Starting phenix.real_space_refine on Tue Apr 29 15:52:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8flr_29284/04_2025/8flr_29284.cif Found real_map, /net/cci-nas-00/data/ceres_data/8flr_29284/04_2025/8flr_29284.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8flr_29284/04_2025/8flr_29284.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8flr_29284/04_2025/8flr_29284.map" model { file = "/net/cci-nas-00/data/ceres_data/8flr_29284/04_2025/8flr_29284.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8flr_29284/04_2025/8flr_29284.cif" } resolution = 2.94 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= -0.002 sd= 0.112 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 56 5.16 5 C 5688 2.51 5 N 1552 2.21 5 O 1632 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 8928 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 1897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1897 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 6, 'TRANS': 226} Chain breaks: 2 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "B" Number of atoms: 2563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2563 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 30 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'ASN:plan1': 2, 'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 25 Chain: "G" Number of atoms: 403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 403 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 4, 'TRANS': 50} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "N" Number of atoms: 957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 957 Classifications: {'peptide': 126} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 120} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "P" Number of atoms: 272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 272 Classifications: {'peptide': 32} Link IDs: {'TRANS': 31} Chain: "R" Number of atoms: 2826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 2826 Classifications: {'peptide': 363} Incomplete info: {'truncation_to_alanine': 43} Link IDs: {'PTRANS': 11, 'TRANS': 351} Chain breaks: 3 Unresolved non-hydrogen bonds: 168 Unresolved non-hydrogen angles: 206 Unresolved non-hydrogen dihedrals: 137 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 4, 'ASP:plan': 2, 'GLU:plan': 7, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 107 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "R" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Time building chain proxies: 5.56, per 1000 atoms: 0.62 Number of scatterers: 8928 At special positions: 0 Unit cell: (73.1, 94.35, 173.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 56 16.00 O 1632 8.00 N 1552 7.00 C 5688 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Simple disulfide: pdb=" SG CYS R 48 " - pdb=" SG CYS R 117 " distance=2.03 Simple disulfide: pdb=" SG CYS R 108 " - pdb=" SG CYS R 148 " distance=2.03 Simple disulfide: pdb=" SG CYS R 131 " - pdb=" SG CYS R 170 " distance=2.03 Simple disulfide: pdb=" SG CYS R 281 " - pdb=" SG CYS R 351 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 2.28 Conformation dependent library (CDL) restraints added in 964.3 milliseconds 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2154 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 12 sheets defined 43.2% alpha, 19.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.96 Creating SS restraints... Processing helix chain 'A' and resid 16 through 39 removed outlier: 3.542A pdb=" N GLN A 29 " --> pdb=" O LYS A 25 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA A 39 " --> pdb=" O GLN A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 51 No H-bonds generated for 'chain 'A' and resid 49 through 51' Processing helix chain 'A' and resid 52 through 64 Processing helix chain 'A' and resid 233 through 239 removed outlier: 3.535A pdb=" N CYS A 237 " --> pdb=" O TRP A 234 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 279 Processing helix chain 'A' and resid 293 through 303 removed outlier: 3.757A pdb=" N GLU A 299 " --> pdb=" O ASP A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 312 removed outlier: 4.492A pdb=" N TYR A 311 " --> pdb=" O