Starting phenix.real_space_refine on Thu Dec 7 22:56:20 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a01_15044/12_2023/8a01_15044.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a01_15044/12_2023/8a01_15044.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a01_15044/12_2023/8a01_15044.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a01_15044/12_2023/8a01_15044.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a01_15044/12_2023/8a01_15044.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a01_15044/12_2023/8a01_15044.pdb" } resolution = 3.2 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= 0.016 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 15 5.16 5 C 3495 2.51 5 N 885 2.21 5 O 1116 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C ASP 29": "OD1" <-> "OD2" Residue "C ASP 108": "OD1" <-> "OD2" Residue "C ASP 147": "OD1" <-> "OD2" Residue "B GLU 91": "OE1" <-> "OE2" Residue "B GLU 100": "OE1" <-> "OE2" Residue "B TYR 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 198": "OD1" <-> "OD2" Residue "A GLU 14": "OE1" <-> "OE2" Residue "A TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 198": "OD1" <-> "OD2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 5511 Number of models: 1 Model: "" Number of chains: 3 Chain: "C" Number of atoms: 1837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1837 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 5, 'TRANS': 233} Chain: "B" Number of atoms: 1837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1837 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 5, 'TRANS': 233} Chain: "A" Number of atoms: 1837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1837 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 5, 'TRANS': 233} Time building chain proxies: 3.58, per 1000 atoms: 0.65 Number of scatterers: 5511 At special positions: 0 Unit cell: (104.16, 97.96, 71.92, 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 15 16.00 O 1116 8.00 N 885 7.00 C 3495 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: 1.93 Conformation dependent library (CDL) restraints added in 1.1 seconds 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1356 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 17 sheets defined 10.2% alpha, 38.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.78 Creating SS restraints... Processing helix chain 'C' and resid 31 through 35 Processing helix chain 'C' and resid 60 through 68 removed outlier: 3.514A pdb=" N SER C 67 " --> pdb=" O PHE C 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 178 through 187 Processing helix chain 'B' and resid 31 through 35 removed outlier: 3.652A pdb=" N LEU B 35 " --> pdb=" O LEU B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 60 through 68 removed outlier: 3.638A pdb=" N SER B 67 " --> pdb=" O PHE B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 187 Processing helix chain 'A' and resid 31 through 35 removed outlier: 3.617A pdb=" N LEU A 35 " --> pdb=" O LEU A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 68 Processing helix chain 'A' and resid 178 through 188 Processing sheet with id=AA1, first strand: chain 'C' and resid 2 through 7 removed outlier: 5.422A pdb=" N LYS C 2 " --> pdb=" O GLY C 119 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N GLY C 119 " --> pdb=" O LYS C 2 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA C 23 " --> pdb=" O ILE C 120 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 15 through 17 removed outlier: 3.557A pdb=" N SER C 101 " --> pdb=" O GLU C 45 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N ILE C 40 " --> pdb=" O ASN C 56 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N ASN C 56 " --> pdb=" O ILE C 40 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ILE C 42 " --> pdb=" O LEU C 54 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 128 through 136 removed outlier: 5.664A pdb=" N ASN C 230 " --> pdb=" O THR C 157 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LEU C 153 " --> pdb=" O ARG C 234 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 143 through 147 removed outlier: 6.570A pdb=" N GLN C 168 " --> pdb=" O VAL C 217 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ILE C 219 " --> pdb=" O SER C 166 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N SER C 166 " --> pdb=" O ILE C 219 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N ILE C 221 " --> pdb=" O ASP C 164 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ASP C 164 " --> pdb=" O ILE C 221 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N LYS C 223 " --> pdb=" O VAL C 162 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N VAL C 162 " --> pdb=" O