Starting phenix.real_space_refine on Sat Aug 3 00:12:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lf6_23300/08_2024/7lf6_23300.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lf6_23300/08_2024/7lf6_23300.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lf6_23300/08_2024/7lf6_23300.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lf6_23300/08_2024/7lf6_23300.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lf6_23300/08_2024/7lf6_23300.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lf6_23300/08_2024/7lf6_23300.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.022 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 40 5.16 5 C 4164 2.51 5 N 1016 2.21 5 O 1068 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 6288 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 407, 3144 Classifications: {'peptide': 407} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 18, 'TRANS': 388} Chain breaks: 2 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'ARG:plan': 3} Unresolved non-hydrogen planarities: 15 Chain: "B" Number of atoms: 3144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 407, 3144 Classifications: {'peptide': 407} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 18, 'TRANS': 388} Chain breaks: 2 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'ARG:plan': 3} Unresolved non-hydrogen planarities: 15 Time building chain proxies: 4.51, per 1000 atoms: 0.72 Number of scatterers: 6288 At special positions: 0 Unit cell: (78.375, 85.8, 81.675, 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 40 16.00 O 1068 8.00 N 1016 7.00 C 4164 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 144 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS B 144 " - pdb=" SG CYS B 196 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.66 Conformation dependent library (CDL) restraints added in 1.2 seconds 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1556 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 0 sheets defined 81.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.54 Creating SS restraints... Processing helix chain 'A' and resid 35 through 50 removed outlier: 3.718A pdb=" N PHE A 39 " --> pdb=" O ARG A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 57 removed outlier: 4.070A pdb=" N VAL A 55 " --> pdb=" O MET A 51 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N HIS A 57 " --> pdb=" O LEU A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 102 removed outlier: 3.631A pdb=" N VAL A 101 " --> pdb=" O ARG A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 133 Proline residue: A 124 - end of helix Processing helix chain 'A' and resid 136 through 164 removed outlier: 4.436A pdb=" N ILE A 140 " --> pdb=" O VAL A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 206 removed outlier: 3.622A pdb=" N HIS A 184 " --> pdb=" O LEU A 180 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N GLY A 192 " --> pdb=" O ILE A 188 " (cutoff:3.500A) Proline residue: A 193 - end of helix removed outlier: 3.854A pdb=" N PHE A 205 " --> pdb=" O ILE A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 223 removed outlier: 4.486A pdb=" N VAL A 217 " --> pdb=" O LEU A 213 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N ILE A 218 " --> pdb=" O MET A 214 " (cutoff:3.500A) Proline residue: A 221 - end of helix Processing helix chain 'A' and resid 257 through 284 removed outlier: 4.806A pdb=" N LEU A 276 " --> pdb=" O VAL A 272 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N ILE A 277 " --> pdb=" O ALA A 273 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ASP A 283 " --> pdb=" O ASP A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 296 removed outlier: 3.676A pdb=" N PHE A 295 " --> pdb=" O LYS A 292 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N SER A 296 " --> pdb=" O GLU A 293 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 292 through 296' Processing helix chain 'A' and resid 298 through 333 removed outlier: 4.412A pdb=" N ALA A 302 " --> pdb=" O SER A 298 " (cutoff:3.500A) Proline residue: A 308 - end of helix removed outlier: 4.286A pdb=" N HIS A 333 " --> pdb=" O SER A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 353 Processing helix chain 'A' and resid 354 through 364 removed outlier: 3.813A pdb=" N ALA A 364 " --> pdb=" O GLN A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 396 removed outlier: 3.728A pdb=" N GLN A 390 " --> pdb=" O ALA A 386 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N MET A 393 " --> pdb=" O PHE A 389 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N TRP A 394 " --> pdb=" O GLN A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 410 Processing helix chain 'A' and resid 415 through 437 removed