Starting phenix.real_space_refine on Sat Jan 18 15:35:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xkf_33250/01_2025/7xkf_33250.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xkf_33250/01_2025/7xkf_33250.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7xkf_33250/01_2025/7xkf_33250.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xkf_33250/01_2025/7xkf_33250.map" model { file = "/net/cci-nas-00/data/ceres_data/7xkf_33250/01_2025/7xkf_33250.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xkf_33250/01_2025/7xkf_33250.cif" } resolution = 2.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 5427 atoms to isotropic. 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 48 5.16 5 C 5087 2.51 5 N 1372 2.21 5 O 1454 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 7961 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1856 Classifications: {'peptide': 226} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 6, 'TRANS': 219} Chain breaks: 3 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 13 Chain: "B" Number of atoms: 2601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2601 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "G" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 424 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 4, 'TRANS': 50} Chain: "N" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "R" Number of atoms: 2086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2086 Classifications: {'peptide': 261} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 4, 'TRANS': 256} Chain breaks: 2 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "R" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'AND': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.69, per 1000 atoms: 0.59 Number of scatterers: 7961 At special positions: 0 Unit cell: (103.887, 109.242, 95.319, 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 48 16.00 O 1454 8.00 N 1372 7.00 C 5087 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, 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 686 " - pdb=" SG CYS R 770 " 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: 2.62 Conformation dependent library (CDL) restraints added in 1.2 seconds 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1886 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 10 sheets defined 41.3% alpha, 20.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.84 Creating SS restraints... Processing helix chain 'A' and resid 10 through 39 removed outlier: 3.550A pdb=" N ASN A 14 " --> pdb=" O GLU A 10 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ALA A 39 " --> pdb=" O GLN A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 58 removed outlier: 3.547A pdb=" N VAL A 57 " --> pdb=" O LYS A 53 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LYS A 58 " --> pdb=" O ASN A 54 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 53 through 58' Processing helix chain 'A' and resid 233 through 239 removed outlier: 3.576A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 278 Processing helix chain 'A' and resid 293 through 303 Processing helix chain 'A' and resid 308 through 312 Processing helix chain 'A' and resid 313 through 316 Processing helix chain 'A' and resid 333 through 353 removed outlier: 3.893A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLY A 353 " --> pdb=" O SER A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 removed outlier: 3.520A pdb=" N GLN A 390 " --> pdb=" O MET A 386 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N TYR A 391 " --> pdb=" O HIS A 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 26 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 9 through 25 removed outlier: 4.026A pdb=" N ILE G 25 " --> pdb=" O MET G 21 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 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 Processing helix chain 'R' and resid 617 through 645 Processing helix chain 'R' and resid 646 through 649 Processing helix chain 'R' and resid 651 through 677 Processing helix chain 'R' and resid 682 through 716 Processing helix chain 'R' and resid 725 through 749 Proline residue: R 738 - end of helix Processing helix chain 'R' and resid 750 through 753 removed outlier: 3.781A pdb=" N TYR R 753 " --> pdb=" O PRO R 750 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 750 through 753' Processing helix chain 'R' and resid 776 through 783 Processing helix chain 'R' and resid 783 through 809 Processing helix chain 'R' and resid 820 through 834 removed outlier: 3.989A pdb=" N LEU R 824 " --> pdb=" O SER R 820 " (cutoff:3.500A) Processing helix chain 'R' and resid 835 through 838 Processing helix chain 'R' and resid 839 through 845 removed outlier: 4.145A pdb=" N PHE R 843 " --> pdb=" O GLY R 839 " (cutoff:3.500A) Processing helix chain 'R' and resid 849 through 862 removed outlier: 3.718A pdb=" N LEU R 862 " --> pdb=" O ILE R 858 " (cutoff:3.500A) Processing helix chain 'R' and resid 862 through 872 Processing helix chain 'R' and resid 875 through 883 removed outlier: 3.505A pdb=" N ARG R 879 " --> pdb=" O LYS R 875 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214 removed outlier: 4.476A pdb=" N VAL A 224 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N GLY A 47 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 8.175A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 8.566A pdb=" N ALA A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.631A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE B 81 " --> pdb=" O HIS B 91 