Starting phenix.real_space_refine on Wed Mar 12 03:08:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ld3_23280/03_2025/7ld3_23280.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ld3_23280/03_2025/7ld3_23280.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ld3_23280/03_2025/7ld3_23280.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ld3_23280/03_2025/7ld3_23280.map" model { file = "/net/cci-nas-00/data/ceres_data/7ld3_23280/03_2025/7ld3_23280.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ld3_23280/03_2025/7ld3_23280.cif" } resolution = 3.2 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= 0.004 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: 6 Type Number sf(0) Gaussians S 53 5.16 5 Cl 1 4.86 5 C 4498 2.51 5 N 1189 2.21 5 O 1269 1.98 5 F 6 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 7016 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1693 Classifications: {'peptide': 210} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 207} Chain breaks: 2 Chain: "R" Number of atoms: 2273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2273 Classifications: {'peptide': 288} Link IDs: {'PTRANS': 14, 'TRANS': 273} Chain breaks: 1 Chain: "B" Number of atoms: 2568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2568 Classifications: {'peptide': 334} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 328} Chain breaks: 1 Chain: "G" Number of atoms: 433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 433 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 4, 'TRANS': 51} Chain: "R" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 49 Unusual residues: {'ADN%rna3p': 1, 'XTD': 1} Classifications: {'undetermined': 2, 'water': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 2} Time building chain proxies: 4.78, per 1000 atoms: 0.68 Number of scatterers: 7016 At special positions: 0 Unit cell: (127.204, 88.382, 102.424, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 1 17.00 S 53 16.00 F 6 9.00 O 1269 8.00 N 1189 7.00 C 4498 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS R 80 " - pdb=" SG CYS R 169 " distance=2.03 Simple disulfide: pdb=" SG CYS R 260 " - pdb=" SG CYS R 263 " distance=2.04 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: 1.80 Conformation dependent library (CDL) restraints added in 1.0 seconds 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1684 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 9 sheets defined 47.1% alpha, 19.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.82 Creating SS restraints... Processing helix chain 'A' and resid 11 through 30 removed outlier: 3.702A pdb=" N ARG A 15 " --> pdb=" O ALA A 11 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 53 removed outlier: 3.671A pdb=" N ILE A 49 " --> pdb=" O GLY A 45 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL A 50 " --> pdb=" O LYS A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 217 removed outlier: 4.834A pdb=" N ILE A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N HIS A 214 " --> pdb=" O LYS A 211 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N PHE A 216 " --> pdb=" O ILE A 213 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLU A 217 " --> pdb=" O HIS A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 232 removed outlier: 4.105A pdb=" N ASP A 232 " --> pdb=" O SER A 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 229 through 232' Processing helix chain 'A' and resid 242 through 256 removed outlier: 3.526A pdb=" N ASN A 256 " --> pdb=" O ASP A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 282 removed outlier: 3.644A pdb=" N GLU A 277 " --> pdb=" O ASP A 273 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N THR A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N HIS A 281 " --> pdb=" O GLU A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 310 Processing helix chain 'A' and resid 328 through 353 removed outlier: 3.704A pdb=" N ASN A 332 " --> pdb=" O THR A 328 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL A 333 " --> pdb=" O ASP A 329 " (cutoff:3.500A) Processing helix chain 'R' and resid 6 through 36 removed outlier: 3.715A pdb=" N ALA R 10 " --> pdb=" O SER R 6 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ALA R 11 " --> pdb=" O ALA R 7 " (cutoff:3.500A) Proline residue: R 25 - end of helix Processing helix chain 'R' and resid 42 through 62 Processing helix chain 'R' and resid 62 through 72 Processing helix chain 'R' and resid 77 through 111 Proline residue: R 86 - end of helix Processing helix chain 'R' and resid 120 through 140 Processing helix chain 'R' and resid 141 through 144 Processing helix chain 'R' and resid 148 through 160 Processing helix chain 'R' and resid 170 through 175 removed outlier: 3.664A pdb=" N VAL R 174 " --> pdb=" O GLU R 170 " (cutoff:3.500A) Processing helix chain 'R' and resid 176 through 183 Processing helix chain 'R' and resid 184 through 189 Processing helix chain 'R' and resid 189 through 211 Processing helix chain 'R' and resid 225 through 260 Proline residue: R 249 - end of helix Processing helix chain 'R' and resid 266 through 279 removed outlier: 3.731A pdb=" N THR R 270 " --> pdb=" O PRO R 266 " (cutoff:3.500A) Processing helix chain 'R' and resid 283 through 288 removed outlier: 3.664A pdb=" N VAL R 287 " --> pdb=" O MET R 283 " (cutoff:3.500A) Processing helix chain 'R' and resid 292 through 300 Processing helix chain 'B' and resid 5 through 25 removed outlier: 3.593A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 9 through 24 removed outlier: 3.778A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 45 through 48 Processing sheet with id=AA1, first strand: chain 'A' and resid 186 through 192 removed outlier: 8.921A pdb=" N ALA A 221 " --> pdb=" O GLU A 33 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N LYS A 35 " --> pdb=" O ALA A 221 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N ILE A 223 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N LEU A 37 " --> pdb=" O ILE A 223 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N CYS A 225 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N LEU A 39 " --> pdb=" O CYS A 225 " (cutoff:3.500A) removed outlier: 9.015A pdb=" N ALA A 227 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N ILE A 222 " --> pdb=" O ILE A 266 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N PHE A 268 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N PHE A 224 " --> pdb=" O PHE A 268 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N ASN A 270 " --> pdb=" O PHE A 224 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N VAL A 226 " --> pdb=" O ASN A 270 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'R' and resid 74 through 76 Processing sheet with id=AA3, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.586A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.590A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105 removed outlier: 7.027A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.648A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.521A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.497A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.773A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) 374 hydrogen bonds defined for protein. 1080 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: 2.00 Time building geometry restraints manager: 2.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1636 1.33 - 1.45: 1604 1.45 - 1.58: 3841 1.58 - 1.70: 0 1.70 - 1.83: 78 Bond restraints: 7159 Sorted by residual: bond pdb=" C VAL R 24 " pdb=" N PRO R 25 " ideal model delta sigma weight residual 1.334 1.403 -0.069 2.34e-02 1.83e+03 8.69e+00 bond pdb=" CA ILE G 28 " pdb=" CB ILE G 28 " ideal model delta sigma weight residual 1.547 1.577 -0.030 1.68e-02 3.54e+03 3.29e+00 bond pdb=" C XTD R 402 " pdb=" C7 XTD R 402 " ideal model delta sigma weight residual 1.448 1.483 -0.035 2.00e-02 2.50e+03 3.11e+00 bond pdb=" CB ASP B 258 " pdb=" CG ASP B 258 " ideal model delta