outlier: 5.617A pdb=" N TYR A 426 " --> pdb=" O LYS A 422 " (cutoff:3.500A) Proline residue: A 427 - end of helix Processing helix chain 'A' and resid 444 through 469 Proline residue: A 456 - end of helix removed outlier: 4.787A pdb=" N LEU A 460 " --> pdb=" O PRO A 456 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N LEU A 461 " --> pdb=" O CYS A 457 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA A 469 " --> pdb=" O LEU A 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 50 removed outlier: 3.719A pdb=" N PHE B 39 " --> pdb=" O ARG B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 57 removed outlier: 4.070A pdb=" N VAL B 55 " --> pdb=" O MET B 51 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N HIS B 57 " --> pdb=" O LEU B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 66 through 102 removed outlier: 3.631A pdb=" N VAL B 101 " --> pdb=" O ARG B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 133 Proline residue: B 124 - end of helix Processing helix chain 'B' and resid 136 through 164 removed outlier: 4.436A pdb=" N ILE B 140 " --> pdb=" O VAL B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 206 removed outlier: 3.622A pdb=" N HIS B 184 " --> pdb=" O LEU B 180 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N GLY B 192 " --> pdb=" O ILE B 188 " (cutoff:3.500A) Proline residue: B 193 - end of helix removed outlier: 3.854A pdb=" N PHE B 205 " --> pdb=" O ILE B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 223 removed outlier: 4.485A pdb=" N VAL B 217 " --> pdb=" O LEU B 213 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N ILE B 218 " --> pdb=" O MET B 214 " (cutoff:3.500A) Proline residue: B 221 - end of helix Processing helix chain 'B' and resid 257 through 284 removed outlier: 4.807A pdb=" N LEU B 276 " --> pdb=" O VAL B 272 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N ILE B 277 " --> pdb=" O ALA B 273 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ASP B 283 " --> pdb=" O ASP B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 296 removed outlier: 3.677A pdb=" N PHE B 295 " --> pdb=" O LYS B 292 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N SER B 296 " --> pdb=" O GLU B 293 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 292 through 296' Processing helix chain 'B' and resid 298 through 333 removed outlier: 4.411A pdb=" N ALA B 302 " --> pdb=" O SER B 298 " (cutoff:3.500A) Proline residue: B 308 - end of helix removed outlier: 4.285A pdb=" N HIS B 333 " --> pdb=" O SER B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 353 Processing helix chain 'B' and resid 354 through 364 removed outlier: 3.813A pdb=" N ALA B 364 " --> pdb=" O GLN B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 396 removed outlier: 3.727A pdb=" N GLN B 390 " --> pdb=" O ALA B 386 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N MET B 393 " --> pdb=" O PHE B 389 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N TRP B 394 " --> pdb=" O GLN B 390 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 415 through 437 removed outlier: 5.617A pdb=" N TYR B 426 " --> pdb=" O LYS B 422 " (cutoff:3.500A) Proline residue: B 427 - end of helix Processing helix chain 'B' and resid 444 through 469 Proline residue: B 456 - end of helix removed outlier: 4.787A pdb=" N LEU B 460 " --> pdb=" O PRO B 456 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N LEU B 461 " --> pdb=" O CYS B 457 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA B 469 " --> pdb=" O LEU B 465 " (cutoff:3.500A) 454 hydrogen bonds defined for protein. 1350 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.88 Time building geometry restraints manager: 2.89 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: 1932 1.34 - 1.47: 1612 1.47 - 1.60: 2836 1.60 - 1.73: 0 1.73 - 1.85: 62 Bond restraints: 6442 Sorted by residual: bond pdb=" CB CYS B 196 " pdb=" SG CYS B 196 " ideal model delta sigma weight residual 1.808 1.853 -0.045 3.30e-02 9.18e+02 1.86e+00 bond pdb=" CB CYS A 196 " pdb=" SG CYS A 196 " ideal model delta sigma weight residual 1.808 1.852 -0.044 3.30e-02 9.18e+02 1.81e+00 bond pdb=" CB MET A 130 " pdb=" CG MET A 130 " ideal model delta sigma weight residual 1.520 1.488 0.032 3.00e-02 1.11e+03 1.15e+00 bond pdb=" CB MET B 130 " pdb=" CG MET B 130 " ideal model delta sigma weight residual 1.520 1.488 0.032 3.00e-02 1.11e+03 1.11e+00 bond pdb=" CB TRP B 394 " pdb=" CG TRP B 394 " ideal model delta sigma weight residual 1.498 1.471 0.027 3.10e-02 1.04e+03 7.83e-01 ... (remaining 6437 not shown) Histogram of bond angle deviations from ideal: 99.19 - 106.17: 172 106.17 - 113.14: 3618 113.14 - 120.11: 2377 120.11 - 127.08: 2553 127.08 - 134.06: 72 Bond angle restraints: 8792 Sorted by residual: angle pdb=" N ILE B 218 " pdb=" CA ILE B 218 " pdb=" C ILE B 218 " ideal model delta sigma weight residual 113.42 108.71 4.71 1.17e+00 7.31e-01 1.62e+01 angle pdb=" N ILE A 218 " pdb=" CA ILE A 218 " pdb=" C ILE A 218 " ideal model delta sigma weight residual 113.42 108.73 4.69 1.17e+00 7.31e-01 1.61e+01 angle pdb=" CB MET A 130 " pdb=" CG MET A 130 " pdb=" SD MET A 130 " ideal model delta sigma weight residual 112.70 101.58 11.12 3.00e+00 1.11e-01 1.37e+01 angle pdb=" CB MET B 130 " pdb=" CG MET B 130 " pdb=" SD MET B 130 " ideal model delta sigma weight residual 112.70 101.59 11.11 3.00e+00 1.11e-01 1.37e+01 angle pdb=" N GLN B 361 " pdb=" CA GLN B 361 " pdb=" CB GLN B 361 " ideal model delta sigma weight residual 110.16 114.90 -4.74 1.48e+00 4.57e-01 1.02e+01 ... (remaining 8787 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.55: 3356 15.55 - 31.11: 302 31.11 - 46.66: 100 46.66 - 62.21: 10 62.21 - 77.77: 8 Dihedral angle restraints: 3776 sinusoidal: 1392 harmonic: 2384 Sorted by residual: dihedral pdb=" CG ARG A 375 " pdb=" CD ARG A 375 " pdb=" NE ARG A 375 " pdb=" CZ ARG A 375 " ideal model delta sinusoidal sigma weight residual 180.00 135.34 44.66 2 1.50e+01 4.44e-03 1.05e+01 dihedral pdb=" CG ARG B 375 " pdb=" CD ARG B 375 " pdb=" NE ARG B 375 " pdb=" CZ ARG B 375 " ideal model delta sinusoidal sigma weight residual 180.00 135.40 44.60 2 1.50e+01 4.44e-03 1.05e+01 dihedral pdb=" CA GLN B 34 " pdb=" C GLN B 34 " pdb=" N ARG B 35 " pdb=" CA ARG B 35 " ideal model delta harmonic sigma weight residual -180.00 -165.41 -14.59 0 5.00e+00 4.00e-02 8.51e+00 ... (remaining 3773 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 798 0.047 - 0.095: 237 0.095 - 0.142: 49 0.142 - 0.190: 0 0.190 - 0.237: 2 Chirality restraints: 1086 Sorted by residual: chirality pdb=" CB VAL A 409 " pdb=" CA VAL A 409 " pdb=" CG1 VAL A 409 " pdb=" CG2 VAL A 409 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.41e+00 chirality pdb=" CB VAL B 409 " pdb=" CA VAL B 409 " pdb=" CG1 VAL B 409 " pdb=" CG2 VAL B 409 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" CA VAL B 455 " pdb=" N VAL B 455 " pdb=" C VAL B 455 " pdb=" CB VAL B 455 " both_signs ideal model delta sigma weight residual False 2.44 2.31 0.14 2.00e-01 2.50e+01 4.62e-01 ... (remaining 1083 not shown) Planarity restraints: 1074 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 377 " 0.158 9.50e-02 1.11e+02 7.08e-02 3.24e+00 pdb=" NE ARG B 377 " -0.012 2.00e-02 2.50e+03 pdb=" CZ ARG B 377 " 0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG B 377 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG B 377 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 377 " -0.157 9.50e-02 1.11e+02 7.05e-02 3.22e+00 pdb=" NE ARG A 377 " 0.012 2.00e-02 2.50e+03 pdb=" CZ ARG A 377 " -0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG A 377 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A 377 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY B 192 " 0.029 5.00e-02 4.00e+02 4.42e-02 3.12e+00 pdb=" N PRO B 193 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO B 193 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 193 " 0.025 5.00e-02 4.00e+02 ... (remaining 1071 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1028 2.76 - 3.29: 6847 3.29 - 3.83: 11021 3.83 - 4.36: 12361 4.36 - 4.90: 20329 Nonbonded interactions: 51586 Sorted by model distance: nonbonded pdb=" O HIS B 400 " pdb=" OG1 THR B 404 " model vdw 2.220 3.040 nonbonded pdb=" O HIS A 400 " pdb=" OG1 THR A 404 " model vdw 2.220 3.040 nonbonded pdb=" NH2 ARG A 335 " pdb=" O ALA A 402 " model vdw 2.258 3.120 nonbonded pdb=" NH2 ARG B 335 " pdb=" O ALA B 402 " model vdw 2.260 3.120 nonbonded pdb=" O LEU B 213 " pdb=" OG1 THR B 216 " model vdw 2.265 3.040 ... (remaining 51581 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.010 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.330 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: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 21.940 Find NCS groups from input model: 0.220 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: 0.000 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7029 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 0.045 6442 Z= 0.211 Angle : 0.710 11.116 8792 Z= 0.374 Chirality : 0.045 0.237 1086 Planarity : 0.005 0.071 1074 Dihedral : 13.859 77.767 2214 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 17.