LYS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 317 Processing helix chain 'A' and resid 331 through 351 removed outlier: 3.639A pdb=" N ALA A 351 " --> pdb=" O ARG A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 Processing helix chain 'B' and resid 4 through 25 Processing helix chain 'B' and resid 29 through 35 Processing helix chain 'G' and resid 9 through 24 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 45 through 48 removed outlier: 3.590A pdb=" N ASP G 48 " --> pdb=" O ALA G 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 45 through 48' Processing helix chain 'N' and resid 28 through 32 Processing helix chain 'N' and resid 62 through 65 Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.537A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing helix chain 'P' and resid 2 through 32 Processing helix chain 'R' and resid 33 through 54 Processing helix chain 'R' and resid 177 through 212 removed outlier: 4.336A pdb=" N ARG R 181 " --> pdb=" O GLU R 177 " (cutoff:3.500A) Processing helix chain 'R' and resid 217 through 245 Processing helix chain 'R' and resid 278 through 312 removed outlier: 3.660A pdb=" N ALA R 284 " --> pdb=" O GLY R 280 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLY R 303 " --> pdb=" O ILE R 299 " (cutoff:3.500A) Processing helix chain 'R' and resid 316 through 347 removed outlier: 3.676A pdb=" N TRP R 322 " --> pdb=" O LYS R 318 " (cutoff:3.500A) Proline residue: R 332 - end of helix Processing helix chain 'R' and resid 356 through 359 removed outlier: 3.987A pdb=" N LYS R 359 " --> pdb=" O SER R 356 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 356 through 359' Processing helix chain 'R' and resid 360 through 391 Proline residue: R 366 - end of helix Processing helix chain 'R' and resid 400 through 418 Proline residue: R 415 - end of helix Processing helix chain 'R' and resid 419 through 423 removed outlier: 3.524A pdb=" N VAL R 423 " --> pdb=" O HIS R 420 " (cutoff:3.500A) Processing helix chain 'R' and resid 434 through 460 removed outlier: 4.293A pdb=" N GLY R 452 " --> pdb=" O ASN R 448 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N PHE R 453 " --> pdb=" O SER R 449 " (cutoff:3.500A) Processing helix chain 'R' and resid 463 through 479 Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 214 removed outlier: 3.811A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.758A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.520A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 4.151A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.984A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.937A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.535A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.670A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'N' and resid 58 through 60 removed outlier: 6.529A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'R' and resid 111 through 112 removed outlier: 3.705A pdb=" N GLU R 111 " --> pdb=" O TRP R 118 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'R' and resid 126 through 130 499 hydrogen bonds defined for protein. 1440 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: 2.59 Time building geometry restraints manager: 2.68 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: 2905 1.34 - 1.46: 2048 1.46 - 1.58: 4089 1.58 - 1.70: 0 1.70 - 1.81: 78 Bond restraints: 9120 Sorted by residual: bond pdb=" N LEU R 321 " pdb=" CA LEU R 321 " ideal model delta sigma weight residual 1.459 1.495 -0.035 1.23e-02 6.61e+03 8.29e+00 bond pdb=" N VAL R 432 " pdb=" CA VAL R 432 " ideal model delta sigma weight residual 1.461 1.494 -0.034 1.19e-02 7.06e+03 8.03e+00 bond pdb=" N VAL R 171 " pdb=" CA VAL R 171 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.25e-02 6.40e+03 7.72e+00 bond pdb=" N ILE P 28 " pdb=" CA ILE P 28 " ideal model delta sigma weight residual 1.461 1.493 -0.032 1.17e-02 7.31e+03 7.36e+00 bond pdb=" N GLU R 317 " pdb=" CA GLU R 317 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.28e-02 6.10e+03 7.20e+00 ... (remaining 9115 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.96: 12143 1.96 - 3.91: 211 3.91 - 5.87: 22 5.87 - 7.82: 2 7.82 - 9.78: 1 Bond angle restraints: 12379 Sorted by residual: angle pdb=" CA CYS R 217 " pdb=" C CYS R 217 " pdb=" O CYS R 217 " ideal model delta sigma weight residual 121.40 116.94 4.46 1.13e+00 7.83e-01 1.56e+01 angle pdb=" N ILE P 31 " pdb=" CA ILE P 31 " pdb=" C ILE P 31 " ideal model delta sigma weight residual 112.80 108.57 4.23 1.15e+00 7.56e-01 1.35e+01 angle pdb=" C VAL R 334 " pdb=" N PHE R 335 " pdb=" CA PHE R 335 " ideal model delta sigma weight residual 121.14 114.94 6.20 1.75e+00 3.27e-01 1.25e+01 angle pdb=" CA TYR R 191 " pdb=" CB TYR R 191 " pdb=" CG TYR R 191 " ideal model delta sigma weight residual 113.90 119.99 -6.09 1.80e+00 3.09e-01 1.15e+01 angle pdb=" CA ARG R 219 " pdb=" C ARG R 219 " pdb=" O ARG R 219 " ideal model delta sigma weight residual 120.82 117.50 3.32 1.05e+00 9.07e-01 9.99e+00 ... (remaining 12374 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 4893 17.93 - 35.86: 365 35.86 - 53.79: 75 53.79 - 71.72: 14 71.72 - 89.65: 9 Dihedral angle restraints: 5356 sinusoidal: 2023 harmonic: 3333 Sorted by residual: dihedral pdb=" CB CYS R 281 " pdb=" SG CYS R 281 " pdb=" SG CYS R 351 " pdb=" CB CYS R 351 " ideal model delta sinusoidal sigma weight residual 93.00 136.17 -43.17 1 1.00e+01 1.00e-02 2.60e+01 dihedral pdb=" CA CYS N 99 " pdb=" C CYS N 99 " pdb=" N PRO N 100 " pdb=" CA PRO N 100 " ideal model delta harmonic sigma weight residual -180.00 -154.56 -25.44 0 5.00e+00 4.00e-02 2.59e+01 dihedral pdb=" CA LEU A 291 " pdb=" C LEU A 291 " pdb=" N ASN A 292 " pdb=" CA ASN A 292 " ideal model delta harmonic sigma weight residual -180.00 -156.25 -23.75 0 5.00e+00 4.00e-02 2.26e+01 ... (remaining 5353 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 1092 0.049 - 0.099: 235 0.099 - 0.148: 52 0.148 - 0.198: 7 0.198 - 0.247: 1 Chirality restraints: 1387 Sorted by residual: chirality pdb=" CA CYS R 217 " pdb=" N CYS R 217 " pdb=" C CYS R 217 " pdb=" CB CYS R 217 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.53e+00 chirality pdb=" CA ILE P 31 " pdb=" N ILE P 31 " pdb=" C ILE P 31 " pdb=" CB ILE P 31 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.17 2.00e-01 2.50e+01 7.37e-01 chirality pdb=" CA PHE R 335 " pdb=" N PHE R 335 " pdb=" C PHE R 335 " pdb=" CB PHE R 335 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.18e-01 ... (remaining 1384 not shown) Planarity restraints: 1575 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA HIS R 216 " -0.011 2.00e-02 2.50e+03 2.23e-02 4.99e+00 pdb=" C HIS R 216 " 0.039 2.00e-02 2.50e+03 pdb=" O HIS R 216 " -0.015 2.00e-02 2.50e+03 pdb=" N CYS R 217 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE R 376 " -0.009 2.00e-02 2.50e+03 1.73e-02 3.00e+00 pdb=" C ILE R 376 " 0.030 2.00e-02 2.50e+03 pdb=" O ILE R 376 " -0.011 2.00e-02 2.50e+03 pdb=" N LEU R 377 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.028 5.00e-02 4.00e+02 4.22e-02 2.85e+00 pdb=" N PRO B 236 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.024 5.00e-02 4.00e+02 ... (remaining 1572 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 701 2.74 - 3.28: 8964 3.28 - 3.82: 15715 3.82 - 4.36: 19096 4.36 - 4.90: 32751 Nonbonded interactions: 77227 Sorted by model distance: nonbonded pdb=" O ARG N 98 " pdb=" OH TYR N 115 " model vdw 2.201 3.040 nonbonded pdb=" O MET B 325 " pdb=" ND2 ASN B 340 " model vdw 2.207 3.120 nonbonded pdb=" OG SER B 147 " pdb=" O VAL B 187 " model vdw 2.216 3.040 nonbonded pdb=" O ALA R 242 " pdb=" OG SER R 246 " model vdw 2.218 3.040 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.221 3.040 ... (remaining 77222 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 ========== 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=0.00 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: 2.340 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: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 23.210 Find NCS groups from input model: 0.120 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:11.