Starting phenix.real_space_refine on Thu Jul 24 14:17:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zoo_60314/07_2025/8zoo_60314.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zoo_60314/07_2025/8zoo_60314.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8zoo_60314/07_2025/8zoo_60314.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zoo_60314/07_2025/8zoo_60314.map" model { file = "/net/cci-nas-00/data/ceres_data/8zoo_60314/07_2025/8zoo_60314.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zoo_60314/07_2025/8zoo_60314.cif" } resolution = 3.14 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= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 3 5.49 5 S 30 5.16 5 C 3883 2.51 5 N 1124 2.21 5 O 1232 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 6272 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3099 Number of conformers: 1 Conformer: "" Number of residues, atoms: 412, 3099 Classifications: {'peptide': 412} Link IDs: {'PTRANS': 12, 'TRANS': 399} Chain breaks: 1 Chain: "B" Number of atoms: 3116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 416, 3116 Classifications: {'peptide': 416} Link IDs: {'PTRANS': 12, 'TRANS': 403} Chain: "B" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 57 Unusual residues: {'NAP': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'VHF:plan-2': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 6.63, per 1000 atoms: 1.06 Number of scatterers: 6272 At special positions: 0 Unit cell: (99.64, 110.24, 61.48, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 30 16.00 P 3 15.00 O 1232 8.00 N 1124 7.00 C 3883 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.32 Conformation dependent library (CDL) restraints added in 1.5 seconds 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1540 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 6 sheets defined 53.2% alpha, 16.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.74 Creating SS restraints... Processing helix chain 'A' and resid 2 through 17 Processing helix chain 'A' and resid 20 through 38 Processing helix chain 'A' and resid 38 through 57 removed outlier: 3.526A pdb=" N ILE A 42 " --> pdb=" O GLN A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 67 Processing helix chain 'A' and resid 69 through 85 removed outlier: 3.545A pdb=" N ASN A 85 " --> pdb=" O ARG A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 137 removed outlier: 4.018A pdb=" N THR A 126 " --> pdb=" O ARG A 122 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N VAL A 127 " --> pdb=" O PRO A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 166 Processing helix chain 'A' and resid 169 through 171 No H-bonds generated for 'chain 'A' and resid 169 through 171' Processing helix chain 'A' and resid 180 through 189 Processing helix chain 'A' and resid 206 through 213 Processing helix chain 'A' and resid 234 through 248 removed outlier: 3.740A pdb=" N GLN A 248 " --> pdb=" O ASN A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 281 removed outlier: 4.385A pdb=" N ASP A 267 " --> pdb=" O LYS A 263 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N SER A 268 " --> pdb=" O ASN A 264 " (cutoff:3.500A) Proline residue: A 271 - end of helix removed outlier: 3.767A pdb=" N GLU A 279 " --> pdb=" O LYS A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 295 Processing helix chain 'A' and resid 305 through 311 Processing helix chain 'A' and resid 325 through 337 Processing helix chain 'A' and resid 348 through 359 Processing helix chain 'A' and resid 370 through 373 removed outlier: 3.799A pdb=" N THR A 373 " --> pdb=" O THR A 370 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 370 through 373' Processing helix chain 'A' and resid 399 through 401 No H-bonds generated for 'chain 'A' and resid 399 through 401' Processing helix chain 'B' and resid 3 through 18 removed outlier: 3.636A pdb=" N LYS B 15 " --> pdb=" O GLN B 11 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 38 removed outlier: 3.557A pdb=" N LYS B 24 " --> pdb=" O SER B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 56 removed outlier: 3.613A pdb=" N ILE B 42 " --> pdb=" O GLN B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 