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % 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: 1.00 (0.31), residues: 802 helix: 1.06 (0.21), residues: 612 sheet: None (None), residues: 0 loop : -0.41 (0.52), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 324 HIS 0.005 0.001 HIS A 416 PHE 0.018 0.001 PHE A 384 TYR 0.017 0.002 TYR A 313 ARG 0.007 0.001 ARG A 377 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 180 time to evaluate : 0.668 Fit side-chains revert: symmetry clash REVERT: A 71 GLN cc_start: 0.7516 (mm110) cc_final: 0.7188 (mm110) REVERT: A 262 GLU cc_start: 0.7075 (tp30) cc_final: 0.6673 (tp30) REVERT: A 361 GLN cc_start: 0.6761 (mp10) cc_final: 0.6292 (mp10) REVERT: A 377 ARG cc_start: 0.6352 (tpm170) cc_final: 0.6020 (tpm170) REVERT: A 418 LEU cc_start: 0.8138 (tp) cc_final: 0.7904 (tp) REVERT: A 451 MET cc_start: 0.7219 (ttp) cc_final: 0.6903 (ttp) REVERT: B 38 SER cc_start: 0.7534 (p) cc_final: 0.7288 (p) REVERT: B 71 GLN cc_start: 0.7508 (mm110) cc_final: 0.6852 (mm110) REVERT: B 72 ARG cc_start: 0.7764 (tmt-80) cc_final: 0.7104 (tmt-80) REVERT: B 85 PHE cc_start: 0.8029 (t80) cc_final: 0.7706 (t80) REVERT: B 130 MET cc_start: 0.6429 (mtt) cc_final: 0.6165 (mtt) REVERT: B 188 ILE cc_start: 0.8165 (tt) cc_final: 0.7847 (tt) REVERT: B 357 LEU cc_start: 0.7020 (tt) cc_final: 0.6343 (pp) REVERT: B 361 GLN cc_start: 0.6736 (mp10) cc_final: 0.6230 (mp10) REVERT: B 414 ARG cc_start: 0.7125 (mtt-85) cc_final: 0.6850 (mtt-85) REVERT: B 451 MET cc_start: 0.7030 (ttp) cc_final: 0.6698 (ttp) outliers start: 0 outliers final: 0 residues processed: 180 average time/residue: 0.2385 time to fit residues: 52.9158 Evaluate side-chains 173 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 173 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 67 optimal weight: 0.5980 chunk 60 optimal weight: 0.9990 chunk 33 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 62 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 chunk 38 optimal weight: 0.0070 chunk 46 optimal weight: 0.6980 chunk 72 optimal weight: 0.7980 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 328 HIS A 452 GLN ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 452 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7145 moved from start: 0.1576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 6442 Z= 0.235 Angle : 0.668 11.692 8792 Z= 0.342 Chirality : 0.045 0.230 1086 Planarity : 0.005 0.040 1074 Dihedral : 4.240 18.775 860 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 14.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.35 % Allowed : 13.97 % Favored : 83.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.30), residues: 802 helix: 1.09 (0.21), residues: 614 sheet: None (None), residues: 0 loop : -0.43 (0.52), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 410 HIS 0.013 0.001 HIS B 449 PHE 0.014 0.001 PHE B 459 TYR 0.019 0.002 TYR B 313 ARG 0.006 0.001 ARG B 35 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 188 time to evaluate : 0.719 Fit side-chains revert: symmetry clash REVERT: A 44 LEU cc_start: 0.8243 (OUTLIER) cc_final: 0.7993 (mp) REVERT: A 71 GLN cc_start: 0.7549 (mm110) cc_final: 0.7169 (mm110) REVERT: A 77 ARG cc_start: 0.8100 (mmt90) cc_final: 0.7856 (mmt90) REVERT: A 262 GLU cc_start: 0.7245 (tp30) cc_final: 0.6559 (tp30) REVERT: A 332 LEU cc_start: 0.7764 (mm) cc_final: 0.7430 (mm) REVERT: A 335 ARG cc_start: 0.6809 (ptt90) cc_final: 0.6598 (ptt90) REVERT: A 357 LEU cc_start: 0.7369 (tt) cc_final: 0.7109 (tt) REVERT: A 377 ARG cc_start: 0.6276 (tpm170) cc_final: 0.5640 (tpm170) REVERT: A 416 HIS cc_start: 0.7343 (t-90) cc_final: 0.7063 (t-170) REVERT: A 451 MET cc_start: 0.7247 (ttp) cc_final: 0.6991 (ttp) REVERT: A 452 GLN cc_start: 0.7706 (tp-100) cc_final: 0.7474 (tp-100) REVERT: B 71 GLN cc_start: 0.7575 (mm110) cc_final: 0.6878 (mm110) REVERT: B 85 PHE cc_start: 0.8054 (t80) cc_final: 0.7741 (t80) REVERT: B 164 PHE cc_start: 0.7066 (m-80) cc_final: 0.6817 (m-80) REVERT: B 357 LEU cc_start: 0.7348 (OUTLIER) cc_final: 0.6922 (tt) REVERT: B 451 MET cc_start: 0.7150 (ttp) cc_final: 0.6793 (ttp) outliers start: 16 outliers final: 9 residues processed: 191 average time/residue: 0.2194 time to fit residues: 52.6402 Evaluate side-chains 185 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 174 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 SER Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 414 ARG Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 357 LEU Chi-restraints excluded: chain B residue 388 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 40 optimal weight: 0.6980 chunk 22 optimal weight: 0.9980 chunk 60 optimal weight: 0.7980 chunk 49 optimal weight: 0.2980 chunk 20 optimal weight: 0.0770 chunk 72 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 chunk 24 optimal weight: 0.6980 chunk 58 optimal weight: 0.2980 chunk 71 optimal weight: 0.9980 overall best weight: 0.4138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 177 HIS B 328 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7147 moved from start: 0.1917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6442 Z= 0.198 Angle : 0.628 9.816 8792 Z= 0.319 Chirality : 0.043 0.234 1086 Planarity : 0.004 0.042 1074 Dihedral : 4.032 17.384 860 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 13.