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6987 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 : 0.003 0.037 9126 Z= 0.213 Angle : 0.591 9.776 12391 Z= 0.365 Chirality : 0.044 0.247 1387 Planarity : 0.004 0.042 1575 Dihedral : 13.800 89.652 3184 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 0.11 % Allowed : 0.65 % Favored : 99.24 % 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: 1.23 (0.25), residues: 1125 helix: 2.06 (0.25), residues: 442 sheet: -0.27 (0.32), residues: 226 loop : 0.28 (0.31), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 82 HIS 0.005 0.001 HIS A 357 PHE 0.012 0.001 PHE A 212 TYR 0.020 0.001 TYR N 60 ARG 0.009 0.000 ARG B 197 Details of bonding type rmsd hydrogen bonds : bond 0.13207 ( 499) hydrogen bonds : angle 5.91908 ( 1440) SS BOND : bond 0.00126 ( 6) SS BOND : angle 1.50256 ( 12) covalent geometry : bond 0.00347 ( 9120) covalent geometry : angle 0.58900 (12379) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 139 time to evaluate : 0.986 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 240 ASP cc_start: 0.6587 (p0) cc_final: 0.6264 (p0) REVERT: B 153 ASP cc_start: 0.7840 (p0) cc_final: 0.7570 (p0) REVERT: R 189 MET cc_start: 0.7184 (tmm) cc_final: 0.6880 (tmt) REVERT: R 390 ARG cc_start: 0.7504 (ttp-110) cc_final: 0.7294 (ttm170) outliers start: 1 outliers final: 0 residues processed: 140 average time/residue: 1.1279 time to fit residues: 169.7117 Evaluate side-chains 113 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.5980 chunk 84 optimal weight: 6.9990 chunk 47 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 57 optimal weight: 10.0000 chunk 45 optimal weight: 1.9990 chunk 87 optimal weight: 0.8980 chunk 33 optimal weight: 0.9980 chunk 53 optimal weight: 4.9990 chunk 65 optimal weight: 0.9980 chunk 101 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 390 GLN B 125 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.202103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.158560 restraints weight = 9032.162| |-----------------------------------------------------------------------------| r_work (start): 0.3737 rms_B_bonded: 1.95 r_work: 0.3542 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3404 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.1033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9126 Z= 0.152 Angle : 0.544 11.575 12391 Z= 0.290 Chirality : 0.042 0.179 1387 Planarity : 0.004 0.047 1575 Dihedral : 4.375 24.259 1244 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.63 % Allowed : 5.99 % Favored : 92.37 % 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: 1.55 (0.25), residues: 1125 helix: 2.63 (0.24), residues: 435 sheet: -0.12 (0.33), residues: 212 loop : 0.13 (0.29), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP R 298 HIS 0.007 0.001 HIS A 357 PHE 0.034 0.002 PHE R 335 TYR 0.036 0.001 TYR R 191 ARG 0.006 0.000 ARG B 197 Details of bonding type rmsd hydrogen bonds : bond 0.04496 ( 499) hydrogen bonds : angle 4.75759 ( 1440) SS BOND : bond 0.00200 ( 6) SS BOND : angle 1.58068 ( 12) covalent geometry : bond 0.00338 ( 9120) covalent geometry : angle 0.54229 (12379) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 121 time to evaluate : 1.116 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 240 ASP cc_start: 0.7318 (p0) cc_final: 0.6840 (p0) REVERT: B 155 ASN cc_start: 0.7881 (t0) cc_final: 0.7581 (t0) REVERT: G 47 GLU cc_start: 0.7813 (mt-10) cc_final: 0.7584 (mt-10) REVERT: N 95 TYR cc_start: 0.8681 (m-80) cc_final: 0.8477 (m-80) REVERT: R 214 ARG cc_start: 0.7392 (ptm160) cc_final: 0.7046 (pmm150) REVERT: R 390 ARG cc_start: 0.7915 (ttp-110) cc_final: 0.7573 (ttm170) REVERT: R 411 LEU cc_start: 0.8009 (OUTLIER) cc_final: 0.7726 (mp) outliers start: 15 outliers final: 7 residues processed: 128 average time/residue: 1.4481 time to fit residues: 198.8742 Evaluate side-chains 114 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 106 time to evaluate : 1.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain R residue 138 PHE Chi-restraints excluded: chain R residue 409 SER Chi-restraints excluded: chain R residue 411 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 44 optimal weight: 5.9990 chunk 18 optimal weight: 0.8980 chunk 101 optimal weight: 0.7980 chunk 58 optimal weight: 7.9990 chunk 88 optimal weight: 1.9990 chunk 6 optimal weight: 0.4980 chunk 64 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 61 optimal weight: 8.9990 chunk 13 optimal weight: 4.