67 Processing helix chain 'B' and resid 69 through 85 Processing helix chain 'B' and resid 123 through 137 removed outlier: 4.026A pdb=" N VAL B 127 " --> pdb=" O PRO B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 167 Processing helix chain 'B' and resid 169 through 171 No H-bonds generated for 'chain 'B' and resid 169 through 171' Processing helix chain 'B' and resid 180 through 190 removed outlier: 3.747A pdb=" N VAL B 184 " --> pdb=" O ASP B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 212 Processing helix chain 'B' and resid 234 through 248 removed outlier: 3.734A pdb=" N GLN B 248 " --> pdb=" O ASN B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 281 removed outlier: 3.937A pdb=" N ASP B 267 " --> pdb=" O LYS B 263 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N SER B 268 " --> pdb=" O ASN B 264 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU B 270 " --> pdb=" O ALA B 266 " (cutoff:3.500A) Proline residue: B 271 - end of helix removed outlier: 3.528A pdb=" N GLU B 279 " --> pdb=" O LYS B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 296 removed outlier: 4.099A pdb=" N ALA B 292 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N GLN B 293 " --> pdb=" O ALA B 289 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N ALA B 296 " --> pdb=" O ALA B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 311 Processing helix chain 'B' and resid 325 through 337 Processing helix chain 'B' and resid 348 through 359 Processing helix chain 'B' and resid 370 through 373 removed outlier: 3.785A pdb=" N THR B 373 " --> pdb=" O THR B 370 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 370 through 373' Processing helix chain 'B' and resid 399 through 401 No H-bonds generated for 'chain 'B' and resid 399 through 401' Processing sheet with id=AA1, first strand: chain 'A' and resid 93 through 98 removed outlier: 6.895A pdb=" N VAL A 93 " --> pdb=" O ARG A 109 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ARG A 109 " --> pdb=" O VAL A 93 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ASP A 95 " --> pdb=" O ARG A 107 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N ALA B 368 " --> pdb=" O GLY A 411 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N TYR A 413 " --> pdb=" O ALA B 368 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ASP B 342 " --> pdb=" O TYR B 365 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N ASN B 367 " --> pdb=" O ASP B 342 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N ILE B 344 " --> pdb=" O ASN B 367 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N HIS B 226 " --> pdb=" O ALA B 343 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N LEU B 345 " --> pdb=" O HIS B 226 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N TYR B 228 " --> pdb=" O LEU B 345 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N CYS B 225 " --> pdb=" O VAL B 256 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N THR B 258 " --> pdb=" O CYS B 225 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N GLU B 257 " --> pdb=" O ASP B 317 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N LEU B 284 " --> pdb=" O VAL B 302 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 173 through 175 removed outlier: 3.512A pdb=" N MET A 196 " --> pdb=" O VAL A 114 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 301 through 303 removed outlier: 6.243A pdb=" N LEU A 284 " --> pdb=" O VAL A 302 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N GLU A 257 " --> pdb=" O ASP A 317 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N CYS A 225 " --> pdb=" O THR A 258 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N LEU A 260 " --> pdb=" O CYS A 225 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N ILE A 227 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N ASN A 262 " --> pdb=" O ILE A 227 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N VAL A 229 " --> pdb=" O ASN A 262 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N HIS A 226 " --> pdb=" O ALA A 343 " (cutoff:3.500A) removed outlier: 8.096A pdb=" N LEU A 345 " --> pdb=" O HIS A 226 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N