0.8980 chunk 72 optimal weight: 10.0000 chunk 54 optimal weight: 0.6980 chunk 73 optimal weight: 0.6980 chunk 47 optimal weight: 3.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 227 GLN ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 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 : 0.003 0.038 9000 Z= 0.199 Angle : 0.553 8.711 12279 Z= 0.281 Chirality : 0.042 0.139 1347 Planarity : 0.003 0.029 1662 Dihedral : 3.980 24.508 1299 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 14.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 1.61 % Allowed : 15.11 % Favored : 83.28 % 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: 0.19 (0.27), residues: 372 sheet: -0.41 (0.28), residues: 258 loop : -0.19 (0.26), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP b 148 HIS 0.004 0.001 HIS b 132 PHE 0.004 0.001 PHE B 130 TYR 0.007 0.001 TYR B 207 ARG 0.002 0.000 ARG a 77 *********************** 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 90 residues out of total 867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 76 time to evaluate : 1.021 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 ASP cc_start: 0.9108 (t0) cc_final: 0.8453 (t0) REVERT: A 61 THR cc_start: 0.9521 (OUTLIER) cc_final: 0.9225 (p) REVERT: A 62 ASP cc_start: 0.9234 (t70) cc_final: 0.8891 (t0) REVERT: B 40 MET cc_start: 0.9199 (ptp) cc_final: 0.8995 (ptp) REVERT: B 46 GLN cc_start: 0.9374 (mm110) cc_final: 0.9006 (mm110) REVERT: B 59 ASP cc_start: 0.9354 (t0) cc_final: 0.8826 (t0) REVERT: B 62 ASP cc_start: 0.9245 (t70) cc_final: 0.9001 (t0) REVERT: B 214 GLU cc_start: 0.8226 (pp20) cc_final: 0.7703 (pp20) REVERT: B 238 ASN cc_start: 0.8908 (OUTLIER) cc_final: 0.8615 (p0) REVERT: C 40 MET cc_start: 0.9242 (ptp) cc_final: 0.8847 (ptp) REVERT: C 46 GLN cc_start: 0.9465 (mm110) cc_final: 0.9033 (mm-40) REVERT: C 59 ASP cc_start: 0.9214 (t0) cc_final: 0.8661 (t0) REVERT: C 214 GLU cc_start: 0.8422 (pp20) cc_final: 0.7838 (pp20) REVERT: a 25 ASN cc_start: 0.8961 (t0) cc_final: 0.8545 (t0) REVERT: b 25 ASN cc_start: 0.8873 (t0) cc_final: 0.8420 (t0) REVERT: c 62 ARG cc_start: 0.8859 (mmm-85) cc_final: 0.8342 (tpt90) REVERT: c 111 ARG cc_start: 0.9772 (mpp80) cc_final: 0.9527 (ptp90) outliers start: 14 outliers final: 4 residues processed: 86 average time/residue: 0.2997 time to fit residues: 33.3732 Evaluate side-chains 78 residues out of total 867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 72 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 100 ASN Chi-restraints excluded: chain B residue 131 ASP Chi-restraints excluded: chain B residue 238 ASN Chi-restraints excluded: chain B residue 239 ASN Chi-restraints excluded: chain C residue 217 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 70 optimal weight: 5.9990 chunk 35 optimal weight: 0.6980 chunk 23 optimal weight: 5.9990 chunk 22 optimal weight: 0.0770 chunk 75 optimal weight: 6.9990 chunk 80 optimal weight: 0.0970 chunk 58 optimal weight: 6.9990 chunk 11 optimal weight: 0.1980 chunk 93 optimal weight: 0.9990 chunk 107 optimal weight: 0.9990 chunk 113 optimal weight: 30.0000 overall best weight: 0.4138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.1827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9000 Z= 0.133 Angle : 0.554 8.724 12279 Z= 0.277 Chirality : 0.042 0.142 1347 Planarity : 0.003 0.031 1662 Dihedral : 3.835 26.264 1299 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 13.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 1.38 % Allowed : 15.80 % Favored : 82.81 % 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: -0.25 (0.23), residues: 1224 helix: 0.17 (0.27), residues: 372 sheet: -0.35 (0.28), residues: 264 loop : -0.14 (0.26), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP b 148 HIS 0.004 0.001 HIS b 132 PHE 0.005 0.001 PHE B 130 TYR 0.008 0.001 TYR B 207 ARG 0.005 0.000 ARG b 62 *********************** 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 91 residues out of total 867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 79 time to evaluate : 1.082 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 ASP cc_start: 0.9170 (t0) cc_final: 0.8523 (t0) REVERT: A 61 THR cc_start: 0.9553 (OUTLIER) cc_final: 0.9272 (p) REVERT: A 62 ASP cc_start: 0.9247 (t70) cc_final: 0.8904 (t0) REVERT: B 40 MET cc_start: 0.9203 (ptp) cc_final: 0.8981 (ptp) REVERT: B 46 GLN cc_start: 0.9424 (mm110) cc_final: 0.9084 (mm110) REVERT: B 59 ASP cc_start: 0.9346 (t0) cc_final: 0.8808 (t0) REVERT: B 62 ASP cc_start: 0.9246 (t70) cc_final: 0.9028 (t0) REVERT: B 214 GLU cc_start: 0.8180 (pp20) cc_final: 0.7745 (pp20) REVERT: C 40 MET cc_start: 0.9244 (ptp) cc_final: 0.8843 (ptp) REVERT: C 46 GLN cc_start: 0.9442 (mm110) cc_final: 0.9090 (mm-40) REVERT: C 59 ASP cc_start: 0.9198 (t0) cc_final: 0.8648 (t0) REVERT: C 214 GLU cc_start: 0.8363 (pp20) cc_final: 0.7779 (pp20) REVERT: a 25 ASN cc_start: 0.8964 (t0) cc_final: 0.8538 (t0) REVERT: b 25 ASN cc_start: 0.8875 (t0) cc_final: 0.8422 (t0) REVERT: c 111 ARG cc_start: 0.9776 (mpp80) cc_final: 0.9494 (ptp90) outliers start: 12 outliers final: 5 residues processed: 86 average time/residue: 0.3142 time to fit residues: 34.4438 Evaluate side-chains 80 residues out of total 867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 74 time to evaluate : 1.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain B residue 131 ASP Chi-restraints excluded: chain B residue 239 ASN 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: 6.9990 chunk 113 optimal weight: 0.8980 chunk 66 optimal weight: 6.9990 chunk 48 optimal weight: 7.9990 chunk 86 optimal weight: 5.9990 chunk 33 optimal weight: 9.9990 chunk 99 optimal weight: 6.9990 chunk 104 optimal weight: 0.6980 chunk 72 optimal weight: 10.0000 chunk 116 optimal weight: 4.9990 overall best weight: 3.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 227 GLN ** 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 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 260 GLN b 137 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.1897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 9000 Z= 0.393 Angle : 0.623 9.501 12279 Z= 0.319 Chirality : 0.043 0.137 1347 Planarity : 0.004 0.046 1662 Dihedral : 4.157 24.755 1299 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 18.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 1.27 % Allowed : 15.69 % Favored : 83.04 % 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: -0.34 (0.24), residues: 1224 helix: 0.12 (0.27), residues: 372 sheet: -0.49 (0.28), residues: 261 loop : -0.16 (0.27), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP c 36 HIS 0.003 0.001 HIS b 132 PHE 0.006 0.001 PHE C 133 TYR 0.009 0.001 TYR B 67 ARG 0.011 0.001 ARG c 130 *********************** 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 84 residues out of total 867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 73 time to evaluate : 1.024 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 MET cc_start: 0.9475 (ptp) cc_final: 0.9253 (ptp) REVERT: A 59 ASP cc_start: 0.9113 (t0) cc_final: 0.8476 (t0) REVERT: A 61 THR cc_start: 0.9543 (OUTLIER) cc_final: 0.9239 (p) REVERT: A 62 ASP cc_start: 0.9228 (t70) cc_final: 0.8889 (t0) REVERT: B 46 GLN cc_start: 0.9350 (mm110) cc_final: 0.9137 (mm110) REVERT: B 59 ASP cc_start: 0.9364 (t0) cc_final: 0.8857 (t0) REVERT: B 62 ASP cc_start: 0.9239 (t70) cc_final: 0.8969 (t0) REVERT: B 214 GLU cc_start: 0.8363 (pp20) cc_final: 0.7910 (pp20) REVERT: C 40 MET cc_start: 0.9249 (ptp) cc_final: 0.8835 (ptp) REVERT: C 46 GLN cc_start: 0.9429 (mm110) cc_final: 0.9008 (mm-40) REVERT: C 59 ASP cc_start: 0.9201 (t0) cc_final: 0.8615 (t0) REVERT: C 214 GLU cc_start: 0.8446 (pp20) cc_final: 0.7864 (pp20) REVERT: b 62 ARG cc_start: 0.8334 (tpt90) cc_final: 0.8055 (tpm170) REVERT: c 1 MET cc_start: 0.7797 (tmm) cc_final: 0.7501 (tmm) REVERT: c 111 ARG cc_start: 0.9786 (mpp80) cc_final: 0.9474 (ptp90) outliers start: 11 outliers final: 8 residues processed: 82 average time/residue: 0.3126 time to fit residues: 33.1631 Evaluate side-chains 80 residues out of total 867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 71 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 100 ASN Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain B residue 131 ASP Chi-restraints excluded: chain B residue 239 ASN Chi-restraints excluded: chain C residue 100 ASN Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain C residue 239 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 71 optimal weight: 0.6980 chunk 55 optimal weight: 2.9990 chunk 81 optimal weight: 0.3980 chunk 122 optimal weight: 0.3980 chunk 112 optimal weight: 4.9990 chunk 97 optimal weight: 0.0980 chunk 10 optimal weight: 0.6980 chunk 75 optimal weight: 3.9990 chunk 59 optimal weight: 4.9990 chunk 77 optimal weight: 0.9990 chunk 103 optimal weight: 6.9990 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 227 GLN ** 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 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 260 GLN b 137 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.1905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 9000 Z= 0.152 Angle : 0.599 10.350 12279 Z= 0.300 Chirality : 0.043 0.142 1347 Planarity : 0.003 0.045 1662 Dihedral : 3.961 26.738 1299 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 15.