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 390 GLN B 176 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.203332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.160066 restraints weight = 9105.818| |-----------------------------------------------------------------------------| r_work (start): 0.3744 rms_B_bonded: 1.94 r_work: 0.3550 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3408 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.1218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9126 Z= 0.137 Angle : 0.522 12.757 12391 Z= 0.277 Chirality : 0.041 0.175 1387 Planarity : 0.004 0.048 1575 Dihedral : 4.265 22.298 1244 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.96 % Allowed : 8.93 % Favored : 89.11 % 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: 1.64 (0.25), residues: 1125 helix: 2.77 (0.24), residues: 435 sheet: -0.20 (0.33), residues: 212 loop : 0.19 (0.30), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP R 298 HIS 0.006 0.001 HIS A 357 PHE 0.013 0.001 PHE R 335 TYR 0.030 0.001 TYR R 191 ARG 0.008 0.000 ARG B 197 Details of bonding type rmsd hydrogen bonds : bond 0.04219 ( 499) hydrogen bonds : angle 4.61139 ( 1440) SS BOND : bond 0.00169 ( 6) SS BOND : angle 1.38654 ( 12) covalent geometry : bond 0.00304 ( 9120) covalent geometry : angle 0.52049 (12379) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 121 time to evaluate : 0.942 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 240 ASP cc_start: 0.7345 (p0) cc_final: 0.6879 (p0) REVERT: B 155 ASN cc_start: 0.7839 (t0) cc_final: 0.7550 (t0) REVERT: N 29 PHE cc_start: 0.7341 (t80) cc_final: 0.7058 (t80) REVERT: N 59 SER cc_start: 0.8712 (m) cc_final: 0.8496 (t) REVERT: N 95 TYR cc_start: 0.8688 (m-80) cc_final: 0.8483 (m-80) REVERT: R 214 ARG cc_start: 0.7407 (ptm160) cc_final: 0.7058 (pmm150) REVERT: R 390 ARG cc_start: 0.7958 (ttp-110) cc_final: 0.7569 (ttm170) outliers start: 18 outliers final: 11 residues processed: 127 average time/residue: 1.4650 time to fit residues: 200.3324 Evaluate side-chains 116 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 105 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain R residue 138 PHE Chi-restraints excluded: chain R residue 409 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 68 optimal weight: 0.4980 chunk 11 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 95 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 79 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 chunk 14 optimal weight: 0.6980 chunk 51 optimal weight: 0.5980 chunk 38 optimal weight: 0.9990 chunk 108 optimal weight: 1.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 125 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 ASN R 438 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.202776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.160144 restraints weight = 9059.740| |-----------------------------------------------------------------------------| r_work (start): 0.3755 rms_B_bonded: 1.79 r_work: 0.3566 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3425 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.1378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9126 Z= 0.127 Angle : 0.511 12.398 12391 Z= 0.271 Chirality : 0.041 0.166 1387 Planarity : 0.004 0.055 1575 Dihedral : 4.200 21.690 1244 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.29 % Allowed : 9.91 % Favored : 87.80 % 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: 1.61 (0.25), residues: 1125 helix: 2.72 (0.24), residues: 443 sheet: -0.23 (0.33), residues: 214 loop : 0.15 (0.30), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 298 HIS 0.005 0.001 HIS A 357 PHE 0.017 0.001 PHE R 335 TYR 0.028 0.001 TYR R 191 ARG 0.009 0.000 ARG B 197 Details of bonding type rmsd hydrogen bonds : bond 0.04024 ( 499) hydrogen bonds : angle 4.52679 ( 1440) SS BOND : bond 0.00181 ( 6) SS BOND : angle 1.29475 ( 12) covalent geometry : bond 0.00281 ( 9120) covalent geometry : angle 0.50958 (12379) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 119 time to evaluate : 0.948 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 MET cc_start: 0.6238 (OUTLIER) cc_final: 0.5084 (mmt) REVERT: A 240 ASP cc_start: 0.7314 (p0) cc_final: 0.6802 (p0) REVERT: B 155 ASN cc_start: 0.7795 (t0) cc_final: 0.7558 (m-40) REVERT: N 29 PHE cc_start: 0.7385 (t80) cc_final: 0.7095 (t80) REVERT: R 214 ARG cc_start: 0.7429 (ptm160) cc_final: 0.7058 (pmm150) REVERT: R 379 ILE cc_start: 0.7320 (pt) cc_final: 0.7093 (pt) REVERT: R 390 ARG cc_start: 0.7978 (ttp-110) cc_final: 0.7550 (ttm170) outliers start: 21 outliers final: 12 residues processed: 130 average time/residue: 1.3743 time to fit residues: 192.8892 Evaluate side-chains 123 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 110 time to evaluate : 1.