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 3.68 % Allowed : 21.32 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.30), residues: 802 helix: 1.19 (0.21), residues: 616 sheet: None (None), residues: 0 loop : -0.39 (0.53), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 92 HIS 0.012 0.001 HIS A 449 PHE 0.017 0.001 PHE B 459 TYR 0.019 0.002 TYR B 313 ARG 0.004 0.000 ARG B 35 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 181 time to evaluate : 0.837 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 44 LEU cc_start: 0.8149 (OUTLIER) cc_final: 0.7850 (mp) REVERT: A 55 VAL cc_start: 0.8760 (t) cc_final: 0.8519 (p) REVERT: A 71 GLN cc_start: 0.7535 (mm110) cc_final: 0.7139 (mm110) REVERT: A 72 ARG cc_start: 0.7820 (tmt-80) cc_final: 0.7591 (tmt-80) REVERT: A 77 ARG cc_start: 0.8107 (mmt90) cc_final: 0.7894 (mmt90) REVERT: A 117 MET cc_start: 0.7030 (mmp) cc_final: 0.6702 (mmt) REVERT: A 262 GLU cc_start: 0.7284 (tp30) cc_final: 0.6930 (tp30) REVERT: A 266 ASP cc_start: 0.7901 (m-30) cc_final: 0.7638 (t0) REVERT: A 332 LEU cc_start: 0.7966 (OUTLIER) cc_final: 0.7670 (mm) REVERT: A 357 LEU cc_start: 0.7437 (OUTLIER) cc_final: 0.7201 (tp) REVERT: A 416 HIS cc_start: 0.7363 (t-90) cc_final: 0.7117 (t-170) REVERT: A 451 MET cc_start: 0.7213 (ttp) cc_final: 0.6975 (ttp) REVERT: A 452 GLN cc_start: 0.7698 (tp-100) cc_final: 0.7231 (tp-100) REVERT: B 71 GLN cc_start: 0.7560 (mm110) cc_final: 0.6850 (mm110) REVERT: B 85 PHE cc_start: 0.8079 (t80) cc_final: 0.7715 (t80) REVERT: B 332 LEU cc_start: 0.7958 (OUTLIER) cc_final: 0.7739 (mm) REVERT: B 357 LEU cc_start: 0.7415 (OUTLIER) cc_final: 0.6997 (tt) REVERT: B 383 ILE cc_start: 0.7820 (mt) cc_final: 0.7542 (tt) REVERT: B 451 MET cc_start: 0.7146 (ttp) cc_final: 0.6812 (ttp) outliers start: 25 outliers final: 10 residues processed: 187 average time/residue: 0.2227 time to fit residues: 51.9076 Evaluate side-chains 194 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 179 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 SER Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 298 SER Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 414 ARG Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 357 LEU Chi-restraints excluded: chain B residue 388 ILE Chi-restraints excluded: chain B residue 420 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 54 optimal weight: 3.9990 chunk 37 optimal weight: 6.9990 chunk 8 optimal weight: 0.7980 chunk 34 optimal weight: 0.9980 chunk 48 optimal weight: 0.2980 chunk 73 optimal weight: 2.9990 chunk 77 optimal weight: 0.8980 chunk 38 optimal weight: 0.7980 chunk 69 optimal weight: 0.6980 chunk 20 optimal weight: 0.6980 chunk 64 optimal weight: 0.0170 overall best weight: 0.5018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 416 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7166 moved from start: 0.2250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6442 Z= 0.214 Angle : 0.652 9.947 8792 Z= 0.326 Chirality : 0.043 0.249 1086 Planarity : 0.004 0.040 1074 Dihedral : 4.026 17.613 860 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 3.38 % Allowed : 22.06 % Favored : 74.56 % 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: 1.03 (0.30), residues: 802 helix: 1.01 (0.20), residues: 630 sheet: None (None), residues: 0 loop : -0.23 (0.56), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 92 HIS 0.013 0.002 HIS B 449 PHE 0.014 0.001 PHE B 420 TYR 0.020 0.002 TYR B 313 ARG 0.003 0.000 ARG A 35 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 177 time to evaluate : 0.680 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 44 LEU cc_start: 0.8179 (OUTLIER) cc_final: 0.7818 (mp) REVERT: A 55 VAL cc_start: 0.8759 (t) cc_final: 0.8513 (p) REVERT: A 71 GLN cc_start: 0.7526 (mm110) cc_final: 0.7124 (mm110) REVERT: A 72 ARG cc_start: 0.7793 (tmt-80) cc_final: 0.7538 (tmt-80) REVERT: A 117 MET cc_start: 0.7062 (mmp) cc_final: 0.6689 (mmt) REVERT: A 262 GLU cc_start: 0.7307 (tp30) cc_final: 0.6972 (tp30) REVERT: A 332 LEU cc_start: 0.8088 (OUTLIER) cc_final: 0.7764 (mm) REVERT: A 357 LEU cc_start: 0.7567 (OUTLIER) cc_final: 0.7187 (tt) REVERT: A 416 HIS cc_start: 0.7528 (t-90) cc_final: 0.7224 (t-170) REVERT: A 451 MET cc_start: 0.7209 (ttp) cc_final: 0.6991 (ttp) REVERT: B 71 GLN cc_start: 0.7563 (mm110) cc_final: 0.6859 (mm110) REVERT: B 85 PHE cc_start: 0.8097 (t80) cc_final: 0.7671 (t80) REVERT: B 196 CYS cc_start: 0.4739 (OUTLIER) cc_final: 