Starting phenix.real_space_refine on Mon Jun 24 23:46:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xbx_38232/06_2024/8xbx_38232.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xbx_38232/06_2024/8xbx_38232.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xbx_38232/06_2024/8xbx_38232.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xbx_38232/06_2024/8xbx_38232.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xbx_38232/06_2024/8xbx_38232.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xbx_38232/06_2024/8xbx_38232.pdb" } resolution = 4.36 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= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 38 5.49 5 S 33 5.16 5 C 3543 2.51 5 N 1047 2.21 5 O 1212 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "K ARG 130": "NH1" <-> "NH2" Residue "K ARG 150": "NH1" <-> "NH2" Residue "K ARG 167": "NH1" <-> "NH2" Residue "K ARG 170": "NH1" <-> "NH2" Residue "K ARG 177": "NH1" <-> "NH2" Residue "K ARG 193": "NH1" <-> "NH2" Residue "K ARG 215": "NH1" <-> "NH2" Residue "K ARG 229": "NH1" <-> "NH2" Residue "K ARG 235": "NH1" <-> "NH2" Residue "K ARG 241": "NH1" <-> "NH2" Residue "K ARG 247": "NH1" <-> "NH2" Residue "K ARG 250": "NH1" <-> "NH2" Residue "K ARG 254": "NH1" <-> "NH2" Residue "K ARG 299": "NH1" <-> "NH2" Residue "K ARG 303": "NH1" <-> "NH2" Residue "K ARG 306": "NH1" <-> "NH2" Residue "K ARG 310": "NH1" <-> "NH2" Residue "L ARG 130": "NH1" <-> "NH2" Residue "L ARG 150": "NH1" <-> "NH2" Residue "L ARG 167": "NH1" <-> "NH2" Residue "L ARG 170": "NH1" <-> "NH2" Residue "L ARG 177": "NH1" <-> "NH2" Residue "L ARG 193": "NH1" <-> "NH2" Residue "L ARG 215": "NH1" <-> "NH2" Residue "L ARG 229": "NH1" <-> "NH2" Residue "L ARG 235": "NH1" <-> "NH2" Residue "L ARG 241": "NH1" <-> "NH2" Residue "L ARG 247": "NH1" <-> "NH2" Residue "L ARG 250": "NH1" <-> "NH2" Residue "L ARG 254": "NH1" <-> "NH2" Residue "L ARG 299": "NH1" <-> "NH2" Residue "L ARG 303": "NH1" <-> "NH2" Residue "L ARG 306": "NH1" <-> "NH2" Residue "L ARG 310": "NH1" <-> "NH2" Residue "M ARG 130": "NH1" <-> "NH2" Residue "M ARG 150": "NH1" <-> "NH2" Residue "M ARG 167": "NH1" <-> "NH2" Residue "M ARG 170": "NH1" <-> "NH2" Residue "M ARG 177": "NH1" <-> "NH2" Residue "M ARG 193": "NH1" <-> "NH2" Residue "M ARG 215": "NH1" <-> "NH2" Residue "M ARG 229": "NH1" <-> "NH2" Residue "M ARG 235": "NH1" <-> "NH2" Residue "M ARG 241": "NH1" <-> "NH2" Residue "M ARG 247": "NH1" <-> "NH2" Residue "M ARG 250": "NH1" <-> "NH2" Residue "M ARG 254": "NH1" <-> "NH2" Residue "M ARG 299": "NH1" <-> "NH2" Residue "M ARG 303": "NH1" <-> "NH2" Residue "M ARG 306": "NH1" <-> "NH2" Residue "M ARG 310": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/chem_data/mon_lib" Total number of atoms: 5873 Number of models: 1 Model: "" Number of chains: 5 Chain: "I" Number of atoms: 389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 389 Classifications: {'DNA': 19} Link IDs: {'rna3p': 18} Chain: "J" Number of atoms: 390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 390 Classifications: {'DNA': 19} Link IDs: {'rna3p': 18} Chain: "K" Number of atoms: 1698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1698 Classifications: {'peptide': 221} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 216} Chain breaks: 1 Chain: "L" Number of atoms: 1698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1698 Classifications: {'peptide': 221} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 216} Chain breaks: 1 Chain: "M" Number of atoms: 1698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1698 Classifications: {'peptide': 221} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 216} Chain breaks: 1 Time building chain proxies: 4.50, per 1000 atoms: 0.77 Number of scatterers: 5873 At special positions: 0 Unit cell: (109.18, 109.18, 85.86, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 33 16.00 P 38 15.00 O 1212 8.00 N 1047 7.00 C 3543 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: 2.41 Conformation dependent library (CDL) restraints