sigma weight residual 1.516 1.559 -0.043 2.50e-02 1.60e+03 2.92e+00 bond pdb=" CB PRO R 142 " pdb=" CG PRO R 142 " ideal model delta sigma weight residual 1.492 1.408 0.084 5.00e-02 4.00e+02 2.80e+00 ... (remaining 7154 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.73: 9458 2.73 - 5.45: 205 5.45 - 8.18: 32 8.18 - 10.91: 7 10.91 - 13.64: 2 Bond angle restraints: 9704 Sorted by residual: angle pdb=" CA CYS R 263 " pdb=" CB CYS R 263 " pdb=" SG CYS R 263 " ideal model delta sigma weight residual 114.40 124.77 -10.37 2.30e+00 1.89e-01 2.03e+01 angle pdb=" CA ILE G 28 " pdb=" CB ILE G 28 " pdb=" CG2 ILE G 28 " ideal model delta sigma weight residual 110.50 117.83 -7.33 1.70e+00 3.46e-01 1.86e+01 angle pdb=" CA CYS R 260 " pdb=" CB CYS R 260 " pdb=" SG CYS R 260 " ideal model delta sigma weight residual 114.40 123.83 -9.43 2.30e+00 1.89e-01 1.68e+01 angle pdb=" CA LEU B 318 " pdb=" CB LEU B 318 " pdb=" CG LEU B 318 " ideal model delta sigma weight residual 116.30 129.94 -13.64 3.50e+00 8.16e-02 1.52e+01 angle pdb=" CA LYS G 29 " pdb=" CB LYS G 29 " pdb=" CG LYS G 29 " ideal model delta sigma weight residual 114.10 106.36 7.74 2.00e+00 2.50e-01 1.50e+01 ... (remaining 9699 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.42: 3900 16.42 - 32.84: 305 32.84 - 49.26: 71 49.26 - 65.68: 13 65.68 - 82.11: 4 Dihedral angle restraints: 4293 sinusoidal: 1703 harmonic: 2590 Sorted by residual: dihedral pdb=" CB CYS R 260 " pdb=" SG CYS R 260 " pdb=" SG CYS R 263 " pdb=" CB CYS R 263 " ideal model delta sinusoidal sigma weight residual -86.00 -43.23 -42.77 1 1.00e+01 1.00e-02 2.55e+01 dihedral pdb=" CA THR B 249 " pdb=" C THR B 249 " pdb=" N CYS B 250 " pdb=" CA CYS B 250 " ideal model delta harmonic sigma weight residual 180.00 158.04 21.96 0 5.00e+00 4.00e-02 1.93e+01 dihedral pdb=" CA GLN R 74 " pdb=" C GLN R 74 " pdb=" N THR R 75 " pdb=" CA THR R 75 " ideal model delta harmonic sigma weight residual 180.00 -160.18 -19.82 0 5.00e+00 4.00e-02 1.57e+01 ... (remaining 4290 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.112: 1028 0.112 - 0.224: 88 0.224 - 0.337: 1 0.337 - 0.449: 0 0.449 - 0.561: 1 Chirality restraints: 1118 Sorted by residual: chirality pdb=" CB VAL A 202 " pdb=" CA VAL A 202 " pdb=" CG1 VAL A 202 " pdb=" CG2 VAL A 202 " both_signs ideal model delta sigma weight residual False -2.63 -2.07 -0.56 2.00e-01 2.50e+01 7.87e+00 chirality pdb=" CB ILE G 9 " pdb=" CA ILE G 9 " pdb=" CG1 ILE G 9 " pdb=" CG2 ILE G 9 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.24 2.00e-01 2.50e+01 1.46e+00 chirality pdb=" CB ILE G 28 " pdb=" CA ILE G 28 " pdb=" CG1 ILE G 28 " pdb=" CG2 ILE G 28 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.21 2.00e-01 2.50e+01 1.16e+00 ... (remaining 1115 not shown) Planarity restraints: 1211 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 XTD R 402 " -0.047 2.00e-02 2.50e+03 2.89e-02 1.88e+01 pdb=" C11 XTD R 402 " 0.023 2.00e-02 2.50e+03 pdb=" C12 XTD R 402 " 0.029 2.00e-02 2.50e+03 pdb=" C13 XTD R 402 " 0.015 2.00e-02 2.50e+03 pdb=" C14 XTD R 402 " -0.037 2.00e-02 2.50e+03 pdb=" C15 XTD R 402 " 0.014 2.00e-02 2.50e+03 pdb=" C16 XTD R 402 " 0.013 2.00e-02 2.50e+03 pdb=" C17 XTD R 402 " -0.035 2.00e-02 2.50e+03 pdb=" C18 XTD R 402 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' ADN R 401 " -0.059 2.00e-02 2.50e+03 2.45e-02 1.65e+01 pdb=" C2 ADN R 401 " 0.008 2.00e-02 2.50e+03 pdb=" C4 ADN R 401 " 0.016 2.00e-02 2.50e+03 pdb=" C5 ADN R 401 " 0.012 2.00e-02 2.50e+03 pdb=" C6 ADN R 401 " -0.010 2.00e-02 2.50e+03 pdb=" C8 ADN R 401 " 0.020 2.00e-02 2.50e+03 pdb=" N1 ADN R 401 " -0.004 2.00e-02 2.50e+03 pdb=" N3 ADN R 401 " 0.022 2.00e-02 2.50e+03 pdb=" N6 ADN R 401 " -0.035 2.00e-02 2.50e+03 pdb=" N7 ADN R 401 " 0.016 2.00e-02 2.50e+03 pdb=" N9 ADN R 401 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 173 " -0.018 2.00e-02 2.50e+03 3.65e-02 1.33e+01 pdb=" C THR B 173 " 0.063 2.00e-02 2.50e+03 pdb=" O THR B 173 " -0.023 2.00e-02 2.50e+03 pdb=" N GLY B 174 " -0.022 2.00e-02 