Starting phenix.real_space_refine on Fri Dec 8 20:09:07 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jlq_36404/12_2023/8jlq_36404_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jlq_36404/12_2023/8jlq_36404.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jlq_36404/12_2023/8jlq_36404.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jlq_36404/12_2023/8jlq_36404.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jlq_36404/12_2023/8jlq_36404_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jlq_36404/12_2023/8jlq_36404_updated.pdb" } resolution = 2.84 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= -0.006 sd= 0.121 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 S 67 5.16 5 Cl 1 4.86 5 C 5767 2.51 5 N 1541 2.21 5 O 1657 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 389": "NH1" <-> "NH2" Residue "B PHE 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 9033 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1902 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 6, 'TRANS': 221} Chain breaks: 3 Chain: "B" Number of atoms: 2587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2587 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "R" Number of atoms: 2294 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2294 Classifications: {'peptide': 283} Link IDs: {'PTRANS': 11, 'TRANS': 271} Chain breaks: 1 Chain: "S" Number of atoms: 1784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1784 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 10, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Chain: "Y" Number of atoms: 445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 445 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 4, 'TRANS': 53} Chain: "R" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'G3C': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.16, per 1000 atoms: 0.57 Number of scatterers: 9033 At special positions: 0 Unit cell: (107.12, 128.96, 101.92, 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) Cl 1 17.00 S 67 16.00 O 1657 8.00 N 1541 7.00 C 5767 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS B 121 " - pdb=" SG CYS B 149 " distance=2.04 Simple disulfide: pdb=" SG CYS R 96 " - pdb=" SG CYS R 182 " distance=2.03 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.03 Simple disulfide: pdb=" SG CYS S 159 " - pdb=" SG CYS S 229 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.33 Conformation dependent library (CDL) restraints added in 1.7 seconds 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2140 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 25 helices and 13 sheets defined 34.9% alpha, 19.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.73 Creating SS restraints... Processing helix chain 'A' and resid 14 through 38 Processing helix chain 'A' and resid 53 through 61 Processing helix chain 'A' and resid 234 through 237 Processing helix chain 'A' and resid 265 through 277 Processing helix chain 'A' and resid 280 through 282 No H-bonds generated for 'chain 'A' and resid 280 through 282' Processing helix chain 'A' and resid 294 through 301 removed outlier: 3.525A pdb=" N LYS A 300 " --> pdb=" O LEU A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 350 removed outlier: 4.572A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N SER A 349 " --> pdb=" O PHE A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 390 removed outlier: 4.031A pdb=" N GLN A 384 " --> pdb=" O ARG A 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 25 Processing helix chain 'B' and resid 30 through 33 No H-bonds generated for 'chain 'B' and resid 30 through 33' Processing helix chain 'R' and resid 23 through 50 Processing helix chain 'R' and resid 52 through 54 No H-bonds generated for 'chain 'R' and resid 52 through 54' Processing helix chain 'R' and resid 57 through 86 removed outlier: 4.269A pdb=" N MET R 77 " --> pdb=" O GLY R 73 " (cutoff:3.500A) Proline residue: R 78 - end of helix Processing helix chain 'R' and resid 93 through 123 Processing helix chain 'R' and resid 128 through 134 removed outlier: 3.571A pdb=" N TYR R 131 " --> pdb=" O PRO R 128 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N LYS R 132 " --> pdb=" O LEU R 129 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ALA R 133 " --> pdb=" O ARG R 130 " (cutoff:3.500A) Processing