Starting phenix.real_space_refine on Fri Aug 2 22:57:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xbx_38232/08_2024/8xbx_38232.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xbx_38232/08_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_38232/08_2024/8xbx_38232.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xbx_38232/08_2024/8xbx_38232.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xbx_38232/08_2024/8xbx_38232.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xbx_38232/08_2024/8xbx_38232.cif" } 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-5409/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: 4.09, per 1000 atoms: 0.70 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: 2.81 Conformation dependent library (CDL) restraints added in 931.6 milliseconds 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: 2.23 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: 1.92 Time building geometry restraints manager: 2.75 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 3.120 nonbonded pdb=" N THR K 103 " pdb=" O GLY K 151 " model vdw 2.260 3.120 nonbonded pdb=" N THR M 103 " pdb=" O GLY M 151 " model vdw 2.261 3.120 nonbonded pdb=" O ARG K 130 " pdb=" NH2 ARG K 310 " model vdw 2.354 3.120 nonbonded pdb=" O ARG M 130 " pdb=" NH2 ARG M 310 " model vdw 2.354 3.120 ... (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 Time spend for trying shortcut: 0.00 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: 0.920 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: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 22.710 Find NCS groups from input model: 0.170 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:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.800 ------------------------------------------------------------------------------- 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 : 0.573 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: 0.2060 time to fit residues: 9.2579 Evaluate side-chains 22 residues out of total 531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 0.633 ------------------------------------------------------------------------------- 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: 5.9990 chunk 51 optimal weight: 20.0000 chunk 28 optimal weight: 5.9990 chunk 17 optimal weight: 8.9990 chunk 34 optimal weight: 0.0370 chunk 27 optimal weight: 10.0000 chunk 53 optimal weight: 6.9990 chunk 20 optimal weight: 1.9990 chunk 32 optimal weight: 0.1980 chunk 39 optimal weight: 6.9990 chunk 61 optimal weight: 7.9990 overall best weight: 2.8464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6075 moved from start: 0.2639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6032 Z= 0.199 Angle : 0.562 5.854 8298 Z= 0.310 Chirality : 0.041 0.167 950 Planarity : 0.004 0.030 944 Dihedral : 22.089 69.187 1144 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 12.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % 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: 0.36 (0.32), residues: 651 helix: 0.67 (0.31), residues: 282 sheet: 0.84 (0.36), residues: 162 loop : -0.72 (0.42), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS L 244 PHE 0.011 0.001 PHE M 126 TYR 0.014 0.002 TYR K 178 ARG 0.005 0.001 ARG M 170 *********************** 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 24 residues out of total 531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 24 time to evaluate : 0.633 Fit side-chains REVERT: K 158 MET cc_start: 0.8999 (mmp) cc_final: 0.8789 (mpp) REVERT: K 210 MET cc_start: 0.5835 (ptm) cc_final: 0.5483 (ptm) REVERT: L 326 MET cc_start: 0.4540 (tpp) cc_final: 0.4242 (mmm) REVERT: M 210 MET cc_start: 0.2085 (ppp) cc_final: 0.1852 (ppp) outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.1929 time to fit residues: 6.7426 Evaluate side-chains 21 residues out of total 531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 21 time to evaluate : 0.616 ------------------------------------------------------------------------------- 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: 20.0000 chunk 19 optimal weight: 9.9990 chunk 51 optimal weight: 50.0000 chunk 42 optimal weight: 9.9990 chunk 17 optimal weight: 5.9990 chunk 61 optimal weight: 7.9990 chunk 66 optimal weight: 30.0000 chunk 55 optimal weight: 30.0000 chunk 21 optimal weight: 6.9990 chunk 49 optimal weight: 6.9990 chunk 46 optimal weight: 8.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- 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 ** M 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6393 moved from start: 0.5820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.097 6032 Z= 0.430 Angle : 0.862 10.342 8298 Z= 0.472 Chirality : 0.052 0.229 950 Planarity : 0.005 0.052 944 Dihedral : 23.891 80.251 1144 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 31.