2.50e+03 ... (remaining 1208 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 1769 2.80 - 3.33: 6327 3.33 - 3.85: 11784 3.85 - 4.38: 14139 4.38 - 4.90: 24289 Nonbonded interactions: 58308 Sorted by model distance: nonbonded pdb=" O SER B 334 " pdb=" OG SER B 334 " model vdw 2.277 3.040 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.295 3.040 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.312 3.040 nonbonded pdb=" O VAL R 138 " pdb=" OH TYR R 179 " model vdw 2.319 3.040 nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 2.322 3.040 ... (remaining 58303 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: 1.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 20.550 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:3.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 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 : 0.006 0.084 7159 Z= 0.395 Angle : 1.018 13.637 9704 Z= 0.566 Chirality : 0.063 0.561 1118 Planarity : 0.008 0.087 1211 Dihedral : 12.923 82.106 2603 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 0.13 % Allowed : 3.83 % Favored : 96.04 % 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: -1.50 (0.25), residues: 872 helix: -1.42 (0.22), residues: 404 sheet: 0.84 (0.38), residues: 173 loop : -1.24 (0.32), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP B 99 HIS 0.006 0.002 HIS A 323 PHE 0.042 0.003 PHE R 275 TYR 0.033 0.003 TYR A 297 ARG 0.012 0.001 ARG G 13 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 120 time to evaluate : 0.706 Fit side-chains revert: symmetry clash REVERT: B 59 TYR cc_start: 0.8398 (m-80) cc_final: 0.7763 (m-80) REVERT: B 259 GLN cc_start: 0.8285 (pt0) cc_final: 0.7913 (pt0) outliers start: 1 outliers final: 0 residues processed: 121 average time/residue: 0.2061 time to fit residues: 32.9050 Evaluate side-chains 76 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 73 optimal weight: 0.9980 chunk 65 optimal weight: 3.9990 chunk 36 optimal weight: 6.9990 chunk 22 optimal weight: 0.6980 chunk 44 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 68 optimal weight: 0.6980 chunk 26 optimal weight: 0.7980 chunk 41 optimal weight: 0.9980 chunk 50 optimal weight: 6.9990 chunk 79 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 332 ASN B 91 HIS B 132 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.168992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.137886 restraints weight = 7524.241| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 1.63 r_work: 0.3383 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3245 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.1659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7159 Z= 0.206 Angle : 0.584 7.778 9704 Z= 0.314 Chirality : 0.043 0.159 1118 Planarity : 0.005 0.063 1211 Dihedral : 7.036 56.449 995 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 0.92 % Allowed : 8.85 % Favored : 90.22 % 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: -0.20 (0.27), residues: 872 helix: 0.17 (0.25), residues: 417 sheet: 0.57 (0.37), residues: 177 loop : -0.87 (0.35), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 82 HIS 0.003 0.001 HIS R 251 PHE 0.032 0.001 PHE R 275 TYR 0.011 0.001 TYR B 124 ARG 0.002 0.000 ARG R 108 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 92 time to evaluate : 0.797 Fit side-chains revert: symmetry clash REVERT: A 32 ARG cc_start: 0.8040 (ptt-90) cc_final: 0.7799 (ptp-170) REVERT: A 208 GLU cc_start: 0.7891 (pt0) cc_final: 0.7669 (pt0) REVERT: A 210 LYS cc_start: 0.9274 (ptmt) cc_final: 0.8974 (pttt) REVERT: B 101 MET cc_start: 0.8893 (mtp) cc_final: 0.8629 (mtp) REVERT: B 146 LEU cc_start: 0.8417 (OUTLIER) cc_final: 0.8136 (mp) outliers start: 7 outliers final: 3 residues processed: 96 average time/residue: 0.1954 time to fit residues: 25.3942 Evaluate side-chains 81 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 77 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 23 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 275 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 27 optimal weight: 0.9980 chunk 82 optimal weight: 20.0000 chunk 35 optimal weight: 7.9990 chunk 23 optimal weight: 0.9990 chunk 56 optimal weight: 3.9990 chunk 71 optimal weight: 3.9990 chunk 81 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 80 optimal weight: 0.9990 overall best weight: 1.