helix chain 'R' and resid 137 through 159 Proline residue: R 151 - end of helix Processing helix chain 'R' and resid 169 through 179 removed outlier: 4.201A pdb=" N ARG R 179 " --> pdb=" O HIS R 175 " (cutoff:3.500A) Processing helix chain 'R' and resid 188 through 198 Processing helix chain 'R' and resid 200 through 231 removed outlier: 3.871A pdb=" N ILE R 224 " --> pdb=" O GLN R 220 " (cutoff:3.500A) Processing helix chain 'R' and resid 249 through 276 Proline residue: R 266 - end of helix Proline residue: R 275 - end of helix Processing helix chain 'R' and resid 283 through 304 Proline residue: R 301 - end of helix Processing helix chain 'R' and resid 309 through 318 Processing helix chain 'S' and resid 221 through 223 No H-bonds generated for 'chain 'S' and resid 221 through 223' Processing helix chain 'Y' and resid 7 through 23 Processing helix chain 'Y' and resid 30 through 43 Processing sheet with id= A, first strand: chain 'A' and resid 359 through 363 removed outlier: 7.368A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 8.067A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ASN A 218 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N LEU A 43 " --> pdb=" O ASN A 218 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N HIS A 220 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N LEU A 45 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N PHE A 222 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 8.121A pdb=" N GLY A 47 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N VAL A 224 " --> pdb=" O GLY A 47 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 48 through 52 removed outlier: 3.809A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.893A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 137 through 139 Processing sheet with id= E, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.752A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER B 161 " --> pdb=" O THR B 165 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N CYS B 166 " --> pdb=" O PHE B 180 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N PHE B 180 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N LEU B 168 " --> pdb=" O THR B 178 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.839A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N ALA B 203 " --> pdb=" O SER B 207 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.658A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 5.230A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 296 through 298 removed outlier: 3.744A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'S' and resid 3 through 7 Processing sheet with id= J, first strand: chain 'S' and resid 97 through 99 removed outlier: 3.978A pdb=" N ALA S 49 " --> pdb=" O TRP S 36 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'S' and resid 140 through 142 Processing sheet with id= L, first strand: chain 'S' and resid 146 through 148 removed outlier: 6.303A pdb=" N LYS S 244 " --> pdb=" O VAL S 147 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'S' and resid 174 through 176 400 hydrogen bonds defined for protein. 1161 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.76 Time building geometry restraints manager: 3.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1446 1.30 - 1.44: 2616 1.44 - 1.57: 5074 1.57 - 1.71: 0 1.71 - 1.84: 101 Bond restraints: 9237 Sorted by residual: bond pdb=" CA HIS R 99 " pdb=" CB HIS R 99 " ideal model delta sigma weight residual 1.530 1.447 0.083 1.57e-02 4.06e+03 2.79e+01 bond pdb=" C ARG B 134 " pdb=" O ARG B 134 " ideal model delta sigma weight residual 1.234 1.170 0.063 1.26e-02 6.30e+03 2.52e+01 bond pdb=" N ARG A 347 " pdb=" CA ARG A 347 " ideal model delta sigma weight residual 1.457 1.393 0.064 1.29e-02 6.01e+03 2.48e+01 bond pdb=" C ARG A 283 " pdb=" O ARG A 283 " ideal model delta sigma weight residual 1.236 1.180 0.057 1.16e-02 7.43e+03 2.39e+01 bond pdb=" CA PHE R 154 " pdb=" C PHE R 154 " ideal model delta sigma weight residual 1.524 1.461 0.063 1.32e-02 5.74e+03 2.28e+01 ... (remaining 9232 not shown) Histogram of bond angle deviations from ideal: 98.15 - 105.37: 149 105.37 - 112.60: 4750 112.60 - 119.83: 3149 119.83 - 127.05: 4348 127.05 - 134.28: 109 Bond angle restraints: 12505 Sorted by residual: angle pdb=" C ARG A 283 " pdb=" N ASP A 284 " pdb=" CA ASP A 284 " ideal model delta sigma weight residual 122.21 110.02 12.19 1.48e+00 4.57e-01 6.78e+01 angle pdb=" C GLU S 234 " pdb=" N TYR S 235 " pdb=" CA TYR S 235 " ideal model delta sigma weight residual 122.89 115.22 7.67 1.12e+00 7.97e-01 4.69e+01 angle pdb=" N VAL R 184 " pdb=" CA VAL R 184 " pdb=" C VAL R 184 " ideal model delta sigma weight residual 109.37 116.64 -7.27 1.35e+00 5.49e-01 2.90e+01 angle pdb=" N TYR A 358 " pdb=" CA TYR A 358 " pdb=" CB TYR A 358 " ideal model delta sigma weight residual 111.43 103.57 7.86 1.59e+00 3.96e-01 2.44e+01 angle pdb=" N THR B 223 " pdb=" CA THR B 223 " pdb=" C THR B 223 " ideal model delta sigma weight residual 110.17 102.80 7.37 1.51e+00 4.39e-01 2.38e+01 ... (remaining 12500 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.77: 4954 16.77 - 33.53: 412 33.53 - 50.30: 101 50.30 - 67.07: 9 67.07 - 83.84: 6 Dihedral angle restraints: 5482 sinusoidal: 2165 harmonic: 3317 Sorted by residual: dihedral pdb=" CB CYS R 96 " pdb=" SG CYS R 96 " pdb=" SG CYS R 182 " pdb=" CB CYS R 182 " ideal model delta sinusoidal sigma weight residual -86.00 -148.00 62.00 1 1.00e+01 1.00e-02 5.09e+01 dihedral pdb=" C ARG B 134 " pdb=" N ARG B 134 " pdb=" CA ARG B 134 " pdb=" CB ARG B 134 " ideal model delta harmonic sigma weight residual -122.60 -110.44 -12.16 0 2.50e+00 1.60e-01 2.37e+01 dihedral pdb=" CA TYR S 235 " pdb=" C TYR S 235 " pdb=" N PRO S 236 " pdb=" CA PRO S 236 " ideal model delta harmonic sigma weight residual 180.00 158.91 21.09 0 5.00e+00 4.00e-02 1.78e+01 ... (remaining 5479 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1085 0.054 - 0.108: 265 0.108 - 0.162: 35 0.162 - 0.216: 7 0.216 - 0.270: 1 Chirality restraints: 1393 Sorted by residual: chirality pdb=" CA ARG B 134 " pdb=" N ARG B 134 " pdb=" C ARG B 134 " pdb=" CB ARG B 134 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.82e+00 chirality pdb=" CA ILE B 338 " pdb=" N ILE B 338 " pdb=" C ILE B 338 " pdb=" CB ILE B 338 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.19 2.00e-01 2.50e+01 9.30e-01 chirality pdb=" CA ILE B 229 " pdb=" N ILE B 229 " pdb=" C ILE B 229 " pdb=" CB ILE B 229 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 8.74e-01 ... (remaining 1390 not shown) Planarity restraints: 1577 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN R 220 " 0.019 2.00e-02 2.50e+03 3.84e-02 1.48e+01 pdb=" C GLN R 220 " -0.066 2.00e-02 2.50e+03 pdb=" O GLN R 220 " 0.024 2.00e-02 2.50e+03 pdb=" N ALA R 221 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS R 99 " -0.028 2.00e-02 2.50e+03 2.33e-02 8.16e+00 pdb=" CG HIS R 99 " 0.048 2.00e-02 2.50e+03 pdb=" ND1 HIS R 99 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 HIS R 99 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 HIS R 99 " -0.008 2.00e-02 2.50e+03 pdb=" NE2 HIS R 99 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE R 292 " 0.014 2.00e-02 2.50e+03 2.84e-02 8.06e+00 pdb=" C PHE R 292 " -0.049 2.00e-02 2.50e+03 pdb=" O PHE R 292 " 0.019 2.00e-02 2.50e+03 pdb=" N GLY R 293 " 0.016 2.00e-02 2.50e+03 ... (remaining 1574 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 840 2.74 - 3.28: 9521 3.28 - 3.82: 16213 3.82 - 4.36: 19166 4.36 - 4.90: 32359 Nonbonded interactions: 78099 Sorted by model distance: nonbonded pdb=" OE2 GLU A 15 " pdb=" OH TYR S 175 " model vdw 2.203 2.440 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.210 2.440 nonbonded pdb=" ND1 HIS A 387 " pdb=" O ALA R 124 " model vdw 2.230 2.520 nonbonded pdb=" OD2 ASP B 83 " pdb=" OG1 THR B 86 " model vdw 2.241 2.440 nonbonded pdb=" OG SER B 108 " pdb=" OD1 ASP B 154 " model vdw 2.261 2.440 ... (remaining 78094 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 2.390 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 27.870 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.040 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: 0.010 Load rotamer database and sin/cos tables:13.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6613 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 0.083 9237 Z= 0.308 Angle : 0.782 12.189 12505 Z= 0.475 Chirality : 0.047 0.270 1393 Planarity : 0.005 0.044 1577 Dihedral : 13.144 83.836 3330 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 18.