0.4533 (t) REVERT: B 332 LEU cc_start: 0.8029 (OUTLIER) cc_final: 0.7769 (mm) REVERT: B 357 LEU cc_start: 0.7490 (OUTLIER) cc_final: 0.6876 (tt) REVERT: B 361 GLN cc_start: 0.7030 (mp10) cc_final: 0.6746 (mp10) REVERT: B 383 ILE cc_start: 0.7852 (mt) cc_final: 0.7562 (tt) REVERT: B 451 MET cc_start: 0.7196 (ttp) cc_final: 0.6888 (ttp) outliers start: 23 outliers final: 12 residues processed: 183 average time/residue: 0.2324 time to fit residues: 53.0978 Evaluate side-chains 190 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 172 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 SER Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 163 HIS Chi-restraints excluded: chain A residue 298 SER Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 414 ARG Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain B residue 117 MET Chi-restraints excluded: chain B residue 196 CYS Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 357 LEU Chi-restraints excluded: chain B residue 388 ILE Chi-restraints excluded: chain B residue 420 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 43 optimal weight: 0.3980 chunk 1 optimal weight: 0.9990 chunk 57 optimal weight: 0.0050 chunk 31 optimal weight: 0.9990 chunk 65 optimal weight: 0.6980 chunk 53 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 69 optimal weight: 0.8980 chunk 19 optimal weight: 4.9990 chunk 26 optimal weight: 0.9990 overall best weight: 0.5394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7178 moved from start: 0.2483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6442 Z= 0.221 Angle : 0.652 10.544 8792 Z= 0.326 Chirality : 0.043 0.279 1086 Planarity : 0.005 0.057 1074 Dihedral : 4.033 17.971 860 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 13.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 5.44 % Allowed : 22.65 % Favored : 71.91 % 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: 0.90 (0.30), residues: 802 helix: 0.93 (0.20), residues: 632 sheet: None (None), residues: 0 loop : -0.35 (0.57), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 92 HIS 0.012 0.002 HIS B 449 PHE 0.016 0.001 PHE A 420 TYR 0.020 0.002 TYR B 313 ARG 0.005 0.000 ARG A 35 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 171 time to evaluate : 0.595 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 44 LEU cc_start: 0.8177 (OUTLIER) cc_final: 0.7945 (mp) REVERT: A 71 GLN cc_start: 0.7535 (mm110) cc_final: 0.7123 (mm110) REVERT: A 72 ARG cc_start: 0.7793 (tmt-80) cc_final: 0.6778 (tmt-80) REVERT: A 77 ARG cc_start: 0.8086 (mmt90) cc_final: 0.7878 (mmt90) REVERT: A 262 GLU cc_start: 0.7298 (tp30) cc_final: 0.7097 (tp30) REVERT: A 332 LEU cc_start: 0.8124 (OUTLIER) cc_final: 0.7812 (mm) REVERT: A 335 ARG cc_start: 0.6990 (ptt90) cc_final: 0.6759 (ptt90) REVERT: A 357 LEU cc_start: 0.7636 (OUTLIER) cc_final: 0.7243 (tt) REVERT: A 387 SER cc_start: 0.7984 (t) cc_final: 0.7671 (t) REVERT: A 416 HIS cc_start: 0.7642 (t-90) cc_final: 0.7334 (t-170) REVERT: A 451 MET cc_start: 0.7162 (ttp) cc_final: 0.6954 (ttp) REVERT: B 71 GLN cc_start: 0.7568 (mm110) cc_final: 0.6870 (mm110) REVERT: B 85 PHE cc_start: 0.8122 (t80) cc_final: 0.7674 (t80) REVERT: B 196 CYS cc_start: 0.4718 (OUTLIER) cc_final: 0.4514 (t) REVERT: B 332 LEU cc_start: 0.8034 (OUTLIER) cc_final: 0.7779 (mm) REVERT: B 357 LEU cc_start: 0.7531 (OUTLIER) cc_final: 0.6857 (tt) REVERT: B 361 GLN cc_start: 0.7059 (OUTLIER) cc_final: 0.6720 (mp10) REVERT: B 383 ILE cc_start: 0.7857 (mt) cc_final: 0.7555 (tt) REVERT: B 451 MET cc_start: 0.7207 (ttp) cc_final: 0.6914 (ttp) outliers start: 37 outliers final: 14 residues processed: 187 average time/residue: 0.2254 time to fit residues: 52.3899 Evaluate side-chains 190 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 169 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 SER Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 163 HIS Chi-restraints excluded: chain A residue 178 ARG Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 414 ARG Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain B residue 117 MET Chi-restraints excluded: chain B residue 183 ARG Chi-restraints excluded: chain B residue 196 CYS Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 357 LEU Chi-restraints excluded: chain B residue 361 GLN Chi-restraints excluded: chain B residue 388 ILE Chi-restraints excluded: chain B residue 420 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 69 optimal weight: 0.7980 chunk 15 optimal weight: 0.9990 chunk 45 optimal weight: 0.7980 chunk 19 optimal weight: 4.9990 chunk 77 optimal weight: 3.9990 chunk 64 optimal weight: 0.0070 chunk 35 optimal weight: 0.7980 chunk 6 optimal weight: 2.9990 chunk 25 optimal weight: 0.1980 chunk 40 optimal weight: 0.6980 chunk 74 optimal weight: 0.4980 overall best weight: 0.4398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 416 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7166 moved from start: 0.2640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6442 Z= 0.211 Angle : 0.649 10.152 8792 Z= 0.321 Chirality : 0.043 0.303 1086 Planarity : 0.005 0.042 1074 Dihedral : 3.966 16.920 860 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 13.