TYR A 228 " --> pdb=" O LEU A 345 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ASP A 342 " --> pdb=" O TYR A 365 " (cutoff:3.500A) removed outlier: 7.940A pdb=" N ASN A 367 " --> pdb=" O ASP A 342 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N ILE A 344 " --> pdb=" O ASN A 367 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N VAL A 364 " --> pdb=" O GLY B 409 " (cutoff:3.500A) removed outlier: 8.085A pdb=" N GLY B 411 " --> pdb=" O VAL A 364 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N VAL A 366 " --> pdb=" O GLY B 411 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N TYR B 413 " --> pdb=" O VAL A 366 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N ALA A 368 " --> pdb=" O TYR B 413 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ASP B 95 " --> pdb=" O ARG B 107 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N ARG B 109 " --> pdb=" O VAL B 93 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N VAL B 93 " --> pdb=" O ARG B 109 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 386 through 387 Processing sheet with id=AA5, first strand: chain 'B' and resid 173 through 176 Processing sheet with id=AA6, first strand: chain 'B' and resid 386 through 387 346 hydrogen bonds defined for protein. 999 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: 2.36 Time building geometry restraints manager: 3.62 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: 1115 1.31 - 1.44: 1416 1.44 - 1.56: 3758 1.56 - 1.69: 5 1.69 - 1.82: 46 Bond restraints: 6340 Sorted by residual: bond pdb=" O2B NAP B 501 " pdb=" P2B NAP B 501 " ideal model delta sigma weight residual 1.736 1.617 0.119 2.00e-02 2.50e+03 3.56e+01 bond pdb=" C5D NAP B 501 " pdb=" O5D NAP B 501 " ideal model delta sigma weight residual 1.403 1.449 -0.046 2.00e-02 2.50e+03 5.34e+00 bond pdb=" O5D NAP B 501 " pdb=" PN NAP B 501 " ideal model delta sigma weight residual 1.649 1.603 0.046 2.00e-02 2.50e+03 5.30e+00 bond pdb=" N ASP B 100 " pdb=" CA ASP B 100 " ideal model delta sigma weight residual 1.459 1.485 -0.026 1.19e-02 7.06e+03 4.81e+00 bond pdb=" O3 NAP B 501 " pdb=" PA NAP B 501 " ideal model delta sigma weight residual 1.647 1.603 0.044 2.00e-02 2.50e+03 4.79e+00 ... (remaining 6335 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.81: 8435 1.81 - 3.62: 131 3.62 - 5.43: 28 5.43 - 7.25: 2 7.25 - 9.06: 2 Bond angle restraints: 8598 Sorted by residual: angle pdb=" CB MET A 62 " pdb=" CG MET A 62 " pdb=" SD MET A 62 " ideal model delta sigma weight residual 112.70 121.76 -9.06 3.00e+00 1.11e-01 9.12e+00 angle pdb=" CA ASP B 100 " pdb=" C ASP B 100 " pdb=" O ASP B 100 " ideal model delta sigma weight residual 120.82 118.09 2.73 1.05e+00 9.07e-01 6.77e+00 angle pdb=" N ASP B 100 " pdb=" CA ASP B 100 " pdb=" C ASP B 100 " ideal model delta sigma weight residual 111.07 108.30 2.77 1.07e+00 8.73e-01 6.68e+00 angle pdb=" CA ASP A 95 " pdb=" C ASP A 95 " pdb=" O ASP A 95 " ideal model delta sigma weight residual 121.31 118.57 2.74 1.07e+00 8.73e-01 6.57e+00 angle pdb=" C ASP A 78 " pdb=" N ASP A 79 " pdb=" CA ASP A 79 " ideal model delta sigma weight residual 121.14 116.99 4.15 1.75e+00 3.27e-01 5.62e+00 ... (remaining 8593 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.20: 3415 17.20 - 34.39: 382 34.39 - 51.59: 99 51.59 - 68.78: 45 68.78 - 85.98: 13 Dihedral angle restraints: 3954 sinusoidal: 1573 harmonic: 2381 Sorted by residual: dihedral pdb=" CA ASN B 152 " pdb=" CB ASN B 152 " pdb=" CG ASN B 152 " pdb=" OD1 ASN B 152 " ideal model delta sinusoidal sigma weight residual -90.00 -160.78 70.78 2 2.00e+01 2.50e-03 1.07e+01 dihedral pdb=" CG ARG B 334 " pdb=" CD ARG B 334 " pdb=" NE ARG B 334 " pdb=" CZ ARG B 334 " ideal model delta sinusoidal sigma weight residual 90.00 134.97 -44.97 2 1.50e+01 4.44e-03 1.07e+01 dihedral pdb=" CG ARG A 65 " pdb=" CD ARG A 65 " pdb=" NE ARG A 65 " pdb=" CZ ARG A 65 " ideal model delta sinusoidal sigma weight residual 180.00 136.45 43.55 2 1.50e+01 4.44e-03 1.01e+01 ... (remaining 3951 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 788 0.044 - 0.088: 174 0.088 - 0.131: 68 0.131 - 0.175: 4 0.175 - 0.219: 2 Chirality restraints: 1036 Sorted