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.934A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.406A 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: 3.791A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N CYS B 166 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N THR B 179 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N LEU B 168 " --> pdb=" O THR B 177 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLN B 175 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.718A pdb=" N ALA B 203 " --> pdb=" O SER B 207 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.745A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.587A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (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 11 through 12 removed outlier: 6.853A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N ALA N 40 " --> pdb=" O GLY N 44 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N GLY N 44 " --> pdb=" O ALA N 40 " (cutoff:3.500A) 401 hydrogen bonds defined for protein. 1131 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: 2.32 Time building geometry restraints manager: 3.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1283 1.31 - 1.44: 2278 1.44 - 1.56: 4493 1.56 - 1.69: 8 1.69 - 1.81: 66 Bond restraints: 8128 Sorted by residual: bond pdb=" C5 AND R1001 " pdb=" C6 AND R1001 " ideal model delta sigma weight residual 1.332 1.680 -0.348 2.00e-02 2.50e+03 3.02e+02 bond pdb=" C15 AND R1001 " pdb=" C16 AND R1001 " ideal model delta sigma weight residual 1.535 1.740 -0.205 2.00e-02 2.50e+03 1.05e+02 bond pdb=" C14 AND R1001 " pdb=" C15 AND R1001 " ideal model delta sigma weight residual 1.529 1.680 -0.151 2.00e-02 2.50e+03 5.74e+01 bond pdb=" C13 AND R1001 " pdb=" C17 AND R1001 " ideal model delta sigma weight residual 1.514 1.661 -0.147 2.00e-02 2.50e+03 5.42e+01 bond pdb=" C11 AND R1001 " pdb=" C12 AND R1001 " ideal model delta sigma weight residual 1.531 1.638 -0.107 2.00e-02 2.50e+03 2.87e+01 ... (remaining 8123 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.55: 10659 1.55 - 3.09: 258 3.09 - 4.64: 59 4.64 - 6.18: 29 6.18 - 7.73: 8 Bond angle restraints: 11013 Sorted by residual: angle pdb=" C ALA N 101 " pdb=" N PRO N 102 " pdb=" CA PRO N 102 " ideal model delta sigma weight residual 120.03 124.44 -4.41 9.90e-01 1.02e+00 1.99e+01 angle pdb=" CA PRO G 53 " pdb=" N PRO G 53 " pdb=" CD PRO G 53 " ideal model delta sigma weight residual 112.00 106.26 5.74 1.40e+00 5.10e-01 1.68e+01 angle pdb=" N ALA B 140 " pdb=" CA ALA B 140 " pdb=" C ALA B 140 " ideal model delta sigma weight residual 108.49 115.17 -6.68 1.65e+00 3.67e-01 1.64e+01 angle pdb=" N PRO N 100 " pdb=" CA PRO N 100 " pdb=" C PRO N 100 " ideal model delta sigma weight residual 113.53 119.12 -5.59 1.39e+00 5.18e-01 1.62e+01 angle pdb=" C CYS N 99 " pdb=" N PRO N 100 " pdb=" CA PRO N 100 " ideal model delta sigma weight residual 119.05 123.35 -4.30 1.11e+00 8.12e-01 1.50e+01 ... (remaining 11008 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.29: 4249 17.29 - 34.57: 460 34.57 - 51.86: 103 51.86 - 69.14: 22 69.14 - 86.43: 6 Dihedral angle restraints: 4840 sinusoidal: 1920 harmonic: 2920 Sorted by residual: dihedral pdb=" CB CYS N 99 " pdb=" SG CYS N 99 " pdb=" SG CYS N 107 " pdb=" CB CYS N 107 " ideal model delta sinusoidal sigma weight residual 93.00 6.57 86.43 1 1.00e+01 1.00e-02 9.00e+01 dihedral pdb=" CA CYS N 107 " pdb=" C CYS N 107 " pdb=" N PHE N 108 " pdb=" CA PHE N 108 " ideal model delta harmonic sigma weight residual -180.00 -156.77 -23.23 0 5.00e+00 4.00e-02 2.16e+01 dihedral pdb=" CB CYS R 686 " pdb=" SG CYS R 686 " pdb=" SG CYS R 770 " pdb=" CB CYS R 770 " ideal model delta sinusoidal sigma weight residual -86.00 -125.04 39.04 1 1.00e+01 1.00e-02 2.14e+01 ... (remaining 4837 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 1093 0.069 - 0.139: 145 0.139 - 0.208: 3 0.208 - 0.277: 1 0.277 - 0.346: 1 Chirality restraints: 1243 Sorted by residual: chirality pdb=" C13 AND R1001 " pdb=" C12 AND R1001 " pdb=" C14 AND R1001 " pdb=" C17 AND R1001 " both_signs ideal model delta sigma weight residual False -2.72 -2.37 -0.35 2.00e-01 2.50e+01 3.00e+00 chirality pdb=" C9 AND R1001 " pdb=" C10 AND R1001 " pdb=" C11 AND R1001 " pdb=" C8 AND R1001 " both_signs ideal model delta sigma weight residual False -2.46 -2.73 0.27 2.00e-01 2.50e+01 1.80e+00 chirality pdb=" CA PRO N 100 " pdb=" N PRO N 100 " pdb=" C PRO N 100 " pdb=" CB PRO N 100 " both_signs ideal model delta sigma weight residual False 2.72 2.51 0.21 2.00e-01 2.50e+01 1.06e+00 ... (remaining 1240 not shown) Planarity restraints: 1394 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG N 98 " 0.024 2.00e-02 2.50e+03 4.84e-02 2.34e+01 pdb=" C ARG N 98 " -0.084 2.00e-02 2.50e+03 pdb=" O ARG N 98 " 0.032 2.00e-02 2.50e+03 pdb=" N CYS N 99 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR G 52 " -0.076 5.00e-02 4.00e+02 1.12e-01 2.00e+01 pdb=" N PRO G 53 " 0.193 5.00e-02 4.00e+02 pdb=" CA PRO G 53 " -0.058 5.00e-02 4.00e+02 pdb=" CD PRO G 53 " -0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN N 13 " -0.030 5.00e-02 4.00e+02 4.63e-02 3.44e+00 pdb=" N PRO N 14 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO N 14 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO N 14 " -0.026 5.00e-02 4.00e+02 ... (remaining 1391 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.62: 118 2.62 - 3.19: 7185 3.19 - 3.76: 12363 3.76 - 4.33: 17452 4.33 - 4.90: 29049 Nonbonded interactions: 66167 Sorted by model distance: nonbonded pdb=" OG SER G 57 " pdb=" OE1 GLU G 58 " model vdw 2.055 3.040 nonbonded pdb=" OD1 ASN A 278 " pdb=" OG SER A 352 " model vdw 2.210 3.040 nonbonded pdb=" O SER N 112 " pdb=" NH2 ARG N 118 " model vdw 2.215 3.120 nonbonded pdb=" CA ASN A 279 " pdb=" OD2 ASP N 106 " model vdw 2.217 3.470 nonbonded pdb=" O SER A 251 " pdb=" NZ LYS A 300 " model vdw 2.222 3.120 ... (remaining 66162 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 22.570 Find NCS groups from input model: 0.080 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:13.