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 132 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.165763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.134405 restraints weight = 7620.549| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 1.63 r_work: 0.3338 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3193 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.2135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 7159 Z= 0.253 Angle : 0.554 7.159 9704 Z= 0.298 Chirality : 0.043 0.160 1118 Planarity : 0.005 0.056 1211 Dihedral : 6.398 55.097 995 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.11 % Allowed : 10.44 % Favored : 87.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.28), residues: 872 helix: 0.70 (0.26), residues: 413 sheet: 0.23 (0.36), residues: 179 loop : -0.78 (0.37), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 82 HIS 0.004 0.001 HIS G 44 PHE 0.029 0.002 PHE R 275 TYR 0.017 0.001 TYR B 111 ARG 0.003 0.000 ARG R 108 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 81 time to evaluate : 0.755 Fit side-chains revert: symmetry clash REVERT: A 32 ARG cc_start: 0.8133 (ptt-90) cc_final: 0.7819 (ptp-170) REVERT: A 208 GLU cc_start: 0.7987 (pt0) cc_final: 0.7744 (pt0) REVERT: A 210 LYS cc_start: 0.9291 (ptmt) cc_final: 0.8902 (pttt) REVERT: B 146 LEU cc_start: 0.8451 (OUTLIER) cc_final: 0.8241 (mp) outliers start: 16 outliers final: 9 residues processed: 95 average time/residue: 0.1867 time to fit residues: 24.2159 Evaluate side-chains 84 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 74 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain R residue 23 SER Chi-restraints excluded: chain R residue 286 ILE Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 28 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 49 optimal weight: 10.0000 chunk 52 optimal weight: 0.0470 chunk 13 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 chunk 45 optimal weight: 0.6980 chunk 6 optimal weight: 0.6980 chunk 77 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 78 optimal weight: 0.9980 chunk 86 optimal weight: 0.7980 chunk 46 optimal weight: 2.9990 overall best weight: 0.6478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 270 ASN ** R 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 132 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.168987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.137488 restraints weight = 7630.793| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 1.65 r_work: 0.3380 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3233 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.2386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7159 Z= 0.171 Angle : 0.507 6.766 9704 Z= 0.272 Chirality : 0.041 0.150 1118 Planarity : 0.004 0.049 1211 Dihedral : 5.890 53.271 995 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.98 % Allowed : 11.10 % Favored : 86.92 % 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: 0.44 (0.29), residues: 872 helix: 1.15 (0.27), residues: 409 sheet: 0.08 (0.36), residues: 176 loop : -0.68 (0.37), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 169 HIS 0.003 0.001 HIS B 91 PHE 0.028 0.001 PHE R 275 TYR 0.014 0.001 TYR B 111 ARG 0.003 0.000 ARG R 108 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 81 time to evaluate : 0.812 Fit side-chains REVERT: A 210 LYS cc_start: 0.9235 (ptmt) cc_final: 0.8901 (ptmt) REVERT: R 29 LEU cc_start: 0.7680 (OUTLIER) cc_final: 0.7270 (mp) REVERT: B 13 GLN cc_start: 0.8431 (pp30) cc_final: 0.8225 (pp30) REVERT: B 101 MET cc_start: 0.8959 (mtp) cc_final: 0.8610 (mtp) REVERT: B 197 ARG cc_start: 