by residual: chirality pdb=" CB ILE A 31 " pdb=" CA ILE A 31 " pdb=" CG1 ILE A 31 " pdb=" CG2 ILE A 31 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" C3B NAP B 501 " pdb=" C2B NAP B 501 " pdb=" C4B NAP B 501 " pdb=" O3B NAP B 501 " both_signs ideal model delta sigma weight residual False -2.52 -2.73 0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" C4D NAP B 501 " pdb=" C3D NAP B 501 " pdb=" C5D NAP B 501 " pdb=" O4D NAP B 501 " both_signs ideal model delta sigma weight residual False -2.58 -2.43 -0.16 2.00e-01 2.50e+01 6.17e-01 ... (remaining 1033 not shown) Planarity restraints: 1121 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP A 360 " -0.011 2.00e-02 2.50e+03 2.32e-02 5.39e+00 pdb=" CG ASP A 360 " 0.040 2.00e-02 2.50e+03 pdb=" OD1 ASP A 360 " -0.015 2.00e-02 2.50e+03 pdb=" OD2 ASP A 360 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 360 " 0.010 2.00e-02 2.50e+03 2.07e-02 4.29e+00 pdb=" C ASP A 360 " -0.036 2.00e-02 2.50e+03 pdb=" O ASP A 360 " 0.014 2.00e-02 2.50e+03 pdb=" N SER A 361 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE B 215 " -0.018 5.00e-02 4.00e+02 2.79e-02 1.24e+00 pdb=" N PRO B 216 " 0.048 5.00e-02 4.00e+02 pdb=" CA PRO B 216 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO B 216 " -0.016 5.00e-02 4.00e+02 ... (remaining 1118 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 1367 2.79 - 3.31: 6154 3.31 - 3.84: 10305 3.84 - 4.37: 11667 4.37 - 4.90: 20744 Nonbonded interactions: 50237 Sorted by model distance: nonbonded pdb=" O PRO B 271 " pdb=" OG SER B 274 " model vdw 2.257 3.040 nonbonded pdb=" OD2 ASP A 342 " pdb=" OG SER A 361 " model vdw 2.277 3.040 nonbonded pdb=" OG SER B 20 " pdb=" OE1 GLU B 23 " model vdw 2.282 3.040 nonbonded pdb=" OE1 GLU B 312 " pdb=" O3D NAP B 501 " model vdw 2.305 3.040 nonbonded pdb=" OE1 GLN A 248 " pdb=" NH2 ARG A 371 " model vdw 2.321 3.120 ... (remaining 50232 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 2 through 200 or resid 205 through 417)) } 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: 41.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 27.060 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 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 : 0.004 0.119 6341 Z= 0.207 Angle : 0.573 9.057 8598 Z= 0.297 Chirality : 0.043 0.219 1036 Planarity : 0.003 0.028 1121 Dihedral : 17.432 85.979 2414 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 0.00 % Allowed : 20.09 % Favored : 79.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (0.30), residues: 822 helix: 2.63 (0.27), residues: 387 sheet: 0.68 (0.46), residues: 132 loop : -0.77 (0.34), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 407 HIS 0.003 0.001 HIS A 226 PHE 0.003 0.001 PHE A 372 TYR 0.010 0.001 TYR B 119 ARG 0.003 0.000 ARG B 150 Details of bonding type rmsd hydrogen bonds : bond 0.15150 ( 346) hydrogen bonds : angle 5.72615 ( 999) covalent geometry : bond 0.00406 ( 6340) covalent geometry : angle 0.57265 ( 8598) Misc. bond : bond 0.04917 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.812 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 52 average time/residue: 0.1581 time to fit residues: 12.1413 Evaluate side-chains 51 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 69 optimal weight: 9.9990 chunk 62 optimal weight: 5.9990 chunk 34 optimal weight: 0.9980 chunk 21 optimal weight: 4.9990 chunk 41 optimal weight: 10.0000 chunk 33 optimal weight: 4.9990 chunk 64 optimal weight: 0.4980 chunk 24 optimal weight: 10.0000 chunk 39 optimal weight: 0.9980 chunk 47 optimal weight: 4.9990 chunk 74 optimal weight: 5.9990 overall best weight: 2.