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 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 : 0.007 0.348 8128 Z= 0.483 Angle : 0.678 7.729 11013 Z= 0.378 Chirality : 0.046 0.346 1243 Planarity : 0.006 0.112 1394 Dihedral : 15.092 85.281 2945 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 14.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 1.06 % Allowed : 17.22 % Favored : 81.72 % 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: 0.77 (0.27), residues: 988 helix: 2.40 (0.26), residues: 375 sheet: -0.04 (0.33), residues: 229 loop : -1.07 (0.30), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 234 HIS 0.011 0.001 HIS A 357 PHE 0.012 0.001 PHE R 634 TYR 0.012 0.001 TYR N 60 ARG 0.014 0.001 ARG G 13 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 159 time to evaluate : 0.952 Fit side-chains revert: symmetry clash REVERT: A 12 GLN cc_start: 0.8813 (mm110) cc_final: 0.8095 (pt0) REVERT: A 381 ASP cc_start: 0.8517 (t70) cc_final: 0.8103 (t70) REVERT: G 13 ARG cc_start: 0.8406 (mtm110) cc_final: 0.7964 (mtm110) outliers start: 9 outliers final: 7 residues processed: 166 average time/residue: 1.4901 time to fit residues: 259.7474 Evaluate side-chains 133 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 126 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 323 ASP Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain R residue 782 VAL Chi-restraints excluded: chain R residue 824 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 0.5980 chunk 74 optimal weight: 0.8980 chunk 41 optimal weight: 0.8980 chunk 25 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 76 optimal weight: 0.9990 chunk 29 optimal weight: 0.7980 chunk 46 optimal weight: 4.9990 chunk 57 optimal weight: 1.9990 chunk 88 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 860 ASN ** 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 = 0.3380 r_free = 0.3380 target = 0.091726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.068024 restraints weight = 14310.031| |-----------------------------------------------------------------------------| r_work (start): 0.2945 rms_B_bonded: 2.88 r_work: 0.2807 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.1215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8128 Z= 0.213 Angle : 0.558 5.468 11013 Z= 0.303 Chirality : 0.042 0.153 1243 Planarity : 0.004 0.067 1394 Dihedral : 5.063 46.406 1163 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 3.54 % Allowed : 20.05 % Favored : 76.42 % 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: 0.88 (0.27), residues: 988 helix: 2.55 (0.26), residues: 373 sheet: 0.02 (0.34), residues: 222 loop : -1.04 (0.30), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 211 HIS 0.008 0.001 HIS A 357 PHE 0.018 0.001 PHE R 671 TYR 0.015 0.001 TYR A 339 ARG 0.009 0.001 ARG R 650 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 137 time to evaluate : 0.999 Fit side-chains REVERT: A 12 GLN cc_start: 0.8252 (mm110) cc_final: 0.7846 (pt0) REVERT: A 38 ARG cc_start: 0.8740 (OUTLIER) cc_final: 0.8373 (mmt90) REVERT: A 216 LYS cc_start: 0.9164 (mtmm) cc_final: 0.8872 (mmpt) REVERT: A 220 HIS cc_start: 0.8669 (m170) cc_final: 0.8397 (m170) REVERT: A 296 LEU cc_start: 0.8942 (OUTLIER) cc_final: 0.8375 (mp) REVERT: B 23 LYS cc_start: 0.8904 (mmmm) cc_final: 0.8632 (tppt) REVERT: B 61 MET cc_start: 0.9410 (OUTLIER) cc_final: 0.9101 (ppp) REVERT: G 13 ARG cc_start: 0.8450 (mtm110) cc_final: 0.8173 (mtm110) REVERT: G 47 GLU cc_start: 0.8727 (pm20) cc_final: 0.8421 (pm20) REVERT: G 58 GLU cc_start: 0.8314 (pm20) cc_final: 0.8084 (pm20) REVERT: R 646 GLU cc_start: 0.7689 (tm-30) cc_final: 0.7405 (tm-30) outliers start: 30 outliers final: 8 residues processed: 154 average time/residue: 1.3843 time to fit residues: 225.3791 Evaluate side-chains 135 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 124 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 204 CYS Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain R residue 711 MET Chi-restraints excluded: chain R residue 782 VAL Chi-restraints excluded: chain R residue 872 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 13 optimal weight: 0.8980 chunk 74 optimal weight: 1.9990 chunk 76 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 chunk 84 optimal weight: 0.9990 chunk 51 optimal weight: 3.9990 chunk 82 optimal weight: 0.0270 chunk 53 optimal weight: 2.9990 chunk 85 optimal weight: 0.9980 chunk 90 optimal weight: 0.8980 chunk 38 optimal weight: 3.9990 overall best weight: 0.7640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 123 GLN ** R 860 ASN ** 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 = 0.3373 r_free = 0.3373 target = 0.091694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.067462 restraints weight = 14463.770| |-----------------------------------------------------------------------------| r_work (start): 0.2942 rms_B_bonded: 2.95 r_work: 0.2800 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.1477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8128 Z= 0.197 Angle : 0.539 8.354 11013 Z= 0.288 Chirality : 0.042 0.147 1243 Planarity : 0.004 0.056 1394 Dihedral : 4.308 36.246 1153 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 3.89 % Allowed : 20.05 % Favored : 76.