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain R residue 138 PHE Chi-restraints excluded: chain R residue 409 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 0.0000 chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 10.0000 chunk 95 optimal weight: 1.9990 chunk 97 optimal weight: 0.8980 chunk 87 optimal weight: 0.7980 chunk 71 optimal weight: 0.4980 chunk 53 optimal weight: 2.9990 chunk 88 optimal weight: 0.6980 chunk 61 optimal weight: 0.9990 chunk 80 optimal weight: 0.2980 overall best weight: 0.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.205773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.163295 restraints weight = 9007.489| |-----------------------------------------------------------------------------| r_work (start): 0.3774 rms_B_bonded: 1.70 r_work: 0.3598 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3462 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.1471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 9126 Z= 0.108 Angle : 0.486 10.651 12391 Z= 0.259 Chirality : 0.040 0.158 1387 Planarity : 0.004 0.053 1575 Dihedral : 4.107 26.523 1244 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.85 % Allowed : 11.76 % Favored : 86.38 % 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: 1.72 (0.26), residues: 1125 helix: 2.84 (0.24), residues: 443 sheet: -0.22 (0.33), residues: 216 loop : 0.22 (0.30), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 298 HIS 0.004 0.001 HIS A 357 PHE 0.033 0.001 PHE R 335 TYR 0.026 0.001 TYR R 191 ARG 0.011 0.000 ARG B 197 Details of bonding type rmsd hydrogen bonds : bond 0.03770 ( 499) hydrogen bonds : angle 4.38694 ( 1440) SS BOND : bond 0.00254 ( 6) SS BOND : angle 1.01105 ( 12) covalent geometry : bond 0.00229 ( 9120) covalent geometry : angle 0.48481 (12379) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 122 time to evaluate : 1.005 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 ARG cc_start: 0.8370 (OUTLIER) cc_final: 0.7444 (mtt90) REVERT: A 60 MET cc_start: 0.6221 (OUTLIER) cc_final: 0.5985 (mmt) REVERT: A 240 ASP cc_start: 0.7368 (p0) cc_final: 0.6897 (p0) REVERT: B 134 ARG cc_start: 0.6758 (ptm160) cc_final: 0.6187 (ptm160) REVERT: B 155 ASN cc_start: 0.7752 (t0) cc_final: 0.7492 (m-40) REVERT: N 29 PHE cc_start: 0.7381 (t80) cc_final: 0.7099 (t80) REVERT: R 189 MET cc_start: 0.7672 (tmm) cc_final: 0.7457 (tmt) REVERT: R 214 ARG cc_start: 0.7389 (ptm160) cc_final: 0.7079 (pmm150) REVERT: R 390 ARG cc_start: 0.7980 (ttp-110) cc_final: 0.7478 (ttm170) outliers start: 17 outliers final: 9 residues processed: 129 average time/residue: 1.1494 time to fit residues: 159.5440 Evaluate side-chains 124 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 113 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain R residue 138 PHE Chi-restraints excluded: chain R residue 409 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 90 optimal weight: 2.9990 chunk 108 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 56 optimal weight: 5.9990 chunk 110 optimal weight: 0.6980 chunk 7 optimal weight: 0.6980 chunk 25 optimal weight: 9.9990 chunk 6 optimal weight: 0.