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.087464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.062183 restraints weight = 15135.295| |-----------------------------------------------------------------------------| r_work (start): 0.2913 rms_B_bonded: 4.01 r_work: 0.2726 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.2726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.0890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.028 6341 Z= 0.198 Angle : 0.495 7.751 8598 Z= 0.260 Chirality : 0.043 0.159 1036 Planarity : 0.003 0.028 1121 Dihedral : 7.728 57.271 966 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.72 % Allowed : 17.82 % Favored : 79.46 % 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: 1.82 (0.30), residues: 822 helix: 2.79 (0.27), residues: 393 sheet: 0.67 (0.45), residues: 131 loop : -0.78 (0.35), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 407 HIS 0.004 0.001 HIS A 226 PHE 0.007 0.001 PHE B 313 TYR 0.006 0.001 TYR A 365 ARG 0.003 0.000 ARG B 150 Details of bonding type rmsd hydrogen bonds : bond 0.03956 ( 346) hydrogen bonds : angle 4.53623 ( 999) covalent geometry : bond 0.00452 ( 6340) covalent geometry : angle 0.49492 ( 8598) Misc. bond : bond 0.00025 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 53 time to evaluate : 1.136 Fit side-chains revert: symmetry clash REVERT: A 190 MET cc_start: 0.8807 (mtm) cc_final: 0.8495 (mtt) REVERT: A 196 MET cc_start: 0.8598 (tmm) cc_final: 0.7925 (tmm) REVERT: A 277 MET cc_start: 0.8978 (tpp) cc_final: 0.8600 (tpp) REVERT: A 360 ASP cc_start: 0.8790 (t0) cc_final: 0.8481 (t0) outliers start: 18 outliers final: 8 residues processed: 68 average time/residue: 0.3112 time to fit residues: 32.2919 Evaluate side-chains 56 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 48 time to evaluate : 1.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 MET Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 209 CYS Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 186 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 66 optimal weight: 6.9990 chunk 58 optimal weight: 5.9990 chunk 49 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 chunk 5 optimal weight: 5.9990 chunk 68 optimal weight: 0.9990 chunk 16 optimal weight: 6.9990 chunk 46 optimal weight: 5.9990 chunk 17 optimal weight: 7.9990 chunk 0 optimal weight: 8.9990 chunk 33 optimal weight: 4.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.085509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.059818 restraints weight = 15372.763| |-----------------------------------------------------------------------------| r_work (start): 0.2878 rms_B_bonded: 4.11 r_work: 0.2689 rms_B_bonded: 4.76 restraints_weight: 0.5000 r_work (final): 0.2689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.1267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.032 6341 Z= 0.244 Angle : 0.526 7.696 8598 Z= 0.277 Chirality : 0.043 0.148 1036 Planarity : 0.003 0.027 1121 Dihedral : 6.978 59.177 966 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 3.47 % Allowed : 18.73 % Favored : 77.79 % 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: 1.76 (0.30), residues: 822 helix: 2.79 (0.26), residues: 392 sheet: 0.65 (0.45), residues: 131 loop : -0.87 (0.35), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 407 HIS 0.004 0.001 HIS A 226 PHE 0.007 0.001 PHE B 313 TYR 0.009 0.001 TYR B 119 ARG 0.003 0.000 ARG B 150 Details of bonding type rmsd hydrogen bonds : bond 0.04103 ( 346) hydrogen bonds : angle 4.46997 ( 999) covalent geometry : bond 0.00562 ( 6340) covalent geometry : angle 0.52629 ( 8598) Misc. bond : bond 0.00047 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 49 time to evaluate : 0.967 Fit side-chains revert: symmetry clash REVERT: A 190 MET cc_start: 0.8916 (mtm) cc_final: 0.8442 (mtt) REVERT: A 196 MET cc_start: 0.8733 (tmm) cc_final: 0.8027 (tmm) REVERT: A 265 ILE cc_start: 0.9223 (OUTLIER) cc_final: 0.8983 (tp) REVERT: A 277 MET cc_start: 0.9039 (tpp) cc_final: 0.8776 (tpp) REVERT: A 360 ASP cc_start: 0.8842 (t0) cc_final: 0.8476 (t0) REVERT: B 234 GLU cc_start: 0.7789 (OUTLIER) cc_final: 0.6990 (mp0) outliers start: 23 outliers final: 13 residues processed: 67 average time/residue: 0.2666 time to fit residues: 25.6935 Evaluate side-chains 61 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 46 time to evaluate : 2.