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 0.41 % Allowed : 1.02 % Favored : 98.57 % Cbeta Deviations : 0.09 % 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: -0.45 (0.25), residues: 1120 helix: 0.90 (0.26), residues: 403 sheet: -0.51 (0.32), residues: 270 loop : -1.19 (0.29), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 82 HIS 0.016 0.001 HIS R 99 PHE 0.018 0.001 PHE R 154 TYR 0.029 0.002 TYR A 358 ARG 0.006 0.000 ARG A 20 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 170 time to evaluate : 1.062 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 173 average time/residue: 1.0387 time to fit residues: 193.6654 Evaluate side-chains 140 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 137 time to evaluate : 0.981 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 3 residues processed: 0 time to fit residues: 1.3932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 0.6980 chunk 84 optimal weight: 10.0000 chunk 46 optimal weight: 0.9990 chunk 28 optimal weight: 0.7980 chunk 56 optimal weight: 5.9990 chunk 44 optimal weight: 2.9990 chunk 87 optimal weight: 0.8980 chunk 33 optimal weight: 0.6980 chunk 52 optimal weight: 4.9990 chunk 64 optimal weight: 1.9990 chunk 100 optimal weight: 7.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS ** B 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 156 GLN B 183 HIS B 220 GLN ** B 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 164 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6773 moved from start: 0.1401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9237 Z= 0.216 Angle : 0.594 7.941 12505 Z= 0.309 Chirality : 0.043 0.204 1393 Planarity : 0.004 0.045 1577 Dihedral : 4.361 22.366 1256 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 16.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 2.34 % Allowed : 11.41 % Favored : 86.25 % 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: -0.22 (0.25), residues: 1120 helix: 1.23 (0.25), residues: 409 sheet: -0.51 (0.32), residues: 275 loop : -1.16 (0.29), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 211 HIS 0.005 0.001 HIS R 55 PHE 0.017 0.002 PHE R 299 TYR 0.019 0.001 TYR A 37 ARG 0.008 0.000 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 142 time to evaluate : 1.090 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 7 residues processed: 151 average time/residue: 0.9981 time to fit residues: 163.0612 Evaluate side-chains 133 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 126 time to evaluate : 0.913 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 4 residues processed: 3 average time/residue: 0.0971 time to fit residues: 1.8346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 56 optimal weight: 0.5980 chunk 31 optimal weight: 0.7980 chunk 83 optimal weight: 6.9990 chunk 68 optimal weight: 6.9990 chunk 27 optimal weight: 4.9990 chunk 100 optimal weight: 6.9990 chunk 109 optimal weight: 5.9990 chunk 89 optimal weight: 0.0270 chunk 34 optimal weight: 0.8980 chunk 81 optimal weight: 0.7980 chunk 99 optimal weight: 0.9980 overall best weight: 0.6238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS A 357 HIS ** B 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 ASN ** B 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 164 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6778 moved from start: 0.1757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9237 Z= 0.185 Angle : 0.562 8.857 12505 Z= 0.292 Chirality : 0.043 0.170 1393 Planarity : 0.004 0.047 1577 Dihedral : 4.237 23.029 1256 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 15.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 2.95 % Allowed : 13.34 % Favored : 83.71 % 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: -0.08 (0.25), residues: 1120 helix: 1.47 (0.26), residues: 405 sheet: -0.46 (0.32), residues: 274 loop : -1.20 (0.29), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 211 HIS 0.005 0.001 HIS A 357 PHE 0.014 0.001 PHE B 253 TYR 0.016 0.001 TYR R 200 ARG 0.005 0.000 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 132 time to evaluate : 0.991 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 10 residues processed: 145 average time/residue: 1.0835 time to fit residues: 169.6085 Evaluate side-chains 136 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 126 time to evaluate : 0.969 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 8 residues