added in 1.1 seconds 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1200 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 3 sheets defined 47.1% alpha, 20.8% beta 19 base pairs and 36 stacking pairs defined. Time for finding SS restraints: 2.18 Creating SS restraints... Processing helix chain 'K' and resid 106 through 113 Processing helix chain 'K' and resid 132 through 144 removed outlier: 3.675A pdb=" N VAL K 142 " --> pdb=" O HIS K 138 " (cutoff:3.500A) Processing helix chain 'K' and resid 145 through 146 No H-bonds generated for 'chain 'K' and resid 145 through 146' Processing helix chain 'K' and resid 147 through 151 Processing helix chain 'K' and resid 167 through 178 Processing helix chain 'K' and resid 181 through 188 Processing helix chain 'K' and resid 196 through 214 removed outlier: 3.933A pdb=" N LEU K 204 " --> pdb=" O GLN K 200 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N TYR K 205 " --> pdb=" O THR K 201 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLN K 206 " --> pdb=" O GLN K 202 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA K 209 " --> pdb=" O TYR K 205 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N VAL K 212 " --> pdb=" O SER K 208 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N GLU K 213 " --> pdb=" O ALA K 209 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N SER K 214 " --> pdb=" O MET K 210 " (cutoff:3.500A) Processing helix chain 'K' and resid 225 through 231 removed outlier: 3.532A pdb=" N ARG K 229 " --> pdb=" O THR K 225 " (cutoff:3.500A) Processing helix chain 'K' and resid 237 through 260 Processing helix chain 'K' and resid 291 through 296 removed outlier: 3.879A pdb=" N ALA K 295 " --> pdb=" O ILE K 291 " (cutoff:3.500A) Processing helix chain 'L' and resid 106 through 113 Processing helix chain 'L' and resid 132 through 144 removed outlier: 3.675A pdb=" N VAL L 142 " --> pdb=" O HIS L 138 " (cutoff:3.500A) Processing helix chain 'L' and resid 145 through 146 No H-bonds generated for 'chain 'L' and resid 145 through 146' Processing helix chain 'L' and resid 147 through 151 Processing helix chain 'L' and resid 167 through 178 Processing helix chain 'L' and resid 181 through 188 Processing helix chain 'L' and resid 196 through 214 removed outlier: 3.933A pdb=" N LEU L 204 " --> pdb=" O GLN L 200 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N TYR L 205 " --> pdb=" O THR L 201 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLN L 206 " --> pdb=" O GLN L 202 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA L 209 " --> pdb=" O TYR L 205 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N VAL L 212 " --> pdb=" O SER L 208 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N GLU L 213 " --> pdb=" O ALA L 209 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N SER L 214 " --> pdb=" O MET L 210 " (cutoff:3.500A) Processing helix chain 'L' and resid 225 through 231 removed outlier: 3.532A pdb=" N ARG L 229 " --> pdb=" O THR L 225 " (cutoff:3.500A) Processing helix chain 'L' and resid 237 through 260 Processing helix chain 'L' and resid 291 through 296 removed outlier: 3.879A pdb=" N ALA L 295 " --> pdb=" O ILE L 291 " (cutoff:3.500A) Processing helix chain 'M' and resid 106 through 113 Processing helix chain 'M' and resid 132 through 144 removed outlier: 3.675A pdb=" N VAL M 142 " --> pdb=" O HIS M 138 " (cutoff:3.500A) Processing helix chain 'M' and resid 145 through 146 No H-bonds generated for 'chain 'M' and resid 145 through 146' Processing helix chain 'M' and resid 147 through 151 Processing helix chain 'M' and resid 167 through 178 Processing helix chain 'M' and resid 181 through 188 Processing helix chain 'M' and resid 196 through 214 removed outlier: 3.933A pdb=" N LEU M 204 " --> pdb=" O GLN M 200 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N TYR M 205 " --> pdb=" O THR M 201 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLN M 206 " --> pdb=" O GLN M 202 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA M 209 " --> pdb=" O