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.27), residues: 988 helix: 2.59 (0.26), residues: 374 sheet: 0.04 (0.34), residues: 221 loop : -1.03 (0.30), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 211 HIS 0.007 0.001 HIS A 357 PHE 0.014 0.001 PHE R 671 TYR 0.012 0.001 TYR A 339 ARG 0.010 0.001 ARG R 650 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 143 time to evaluate : 0.981 Fit side-chains REVERT: A 12 GLN cc_start: 0.8345 (mm110) cc_final: 0.7825 (pt0) REVERT: A 13 ARG cc_start: 0.8200 (mpt180) cc_final: 0.7970 (mtm-85) REVERT: A 38 ARG cc_start: 0.8730 (OUTLIER) cc_final: 0.8361 (mmt90) REVERT: A 216 LYS cc_start: 0.9187 (mtmm) cc_final: 0.8913 (mmpt) REVERT: B 10 GLU cc_start: 0.8554 (tp30) cc_final: 0.8276 (tp30) REVERT: B 23 LYS cc_start: 0.8901 (mmmm) cc_final: 0.8620 (tppt) REVERT: B 61 MET cc_start: 0.9367 (OUTLIER) cc_final: 0.9151 (ppp) REVERT: B 215 GLU cc_start: 0.8894 (pm20) cc_final: 0.8694 (pm20) REVERT: B 234 PHE cc_start: 0.9119 (OUTLIER) cc_final: 0.7504 (t80) REVERT: G 47 GLU cc_start: 0.8726 (pm20) cc_final: 0.8414 (pm20) REVERT: N 3 GLN cc_start: 0.8411 (tt0) cc_final: 0.8185 (tt0) REVERT: R 646 GLU cc_start: 0.7616 (tm-30) cc_final: 0.7299 (tm-30) outliers start: 33 outliers final: 12 residues processed: 167 average time/residue: 1.3198 time to fit residues: 232.6603 Evaluate side-chains 137 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 122 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 204 CYS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 86 LEU Chi-restraints excluded: chain R residue 680 TYR Chi-restraints excluded: chain R residue 711 MET Chi-restraints excluded: chain R residue 782 VAL Chi-restraints excluded: chain R residue 824 LEU Chi-restraints excluded: chain R residue 872 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 17 optimal weight: 0.7980 chunk 30 optimal weight: 0.7980 chunk 56 optimal weight: 0.8980 chunk 20 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 chunk 4 optimal weight: 10.0000 chunk 19 optimal weight: 2.9990 chunk 13 optimal weight: 6.9990 chunk 94 optimal weight: 8.9990 chunk 55 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 123 GLN R 668 ASN ** R 860 ASN ** 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 = 0.3383 r_free = 0.3383 target = 0.091869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.068109 restraints weight = 14409.351| |-----------------------------------------------------------------------------| r_work (start): 0.2941 rms_B_bonded: 2.90 r_work: 0.2802 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.1650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8128 Z= 0.215 Angle : 0.553 6.960 11013 Z= 0.295 Chirality : 0.042 0.145 1243 Planarity : 0.004 0.052 1394 Dihedral : 4.307 35.628 1153 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 3.89 % Allowed : 20.87 % Favored : 75.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.17 % 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: 0.89 (0.27), residues: 988 helix: 2.53 (0.26), residues: 375 sheet: 0.05 (0.34), residues: 221 loop : -1.03 (0.30), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 211 HIS 0.006 0.001 HIS A 357 PHE 0.012 0.001 PHE R 671 TYR 0.012 0.001 TYR A 339 ARG 0.009 0.001 ARG R 650 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 126 time to evaluate : 0.863 Fit side-chains REVERT: A 12 GLN cc_start: 0.8275 (mm110) cc_final: 0.7827 (pt0) REVERT: A 13 ARG cc_start: 0.8211 (mpt180) cc_final: 0.7972 (mpp-170) REVERT: A 38 ARG cc_start: 0.8747 (OUTLIER) cc_final: 0.8366 (mmt90) REVERT: A 216 LYS cc_start: 0.9178 (mtmm) cc_final: 0.8915 (mmpt) REVERT: B 10 GLU cc_start: 0.8627 (tp30) cc_final: 0.8244 (tp30) REVERT: B 19 ARG cc_start: 0.8916 (ttp80) cc_final: 0.8711 (ttp80) REVERT: B 23 LYS cc_start: 0.8921 (mmmm) cc_final: 0.8645 (tppt) REVERT: B 61 MET cc_start: 0.9369 (OUTLIER) cc_final: 0.9114 (ppp) REVERT: B 234 PHE cc_start: 0.9150 (OUTLIER) cc_final: 0.7570 (t80) REVERT: B 256 ARG cc_start: 0.8262 (OUTLIER) cc_final: 0.7656 (ptt-90) REVERT: G 13 ARG cc_start: 0.8428 (mtm110) cc_final: 0.8223 (mtm110) REVERT: G 47 GLU cc_start: 0.8714 (pm20) cc_final: 0.8412 (pm20) REVERT: R 646 GLU cc_start: 0.7585 (tm-30) cc_final: 0.7211 (tm-30) outliers start: 33 outliers final: 16 residues processed: 151 average time/residue: 1.4077 time to fit residues: 223.5616 Evaluate side-chains 146 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 126 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 204 CYS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 256 ARG Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 86 LEU Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain R residue 680 TYR Chi-restraints excluded: chain R residue 711 MET Chi-restraints excluded: chain R residue 782 VAL Chi-restraints excluded: chain R residue 824 LEU Chi-restraints excluded: chain R residue 869 ILE Chi-restraints excluded: chain R residue 872 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 3 optimal weight: 0.9980 chunk 52 optimal weight: 0.0050 chunk 78 optimal weight: 0.9990 chunk 19 optimal weight: 0.5980 chunk 96 optimal weight: 0.5980 chunk 81 optimal weight: 0.8980 chunk 93 optimal weight: 0.8980 chunk 58 optimal weight: 3.9990 chunk 83 optimal weight: 0.8980 chunk 13 optimal weight: 7.9990 chunk 5 optimal weight: 3.9990 overall best weight: 0.