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 1.38 % Allowed : 15.69 % Favored : 82.93 % 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: -0.25 (0.23), residues: 1224 helix: 0.13 (0.27), residues: 372 sheet: -0.03 (0.30), residues: 228 loop : -0.28 (0.25), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP b 148 HIS 0.004 0.001 HIS b 132 PHE 0.004 0.001 PHE c 162 TYR 0.008 0.001 TYR B 207 ARG 0.010 0.001 ARG c 130 ********************** 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 91 residues out of total 867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 79 time to evaluate : 0.966 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 MET cc_start: 0.9473 (ptp) cc_final: 0.9228 (ptp) REVERT: A 59 ASP cc_start: 0.9103 (t0) cc_final: 0.8469 (t0) REVERT: A 61 THR cc_start: 0.9557 (OUTLIER) cc_final: 0.9260 (p) REVERT: A 62 ASP cc_start: 0.9279 (t70) cc_final: 0.8926 (t0) REVERT: B 46 GLN cc_start: 0.9408 (mm110) cc_final: 0.9060 (mm110) REVERT: B 59 ASP cc_start: 0.9347 (t0) cc_final: 0.8818 (t0) REVERT: B 62 ASP cc_start: 0.9269 (t70) cc_final: 0.9063 (t0) REVERT: B 214 GLU cc_start: 0.8318 (pp20) cc_final: 0.7909 (pp20) REVERT: C 40 MET cc_start: 0.9228 (ptp) cc_final: 0.8863 (ptp) REVERT: C 46 GLN cc_start: 0.9447 (mm110) cc_final: 0.9087 (mm-40) REVERT: C 59 ASP cc_start: 0.9178 (t0) cc_final: 0.8611 (t0) REVERT: C 214 GLU cc_start: 0.8421 (pp20) cc_final: 0.7857 (pp20) REVERT: a 25 ASN cc_start: 0.8962 (t0) cc_final: 0.8529 (t0) REVERT: a 62 ARG cc_start: 0.8766 (tpt90) cc_final: 0.8493 (tpm170) REVERT: b 25 ASN cc_start: 0.8909 (t0) cc_final: 0.8468 (t0) REVERT: b 62 ARG cc_start: 0.8401 (tpt90) cc_final: 0.8152 (tpm170) REVERT: c 1 MET cc_start: 0.7696 (tmm) cc_final: 0.7403 (tmm) REVERT: c 111 ARG cc_start: 0.9781 (mpp80) cc_final: 0.9471 (ptp90) outliers start: 12 outliers final: 7 residues processed: 88 average time/residue: 0.2936 time to fit residues: 33.3840 Evaluate side-chains 84 residues out of total 867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 76 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain B residue 131 ASP Chi-restraints excluded: chain B residue 204 GLU Chi-restraints excluded: chain B residue 239 ASN Chi-restraints excluded: chain C residue 100 ASN 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: 3.9990 chunk 89 optimal weight: 7.9990 chunk 14 optimal weight: 7.9990 chunk 27 optimal weight: 5.9990 chunk 97 optimal weight: 0.2980 chunk 40 optimal weight: 6.9990 chunk 100 optimal weight: 0.7980 chunk 12 optimal weight: 9.9990 chunk 18 optimal weight: 10.0000 chunk 85 optimal weight: 0.9990 chunk 5 optimal weight: 0.7980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 227 GLN ** 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 ** 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 = 0.3489 r_free = 0.3489 target = 0.055102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.035412 restraints weight = 41282.891| |-----------------------------------------------------------------------------| r_work (start): 0.2762 rms_B_bonded: 4.33 r_work: 0.2610 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.2610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.1948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9000 Z= 0.224 Angle : 0.608 9.746 12279 Z= 0.307 Chirality : 0.043 0.138 1347 Planarity : 0.003 0.039 1662 Dihedral : 3.991 25.867 1299 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 16.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 1.04 % Allowed : 16.38 % Favored : 82.58 % 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 (0.23), residues: 1224 helix: 0.11 (0.27), residues: 372 sheet: -0.07 (0.30), residues: 228 loop : -0.27 (0.25), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP b 148 HIS 0.003 0.001 HIS b 132 PHE 0.004 0.001 PHE a 24 TYR 0.012 0.001 TYR C 67 ARG 0.008 0.000 ARG c 130 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2107.07 seconds wall clock time: 38 minutes 53.37 seconds (2333.37 seconds total)