TYR M 205 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N VAL M 212 " --> pdb=" O SER M 208 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N GLU M 213 " --> pdb=" O ALA M 209 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N SER M 214 " --> pdb=" O MET M 210 " (cutoff:3.500A) Processing helix chain 'M' and resid 225 through 231 removed outlier: 3.533A pdb=" N ARG M 229 " --> pdb=" O THR M 225 " (cutoff:3.500A) Processing helix chain 'M' and resid 237 through 260 Processing helix chain 'M' and resid 291 through 296 removed outlier: 3.879A pdb=" N ALA M 295 " --> pdb=" O ILE M 291 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'K' and resid 189 through 193 removed outlier: 5.370A pdb=" N LYS K 156 " --> pdb=" O TYR K 216 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU K 218 " --> pdb=" O LYS K 156 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N ALA K 217 " --> pdb=" O ALA K 262 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N VAL K 264 " --> pdb=" O ALA K 217 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N LEU K 219 " --> pdb=" O VAL K 264 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N THR K 266 " --> pdb=" O LEU K 219 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N VAL K 221 " --> pdb=" O THR K 266 " (cutoff:3.500A) removed outlier: 8.633A pdb=" N GLN K 268 " --> pdb=" O VAL K 221 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ILE K 265 " --> pdb=" O THR K 123 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N MET K 125 " --> pdb=" O ILE K 265 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ASN K 267 " --> pdb=" O MET K 125 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLY K 127 " --> pdb=" O ASN K 267 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N ILE K 122 " --> pdb=" O THR K 298 " (cutoff:3.500A) removed outlier: 8.606A pdb=" N LEU K 300 " --> pdb=" O ILE K 122 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N GLU K 124 " --> pdb=" O LEU K 300 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N LEU K 302 " --> pdb=" O GLU K 124 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N PHE K 126 " --> pdb=" O LEU K 302 " (cutoff:3.500A) removed outlier: 9.077A pdb=" N LYS K 304 " --> pdb=" O PHE K 126 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ARG K 299 " --> pdb=" O TYR K 315 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'L' and resid 189 through 193 removed outlier: 5.370A pdb=" N LYS L 156 " --> pdb=" O TYR L 216 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU L 218 " --> pdb=" O LYS L 156 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N ALA L 217 " --> pdb=" O ALA L 262 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N VAL L 264 " --> pdb=" O ALA L 217 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N LEU L 219 " --> pdb=" O VAL L 264 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N THR L 266 " --> pdb=" O LEU L 219 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N VAL L 221 " --> pdb=" O THR L 266 " (cutoff:3.500A) removed outlier: 8.633A pdb=" N GLN L 268 " --> pdb=" O VAL L 221 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ILE L 265 " --> pdb=" O THR L 123 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N MET L 125 " --> pdb=" O ILE L 265 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ASN L 267 " --> pdb=" O MET L 125 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLY L 127 " --> pdb=" O ASN L 267 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N ILE L 122 " --> pdb=" O THR L 298 " (cutoff:3.500A) removed outlier: 8.606A pdb=" N LEU L 300 " --> pdb=" O ILE L 122 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N GLU L 124 " --> pdb=" O LEU L 300 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N LEU L 302 " --> pdb=" O GLU L 124 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N PHE L 126 " --> pdb=" O LEU L 302 " (cutoff:3.500A) removed outlier: 9.077A pdb=" N LYS L 304 " --> pdb=" O PHE L 126 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N ARG L 