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 MET Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 209 CYS Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 234 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 5 optimal weight: 20.0000 chunk 0 optimal weight: 7.9990 chunk 30 optimal weight: 9.9990 chunk 20 optimal weight: 3.9990 chunk 74 optimal weight: 7.9990 chunk 64 optimal weight: 7.9990 chunk 67 optimal weight: 0.9980 chunk 8 optimal weight: 3.9990 chunk 76 optimal weight: 0.4980 chunk 26 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.085806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.060149 restraints weight = 15560.764| |-----------------------------------------------------------------------------| r_work (start): 0.2887 rms_B_bonded: 4.14 r_work: 0.2690 rms_B_bonded: 4.83 restraints_weight: 0.5000 r_work (final): 0.2690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.1413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.027 6341 Z= 0.208 Angle : 0.496 7.882 8598 Z= 0.260 Chirality : 0.042 0.148 1036 Planarity : 0.003 0.028 1121 Dihedral : 6.433 53.333 966 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 3.17 % Allowed : 19.34 % Favored : 77.49 % 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: 1.73 (0.30), residues: 822 helix: 2.79 (0.26), residues: 392 sheet: 0.62 (0.46), residues: 131 loop : -0.92 (0.35), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 407 HIS 0.004 0.001 HIS A 226 PHE 0.006 0.001 PHE B 313 TYR 0.014 0.001 TYR B 119 ARG 0.002 0.000 ARG B 150 Details of bonding type rmsd hydrogen bonds : bond 0.03722 ( 346) hydrogen bonds : angle 4.32374 ( 999) covalent geometry : bond 0.00478 ( 6340) covalent geometry : angle 0.49627 ( 8598) Misc. bond : bond 0.00041 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 48 time to evaluate : 0.792 Fit side-chains revert: symmetry clash REVERT: A 190 MET cc_start: 0.8884 (mtm) cc_final: 0.8356 (mtp) REVERT: A 196 MET cc_start: 0.8725 (tmm) cc_final: 0.8023 (tmm) REVERT: A 265 ILE cc_start: 0.9207 (OUTLIER) cc_final: 0.8964 (tp) REVERT: A 360 ASP cc_start: 0.8876 (t0) cc_final: 0.8493 (t0) REVERT: B 104 ARG cc_start: 0.8400 (OUTLIER) cc_final: 0.8003 (mmt180) REVERT: B 234 GLU cc_start: 0.7766 (OUTLIER) cc_final: 0.6849 (mp0) REVERT: B 414 THR cc_start: 0.9176 (m) cc_final: 0.8608 (p) outliers start: 21 outliers final: 13 residues processed: 65 average time/residue: 0.1631 time to fit residues: 15.0919 Evaluate side-chains 62 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 46 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 MET Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 209 CYS Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain B residue 104 ARG Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 234 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 23 optimal weight: 0.8980 chunk 57 optimal weight: 8.9990 chunk 32 optimal weight: 6.9990 chunk 51 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 74 optimal weight: 8.9990 chunk 79 optimal weight: 8.9990 chunk 61 optimal weight: 6.9990 chunk 43 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 21 optimal weight: 0.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.086217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.060793 restraints weight = 15405.238| |-----------------------------------------------------------------------------| r_work (start): 0.2889 rms_B_bonded: 4.06 r_work: 0.2699 rms_B_bonded: 4.74 restraints_weight: 0.5000 r_work (final): 0.2699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.1504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 6341 Z= 0.200 Angle : 0.502 9.479 8598 Z= 0.258 Chirality : 0.042 0.151 1036 Planarity : 0.003 0.029 1121 Dihedral : 6.091 42.191 966 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 3.47 % Allowed : 19.64 % Favored : 76.89 % 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: 1.75 (0.30), residues: 822 helix: 2.82 (0.26), residues: 392 sheet: 0.66 (0.45), residues: 129 loop : -0.94 (0.34), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 407 HIS 0.003 0.001 HIS A 226 PHE 0.006 0.001 PHE B 313 TYR 0.008 0.001 TYR A 193 ARG 0.002 0.000 ARG B 150 Details of bonding type rmsd hydrogen bonds : bond 0.03669 ( 346) hydrogen bonds : angle 4.27071 ( 999) covalent geometry : bond 0.00461 ( 6340) covalent geometry : angle 0.50183 ( 8598) Misc. bond : bond 0.00038 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 50 time to evaluate : 1.850 Fit side-chains revert: symmetry clash