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 0.19 % Allowed : 1.13 % 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: -0.53 (0.30), residues: 651 helix: -0.48 (0.28), residues: 282 sheet: 0.84 (0.36), residues: 156 loop : -0.86 (0.39), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.002 HIS K 244 PHE 0.015 0.002 PHE M 126 TYR 0.017 0.002 TYR K 178 ARG 0.009 0.001 ARG M 170 *********************** 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: 1 poor density : 25 time to evaluate : 0.625 Fit side-chains revert: symmetry clash REVERT: K 210 MET cc_start: 0.5673 (ptm) cc_final: 0.5364 (ptm) REVERT: K 251 MET cc_start: 0.4450 (mtm) cc_final: 0.3858 (mmt) REVERT: L 149 ASP cc_start: 0.8605 (t70) cc_final: 0.8402 (p0) REVERT: L 210 MET cc_start: 0.1708 (ppp) cc_final: 0.1313 (ppp) REVERT: M 210 MET cc_start: 0.2625 (ppp) cc_final: 0.2333 (ppp) outliers start: 1 outliers final: 1 residues processed: 26 average time/residue: 0.1687 time to fit residues: 6.6366 Evaluate side-chains 23 residues out of total 531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 22 time to evaluate : 0.611 ------------------------------------------------------------------------------- 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: 8.9990 chunk 6 optimal weight: 50.0000 chunk 29 optimal weight: 3.9990 chunk 41 optimal weight: 40.0000 chunk 62 optimal weight: 40.0000 chunk 65 optimal weight: 8.9990 chunk 58 optimal weight: 8.9990 chunk 17 optimal weight: 5.9990 chunk 54 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 0 optimal weight: 0.5980 overall best weight: 3.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6225 moved from start: 0.5949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 6032 Z= 0.218 Angle : 0.575 7.161 8298 Z= 0.317 Chirality : 0.041 0.146 950 Planarity : 0.003 0.030 944 Dihedral : 23.497 84.081 1144 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 16.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % 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: -0.21 (0.31), residues: 651 helix: -0.09 (0.29), residues: 282 sheet: 0.97 (0.39), residues: 150 loop : -0.82 (0.38), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS K 244 PHE 0.010 0.001 PHE M 327 TYR 0.009 0.001 TYR K 232 ARG 0.004 0.000 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 25 residues out of total 531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 25 time to evaluate : 0.608 Fit side-chains REVERT: K 210 MET cc_start: 0.5838 (ptm) cc_final: 0.5600 (ptm) REVERT: K 251 MET cc_start: 0.4486 (mtm) cc_final: 0.3920 (mmt) REVERT: L 149 ASP cc_start: 0.8592 (t70) cc_final: 0.8387 (p0) REVERT: L 210 MET cc_start: 0.1415 (ppp) cc_final: 0.0851 (ppp) REVERT: M 210 MET cc_start: 0.2494 (ppp) cc_final: 0.2281 (ppp) outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.1812 time to fit residues: 6.7989 Evaluate side-chains 23 residues out of total 531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 23 time to evaluate : 0.662 ------------------------------------------------------------------------------- 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: 7.9990 chunk 56 optimal weight: 6.9990 chunk 45 optimal weight: 30.0000 chunk 0 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 58 optimal weight: 6.9990 chunk 16 optimal weight: 10.0000 chunk 22 optimal weight: 20.0000 chunk 59 optimal weight: 6.9990 chunk 12 optimal weight: 3.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 206 GLN M 101 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6365 moved from start: 0.7304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 6032 Z= 0.316 Angle : 0.675 9.244 8298 Z= 0.368 Chirality : 0.045 0.148 950 Planarity : 0.004 0.032 944 Dihedral : 23.564 84.326 1144 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 27.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % 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: -0.39 (0.31), residues: 651 helix: -0.24 (0.29), residues: 282 sheet: 0.77 (0.40), residues: 150 loop : -0.81 (0.38), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.001 HIS K 244 PHE 0.012 0.002 PHE M 248 TYR 0.016 0.002 TYR K 159 ARG 0.007 0.001 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 25 residues out of total 531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 25 time to evaluate : 0.619 Fit side-chains REVERT: K 210 MET cc_start: 0.5877 (ptm) cc_final: 0.5675 (ptm) REVERT: K 251 MET cc_start: 0.4725 (mtm) cc_final: 0.4052 (mmt) REVERT: L 149 ASP cc_start: 0.8645 (t70) cc_final: 0.8428 (p0) REVERT: L 210 MET cc_start: 0.4384 (ppp) cc_final: 0.3985 (ppp) outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.1430 time to fit residues: 5.6956 Evaluate side-chains 24 residues out of total 531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 24 time to evaluate : 0.654 ------------------------------------------------------------------------------- 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: 20.0000 chunk 16 optimal weight: 6.9990 chunk 65 optimal weight: 10.0000 chunk 54 optimal weight: 0.9990 chunk 30 optimal weight: 6.9990 chunk 5 optimal weight: 30.0000 chunk 21 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 63 optimal weight: 9.9990 chunk 7 optimal weight: 20.0000 chunk 37 optimal weight: 5.