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 5.15 % Allowed : 24.12 % Favored : 70.74 % 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: 0.98 (0.31), residues: 802 helix: 0.99 (0.20), residues: 632 sheet: None (None), residues: 0 loop : -0.34 (0.57), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 92 HIS 0.013 0.002 HIS B 449 PHE 0.017 0.001 PHE B 420 TYR 0.020 0.002 TYR B 313 ARG 0.005 0.000 ARG A 35 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 181 time to evaluate : 0.659 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 44 LEU cc_start: 0.8134 (OUTLIER) cc_final: 0.7914 (mp) REVERT: A 71 GLN cc_start: 0.7530 (mm110) cc_final: 0.7143 (mm110) REVERT: A 72 ARG cc_start: 0.7778 (tmt-80) cc_final: 0.7500 (tmt-80) REVERT: A 262 GLU cc_start: 0.7345 (tp30) cc_final: 0.7113 (tp30) REVERT: A 266 ASP cc_start: 0.7929 (m-30) cc_final: 0.7608 (t0) REVERT: A 332 LEU cc_start: 0.8106 (OUTLIER) cc_final: 0.7815 (mm) REVERT: A 357 LEU cc_start: 0.7593 (OUTLIER) cc_final: 0.6991 (tt) REVERT: A 361 GLN cc_start: 0.7039 (OUTLIER) cc_final: 0.6704 (mp10) REVERT: A 387 SER cc_start: 0.7981 (t) cc_final: 0.7657 (t) REVERT: A 416 HIS cc_start: 0.7669 (t-90) cc_final: 0.7452 (t-170) REVERT: A 451 MET cc_start: 0.7101 (ttp) cc_final: 0.6898 (ttp) REVERT: B 71 GLN cc_start: 0.7568 (mm110) cc_final: 0.6859 (mm110) REVERT: B 85 PHE cc_start: 0.8126 (t80) cc_final: 0.7648 (t80) REVERT: B 196 CYS cc_start: 0.4703 (OUTLIER) cc_final: 0.4443 (t) REVERT: B 332 LEU cc_start: 0.8026 (OUTLIER) cc_final: 0.7796 (mm) REVERT: B 357 LEU cc_start: 0.7527 (OUTLIER) cc_final: 0.6814 (tt) REVERT: B 361 GLN cc_start: 0.7061 (OUTLIER) cc_final: 0.6646 (mp10) REVERT: B 383 ILE cc_start: 0.7840 (mt) cc_final: 0.7543 (tt) REVERT: B 451 MET cc_start: 0.7219 (ttp) cc_final: 0.6847 (ttp) outliers start: 35 outliers final: 20 residues processed: 192 average time/residue: 0.2169 time to fit residues: 51.9950 Evaluate side-chains 207 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 179 time to evaluate : 0.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 SER Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 163 HIS Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 178 ARG Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 298 SER Chi-restraints excluded: chain A residue 314 PHE Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 361 GLN Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 414 ARG Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 117 MET Chi-restraints excluded: chain B residue 183 ARG Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 196 CYS Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 357 LEU Chi-restraints excluded: chain B residue 361 GLN Chi-restraints excluded: chain B residue 388 ILE Chi-restraints excluded: chain B residue 420 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 8 optimal weight: 0.5980 chunk 44 optimal weight: 0.5980 chunk 56 optimal weight: 0.6980 chunk 43 optimal weight: 0.4980 chunk 65 optimal weight: 0.8980 chunk 77 optimal weight: 4.9990 chunk 48 optimal weight: 0.5980 chunk 47 optimal weight: 0.7980 chunk 35 optimal weight: 0.9980 chunk 30 optimal weight: 0.6980 chunk 46 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 416 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7191 moved from start: 0.2796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 6442 Z= 0.249 Angle : 0.686 11.350 8792 Z= 0.338 Chirality : 0.044 0.262 1086 Planarity : 0.004 0.040 1074 Dihedral : 4.033 18.305 860 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 14.