REVERT: A 190 MET cc_start: 0.8875 (mtm) cc_final: 0.8509 (mtp) REVERT: A 196 MET cc_start: 0.8751 (tmm) cc_final: 0.7996 (tmm) REVERT: A 265 ILE cc_start: 0.9222 (OUTLIER) cc_final: 0.8979 (tp) REVERT: A 277 MET cc_start: 0.9020 (tpp) cc_final: 0.8610 (tpp) REVERT: A 360 ASP cc_start: 0.8856 (t0) cc_final: 0.8474 (t0) REVERT: B 104 ARG cc_start: 0.8422 (OUTLIER) cc_final: 0.8018 (mmt180) REVERT: B 234 GLU cc_start: 0.7765 (OUTLIER) cc_final: 0.6934 (mp0) REVERT: B 414 THR cc_start: 0.9170 (m) cc_final: 0.8603 (p) outliers start: 23 outliers final: 17 residues processed: 68 average time/residue: 0.2101 time to fit residues: 21.1443 Evaluate side-chains 68 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 48 time to evaluate : 1.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 MET Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 209 CYS Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 104 ARG Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 234 GLU Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 349 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 41 optimal weight: 10.0000 chunk 29 optimal weight: 20.0000 chunk 44 optimal weight: 5.9990 chunk 56 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 21 optimal weight: 5.9990 chunk 71 optimal weight: 5.9990 chunk 60 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 chunk 42 optimal weight: 4.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 152 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.086684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.061301 restraints weight = 15347.260| |-----------------------------------------------------------------------------| r_work (start): 0.2900 rms_B_bonded: 4.05 r_work: 0.2711 rms_B_bonded: 4.74 restraints_weight: 0.5000 r_work (final): 0.2711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.1582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 6341 Z= 0.173 Angle : 0.483 8.198 8598 Z= 0.248 Chirality : 0.042 0.146 1036 Planarity : 0.003 0.030 1121 Dihedral : 5.717 35.423 966 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 3.17 % Allowed : 20.69 % Favored : 76.13 % 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: 1.85 (0.30), residues: 822 helix: 2.89 (0.26), residues: 392 sheet: 0.73 (0.45), residues: 129 loop : -0.89 (0.34), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 407 HIS 0.003 0.001 HIS A 226 PHE 0.005 0.001 PHE B 313 TYR 0.007 0.001 TYR B 119 ARG 0.002 0.000 ARG B 54 Details of bonding type rmsd hydrogen bonds : bond 0.03436 ( 346) hydrogen bonds : angle 4.17645 ( 999) covalent geometry : bond 0.00398 ( 6340) covalent geometry : angle 0.48295 ( 8598) Misc. bond : bond 0.00021 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 50 time to evaluate : 0.870 Fit side-chains revert: symmetry clash REVERT: A 190 MET cc_start: 0.8854 (mtm) cc_final: 0.8457 (mtp) REVERT: A 196 MET cc_start: 0.8730 (tmm) cc_final: 0.7980 (tmm) REVERT: A 265 ILE cc_start: 0.9219 (OUTLIER) cc_final: 0.8975 (tp) REVERT: A 360 ASP cc_start: 0.8914 (t0) cc_final: 0.8552 (t0) REVERT: B 234 GLU cc_start: 0.7728 (OUTLIER) cc_final: 0.6892 (mp0) REVERT: B 414 THR cc_start: 0.9187 (m) cc_final: 0.8614 (p) outliers start: 21 outliers final: 15 residues processed: 68 average time/residue: 0.2019 time to fit residues: 20.8378 Evaluate side-chains 64 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 47 time to evaluate : 1.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 MET Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 209 CYS Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 234 GLU Chi-restraints excluded: chain B residue 243 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 72 optimal weight: 3.9990 chunk 68 optimal weight: 0.9990 chunk 66 optimal weight: 0.9980 chunk 4 optimal weight: 6.9990 chunk 20 optimal weight: 4.9990 chunk 67 optimal weight: 0.0870 chunk 35 optimal weight: 4.9990 chunk 25 optimal weight: 7.9990 chunk 0 optimal weight: 8.9990 chunk 76 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 overall best weight: 1.8164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.087153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.061762 