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 849 ASN ** R 860 ASN ** 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 = 0.3383 r_free = 0.3383 target = 0.092274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.068193 restraints weight = 14446.022| |-----------------------------------------------------------------------------| r_work (start): 0.2957 rms_B_bonded: 2.93 r_work: 0.2819 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.1741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8128 Z= 0.179 Angle : 0.545 6.403 11013 Z= 0.291 Chirality : 0.042 0.141 1243 Planarity : 0.004 0.050 1394 Dihedral : 4.216 34.189 1153 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 4.13 % Allowed : 21.58 % Favored : 74.29 % 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: 0.92 (0.27), residues: 988 helix: 2.53 (0.26), residues: 375 sheet: 0.09 (0.34), residues: 221 loop : -1.01 (0.31), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 211 HIS 0.005 0.001 HIS A 357 PHE 0.011 0.001 PHE R 856 TYR 0.009 0.001 TYR A 339 ARG 0.012 0.001 ARG R 650 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 139 time to evaluate : 0.833 Fit side-chains revert: symmetry clash REVERT: A 12 GLN cc_start: 0.8265 (mm110) cc_final: 0.7835 (pt0) REVERT: A 13 ARG cc_start: 0.8251 (OUTLIER) cc_final: 0.7959 (mpp-170) REVERT: A 38 ARG cc_start: 0.8710 (OUTLIER) cc_final: 0.8327 (mmt90) REVERT: A 216 LYS cc_start: 0.9222 (mtmm) cc_final: 0.8982 (mmpt) REVERT: B 10 GLU cc_start: 0.8661 (tp30) cc_final: 0.8208 (tp30) REVERT: B 23 LYS cc_start: 0.8919 (mmmm) cc_final: 0.8673 (tppt) REVERT: B 127 LYS cc_start: 0.9021 (OUTLIER) cc_final: 0.8719 (ptpt) REVERT: B 215 GLU cc_start: 0.8930 (pm20) cc_final: 0.8728 (pm20) REVERT: B 234 PHE cc_start: 0.9127 (OUTLIER) cc_final: 0.7532 (t80) REVERT: G 47 GLU cc_start: 0.8718 (pm20) cc_final: 0.8421 (pm20) REVERT: R 623 ILE cc_start: 0.9163 (mt) cc_final: 0.8816 (OUTLIER) REVERT: R 646 GLU cc_start: 0.7493 (tm-30) cc_final: 0.7185 (tm-30) REVERT: R 862 LEU cc_start: 0.8277 (OUTLIER) cc_final: 0.7919 (pp) outliers start: 35 outliers final: 15 residues processed: 163 average time/residue: 1.3115 time to fit residues: 225.8263 Evaluate side-chains 146 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 127 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ARG Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 127 LYS Chi-restraints excluded: chain B residue 204 CYS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain R residue 680 TYR Chi-restraints excluded: chain R residue 711 MET Chi-restraints excluded: chain R residue 782 VAL Chi-restraints excluded: chain R residue 810 LYS Chi-restraints excluded: chain R residue 824 LEU Chi-restraints excluded: chain R residue 862 LEU Chi-restraints excluded: chain R residue 869 ILE Chi-restraints excluded: chain R residue 872 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 93 optimal weight: 0.9980 chunk 74 optimal weight: 0.7980 chunk 31 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 79 optimal weight: 0.7980 chunk 18 optimal weight: 4.9990 chunk 7 optimal weight: 0.6980 chunk 75 optimal weight: 0.8980 chunk 3 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 123 GLN ** R 860 ASN ** 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 = 0.3391 r_free = 0.3391 target = 0.092455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.068329 restraints weight = 14440.167| |-----------------------------------------------------------------------------| r_work (start): 0.2947 rms_B_bonded: 2.92 r_work: 0.2808 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.1845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8128 Z= 0.203 Angle : 0.568 7.794 11013 Z= 0.301 Chirality : 0.042 0.141 1243 Planarity : 0.004 0.049 1394 Dihedral : 4.217 34.356 1153 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 4.25 % Allowed : 22.05 % Favored : 73.70 % 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: 0.91 (0.27), residues: 988 helix: 2.52 (0.26), residues: 375 sheet: 0.13 (0.34), residues: 221 loop : -1.03 (0.31), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 211 HIS 0.005 0.001 HIS A 357 PHE 0.011 0.001 PHE R 856 TYR 0.012 0.001 TYR A 339 ARG 0.010 0.001 ARG R 650 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 132 time to evaluate : 1.035 Fit side-chains REVERT: A 12 GLN cc_start: 0.8288 (mm110) cc_final: 0.7850 (pt0) REVERT: A 38 ARG cc_start: 0.8742 (OUTLIER) cc_final: 0.8352 (mmt90) REVERT: A 216 LYS cc_start: 0.9223 (mtmm) cc_final: 0.8996 (mmpt) REVERT: B 10 GLU cc_start: 0.8629 (tp30) cc_final: 0.8161 (tp30) REVERT: B 23 LYS cc_start: 0.8912 (mmmm) cc_final: 0.8678 (tppt) REVERT: B 127 LYS cc_start: 0.9022 (OUTLIER) cc_final: 0.8759 (ptpt) REVERT: B 215 GLU cc_start: 0.8991 (pm20) cc_final: 0.8772 (pm20) REVERT: B 234 PHE cc_start: 0.9152 (OUTLIER) cc_final: 0.7568 (t80) REVERT: B 256 ARG cc_start: 0.8227 (OUTLIER) cc_final: 0.7457 (ptt-90) REVERT: G 13 ARG cc_start: 0.8360 (mtm110) cc_final: 0.8114 (mtm110) REVERT: G 20 LYS cc_start: 0.8300 (pttm) cc_final: 0.8075 (pttm) REVERT: G 47 GLU cc_start: 0.8719 (pm20) cc_final: 0.8438 (pm20) REVERT: R 623 ILE cc_start: 0.9198 (mt) cc_final: 0.8841 (OUTLIER) REVERT: R 646 GLU cc_start: 0.7489 (tm-30) cc_final: 0.7248 (tm-30) REVERT: R 822 GLN cc_start: 0.8605 (tm-30) cc_final: 0.8071 (tm-30) REVERT: R 862 LEU cc_start: 0.8288 (OUTLIER) cc_final: 0.7921 (pp) outliers start: 36 outliers final: 18 residues processed: 159 average time/residue: 1.3735 time to fit residues: 230.4895 Evaluate side-chains 145 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 123 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 127 