299 " --> pdb=" O TYR L 315 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'M' and resid 189 through 193 removed outlier: 5.370A pdb=" N LYS M 156 " --> pdb=" O TYR M 216 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU M 218 " --> pdb=" O LYS M 156 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ALA M 217 " --> pdb=" O ALA M 262 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N VAL M 264 " --> pdb=" O ALA M 217 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N LEU M 219 " --> pdb=" O VAL M 264 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N THR M 266 " --> pdb=" O LEU M 219 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N VAL M 221 " --> pdb=" O THR M 266 " (cutoff:3.500A) removed outlier: 8.633A pdb=" N GLN M 268 " --> pdb=" O VAL M 221 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ILE M 265 " --> pdb=" O THR M 123 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N MET M 125 " --> pdb=" O ILE M 265 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ASN M 267 " --> pdb=" O MET M 125 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLY M 127 " --> pdb=" O ASN M 267 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N ILE M 122 " --> pdb=" O THR M 298 " (cutoff:3.500A) removed outlier: 8.606A pdb=" N LEU M 300 " --> pdb=" O ILE M 122 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N GLU M 124 " --> pdb=" O LEU M 300 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N LEU M 302 " --> pdb=" O GLU M 124 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N PHE M 126 " --> pdb=" O LEU M 302 " (cutoff:3.500A) removed outlier: 9.076A pdb=" N LYS M 304 " --> pdb=" O PHE M 126 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N ARG M 299 " --> pdb=" O TYR M 315 " (cutoff:3.500A) 231 hydrogen bonds defined for protein. 675 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 49 hydrogen bonds 98 hydrogen bond angles 0 basepair planarities 19 basepair parallelities 36 stacking parallelities Total time for adding SS restraints: 1.81 Time building geometry restraints manager: 2.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1849 1.34 - 1.46: 1254 1.46 - 1.57: 2801 1.57 - 1.69: 74 1.69 - 1.81: 54 Bond restraints: 6032 Sorted by residual: bond pdb=" C1' DC J 16 " pdb=" N1 DC J 16 " ideal model delta sigma weight residual 1.490 1.557 -0.067 3.00e-02 1.11e+03 5.05e+00 bond pdb=" C1' DC J 1 " pdb=" N1 DC J 1 " ideal model delta sigma weight residual 1.490 1.557 -0.067 3.00e-02 1.11e+03 4.91e+00 bond pdb=" C1' DC I 154 " pdb=" N1 DC I 154 " ideal model delta sigma weight residual 1.490 1.556 -0.066 3.00e-02 1.11e+03 4.83e+00 bond pdb=" C1' DC I 155 " pdb=" N1 DC I 155 " ideal model delta sigma weight residual 1.490 1.556 -0.066 3.00e-02 1.11e+03 4.83e+00 bond pdb=" C1' DC I 152 " pdb=" N1 DC I 152 " ideal model delta sigma weight residual 1.490 1.556 -0.066 3.00e-02 1.11e+03 4.82e+00 ... (remaining 6027 not shown) Histogram of bond angle deviations from ideal: 96.98 - 104.09: 157 104.09 - 111.19: 2589 111.19 - 118.30: 2028 118.30 - 125.41: 3389 125.41 - 132.52: 135 Bond angle restraints: 8298 Sorted by residual: angle pdb=" O3' DC J 10 " pdb=" P DG J 11 " pdb=" O5' DG J 11 " ideal model delta sigma weight residual 104.00 96.98 7.02 1.50e+00 4.44e-01 2.19e+01 angle pdb=" O3' DG J 2 " pdb=" P DT J 3 " pdb=" O5' DT J 3 " ideal model delta sigma weight residual 104.00 97.02 6.98 1.50e+00 4.44e-01 2.17e+01 angle pdb=" O3' DA I 153 " pdb=" P DC I 154 " pdb=" O5' DC I 154 " ideal model delta sigma weight residual 104.00 97.02 6.98 1.50e+00 4.44e-01 2.17e+01 angle pdb=" O3' DG J 4 " pdb=" P DG J 5 " pdb=" O5' DG J 5 " ideal model delta sigma weight residual 104.00 97.04 6.96 1.50e+00 4.44e-01 2.16e+01 angle pdb=" O3' DC I 151 " pdb=" P DC I 152 " pdb=" O5' DC I 152 " ideal model delta sigma weight residual 104.00 97.04 6.96 1.50e+00 4.44e-01 2.15e+01 ... (remaining 8293 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.90: 2999 15.90 - 31.80: 311 31.80 - 47.69: 122 47.69 - 63.59: 79 63.59 - 79.49: 6 