processed: 2 average time/residue: 0.1066 time to fit residues: 1.7515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 75 optimal weight: 0.8980 chunk 52 optimal weight: 0.7980 chunk 11 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 chunk 67 optimal weight: 0.6980 chunk 101 optimal weight: 0.1980 chunk 107 optimal weight: 10.0000 chunk 96 optimal weight: 20.0000 chunk 28 optimal weight: 0.8980 chunk 89 optimal weight: 20.0000 chunk 60 optimal weight: 0.0070 overall best weight: 0.4998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS A 357 HIS B 32 GLN ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 ASN ** B 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6769 moved from start: 0.2001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9237 Z= 0.172 Angle : 0.563 7.893 12505 Z= 0.288 Chirality : 0.042 0.183 1393 Planarity : 0.004 0.047 1577 Dihedral : 4.161 23.285 1256 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 15.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 3.36 % Allowed : 16.09 % Favored : 80.55 % 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: -0.03 (0.25), residues: 1120 helix: 1.50 (0.26), residues: 405 sheet: -0.39 (0.32), residues: 274 loop : -1.18 (0.29), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 211 HIS 0.004 0.001 HIS A 357 PHE 0.013 0.001 PHE A 212 TYR 0.015 0.001 TYR R 200 ARG 0.005 0.000 ARG A 283 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 135 time to evaluate : 1.012 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 33 outliers final: 11 residues processed: 156 average time/residue: 0.9951 time to fit residues: 168.2375 Evaluate side-chains 133 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 122 time to evaluate : 0.875 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 9 residues processed: 2 average time/residue: 0.1112 time to fit residues: 1.7344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 1 optimal weight: 1.9990 chunk 79 optimal weight: 0.1980 chunk 44 optimal weight: 5.9990 chunk 91 optimal weight: 20.0000 chunk 74 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 54 optimal weight: 4.9990 chunk 96 optimal weight: 10.0000 chunk 27 optimal weight: 4.9990 chunk 36 optimal weight: 4.9990 chunk 21 optimal weight: 0.6980 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS ** B 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 GLN B 230 ASN B 268 ASN ** B 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 59 ASN ** R 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 164 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6969 moved from start: 0.2674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 9237 Z= 0.396 Angle : 0.701 11.822 12505 Z= 0.357 Chirality : 0.048 0.325 1393 Planarity : 0.005 0.047 1577 Dihedral : 4.685 25.593 1256 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 20.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 4.68 % Allowed : 16.50 % Favored : 78.82 % 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: -0.19 (0.25), residues: 1120 helix: 1.27 (0.25), residues: 405 sheet: -0.46 (0.32), residues: 276 loop : -1.17 (0.29), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 82 HIS 0.010 0.002 HIS A 357 PHE 0.017 0.002 PHE A 212 TYR 0.026 0.002 TYR B 105 ARG 0.006 0.001 ARG A 283 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 136 time to evaluate : 0.927 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 46 outliers final: 20 residues processed: 165 average time/residue: 0.9650 time to fit residues: 172.7505 Evaluate side-chains 146 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 126 time to evaluate : 0.923 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 13 residues processed: 7 average time/residue: 0.2628 time to fit residues: 3.6932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 62 optimal weight: 0.8980 chunk 26 optimal weight: 3.9990 chunk 107 optimal weight: 10.0000 chunk 89 optimal weight: 10.0000 chunk 49 optimal weight: 0.6980 chunk 8 optimal weight: 0.9990 chunk 35 optimal weight: 4.9990 chunk 56 optimal weight: 20.0000 chunk 103 optimal weight: 0.6980 chunk 12 optimal weight: 0.7980 chunk 61 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS ** B 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 GLN B 268 ASN ** B 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 164 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6884 moved from start: 0.2674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9237 Z= 0.215 Angle : 0.621 8.855 12505 Z= 0.316 Chirality : 0.044 0.192 1393 Planarity : 0.004 0.048 1577 Dihedral : 4.494 25.265 1256 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 17.