LYS C 223 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 194 through 195 Processing sheet with id=AA6, first strand: chain 'B' and resid 2 through 7 removed outlier: 6.711A pdb=" N LEU B 117 " --> pdb=" O ILE B 3 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N THR B 5 " --> pdb=" O TYR B 115 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N TYR B 115 " --> pdb=" O THR B 5 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N ARG B 114 " --> pdb=" O SER B 28 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N SER B 28 " --> pdb=" O ARG B 114 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N ASP B 116 " --> pdb=" O LEU B 26 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N LEU B 26 " --> pdb=" O ASP B 116 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N HIS B 118 " --> pdb=" O LEU B 24 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N LEU B 24 " --> pdb=" O HIS B 118 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ILE B 120 " --> pdb=" O GLY B 22 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 15 through 17 removed outlier: 7.237A pdb=" N ILE B 40 " --> pdb=" O ASN B 56 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N ASN B 56 " --> pdb=" O ILE B 40 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ILE B 42 " --> pdb=" O LEU B 54 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 93 through 94 removed outlier: 5.260A pdb=" N SER B 93 " --> pdb=" O THR B 126 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 128 through 137 removed outlier: 5.983A pdb=" N ASN B 230 " --> pdb=" O THR B 157 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N THR B 157 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N LEU B 153 " --> pdb=" O ARG B 234 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 143 through 146 removed outlier: 6.457A pdb=" N GLN B 168 " --> pdb=" O VAL B 217 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N ILE B 219 " --> pdb=" O SER B 166 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N SER B 166 " --> pdb=" O ILE B 219 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N ILE B 221 " --> pdb=" O ASP B 164 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ASP B 164 " --> pdb=" O ILE B 221 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N LYS B 223 " --> pdb=" O VAL B 162 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N VAL B 162 " --> pdb=" O LYS B 223 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 194 through 195 Processing sheet with id=AB3, first strand: chain 'A' and resid 2 through 6 removed outlier: 5.584A pdb=" N LYS A 2 " --> pdb=" O GLY A 119 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N GLY A 119 " --> pdb=" O LYS A 2 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA A 4 " --> pdb=" O LEU A 117 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N SER A 27 " --> pdb=" O ASP A 116 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 15 through 17 removed outlier: 7.006A pdb=" N ILE A 40 " --> pdb=" O ASN A 56 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N ASN A 56 " --> pdb=" O ILE A 40 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ILE A 42 " --> pdb=" O LEU A 54 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 93 through 94 removed outlier: 5.757A pdb=" N SER A 93 " --> pdb=" O THR A 126 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 128 through 137 removed outlier: 5.535A pdb=" N ASN A 230 " --> pdb=" O THR A 157 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N LEU A 153 " --> pdb=" O ARG A 234 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 143 through 147 removed outlier: 6.525A pdb=" N GLN A 168 " --> pdb=" O VAL A 217 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ILE A 219 " --> pdb=" O SER A 166 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N SER A 166 " --> pdb=" O ILE A 219 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N ILE A 221 " --> pdb=" O ASP A 164 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ASP A 164 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N LYS A 223 " --> pdb=" O VAL A 162 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N VAL A 162 " --> pdb=" O LYS A 223 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 194 through 195 201 hydrogen bonds defined for protein. 531 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.66 Time building geometry restraints manager: 2.