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 5.00 % Allowed : 25.59 % Favored : 69.41 % 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: 0.90 (0.30), residues: 802 helix: 0.83 (0.20), residues: 646 sheet: None (None), residues: 0 loop : 0.06 (0.61), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 92 HIS 0.014 0.002 HIS B 449 PHE 0.016 0.001 PHE B 420 TYR 0.021 0.002 TYR B 313 ARG 0.007 0.000 ARG A 35 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 181 time to evaluate : 0.666 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 44 LEU cc_start: 0.8143 (OUTLIER) cc_final: 0.7904 (mp) REVERT: A 71 GLN cc_start: 0.7552 (mm110) cc_final: 0.7163 (mm110) REVERT: A 72 ARG cc_start: 0.7787 (tmt-80) cc_final: 0.6758 (tmt-80) REVERT: A 77 ARG cc_start: 0.8088 (mmt90) cc_final: 0.7872 (mtt90) REVERT: A 196 CYS cc_start: 0.4725 (OUTLIER) cc_final: 0.4300 (t) REVERT: A 262 GLU cc_start: 0.7392 (tp30) cc_final: 0.7191 (tp30) REVERT: A 332 LEU cc_start: 0.8078 (OUTLIER) cc_final: 0.7795 (mm) REVERT: A 361 GLN cc_start: 0.7101 (OUTLIER) cc_final: 0.6900 (mp10) REVERT: A 387 SER cc_start: 0.7956 (t) cc_final: 0.7605 (t) REVERT: A 416 HIS cc_start: 0.7762 (t-90) cc_final: 0.7490 (t-170) REVERT: B 71 GLN cc_start: 0.7582 (mm110) cc_final: 0.6875 (mm110) REVERT: B 85 PHE cc_start: 0.8149 (t80) cc_final: 0.7615 (t80) REVERT: B 196 CYS cc_start: 0.4747 (OUTLIER) cc_final: 0.4477 (t) REVERT: B 262 GLU cc_start: 0.7285 (tp30) cc_final: 0.6626 (tp30) REVERT: B 332 LEU cc_start: 0.8062 (OUTLIER) cc_final: 0.7820 (mm) REVERT: B 335 ARG cc_start: 0.7198 (ptt90) cc_final: 0.6970 (ptt90) REVERT: B 357 LEU cc_start: 0.7506 (OUTLIER) cc_final: 0.6808 (tt) REVERT: B 361 GLN cc_start: 0.7052 (OUTLIER) cc_final: 0.6673 (mp10) REVERT: B 383 ILE cc_start: 0.7863 (mt) cc_final: 0.7544 (tt) REVERT: B 451 MET cc_start: 0.7209 (ttp) cc_final: 0.6930 (ttp) outliers start: 34 outliers final: 21 residues processed: 194 average time/residue: 0.2191 time to fit residues: 52.9089 Evaluate side-chains 206 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 177 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 SER Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 163 HIS Chi-restraints excluded: chain A residue 178 ARG Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 196 CYS Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 335 ARG Chi-restraints excluded: chain A residue 361 GLN Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 414 ARG Chi-restraints excluded: chain A residue 452 GLN Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 117 MET Chi-restraints excluded: chain B residue 183 ARG Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 196 CYS Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 344 LEU Chi-restraints excluded: chain B residue 357 LEU Chi-restraints excluded: chain B residue 361 GLN Chi-restraints excluded: chain B residue 388 ILE Chi-restraints excluded: chain B residue 420 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/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-5409/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-5409/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-5409/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-5409/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-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/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-5409/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-dev-5409/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-dev-5409/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: 70.2461 > 50: distance: 4 - 9: 30.237 distance: 9 - 10: 8.849 distance: 9 - 15: 55.368 distance: 10 - 13: 56.448 distance: 11 - 12: 40.453 distance: 11 - 16: 33.430 distance: 14 - 15: 44.683 distance: 16 - 17: 53.943 distance: 17 - 18: 39.569 distance: 18 - 19: 39.927 distance: 18 - 24: 32.450 distance: 20 - 21: 38.872 distance: 21 - 22: 63.827 distance: 21 - 23: 39.244 distance: 24 - 25: 9.879 distance: 24 - 30: 51.753 distance: 25 - 26: 46.382 distance: 25 - 28: 40.938 distance: 26 - 27: 33.591 distance: 26 - 31: 18.607 distance: 28 - 29: 51.618 distance: 29 - 30: 41.406 distance: 31 - 32: 47.745 distance: 32 - 33: 51.150 distance: 32 - 35: 50.519 distance: 33 - 34: 46.667 distance: 35 - 36: 39.939 distance: 36 - 37: 28.173 distance: 37 - 38: 29.983 distance: 38 - 39: 41.301 distance: 40 - 41: 53.746 distance: 41 - 42: 56.695 distance: 41 - 44: 40.796 distance: 42 - 48: 40.805 distance: 44 - 45: 30.180 distance: 45 - 46: 4.463 distance: 45 - 47: 9.469 distance: 48 - 49: 42.029 distance: 49 - 50: 28.005 distance: 49 - 52: 29.520 distance: 50 - 55: 12.051 distance: 52 - 53: 14.862 distance: 52 - 54: 45.425 distance: 55 - 56: 36.353 distance: 56 - 57: 45.141 distance: 56 - 59: 22.022 distance: 57 - 58: 7.176 distance: 57 - 60: 29.054 distance: 60 - 61: 26.458 distance: 61 - 62: 19.823 distance: 61 - 64: 28.988 distance: 62 - 63: 28.184 distance: 62 - 69: 41.761 distance: 64 - 65: 59.965 distance: 65 - 66: 38.773 distance: 66 - 67: 39.576 distance: 66 - 68: 57.280 distance: 70 - 71: 39.315 distance: 70 - 73: 45.831 distance: 71 - 74: 11.000 distance: 74 - 75: 41.278 distance: 75 - 76: 54.429 distance: 75 - 78: 40.934 distance: 76 - 85: 34.960 distance: 78 - 79: 41.375 distance: 79 - 80: 32.432 distance: 79 - 81: 51.191 distance: 80 - 82: 33.463 distance: 81 - 83: 13.106 distance: 82 - 84: 40.164 distance: 83 - 84: 36.530