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 390 GLN ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.201974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.158713 restraints weight = 9046.410| |-----------------------------------------------------------------------------| r_work (start): 0.3730 rms_B_bonded: 1.76 r_work: 0.3541 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3404 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.1542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9126 Z= 0.161 Angle : 0.548 13.121 12391 Z= 0.287 Chirality : 0.042 0.214 1387 Planarity : 0.004 0.055 1575 Dihedral : 4.311 25.324 1244 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.51 % Allowed : 12.96 % Favored : 84.53 % 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: 1.65 (0.26), residues: 1125 helix: 2.72 (0.24), residues: 443 sheet: -0.18 (0.33), residues: 216 loop : 0.20 (0.30), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 82 HIS 0.006 0.001 HIS A 357 PHE 0.031 0.002 PHE R 335 TYR 0.026 0.002 TYR R 191 ARG 0.012 0.000 ARG B 197 Details of bonding type rmsd hydrogen bonds : bond 0.04153 ( 499) hydrogen bonds : angle 4.53675 ( 1440) SS BOND : bond 0.00161 ( 6) SS BOND : angle 1.56234 ( 12) covalent geometry : bond 0.00370 ( 9120) covalent geometry : angle 0.54653 (12379) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 115 time to evaluate : 0.876 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 MET cc_start: 0.6259 (OUTLIER) cc_final: 0.5973 (mmt) REVERT: A 240 ASP cc_start: 0.7406 (p0) cc_final: 0.6955 (p0) REVERT: B 134 ARG cc_start: 0.6786 (ptm160) cc_final: 0.6222 (ptm160) REVERT: B 155 ASN cc_start: 0.7972 (t0) cc_final: 0.7687 (m-40) REVERT: B 173 THR cc_start: 0.8376 (p) cc_final: 0.8171 (p) REVERT: N 29 PHE cc_start: 0.7439 (t80) cc_final: 0.7185 (t80) REVERT: R 214 ARG cc_start: 0.7401 (ptm160) cc_final: 0.6889 (pmm150) REVERT: R 390 ARG cc_start: 0.7994 (ttp-110) cc_final: 0.7474 (ttm170) outliers start: 23 outliers final: 11 residues processed: 128 average time/residue: 1.1141 time to fit residues: 153.9098 Evaluate side-chains 122 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 110 time to evaluate : 1.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain R residue 138 PHE Chi-restraints excluded: chain R residue 409 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 53.9421 > 50: distance: 95 - 174: 15.478 distance: 98 - 171: 22.849 distance: 108 - 161: 17.089 distance: 111 - 158: 10.438 distance: 120 - 148: 16.191 distance: 122 - 126: 14.368 distance: 126 - 127: 34.149 distance: 127 - 128: 25.470 distance: 128 - 129: 20.960 distance: 128 - 130: 24.555 distance: 130 - 131: 21.435 distance: 131 - 132: 50.929 distance: 131 - 134: 30.951 distance: 132 - 133: 32.940 distance: 132 - 138: 45.006 distance: 134 - 135: 11.511 distance: 135 - 136: 16.475 distance: 135 - 137: 7.060 distance: 138 - 139: 31.079 distance: 139 - 140: 25.752 distance: 139 - 142: 14.624 distance: 140 - 141: 19.896 distance: 140 - 145: 7.572 distance: 142 - 143: 8.550 distance: 142 - 144: 17.528 distance: 145 - 146: 31.907 distance: 146 - 147: 14.159 distance: 146 - 149: 23.726 distance: 147 - 148: 16.782 distance: 147 - 152: 18.491 distance: 149 - 150: 15.131 distance: 149 - 151: 39.202 distance: 152 - 153: 15.579 distance: 152 - 252: 27.501 distance: 153 - 154: 19.688 distance: 153 - 156: 9.344 distance: 154 - 155: 9.444 distance: 154 - 158: 7.656 distance: 155 - 249: 12.012 distance: 156 - 157: 35.532 distance: 158 - 159: 26.112 distance: 159 - 160: 53.942 distance: 159 - 162: 29.052 distance: 160 - 161: 48.779 distance: 160 - 163: 51.366 distance: 163 - 164: 33.749 distance: 163 - 240: 24.196 distance: 164 - 165: 39.479 distance: 164 - 167: 18.615 distance: 165 - 166: 27.670 distance: 165 - 171: 42.649 distance: 166 - 237: 13.522 distance: 167 - 168: 8.245 distance: 168 - 169: 21.802 distance: 168 - 170: 10.181 distance: 171 - 172: 30.096 distance: 172 - 173: 26.823 distance: 172 - 175: 19.873 distance: 173 - 174: 25.997 distance: 173 - 185: 19.621 distance: 175 - 176: 12.412 distance: 176 - 177: 7.525 distance: 176 - 178: 27.209 distance: 177 - 179: 10.884 distance: 178 - 180: 47.541 distance: 178 - 181: 34.139 distance: 179 - 180: 39.027 distance: 180 - 182: 31.623 distance: 181 - 183: 17.685 distance: 182 - 184: 10.748 distance: 185 - 186: 17.442 distance: 186 - 187: 27.927 distance: 186 - 189: 11.584 distance: 187 - 188: 30.357 distance: 187 - 193: 24.273 distance: 189 - 190: 12.979 distance: 190 - 191: 8.953 distance: 190 - 192: 10.684 distance: 193 - 194: 16.971 distance: 194 - 195: 25.583 distance: 194 - 197: 12.919 distance: 195 - 196: 9.615 distance: 195 - 201: 12.715 distance: 197 - 198: 8.857 distance: 198 - 200: 4.401