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1818 1.34 - 1.46: 1045 1.46 - 1.58: 2684 1.58 - 1.69: 0 1.69 - 1.81: 24 Bond restraints: 5571 Sorted by residual: bond pdb=" CB ASN C 143 " pdb=" CG ASN C 143 " ideal model delta sigma weight residual 1.516 1.537 -0.021 2.50e-02 1.60e+03 7.18e-01 bond pdb=" CA ASN C 143 " pdb=" CB ASN C 143 " ideal model delta sigma weight residual 1.536 1.553 -0.017 2.08e-02 2.31e+03 6.77e-01 bond pdb=" CB ASP C 29 " pdb=" CG ASP C 29 " ideal model delta sigma weight residual 1.516 1.535 -0.019 2.50e-02 1.60e+03 5.77e-01 bond pdb=" CA ASN B 143 " pdb=" CB ASN B 143 " ideal model delta sigma weight residual 1.534 1.546 -0.012 1.76e-02 3.23e+03 4.52e-01 bond pdb=" CB ASN B 143 " pdb=" CG ASN B 143 " ideal model delta sigma weight residual 1.516 1.532 -0.016 2.50e-02 1.60e+03 4.19e-01 ... (remaining 5566 not shown) Histogram of bond angle deviations from ideal: 100.74 - 106.84: 70 106.84 - 112.94: 3152 112.94 - 119.04: 1509 119.04 - 125.14: 2796 125.14 - 131.24: 21 Bond angle restraints: 7548 Sorted by residual: angle pdb=" N LYS C 223 " pdb=" CA LYS C 223 " pdb=" C LYS C 223 " ideal model delta sigma weight residual 108.34 111.92 -3.58 1.31e+00 5.83e-01 7.46e+00 angle pdb=" C ALA C 138 " pdb=" N SER C 139 " pdb=" CA SER C 139 " ideal model delta sigma weight residual 121.54 125.84 -4.30 1.91e+00 2.74e-01 5.07e+00 angle pdb=" CA ASN C 143 " pdb=" CB ASN C 143 " pdb=" CG ASN C 143 " ideal model delta sigma weight residual 112.60 114.26 -1.66 1.00e+00 1.00e+00 2.75e+00 angle pdb=" C ILE C 3 " pdb=" N ALA C 4 " pdb=" CA ALA C 4 " ideal model delta sigma weight residual 121.62 118.94 2.68 1.83e+00 2.99e-01 2.14e+00 angle pdb=" CA TYR B 167 " pdb=" CB TYR B 167 " pdb=" CG TYR B 167 " ideal model delta sigma weight residual 113.90 116.48 -2.58 1.80e+00 3.09e-01 2.05e+00 ... (remaining 7543 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.43: 3068 17.43 - 34.86: 270 34.86 - 52.29: 60 52.29 - 69.73: 13 69.73 - 87.16: 9 Dihedral angle restraints: 3420 sinusoidal: 1329 harmonic: 2091 Sorted by residual: dihedral pdb=" CB LYS A 57 " pdb=" CG LYS A 57 " pdb=" CD LYS A 57 " pdb=" CE LYS A 57 " ideal model delta sinusoidal sigma weight residual -180.00 -126.25 -53.75 3 1.50e+01 4.44e-03 9.23e+00 dihedral pdb=" CB LYS B 200 " pdb=" CG LYS B 200 " pdb=" CD LYS B 200 " pdb=" CE LYS B 200 " ideal model delta sinusoidal sigma weight residual 60.00 112.52 -52.52 3 1.50e+01 4.44e-03 9.12e+00 dihedral pdb=" CB GLU B 141 " pdb=" CG GLU B 141 " pdb=" CD GLU B 141 " pdb=" OE1 GLU B 141 " ideal model delta sinusoidal sigma weight residual 0.00 80.58 -80.58 1 3.00e+01 1.11e-03 8.92e+00 ... (remaining 3417 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 564 0.027 - 0.054: 188 0.054 - 0.081: 71 0.081 - 0.109: 72 0.109 - 0.136: 41 Chirality restraints: 936 Sorted by residual: chirality pdb=" CA ILE C 155 " pdb=" N ILE C 155 " pdb=" C ILE C 155 " pdb=" CB ILE C 155 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.60e-01 chirality pdb=" CA ILE C 42 " pdb=" N ILE C 42 " pdb=" C ILE C 42 " pdb=" CB ILE C 42 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.48e-01 chirality pdb=" CA ILE C 221 " pdb=" N ILE C 221 " pdb=" C ILE C 221 " pdb=" CB ILE C 221 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.48e-01 ... (remaining 933 not shown) Planarity restraints: 960 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 178 " 0.016 5.00e-02 4.00e+02 2.38e-02 9.03e-01 pdb=" N PRO B 179 " -0.041 5.00e-02 4.00e+02 pdb=" CA PRO B 179 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO B 179 " 0.013 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 178 " 0.015 5.00e-02 4.00e+02 2.24e-02 8.03e-01 pdb=" N PRO C 179 " -0.039 5.00e-02 4.00e+02 pdb=" CA PRO C 179 " 0.011 5.00e-02 4.00e+02 pdb=" CD PRO C 179 " 0.013 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 211 " -0.013 5.00e-02 4.00e+02 2.04e-02 6.67e-01 pdb=" N PRO A 212 " 0.035 5.00e-02 4.00e+02 pdb=" CA PRO A 212 " -0.011 5.00e-02 4.00e+02 pdb=" CD PRO A 212 " -0.011 5.00e-02 4.00e+02 ... (remaining 957 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 1470 2.81 - 3.33: 4379 3.33 - 3.86: 8347 3.86 - 4.38: 9858 4.38 - 4.90: 18283 Nonbonded interactions: 42337 Sorted by model distance: nonbonded pdb=" OG SER C 163 " pdb=" O ASN C 222 " model vdw 2.289 2.440 nonbonded pdb=" O ILE A 64 " pdb=" OG1 THR A 68 " model vdw 2.297 2.440 nonbonded pdb=" NE2 GLN B 183 " pdb=" OD2 ASP A 77 " model vdw 2.328 2.520 nonbonded pdb=" OD1 ASN B 128 " pdb=" OG1 THR B 238 " model vdw 2.335 2.440 nonbonded pdb=" OD1 ASP C 98 " pdb=" N LYS C 99 " model vdw 2.375 2.520 ... (remaining 42332 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' } 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: 0.