LYS Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 204 CYS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 256 ARG Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 86 LEU Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain R residue 711 MET Chi-restraints excluded: chain R residue 782 VAL Chi-restraints excluded: chain R residue 810 LYS Chi-restraints excluded: chain R residue 824 LEU Chi-restraints excluded: chain R residue 862 LEU Chi-restraints excluded: chain R residue 869 ILE Chi-restraints excluded: chain R residue 872 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 69 optimal weight: 0.9990 chunk 77 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 chunk 15 optimal weight: 6.9990 chunk 48 optimal weight: 0.9990 chunk 53 optimal weight: 0.6980 chunk 20 optimal weight: 0.9990 chunk 70 optimal weight: 0.7980 chunk 71 optimal weight: 0.6980 chunk 12 optimal weight: 0.9980 chunk 59 optimal weight: 0.8980 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 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 ASN ** R 860 ASN ** 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 = 0.3393 r_free = 0.3393 target = 0.092488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.068431 restraints weight = 14436.417| |-----------------------------------------------------------------------------| r_work (start): 0.2949 rms_B_bonded: 2.90 r_work: 0.2811 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.1851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8128 Z= 0.208 Angle : 0.567 7.146 11013 Z= 0.300 Chirality : 0.042 0.140 1243 Planarity : 0.004 0.048 1394 Dihedral : 4.250 34.184 1153 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 3.89 % Allowed : 22.64 % Favored : 73.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.17 % 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: 0.93 (0.27), residues: 988 helix: 2.53 (0.26), residues: 375 sheet: 0.11 (0.34), residues: 221 loop : -1.01 (0.31), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 211 HIS 0.005 0.001 HIS A 357 PHE 0.012 0.001 PHE R 856 TYR 0.012 0.001 TYR N 60 ARG 0.011 0.001 ARG R 650 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 125 time to evaluate : 0.933 Fit side-chains REVERT: A 12 GLN cc_start: 0.8274 (mm110) cc_final: 0.7853 (pt0) REVERT: A 13 ARG cc_start: 0.8276 (mpt180) cc_final: 0.8055 (mpt180) REVERT: A 38 ARG cc_start: 0.8736 (OUTLIER) cc_final: 0.8341 (mmt90) REVERT: A 216 LYS cc_start: 0.9222 (mtmm) cc_final: 0.8995 (mmpt) REVERT: A 331 ASP cc_start: 0.8189 (OUTLIER) cc_final: 0.7887 (OUTLIER) REVERT: B 10 GLU cc_start: 0.8675 (tp30) cc_final: 0.8210 (tp30) REVERT: B 23 LYS cc_start: 0.8911 (mmmm) cc_final: 0.8709 (tppt) REVERT: B 127 LYS cc_start: 0.9022 (OUTLIER) cc_final: 0.8717 (ptpt) REVERT: B 234 PHE cc_start: 0.9156 (OUTLIER) cc_final: 0.7587 (t80) REVERT: B 256 ARG cc_start: 0.8198 (OUTLIER) cc_final: 0.7528 (ptt-90) REVERT: B 325 MET cc_start: 0.9110 (mmt) cc_final: 0.8906 (mmm) REVERT: G 13 ARG cc_start: 0.8397 (mtm110) cc_final: 0.8174 (mtm110) REVERT: G 20 LYS cc_start: 0.8291 (pttm) cc_final: 0.8038 (pttm) REVERT: G 47 GLU cc_start: 0.8739 (pm20) cc_final: 0.8453 (pm20) REVERT: R 646 GLU cc_start: 0.7421 (tm-30) cc_final: 0.7156 (tm-30) REVERT: R 822 GLN cc_start: 0.8605 (tm-30) cc_final: 0.8070 (tm-30) REVERT: R 862 LEU cc_start: 0.8300 (OUTLIER) cc_final: 0.7929 (pp) outliers start: 33 outliers final: 18 residues processed: 150 average time/residue: 1.4036 time to fit residues: 221.9335 Evaluate side-chains 147 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 124 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 331 ASP Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 127 LYS Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 204 CYS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 256 ARG Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 86 LEU Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain R residue 711 MET Chi-restraints excluded: chain R residue 782 VAL Chi-restraints excluded: chain R residue 810 LYS Chi-restraints excluded: chain R residue 824 LEU Chi-restraints excluded: chain R residue 862 LEU Chi-restraints excluded: chain R residue 869 ILE Chi-restraints excluded: chain R residue 872 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 53 optimal weight: 4.9990 chunk 20 optimal weight: 0.9980 chunk 28 optimal weight: 0.8980 chunk 9 optimal weight: 0.6980 chunk 93 optimal weight: 3.9990 chunk 8 optimal weight: 0.0670 chunk 81 optimal weight: 0.9990 chunk 76 optimal weight: 0.5980 chunk 77 optimal weight: 0.6980 chunk 5 optimal weight: 2.9990 chunk 80 optimal weight: 0.9980 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 860 ASN ** 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 = 0.3403 r_free = 0.3403 target = 0.093066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.069032 restraints weight = 14458.192| |-----------------------------------------------------------------------------| r_work (start): 0.2962 rms_B_bonded: 2.91 r_work: 0.2824 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.1960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8128 Z= 0.190 Angle : 0.577 7.299 11013 Z= 0.307 Chirality : 0.042 0.146 1243 Planarity : 0.004 0.052 1394 Dihedral : 4.201 33.387 1153 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 3.54 % Allowed : 23.23 % Favored : 73.