Dihedral angle restraints: 3517 sinusoidal: 1633 harmonic: 1884 Sorted by residual: dihedral pdb=" CA VAL L 334 " pdb=" C VAL L 334 " pdb=" N GLY L 335 " pdb=" CA GLY L 335 " ideal model delta harmonic sigma weight residual -180.00 -152.12 -27.88 0 5.00e+00 4.00e-02 3.11e+01 dihedral pdb=" CA VAL M 334 " pdb=" C VAL M 334 " pdb=" N GLY M 335 " pdb=" CA GLY M 335 " ideal model delta harmonic sigma weight residual -180.00 -152.14 -27.86 0 5.00e+00 4.00e-02 3.10e+01 dihedral pdb=" CA VAL K 334 " pdb=" C VAL K 334 " pdb=" N GLY K 335 " pdb=" CA GLY K 335 " ideal model delta harmonic sigma weight residual -180.00 -152.16 -27.84 0 5.00e+00 4.00e-02 3.10e+01 ... (remaining 3514 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 546 0.030 - 0.060: 252 0.060 - 0.090: 91 0.090 - 0.120: 43 0.120 - 0.150: 18 Chirality restraints: 950 Sorted by residual: chirality pdb=" CA ILE M 311 " pdb=" N ILE M 311 " pdb=" C ILE M 311 " pdb=" CB ILE M 311 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.61e-01 chirality pdb=" CA ILE K 311 " pdb=" N ILE K 311 " pdb=" C ILE K 311 " pdb=" CB ILE K 311 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.54e-01 chirality pdb=" CA ILE L 311 " pdb=" N ILE L 311 " pdb=" C ILE L 311 " pdb=" CB ILE L 311 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.48e-01 ... (remaining 947 not shown) Planarity restraints: 944 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE K 126 " 0.008 2.00e-02 2.50e+03 1.71e-02 2.94e+00 pdb=" C PHE K 126 " -0.030 2.00e-02 2.50e+03 pdb=" O PHE K 126 " 0.011 2.00e-02 2.50e+03 pdb=" N GLY K 127 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE L 126 " -0.008 2.00e-02 2.50e+03 1.71e-02 2.92e+00 pdb=" C PHE L 126 " 0.030 2.00e-02 2.50e+03 pdb=" O PHE L 126 " -0.011 2.00e-02 2.50e+03 pdb=" N GLY L 127 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE M 126 " 0.008 2.00e-02 2.50e+03 1.71e-02 2.92e+00 pdb=" C PHE M 126 " -0.030 2.00e-02 2.50e+03 pdb=" O PHE M 126 " 0.011 2.00e-02 2.50e+03 pdb=" N GLY M 127 " 0.010 2.00e-02 2.50e+03 ... (remaining 941 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 1277 2.79 - 3.32: 5585 3.32 - 3.84: 10197 3.84 - 4.37: 12539 4.37 - 4.90: 19772 Nonbonded interactions: 49370 Sorted by model distance: nonbonded pdb=" N THR L 103 " pdb=" O GLY L 151 " model vdw 2.260 2.520 nonbonded pdb=" N THR K 103 " pdb=" O GLY K 151 " model vdw 2.260 2.520 nonbonded pdb=" N THR M 103 " pdb=" O GLY M 151 " model vdw 2.261 2.520 nonbonded pdb=" O ARG K 130 " pdb=" NH2 ARG K 310 " model vdw 2.354 2.520 nonbonded pdb=" O ARG M 130 " pdb=" NH2 ARG M 310 " model vdw 2.354 2.520 ... (remaining 49365 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 'K' selection = chain 'L' selection = chain 'M' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.080 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: 4.440 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 22.500 Find NCS groups from input model: 0.310 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:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5805 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 : 0.005 0.067 6032 Z= 0.267 Angle : 0.898 8.000 8298 Z= 0.538 Chirality : 0.044 0.150 950 Planarity : 0.006 0.059 944 Dihedral : 18.157 79.490 2317 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 13.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % 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: -0.16 (0.30), residues: 651 helix: 0.12 (0.30), residues: 264 sheet: 0.76 (0.36), residues: 159 loop : -0.86 (0.37), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS M 294 PHE 0.009 0.002 PHE L 248 TYR 0.010 0.002 TYR K 178 ARG 0.015 0.002 ARG M 299 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 33 time to evaluate : 0.566 Fit side-chains REVERT: L 210 MET cc_start: 0.2434 (tmm) cc_final: 0.1427 (ppp) outliers start: 0 outliers final: 0 residues processed: 33 average time/residue: 0.1950 time to fit residues: 8.8459 Evaluate side-chains 22 residues out of total 531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 57 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 chunk 28 optimal weight: 6.9990 chunk 17 optimal weight: 5.9990 chunk 34 optimal weight: 3.9990 chunk 27 optimal weight: 7.9990 chunk 53 optimal weight: 5.9990 chunk 20 optimal weight: 9.9990 chunk 32 optimal weight: 8.9990 chunk 39 optimal weight: 10.0000 chunk 61 optimal weight: 6.