0.8332 (mtp85) cc_final: 0.8130 (mtp85) outliers start: 15 outliers final: 9 residues processed: 92 average time/residue: 0.2070 time to fit residues: 25.9726 Evaluate side-chains 76 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 66 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 ASN Chi-restraints excluded: chain R residue 23 SER Chi-restraints excluded: chain R residue 29 LEU Chi-restraints excluded: chain R residue 104 ASP Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 38 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 71 optimal weight: 0.0970 chunk 56 optimal weight: 0.7980 chunk 42 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 80 optimal weight: 0.6980 chunk 66 optimal weight: 0.7980 chunk 23 optimal weight: 0.3980 chunk 20 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 34 optimal weight: 0.8980 chunk 70 optimal weight: 0.6980 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 GLN ** R 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 132 ASN B 230 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.168387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.135706 restraints weight = 7610.072| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 1.62 r_work: 0.3375 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3230 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.2547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 7159 Z= 0.160 Angle : 0.500 6.668 9704 Z= 0.267 Chirality : 0.041 0.149 1118 Planarity : 0.004 0.046 1211 Dihedral : 5.748 52.447 995 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.11 % Allowed : 12.29 % Favored : 85.60 % 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: 0.60 (0.29), residues: 872 helix: 1.35 (0.27), residues: 409 sheet: 0.11 (0.36), residues: 176 loop : -0.69 (0.37), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 169 HIS 0.003 0.001 HIS A 323 PHE 0.027 0.001 PHE R 275 TYR 0.011 0.001 TYR B 111 ARG 0.002 0.000 ARG R 108 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 74 time to evaluate : 0.703 Fit side-chains REVERT: R 29 LEU cc_start: 0.7668 (OUTLIER) cc_final: 0.7246 (mp) outliers start: 16 outliers final: 11 residues processed: 87 average time/residue: 0.1937 time to fit residues: 23.2948 Evaluate side-chains 80 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 68 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 23 SER Chi-restraints excluded: chain R residue 29 LEU Chi-restraints excluded: chain R residue 104 ASP Chi-restraints excluded: chain R residue 166 VAL Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 38 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 49 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 73 optimal weight: 3.9990 chunk 18 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 chunk 59 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 45 optimal weight: 0.2980 chunk 9 optimal weight: 3.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 132 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.165955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.134561 restraints weight = 7631.831| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 1.60 r_work: 0.3338 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3195 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.2622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7159 Z= 0.218 Angle : 0.526 7.252 9704 Z= 0.277 Chirality : 0.042 0.145 1118 Planarity : 0.004 0.046 1211 Dihedral : 5.810 53.153 995 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.64 % Allowed : 12.55 % Favored : 84.81 % 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: 0.58 (0.29), residues: 872 helix: 1.34 (0.27), residues: 413 sheet: -0.01 (0.37), residues: 176 loop : -0.67 (0.37), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.003 0.001 HIS R 251 PHE 0.026 0.001 PHE R 275 TYR 0.011 0.001 TYR B 111 ARG 0.002 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 74 time to evaluate : 0.783 Fit side-chains