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.17 % 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: 0.93 (0.27), residues: 988 helix: 2.52 (0.26), residues: 375 sheet: 0.12 (0.34), residues: 220 loop : -1.01 (0.31), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 211 HIS 0.005 0.001 HIS A 357 PHE 0.012 0.001 PHE R 856 TYR 0.012 0.001 TYR N 60 ARG 0.013 0.001 ARG N 105 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 126 time to evaluate : 0.814 Fit side-chains REVERT: A 12 GLN cc_start: 0.8268 (mm110) cc_final: 0.7764 (pt0) REVERT: A 13 ARG cc_start: 0.8292 (mpt180) cc_final: 0.7799 (mpp-170) REVERT: A 38 ARG cc_start: 0.8734 (OUTLIER) cc_final: 0.8337 (mmt90) REVERT: A 216 LYS cc_start: 0.9211 (mtmm) cc_final: 0.8980 (mmpt) REVERT: B 10 GLU cc_start: 0.8672 (tp30) cc_final: 0.8197 (tp30) REVERT: B 127 LYS cc_start: 0.9018 (OUTLIER) cc_final: 0.8720 (ptpt) REVERT: B 234 PHE cc_start: 0.9128 (OUTLIER) cc_final: 0.7542 (t80) REVERT: B 325 MET cc_start: 0.9103 (mmt) cc_final: 0.8899 (mmm) REVERT: G 20 LYS cc_start: 0.8266 (pttm) cc_final: 0.8046 (pttm) REVERT: G 47 GLU cc_start: 0.8731 (pm20) cc_final: 0.8441 (pm20) REVERT: R 646 GLU cc_start: 0.7470 (tm-30) cc_final: 0.7187 (tm-30) REVERT: R 768 ASP cc_start: 0.5438 (p0) cc_final: 0.4877 (m-30) REVERT: R 822 GLN cc_start: 0.8598 (tm-30) cc_final: 0.8066 (tm-30) REVERT: R 862 LEU cc_start: 0.8284 (OUTLIER) cc_final: 0.7919 (pp) outliers start: 30 outliers final: 17 residues processed: 149 average time/residue: 1.3910 time to fit residues: 218.6969 Evaluate side-chains 151 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 130 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 127 LYS Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 204 CYS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain R residue 711 MET Chi-restraints excluded: chain R residue 782 VAL Chi-restraints excluded: chain R residue 810 LYS Chi-restraints excluded: chain R residue 824 LEU Chi-restraints excluded: chain R residue 862 LEU Chi-restraints excluded: chain R residue 869 ILE Chi-restraints excluded: chain R residue 872 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 69 optimal weight: 3.9990 chunk 59 optimal weight: 0.2980 chunk 81 optimal weight: 0.9990 chunk 56 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 94 optimal weight: 6.9990 chunk 86 optimal weight: 0.7980 chunk 72 optimal weight: 1.9990 chunk 89 optimal weight: 0.6980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 860 ASN ** 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 = 0.3383 r_free = 0.3383 target = 0.091844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.067528 restraints weight = 14628.231| |-----------------------------------------------------------------------------| r_work (start): 0.2935 rms_B_bonded: 2.94 r_work: 0.2796 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.1931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8128 Z= 0.239 Angle : 0.609 7.930 11013 Z= 0.323 Chirality : 0.043 0.156 1243 Planarity : 0.004 0.055 1394 Dihedral : 4.309 34.766 1153 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 2.95 % Allowed : 23.82 % Favored : 73.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.17 % 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: 0.85 (0.27), residues: 988 helix: 2.47 (0.26), residues: 375 sheet: -0.01 (0.34), residues: 223 loop : -1.00 (0.31), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 234 HIS 0.006 0.001 HIS A 357 PHE 0.012 0.001 PHE R 856 TYR 0.014 0.001 TYR N 60 ARG 0.013 0.001 ARG N 105 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 123 time to evaluate : 0.891 Fit side-chains revert: symmetry clash REVERT: A 12 GLN cc_start: 0.8197 (mm110) cc_final: 0.7825 (pt0) REVERT: A 13 ARG cc_start: 0.8344 (mpt180) cc_final: 0.7789 (mpp-170) REVERT: A 38 ARG cc_start: 0.8744 (OUTLIER) cc_final: 0.8341 (mmt90) REVERT: A 216 LYS cc_start: 0.9218 (mtmm) cc_final: 0.8994 (mmpt) REVERT: B 10 GLU cc_start: 0.8656 (tp30) cc_final: 0.8196 (tp30) REVERT: B 127 LYS cc_start: 0.9020 (OUTLIER) cc_final: 0.8697 (ptpt) REVERT: B 234 PHE cc_start: 0.9172 (OUTLIER) cc_final: 0.7500 (t80) REVERT: G 20 LYS cc_start: 0.8282 (pttm) cc_final: 0.8081 (pttm) REVERT: G 47 GLU cc_start: 0.8764 (pm20) cc_final: 0.8485 (pm20) REVERT: R 646 GLU cc_start: 0.7459 (tm-30) cc_final: 0.7175 (tm-30) REVERT: R 803 GLN cc_start: 0.8486 (OUTLIER) cc_final: 0.7968 (mt0) REVERT: R 822 GLN cc_start: 0.8608 (tm-30) cc_final: 0.8076 (tm-30) REVERT: R 862 LEU cc_start: 0.8285 (OUTLIER) cc_final: 0.7939 (pp) outliers start: 25 outliers final: 17 residues processed: 142 average time/residue: 1.3689 time to fit residues: 204.8933 Evaluate side-chains 147 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 125 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 127 LYS Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 204 CYS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain R residue 711 MET Chi-restraints excluded: chain R residue 782 VAL Chi-restraints excluded: chain R residue 803 GLN Chi-restraints excluded: chain R residue 810 LYS Chi-restraints excluded: chain R residue 824 LEU Chi-restraints excluded: chain R residue 862 LEU Chi-restraints excluded: chain R residue 869 ILE Chi-restraints excluded: chain R residue 872 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 97 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 10 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 74 optimal weight: 0.8980 chunk 53 optimal weight: 0.5980 chunk 83 optimal weight: 0.6980 chunk 85 optimal weight: 2.9990 chunk 82 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 860 ASN ** 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 = 0.3386 r_free = 0.3386 target = 0.092060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.068365 restraints weight = 14352.218| |-----------------------------------------------------------------------------| r_work (start): 0.2946 rms_B_bonded: 2.89 r_work: 0.2805 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.2008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8128 Z= 0.222 Angle : 0.609 7.972 11013 Z= 0.325 Chirality : 0.043 0.172 1243 Planarity : 0.004 0.059 1394 Dihedral : 4.306 34.148 1153 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 2.71 % Allowed : 24.53 % Favored : 72.