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 2.040 Check model and map are aligned: 0.090 Set scattering table: 0.050 Process input model: 19.550 Find NCS groups from input model: 0.330 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:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 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 : 0.002 0.021 5571 Z= 0.118 Angle : 0.437 4.302 7548 Z= 0.240 Chirality : 0.046 0.136 936 Planarity : 0.002 0.024 960 Dihedral : 14.812 87.157 2064 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.02 (0.31), residues: 711 helix: 1.53 (0.67), residues: 63 sheet: 0.94 (0.31), residues: 282 loop : -1.06 (0.30), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS B 118 PHE 0.006 0.001 PHE A 231 TYR 0.010 0.001 TYR C 43 ARG 0.001 0.000 ARG C 114 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 117 time to evaluate : 0.665 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 117 average time/residue: 0.1674 time to fit residues: 25.7692 Evaluate side-chains 90 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 0.651 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 58 optimal weight: 8.9990 chunk 52 optimal weight: 6.9990 chunk 29 optimal weight: 5.9990 chunk 17 optimal weight: 7.9990 chunk 35 optimal weight: 10.0000 chunk 27 optimal weight: 10.0000 chunk 54 optimal weight: 6.9990 chunk 20 optimal weight: 10.0000 chunk 32 optimal weight: 7.9990 chunk 40 optimal weight: 6.9990 chunk 62 optimal weight: 9.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 80 ASN C 203 GLN B 149 GLN B 173 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.1663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.042 5571 Z= 0.575 Angle : 0.682 5.531 7548 Z= 0.361 Chirality : 0.054 0.157 936 Planarity : 0.004 0.029 960 Dihedral : 4.936 18.263 750 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 2.22 % Allowed : 9.52 % Favored : 88.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.30), residues: 711 helix: 0.77 (0.65), residues: 63 sheet: 0.52 (0.31), residues: 291 loop : -1.28 (0.29), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 118 PHE 0.012 0.002 PHE B 231 TYR 0.016 0.002 TYR C 43 ARG 0.003 0.001 ARG C 187 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 83 time to evaluate : 0.662 Fit side-chains outliers start: 14 outliers final: 10 residues processed: 91 average time/residue: 0.1824 time to fit residues: 21.6197 Evaluate side-chains 86 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 76 time to evaluate : 0.664 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0555 time to fit residues: 1.8940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 52.8167 > 50: distance: 14 - 108: 33.220 distance: 17 - 105: 8.728 distance: 25 - 92: 22.672 distance: 28 - 89: 11.469 distance: 46 - 55: 12.718 distance: 55 - 56: 15.284 distance: 56 - 57: 17.645 distance: 56 - 59: 42.780 distance: 57 - 58: 21.851 distance: 57 - 61: 13.955 distance: 59 - 60: 9.690 distance: 61 - 62: 7.032 distance: 62 - 63: 14.854 distance: 62 - 65: 16.787 distance: 63 - 64: 21.708 distance: 63 - 69: 17.497 distance: 65 - 66: 16.298 distance: 66 - 67: 13.986 distance: 66 - 68: 13.554 distance: 69 - 70: 5.176 distance: 70 - 71: 3.696 distance: 71 - 72: 13.041 distance: 71 - 73: 36.070 distance: 73 - 74: 13.361 distance: 74 - 75: 18.268 distance: 74 - 77: 7.175 distance: 75 - 76: 9.765 distance: 75 - 82: 5.801 distance: 77 - 78: 7.794 distance: 78 - 79: 10.030 distance: 79 - 80: 6.248 distance: 79 - 81: 7.308 distance: 82 - 83: 13.212 distance: 83 - 84: 10.911 distance: 83 - 86: 11.680 distance: 84 - 85: 6.200 distance: 84 - 89: 15.589 distance: 86 - 87: 9.317 distance: 86 - 88: 10.865 distance: 89 - 90: 11.932 distance: 90 - 91: 5.364 distance: 90 - 93: 10.062 distance: 91 - 92: 6.713 distance: 91 - 96: 28.408 distance: 93 - 94: 16.792 distance: 93 - 95: 5.760 distance: 96 - 97: 6.391 distance: 97 - 98: 8.432 distance: 97 - 100: 9.268 distance: 98 - 99: 7.434 distance: 98 - 105: 13.636 distance: 100 - 101: 15.293 distance: 101 - 102: 4.957 distance: 102 - 103: 3.035 distance: 105 - 106: 10.549 distance: 106 - 107: 9.028 distance: 106 - 109: 12.385 distance: 107 - 108: 28.069 distance: 107 - 117: 19.365 distance: 109 - 110: 6.084 distance: 110 - 111: 5.369 distance: 110 - 112: 3.621 distance: 111 - 113: 10.421 distance: 112 - 114: 13.734 distance: 113 - 115: 9.596 distance: 114 - 115: 10.773 distance: 115 - 116: 8.228 distance: 117 - 118: 24.465 distance: 118 - 119: 11.233 distance: 118 - 121: 16.740 distance: 119 - 120: 17.550 distance: 119 - 125: 8.283 distance: 120 - 147: 30.318 distance: 121 - 122: 17.864 distance: 122 - 123: 11.803 distance: 122 - 124: 6.499 distance: 125 - 126: 10.138 distance: 125 - 131: 12.465 distance: 126 - 127: 8.700 distance: 126 - 129: 14.866 distance: 127 - 132: 7.055 distance: 128 - 155: 8.474 distance: 129 - 130: 5.197 distance: 130 - 131: 16.127