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 206 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6255 moved from start: 0.7456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 6032 Z= 0.216 Angle : 0.588 7.918 8298 Z= 0.319 Chirality : 0.041 0.141 950 Planarity : 0.003 0.054 944 Dihedral : 23.628 87.474 1144 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 18.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % 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: -0.23 (0.31), residues: 651 helix: -0.01 (0.30), residues: 282 sheet: 0.88 (0.43), residues: 141 loop : -0.84 (0.37), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS K 244 PHE 0.017 0.001 PHE L 248 TYR 0.008 0.001 TYR K 216 ARG 0.005 0.000 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 25 residues out of total 531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 25 time to evaluate : 0.581 Fit side-chains REVERT: K 210 MET cc_start: 0.5840 (ptm) cc_final: 0.5555 (ptm) REVERT: K 251 MET cc_start: 0.4473 (mtm) cc_final: 0.3669 (mmt) REVERT: L 149 ASP cc_start: 0.8685 (t70) cc_final: 0.8472 (p0) REVERT: L 210 MET cc_start: 0.3553 (ppp) cc_final: 0.3286 (ppp) REVERT: L 211 MET cc_start: 0.5295 (mtt) cc_final: 0.4958 (mtt) outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.1419 time to fit residues: 5.6513 Evaluate side-chains 24 residues out of total 531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 24 time to evaluate : 0.652 ------------------------------------------------------------------------------- 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: 8.9990 chunk 37 optimal weight: 1.9990 chunk 55 optimal weight: 20.0000 chunk 36 optimal weight: 0.3980 chunk 65 optimal weight: 1.9990 chunk 41 optimal weight: 30.0000 chunk 39 optimal weight: 7.9990 chunk 30 optimal weight: 7.9990 chunk 40 optimal weight: 5.9990 chunk 26 optimal weight: 6.9990 chunk 19 optimal weight: 5.9990 overall best weight: 3.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6292 moved from start: 0.8008 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= 0.214 Angle : 0.575 7.768 8298 Z= 0.315 Chirality : 0.041 0.141 950 Planarity : 0.003 0.054 944 Dihedral : 23.623 88.994 1144 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 18.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % 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: -0.09 (0.32), residues: 651 helix: 0.09 (0.30), residues: 282 sheet: 0.81 (0.42), residues: 150 loop : -0.69 (0.38), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS M 244 PHE 0.012 0.001 PHE L 248 TYR 0.023 0.001 TYR K 159 ARG 0.005 0.000 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 27 residues out of total 531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 27 time to evaluate : 0.572 Fit side-chains revert: symmetry clash REVERT: K 251 MET cc_start: 0.4340 (mtm) cc_final: 0.3576 (mmt) REVERT: L 149 ASP cc_start: 0.8599 (t70) cc_final: 0.8381 (p0) outliers start: 0 outliers final: 0 residues processed: 27 average time/residue: 0.1873 time to fit residues: 7.3492 Evaluate side-chains 25 residues out of total 531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 25 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 12 optimal weight: 10.0000 chunk 41 optimal weight: 6.9990 chunk 44 optimal weight: 0.3980 chunk 32 optimal weight: 0.7980 chunk 6 optimal weight: 30.0000 chunk 51 optimal weight: 50.0000 chunk 59 optimal weight: 7.9990 chunk 62 optimal weight: 50.0000 chunk 57 optimal weight: 10.0000 chunk 61 optimal weight: 9.9990 chunk 36 optimal weight: 20.0000 overall best weight: 5.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6370 moved from start: 0.9244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.084 6032 Z= 0.316 Angle : 0.695 9.806 8298 Z= 0.373 Chirality : 0.044 0.147 950 Planarity : 0.005 0.058 944 Dihedral : 24.069 88.904 1144 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 28.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % 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: -0.67 (0.31), residues: 651 helix: -0.36 (0.29), residues: 282 sheet: 0.74 (0.47), residues: 129 loop : -1.05 (0.35), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS K 244 PHE 0.011 0.002 PHE L 327 TYR 0.018 0.002 TYR L 232 ARG 0.008 0.001 ARG M 170 *********************** REFINEMENT MACRO_CYCLE 8 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 : 0.836 Fit side-chains revert: symmetry clash REVERT: K 251 MET cc_start: 0.4325 (mtm) cc_final: 0.3645 (mmt) REVERT: L 149 ASP cc_start: 0.8628 (t70) cc_final: 0.8383 (p0) outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.2042 time to fit residues: 7.3367 Evaluate side-chains 23 residues out of total 531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 23 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 26 optimal weight: 20.0000 chunk 47 optimal weight: 5.9990 chunk 18 optimal weight: 6.9990 chunk 55 optimal weight: 6.9990 chunk 57 optimal weight: 7.9990 chunk 60 optimal weight: 20.0000 chunk 40 optimal weight: 9.9990 chunk 64 optimal weight: 10.0000 chunk 39 optimal weight: 5.9990 chunk 30 optimal weight: 0.6980 chunk 44 optimal weight: 7.9990 overall best weight: 5.