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.17 % 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: 0.85 (0.27), residues: 988 helix: 2.45 (0.26), residues: 375 sheet: 0.04 (0.34), residues: 221 loop : -1.01 (0.31), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 211 HIS 0.005 0.001 HIS A 357 PHE 0.012 0.001 PHE R 856 TYR 0.012 0.001 TYR N 60 ARG 0.014 0.001 ARG N 105 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 128 time to evaluate : 0.864 Fit side-chains revert: symmetry clash REVERT: A 12 GLN cc_start: 0.8224 (mm110) cc_final: 0.7837 (pt0) REVERT: A 13 ARG cc_start: 0.8339 (mpt180) cc_final: 0.7793 (mpp-170) REVERT: A 38 ARG cc_start: 0.8737 (OUTLIER) cc_final: 0.8327 (mmt90) REVERT: A 216 LYS cc_start: 0.9211 (mtmm) cc_final: 0.8983 (mmpt) REVERT: A 296 LEU cc_start: 0.8911 (mp) cc_final: 0.8351 (mp) REVERT: B 10 GLU cc_start: 0.8692 (tp30) cc_final: 0.8223 (tp30) REVERT: B 127 LYS cc_start: 0.9016 (OUTLIER) cc_final: 0.8710 (ptpt) REVERT: B 215 GLU cc_start: 0.8858 (pm20) cc_final: 0.8281 (pm20) REVERT: B 217 MET cc_start: 0.7514 (pmt) cc_final: 0.6857 (pmt) REVERT: B 234 PHE cc_start: 0.9162 (OUTLIER) cc_final: 0.7489 (t80) REVERT: G 20 LYS cc_start: 0.8223 (pttm) cc_final: 0.7981 (pttm) REVERT: G 47 GLU cc_start: 0.8772 (pm20) cc_final: 0.8490 (pm20) REVERT: R 803 GLN cc_start: 0.8468 (OUTLIER) cc_final: 0.7972 (mt0) REVERT: R 822 GLN cc_start: 0.8599 (tm-30) cc_final: 0.8066 (tm-30) REVERT: R 862 LEU cc_start: 0.8269 (OUTLIER) cc_final: 0.7925 (pp) outliers start: 23 outliers final: 18 residues processed: 145 average time/residue: 1.3284 time to fit residues: 203.4937 Evaluate side-chains 154 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 131 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 274 ASP Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 127 LYS Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 204 CYS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain R residue 711 MET Chi-restraints excluded: chain R residue 782 VAL Chi-restraints excluded: chain R residue 803 GLN Chi-restraints excluded: chain R residue 810 LYS Chi-restraints excluded: chain R residue 824 LEU Chi-restraints excluded: chain R residue 862 LEU Chi-restraints excluded: chain R residue 869 ILE Chi-restraints excluded: chain R residue 872 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/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-5571/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-5571/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-5571/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-5571/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-5571/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-5571/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-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/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-5571/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-5571/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-5571/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: 56.2337 > 50: distance: 35 - 54: 9.120 distance: 39 - 61: 14.618 distance: 45 - 69: 33.867 distance: 48 - 54: 9.268 distance: 49 - 76: 30.866 distance: 54 - 55: 7.237 distance: 55 - 56: 16.385 distance: 55 - 58: 15.095 distance: 56 - 57: 17.935 distance: 56 - 61: 4.690 distance: 57 - 84: 39.723 distance: 58 - 59: 8.086 distance: 61 - 62: 15.126 distance: 62 - 63: 7.863 distance: 62 - 65: 10.637 distance: 63 - 64: 10.006 distance: 63 - 69: 15.996 distance: 65 - 66: 10.347 distance: 66 - 67: 11.608 distance: 69 - 70: 6.051 distance: 70 - 71: 26.177 distance: 70 - 73: 19.022 distance: 71 - 72: 8.442 distance: 71 - 76: 19.627 distance: 73 - 74: 16.257 distance: 73 - 75: 16.051 distance: 76 - 77: 12.078 distance: 77 - 78: 34.372 distance: 77 - 80: 15.023 distance: 78 - 79: 21.634 distance: 78 - 84: 32.659 distance: 80 - 81: 18.538 distance: 80 - 82: 11.878 distance: 81 - 83: 21.984 distance: 84 - 85: 11.893 distance: 85 - 86: 10.737 distance: 85 - 88: 3.397 distance: 86 - 87: 17.498 distance: 86 - 90: 13.730 distance: 88 - 89: 4.854 distance: 90 - 91: 17.416 distance: 90 - 96: 9.608 distance: 91 - 92: 6.606 distance: 91 - 94: 7.943 distance: 92 - 93: 10.093 distance: 92 - 97: 12.037 distance: 94 - 95: 21.548 distance: 95 - 96: 8.399 distance: 97 - 98: 10.436 distance: 98 - 99: 15.910 distance: 98 - 101: 22.440 distance: 99 - 100: 17.665 distance: 99 - 105: 20.202 distance: 101 - 102: 19.307 distance: 102 - 103: 9.972 distance: 102 - 104: 15.239 distance: 106 - 109: 12.944 distance: 107 - 108: 5.627 distance: 109 - 110: 18.314 distance: 110 - 111: 20.026 distance: 110 - 112: 8.249 distance: 113 - 114: 15.417 distance: 114 - 115: 7.237 distance: 114 - 117: 6.761 distance: 115 - 116: 18.433 distance: 115 - 125: 20.920 distance: 117 - 118: 11.212 distance: 118 - 119: 8.751 distance: 118 - 120: 23.223 distance: 119 - 121: 13.078 distance: 120 - 122: 17.831 distance: 121 - 123: 21.670 distance: 122 - 123: 9.212 distance: 123 - 124: 11.407 distance: 125 - 126: 14.718 distance: 127 - 128: 9.788 distance: 127 - 129: 30.199