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 101 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6129 moved from start: 0.2954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 6032 Z= 0.258 Angle : 0.627 7.168 8298 Z= 0.346 Chirality : 0.043 0.167 950 Planarity : 0.004 0.025 944 Dihedral : 23.243 76.757 1144 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 17.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Rotamer: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % 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: 0.23 (0.31), residues: 651 helix: 0.61 (0.31), residues: 279 sheet: 0.86 (0.36), residues: 159 loop : -0.91 (0.40), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS K 244 PHE 0.012 0.002 PHE M 126 TYR 0.019 0.002 TYR K 178 ARG 0.006 0.000 ARG L 177 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 23 time to evaluate : 0.669 Fit side-chains REVERT: K 210 MET cc_start: 0.5636 (ptm) cc_final: 0.5302 (ptm) REVERT: L 210 MET cc_start: 0.1806 (tmm) cc_final: 0.1441 (ppp) REVERT: L 326 MET cc_start: 0.4520 (tpp) cc_final: 0.4242 (mmm) outliers start: 0 outliers final: 0 residues processed: 23 average time/residue: 0.1804 time to fit residues: 6.2683 Evaluate side-chains 21 residues out of total 531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 21 time to evaluate : 0.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 34 optimal weight: 7.9990 chunk 19 optimal weight: 0.0070 chunk 51 optimal weight: 20.0000 chunk 42 optimal weight: 0.7980 chunk 17 optimal weight: 6.9990 chunk 61 optimal weight: 8.9990 chunk 66 optimal weight: 6.9990 chunk 55 optimal weight: 3.9990 chunk 21 optimal weight: 20.0000 chunk 49 optimal weight: 50.0000 chunk 46 optimal weight: 6.9990 overall best weight: 3.7604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 114 GLN K 206 GLN K 268 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6246 moved from start: 0.4564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 6032 Z= 0.230 Angle : 0.574 6.716 8298 Z= 0.316 Chirality : 0.041 0.147 950 Planarity : 0.003 0.024 944 Dihedral : 23.355 81.310 1144 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 22.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Rotamer: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % 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: 0.38 (0.31), residues: 651 helix: 0.68 (0.30), residues: 279 sheet: 1.29 (0.37), residues: 153 loop : -1.00 (0.37), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS M 138 PHE 0.011 0.001 PHE M 248 TYR 0.012 0.002 TYR K 178 ARG 0.005 0.001 ARG L 177 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 26 time to evaluate : 0.703 Fit side-chains revert: symmetry clash REVERT: K 251 MET cc_start: 0.4227 (mtm) cc_final: 0.3618 (mmt) REVERT: L 149 ASP cc_start: 0.8670 (t70) cc_final: 0.8458 (p0) REVERT: L 210 MET cc_start: 0.1908 (tmm) cc_final: 0.1591 (ppp) REVERT: L 326 MET cc_start: 0.4357 (tpp) cc_final: 0.4104 (mmm) outliers start: 0 outliers final: 0 residues processed: 26 average time/residue: 0.1789 time to fit residues: 6.9925 Evaluate side-chains 23 residues out of total 531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 23 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 32 optimal weight: 30.0000 chunk 6 optimal weight: 50.0000 chunk 29 optimal weight: 7.9990 chunk 41 optimal weight: 9.9990 chunk 62 optimal weight: 50.0000 chunk 65 optimal weight: 30.0000 chunk 58 optimal weight: 7.9990 chunk 17 optimal weight: 9.9990 chunk 54 optimal weight: 5.9990 chunk 37 optimal weight: 10.0000 chunk 0 optimal weight: 1.