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 3.36 % Allowed : 18.33 % Favored : 78.31 % 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: -0.13 (0.25), residues: 1120 helix: 1.36 (0.25), residues: 404 sheet: -0.39 (0.32), residues: 270 loop : -1.20 (0.29), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 82 HIS 0.004 0.001 HIS R 55 PHE 0.012 0.001 PHE A 212 TYR 0.012 0.001 TYR S 101 ARG 0.008 0.000 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 130 time to evaluate : 0.961 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 33 outliers final: 19 residues processed: 150 average time/residue: 1.0599 time to fit residues: 171.6832 Evaluate side-chains 137 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 118 time to evaluate : 0.969 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 13 residues processed: 6 average time/residue: 0.2691 time to fit residues: 3.4603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 78 optimal weight: 2.9990 chunk 60 optimal weight: 0.7980 chunk 90 optimal weight: 6.9990 chunk 59 optimal weight: 0.9990 chunk 106 optimal weight: 0.3980 chunk 66 optimal weight: 2.9990 chunk 65 optimal weight: 0.8980 chunk 49 optimal weight: 0.9980 chunk 42 optimal weight: 5.9990 chunk 63 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS ** B 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 ASN ** B 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6871 moved from start: 0.2739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9237 Z= 0.211 Angle : 0.622 11.229 12505 Z= 0.314 Chirality : 0.044 0.228 1393 Planarity : 0.004 0.049 1577 Dihedral : 4.460 25.195 1256 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 17.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 2.85 % Allowed : 19.96 % Favored : 77.19 % 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: -0.07 (0.25), residues: 1120 helix: 1.41 (0.25), residues: 405 sheet: -0.35 (0.33), residues: 256 loop : -1.15 (0.29), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 82 HIS 0.004 0.001 HIS R 55 PHE 0.013 0.001 PHE A 212 TYR 0.013 0.001 TYR R 200 ARG 0.008 0.000 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 131 time to evaluate : 0.981 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 15 residues processed: 147 average time/residue: 1.0847 time to fit residues: 172.1731 Evaluate side-chains 141 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 126 time to evaluate : 1.075 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 9 residues processed: 6 average time/residue: 0.4707 time to fit residues: 4.7131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 21 optimal weight: 0.6980 chunk 20 optimal weight: 0.7980 chunk 68 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 9 optimal weight: 0.9980 chunk 84 optimal weight: 0.9980 chunk 97 optimal weight: 10.0000 chunk 102 optimal weight: 7.9990 chunk 93 optimal weight: 3.9990 chunk 99 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS ** B 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 ASN ** B 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 59 ASN ** R 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6883 moved from start: 0.2843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 9237 Z= 0.228 Angle : 0.638 9.711 12505 Z= 0.321 Chirality : 0.044 0.187 1393 Planarity : 0.004 0.048 1577 Dihedral : 4.485 25.340 1256 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 17.