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6335 moved from start: 1.0125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 6032 Z= 0.292 Angle : 0.679 9.412 8298 Z= 0.366 Chirality : 0.044 0.150 950 Planarity : 0.004 0.054 944 Dihedral : 24.039 88.621 1144 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 25.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % 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: -0.84 (0.31), residues: 651 helix: -0.52 (0.30), residues: 282 sheet: 0.58 (0.48), residues: 123 loop : -1.03 (0.36), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS K 244 PHE 0.013 0.002 PHE L 248 TYR 0.017 0.002 TYR K 159 ARG 0.008 0.001 ARG M 170 *********************** REFINEMENT MACRO_CYCLE 9 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 : 0.625 Fit side-chains revert: symmetry clash REVERT: K 251 MET cc_start: 0.4059 (mtm) cc_final: 0.3059 (mmt) REVERT: L 149 ASP cc_start: 0.8528 (t70) cc_final: 0.8320 (p0) REVERT: L 243 MET cc_start: 0.6665 (tpt) cc_final: 0.6423 (mmt) outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.1877 time to fit residues: 6.6595 Evaluate side-chains 23 residues out of total 531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 23 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 67 optimal weight: 6.9990 chunk 62 optimal weight: 9.9990 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 5.9990 chunk 41 optimal weight: 9.9990 chunk 33 optimal weight: 9.9990 chunk 42 optimal weight: 10.0000 chunk 57 optimal weight: 2.9990 chunk 16 optimal weight: 7.9990 chunk 49 optimal weight: 6.9990 chunk 7 optimal weight: 40.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6395 moved from start: 1.1126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.089 6032 Z= 0.341 Angle : 0.733 10.549 8298 Z= 0.393 Chirality : 0.047 0.206 950 Planarity : 0.005 0.053 944 Dihedral : 24.224 88.966 1144 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 32.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -1.25 (0.32), residues: 651 helix: -0.88 (0.29), residues: 285 sheet: 0.14 (0.48), residues: 129 loop : -1.10 (0.38), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS L 199 PHE 0.012 0.002 PHE M 259 TYR 0.029 0.002 TYR L 159 ARG 0.011 0.001 ARG M 170 ********************** REFINEMENT MACRO_CYCLE 10 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 : 0.577 Fit side-chains REVERT: K 251 MET cc_start: 0.4141 (mtm) cc_final: 0.3171 (mmt) REVERT: L 149 ASP cc_start: 0.8495 (t70) cc_final: 0.8270 (p0) REVERT: L 210 MET cc_start: 0.2890 (ppp) cc_final: 0.2644 (ppp) REVERT: L 211 MET cc_start: 0.5630 (mtt) cc_final: 0.5117 (mtt) REVERT: L 243 MET cc_start: 0.6755 (tpt) cc_final: 0.6536 (mmt) outliers start: 0 outliers final: 0 residues processed: 23 average time/residue: 0.1468 time to fit residues: 5.3380 Evaluate side-chains 22 residues out of total 531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 14 optimal weight: 40.0000 chunk 54 optimal weight: 5.9990 chunk 22 optimal weight: 10.0000 chunk 55 optimal weight: 6.9990 chunk 6 optimal weight: 7.9990 chunk 9 optimal weight: 6.9990 chunk 47 optimal weight: 8.9990 chunk 3 optimal weight: 20.0000 chunk 39 optimal weight: 40.0000 chunk 61 optimal weight: 6.9990 chunk 36 optimal weight: 6.9990 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 138 HIS ** L 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 290 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.055292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.052255 restraints weight = 85121.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 91)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.048720 restraints weight = 113086.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.048720 restraints weight = 187897.958| |-----------------------------------------------------------------------------| r_work (final): 0.3674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5786 moved from start: 1.2689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.093 6032 Z= 0.383 Angle : 0.804 10.486 8298 Z= 0.427 Chirality : 0.048 0.156 950 Planarity : 0.005 0.052 944 Dihedral : 24.566 88.218 1144 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 35.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -1.74 (0.31), residues: 651 helix: -1.14 (0.29), residues: 278 sheet: -0.48 (0.47), residues: 128 loop : -1.31 (0.38), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS M 244 PHE 0.014 0.002 PHE M 126 TYR 0.018 0.002 TYR L 159 ARG 0.012 0.001 ARG M 170 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1178.35 seconds wall clock time: 22 minutes 0.24 seconds (1320.24 seconds total)