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 268 GLN L 206 GLN M 242 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6355 moved from start: 0.7584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.099 6032 Z= 0.416 Angle : 0.830 12.530 8298 Z= 0.445 Chirality : 0.050 0.172 950 Planarity : 0.006 0.055 944 Dihedral : 24.050 87.992 1144 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 43.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % 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: -0.68 (0.30), residues: 651 helix: -0.41 (0.29), residues: 279 sheet: 0.71 (0.39), residues: 159 loop : -1.23 (0.38), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.002 HIS L 244 PHE 0.012 0.002 PHE M 126 TYR 0.015 0.002 TYR K 232 ARG 0.012 0.001 ARG M 170 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 26 time to evaluate : 0.635 Fit side-chains revert: symmetry clash REVERT: K 251 MET cc_start: 0.5006 (mtm) cc_final: 0.4681 (mmm) REVERT: L 210 MET cc_start: 0.1606 (tmm) cc_final: 0.0985 (ppp) REVERT: M 210 MET cc_start: 0.2397 (ppp) cc_final: 0.2172 (ppp) outliers start: 0 outliers final: 0 residues processed: 26 average time/residue: 0.1873 time to fit residues: 7.0799 Evaluate side-chains 24 residues out of total 531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 24 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 48 optimal weight: 40.0000 chunk 27 optimal weight: 6.9990 chunk 56 optimal weight: 6.9990 chunk 45 optimal weight: 6.9990 chunk 0 optimal weight: 0.6980 chunk 33 optimal weight: 8.9990 chunk 58 optimal weight: 30.0000 chunk 16 optimal weight: 5.9990 chunk 22 optimal weight: 20.0000 chunk 59 optimal weight: 2.9990 chunk 12 optimal weight: 0.0170 overall best weight: 3.3424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 242 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6221 moved from start: 0.7499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 6032 Z= 0.214 Angle : 0.603 8.458 8298 Z= 0.326 Chirality : 0.041 0.148 950 Planarity : 0.003 0.050 944 Dihedral : 23.897 89.400 1144 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 23.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % 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: -0.34 (0.31), residues: 651 helix: 0.03 (0.30), residues: 279 sheet: 0.69 (0.40), residues: 159 loop : -1.12 (0.37), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS M 138 PHE 0.009 0.001 PHE M 248 TYR 0.008 0.001 TYR L 228 ARG 0.008 0.000 ARG M 170 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 24 time to evaluate : 0.583 Fit side-chains REVERT: K 251 MET cc_start: 0.4501 (mtm) cc_final: 0.3709 (mmt) REVERT: L 210 MET cc_start: 0.1708 (tmm) cc_final: 0.1156 (ppp) REVERT: M 210 MET cc_start: 0.2329 (ppp) cc_final: 0.2077 (ppp) outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.1771 time to fit residues: 6.2164 Evaluate side-chains 22 residues out of total 531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 38 optimal weight: 5.9990 chunk 16 optimal weight: 8.9990 chunk 65 optimal weight: 10.0000 chunk 54 optimal weight: 20.0000 chunk 30 optimal weight: 30.0000 chunk 5 optimal weight: 6.9990 chunk 21 optimal weight: 6.9990 chunk 34 optimal weight: 3.9990 chunk 63 optimal weight: 30.0000 chunk 7 optimal weight: 50.0000 chunk 37 optimal weight: 10.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 206 GLN ** M 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6371 moved from start: 0.9118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.103 6032 Z= 0.389 Angle : 0.775 11.300 8298 Z= 0.417 Chirality : 0.048 0.167 950 Planarity : 0.005 0.052 944 Dihedral : 24.239 86.990 1144 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 41.