REVERT: R 29 LEU cc_start: 0.7729 (OUTLIER) cc_final: 0.7341 (mp) outliers start: 20 outliers final: 16 residues processed: 90 average time/residue: 0.1992 time to fit residues: 24.7894 Evaluate side-chains 88 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 71 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 23 SER Chi-restraints excluded: chain R residue 29 LEU Chi-restraints excluded: chain R residue 104 ASP Chi-restraints excluded: chain R residue 166 VAL Chi-restraints excluded: chain R residue 225 TYR Chi-restraints excluded: chain R residue 286 ILE Chi-restraints excluded: chain B residue 132 ASN Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 38 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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-5624/modules/cctbx_project/iotbx/cli_parser.py", line 980, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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-5624/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-5624/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-5624/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-5624/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-5624/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-5624/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-5624/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-5624/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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-5624/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-5624/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-5624/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-5624/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: 55.5042 > 50: distance: 96 - 115: 19.569 distance: 100 - 120: 13.478 distance: 106 - 128: 22.678 distance: 110 - 115: 16.600 distance: 111 - 139: 15.292 distance: 115 - 116: 17.257 distance: 116 - 117: 28.149 distance: 116 - 119: 7.954 distance: 117 - 118: 19.491 distance: 117 - 120: 21.191 distance: 118 - 147: 20.180 distance: 120 - 121: 33.790 distance: 121 - 122: 31.421 distance: 121 - 124: 31.252 distance: 122 - 123: 7.368 distance: 122 - 128: 39.000 distance: 123 - 154: 31.530 distance: 124 - 125: 15.674 distance: 124 - 126: 27.389 distance: 125 - 127: 17.555 distance: 128 - 129: 29.974 distance: 129 - 130: 19.923 distance: 129 - 132: 8.832 distance: 130 - 131: 19.079 distance: 130 - 139: 22.313 distance: 131 - 164: 29.299 distance: 132 - 133: 13.280 distance: 133 - 134: 25.231 distance: 133 - 135: 12.833 distance: 134 - 136: 8.322 distance: 135 - 137: 18.025 distance: 136 - 138: 6.373 distance: 137 - 138: 9.198 distance: 139 - 140: 34.731 distance: 140 - 141: 12.766 distance: 140 - 143: 28.812 distance: 141 - 142: 28.045 distance: 141 - 147: 9.762 distance: 143 - 144: 32.360 distance: 144 - 145: 6.028 distance: 144 - 146: 32.327 distance: 147 - 148: 7.661 distance: 148 - 149: 8.944 distance: 148 - 151: 29.924 distance: 149 - 150: 18.635 distance: 149 - 154: 14.254 distance: 151 - 152: 28.804 distance: 151 - 153: 24.046 distance: 154 - 155: 15.735 distance: 155 - 156: 11.582 distance: 155 - 158: 23.431 distance: 156 - 157: 29.692 distance: 156 - 164: 9.879 distance: 158 - 159: 12.247 distance: 159 - 160: 19.038 distance: 159 - 161: 23.211 distance: 160 - 162: 17.950 distance: 161 - 163: 29.860 distance: 162 - 163: 23.077 distance: 164 - 165: 18.031 distance: 165 - 166: 12.542 distance: 166 - 167: 16.810 distance: 166 - 168: 3.906 distance: 168 - 169: 10.495 distance: 169 - 170: 31.295 distance: 169 - 172: 31.939 distance: 170 - 171: 16.554 distance: 170 - 176: 13.374 distance: 172 - 173: 13.917 distance: 173 - 174: 12.815 distance: 173 - 175: 18.017 distance: 176 - 177: 14.185 distance: 177 - 178: 14.164 distance: 177 - 180: 17.782 distance: 178 - 179: 18.997 distance: 178 - 182: 9.534 distance: 180 - 181: 13.543 distance: 182 - 183: 16.439 distance: 183 - 184: 16.047 distance: 183 - 186: 11.516 distance: 184 - 185: 26.490 distance: 184 - 187: 11.473