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 3.05 % Allowed : 20.47 % Favored : 76.48 % 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 (0.25), residues: 1120 helix: 1.35 (0.25), residues: 405 sheet: -0.33 (0.33), residues: 256 loop : -1.14 (0.29), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 82 HIS 0.008 0.001 HIS A 357 PHE 0.014 0.001 PHE R 299 TYR 0.015 0.001 TYR R 123 ARG 0.009 0.001 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 129 time to evaluate : 1.042 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 18 residues processed: 147 average time/residue: 1.1798 time to fit residues: 187.6566 Evaluate side-chains 138 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 120 time to evaluate : 1.236 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 13 residues processed: 6 average time/residue: 0.1638 time to fit residues: 3.2492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 102 optimal weight: 20.0000 chunk 60 optimal weight: 0.9990 chunk 43 optimal weight: 0.9990 chunk 78 optimal weight: 0.7980 chunk 30 optimal weight: 0.9990 chunk 90 optimal weight: 6.9990 chunk 94 optimal weight: 20.0000 chunk 99 optimal weight: 0.0970 chunk 65 optimal weight: 1.9990 chunk 105 optimal weight: 3.9990 chunk 64 optimal weight: 0.5980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS ** B 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 ASN ** B 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6862 moved from start: 0.2873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 9237 Z= 0.199 Angle : 0.627 10.385 12505 Z= 0.315 Chirality : 0.043 0.189 1393 Planarity : 0.004 0.048 1577 Dihedral : 4.415 25.203 1256 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 17.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 2.44 % Allowed : 21.69 % Favored : 75.87 % 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: -0.02 (0.25), residues: 1120 helix: 1.46 (0.25), residues: 404 sheet: -0.33 (0.32), residues: 256 loop : -1.12 (0.29), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 82 HIS 0.007 0.001 HIS A 357 PHE 0.016 0.001 PHE R 299 TYR 0.012 0.001 TYR R 200 ARG 0.009 0.001 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 128 time to evaluate : 1.113 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 16 residues processed: 144 average time/residue: 1.0712 time to fit residues: 166.4252 Evaluate side-chains 142 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 126 time to evaluate : 0.981 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 12 residues processed: 4 average time/residue: 0.1601 time to fit residues: 2.2586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 61.0625 > 50: distance: 20 - 25: 26.700 distance: 25 - 26: 18.417 distance: 26 - 27: 6.239 distance: 26 - 29: 11.743 distance: 27 - 28: 32.887 distance: 27 - 33: 35.741 distance: 29 - 30: 40.674 distance: 30 - 31: 38.477 distance: 30 - 32: 44.393 distance: 33 - 34: 21.035 distance: 34 - 35: 16.592 distance: 34 - 37: 9.903 distance: 35 - 36: 27.977 distance: 35 - 42: 28.339 distance: 37 - 38: 34.116 distance: 38 - 39: 12.752 distance: 39 - 40: 12.322 distance: 39 - 41: 19.493 distance: 42 - 43: 13.427 distance: 43 - 44: 15.861 distance: 43 - 46: 13.568 distance: 44 - 45: 4.510 distance: 44 - 50: 7.875 distance: 46 - 47: 15.539 distance: 47 - 48: 16.913 distance: 47 - 49: 37.792 distance: 50 - 51: 21.148 distance: 51 - 52: 25.772 distance: 51 - 54: 20.797 distance: 52 - 53: 31.988 distance: 52 - 58: 19.723 distance: 54 - 55: 23.122 distance: 55 - 56: 36.265 distance: 55 - 57: 46.207 distance: 58 - 59: 41.429 distance: 59 - 60: 34.477 distance: 59 - 62: 36.976 distance: 60 - 61: 48.036 distance: 60 - 69: 43.112 distance: 62 - 63: 39.963 distance: 63 - 64: 19.901 distance: 63 - 65: 35.933 distance: 64 - 66: 17.485 distance: 65 - 67: 42.270 distance: 66 - 68: 19.467 distance: 67 - 68: 26.107 distance: 69 - 70: 19.544 distance: 70 - 71: 35.554 distance: 70 - 73: 11.673 distance: 71 - 72: 25.544 distance: 71 - 78: 29.680 distance: 73 - 74: 30.701 distance: 74 - 75: 29.988 distance: 75 - 76: 42.484 distance: 76 - 77: 48.815 distance: 78 - 79: 29.720 distance: 79 - 80: 43.134 distance: 80 - 81: 33.084 distance: 80 - 82: 41.796 distance: 82 - 83: 4.738 distance: 83 - 84: 48.356 distance: 83 - 86: 38.598 distance: 84 - 85: 12.613 distance: 84 - 87: 30.725 distance: 87 - 88: 9.512 distance: 88 - 89: 18.293 distance: 88 - 91: 11.740 distance: 89 - 90: 6.369 distance: 89 - 96: 34.661 distance: 90 - 125: 18.571 distance: 91 - 92: 25.874 distance: 92 - 93: 27.343 distance: 93 - 94: 13.158 distance: 93 - 95: 27.443 distance: 96 - 97: 11.317 distance: 97 - 98: 17.579 distance: 97 - 100: 19.520 distance: 98 - 99: 32.619 distance: 98 - 105: 16.396 distance: 99 - 136: 22.583 distance: 100 - 101: 21.527 distance: 101 - 102: 18.813 distance: 102 - 103: 14.099 distance: 102 - 104: 19.002