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % 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: -1.10 (0.31), residues: 651 helix: -0.49 (0.29), residues: 282 sheet: 0.58 (0.47), residues: 126 loop : -1.62 (0.34), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS K 244 PHE 0.017 0.002 PHE L 248 TYR 0.027 0.002 TYR L 232 ARG 0.012 0.001 ARG M 170 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 24 time to evaluate : 0.608 Fit side-chains REVERT: K 251 MET cc_start: 0.4675 (mtm) cc_final: 0.3904 (mmt) REVERT: L 210 MET cc_start: 0.1717 (tmm) cc_final: 0.1131 (ppp) REVERT: M 210 MET cc_start: 0.2594 (ppp) cc_final: 0.2296 (ppp) outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.1467 time to fit residues: 5.7062 Evaluate side-chains 22 residues out of total 531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 48 optimal weight: 30.0000 chunk 37 optimal weight: 0.7980 chunk 55 optimal weight: 8.9990 chunk 36 optimal weight: 9.9990 chunk 65 optimal weight: 0.7980 chunk 41 optimal weight: 40.0000 chunk 39 optimal weight: 20.0000 chunk 30 optimal weight: 7.9990 chunk 40 optimal weight: 8.9990 chunk 26 optimal weight: 5.9990 chunk 19 optimal weight: 1.9990 overall best weight: 3.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6237 moved from start: 0.9110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 6032 Z= 0.231 Angle : 0.622 9.226 8298 Z= 0.337 Chirality : 0.042 0.153 950 Planarity : 0.004 0.051 944 Dihedral : 24.033 89.351 1144 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 27.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % 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: -0.70 (0.32), residues: 651 helix: -0.30 (0.30), residues: 282 sheet: 0.32 (0.42), residues: 159 loop : -1.08 (0.39), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS L 199 PHE 0.023 0.002 PHE L 248 TYR 0.011 0.001 TYR L 232 ARG 0.008 0.001 ARG M 170 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 23 time to evaluate : 0.663 Fit side-chains REVERT: K 251 MET cc_start: 0.4106 (mtm) cc_final: 0.3601 (mmt) REVERT: L 210 MET cc_start: 0.1869 (tmm) cc_final: 0.1296 (ppp) outliers start: 0 outliers final: 0 residues processed: 23 average time/residue: 0.1533 time to fit residues: 5.7128 Evaluate side-chains 22 residues out of total 531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1477, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1379, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1260, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 71.6612 > 50: distance: 61 - 173: 36.201 distance: 64 - 170: 34.720 distance: 75 - 160: 31.329 distance: 78 - 157: 34.093 distance: 102 - 106: 35.664 distance: 106 - 107: 38.995 distance: 106 - 112: 39.769 distance: 107 - 108: 39.159 distance: 108 - 113: 56.903 distance: 110 - 111: 56.355 distance: 113 - 114: 39.522 distance: 114 - 115: 44.384 distance: 114 - 117: 39.653 distance: 115 - 116: 43.707 distance: 115 - 119: 42.776 distance: 119 - 120: 57.847 distance: 120 - 121: 40.052 distance: 120 - 123: 35.346 distance: 121 - 122: 40.165 distance: 121 - 127: 55.490 distance: 123 - 124: 39.966 distance: 124 - 125: 41.341 distance: 124 - 126: 39.513 distance: 127 - 128: 29.587 distance: 127 - 133: 40.593 distance: 128 - 129: 58.784 distance: 128 - 131: 48.152 distance: 129 - 130: 40.229 distance: 129 - 134: 39.703 distance: 131 - 132: 56.577 distance: 132 - 133: 57.657 distance: 135 - 138: 39.610 distance: 136 - 137: 40.633 distance: 138 - 139: 39.980 distance: 139 - 140: 55.651 distance: 140 - 142: 39.691 distance: 144 - 145: 40.016 distance: 145 - 146: 23.874 distance: 145 - 148: 39.422 distance: 149 - 150: 68.226 distance: 149 - 152: 44.324 distance: 150 - 157: 38.701 distance: 152 - 153: 45.684 distance: 153 - 154: 57.802 distance: 154 - 155: 56.040 distance: 154 - 156: 4.422 distance: 157 - 158: 40.668 distance: 158 - 161: 57.226 distance: 159 - 160: 34.547 distance: 159 - 162: 69.234 distance: 162 - 163: 38.617 distance: 163 - 164: 41.010 distance: 163 - 166: 40.185 distance: 164 - 165: 69.481 distance: 164 - 170: 68.030 distance: 166 - 167: 38.810 distance: 167 - 168: 40.078 distance: 168 - 169: 40.079 distance: 170 - 171: 33.341 distance: 171 - 172: 31.178 distance: 171 - 174: 32.104 distance: 172 - 173: 55.873 distance: 172 - 181: 35.294 distance: 174 - 175: 39.847 distance: 175 - 176: 19.325 distance: 176 - 178: 18.857