restraints weight = 15436.902| |-----------------------------------------------------------------------------| r_work (start): 0.2909 rms_B_bonded: 4.08 r_work: 0.2720 rms_B_bonded: 4.76 restraints_weight: 0.5000 r_work (final): 0.2720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.1619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6341 Z= 0.148 Angle : 0.471 8.290 8598 Z= 0.242 Chirality : 0.041 0.147 1036 Planarity : 0.003 0.030 1121 Dihedral : 5.507 34.308 966 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.72 % Allowed : 21.45 % Favored : 75.83 % 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: 1.93 (0.30), residues: 822 helix: 2.96 (0.26), residues: 392 sheet: 0.70 (0.45), residues: 132 loop : -0.82 (0.35), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 407 HIS 0.003 0.000 HIS A 226 PHE 0.004 0.001 PHE B 313 TYR 0.008 0.001 TYR B 405 ARG 0.001 0.000 ARG B 54 Details of bonding type rmsd hydrogen bonds : bond 0.03298 ( 346) hydrogen bonds : angle 4.11237 ( 999) covalent geometry : bond 0.00340 ( 6340) covalent geometry : angle 0.47070 ( 8598) Misc. bond : bond 0.00010 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 50 time to evaluate : 0.791 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 190 MET cc_start: 0.8821 (mtm) cc_final: 0.8429 (mtp) REVERT: A 196 MET cc_start: 0.8713 (tmm) cc_final: 0.7969 (tmm) REVERT: A 265 ILE cc_start: 0.9218 (OUTLIER) cc_final: 0.8977 (tp) REVERT: A 277 MET cc_start: 0.9020 (tpp) cc_final: 0.8654 (tpp) REVERT: A 360 ASP cc_start: 0.8923 (t0) cc_final: 0.8548 (t0) REVERT: B 414 THR cc_start: 0.9181 (m) cc_final: 0.8606 (p) outliers start: 18 outliers final: 15 residues processed: 66 average time/residue: 0.1375 time to fit residues: 13.5942 Evaluate side-chains 63 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 47 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 MET Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 209 CYS Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 234 GLU Chi-restraints excluded: chain B residue 243 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 48 optimal weight: 1.9990 chunk 56 optimal weight: 4.9990 chunk 77 optimal weight: 0.7980 chunk 34 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 15 optimal weight: 4.9990 chunk 35 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 chunk 18 optimal weight: 10.0000 chunk 61 optimal weight: 2.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.086839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.061425 restraints weight = 15337.379| |-----------------------------------------------------------------------------| r_work (start): 0.2902 rms_B_bonded: 4.05 r_work: 0.2712 rms_B_bonded: 4.74 restraints_weight: 0.5000 r_work (final): 0.2712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.1693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 6341 Z= 0.172 Angle : 0.490 8.447 8598 Z= 0.251 Chirality : 0.042 0.145 1036 Planarity : 0.003 0.030 1121 Dihedral : 5.482 34.506 966 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 3.02 % Allowed : 21.45 % Favored : 75.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.92 (0.30), residues: 822 helix: 2.94 (0.26), residues: 392 sheet: 0.68 (0.45), residues: 138 loop : -0.83 (0.35), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 407 HIS 0.003 0.001 HIS A 226 PHE 0.005 0.001 PHE B 313 TYR 0.007 0.001 TYR B 405 ARG 0.002 0.000 ARG A 54 Details of bonding type rmsd hydrogen bonds : bond 0.03405 ( 346) hydrogen bonds : angle 4.11804 ( 999) covalent geometry : bond 0.00396 ( 6340) covalent geometry : angle 0.48981 ( 8598) Misc. bond : bond 0.00013 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 50 time to evaluate : 0.767 Fit side-chains revert: symmetry clash REVERT: A 190 MET cc_start: 0.8829 (mtm) cc_final: 0.8414 (mtp) REVERT: A 196 MET cc_start: 0.8746 (tmm) cc_final: 0.8000 (tmm) REVERT: A 265 ILE cc_start: 0.9223 (OUTLIER) cc_final: 0.8983 (tp) REVERT: A 360 ASP cc_start: 0.8928 (t0) cc_final: 0.8541 (t0) REVERT: B 104 ARG cc_start: 0.8406 (OUTLIER) cc_final: 0.8016 (mmt180) REVERT: B 234 GLU cc_start: 0.7760 (OUTLIER) cc_final: 0.6870 (mp0) REVERT: B 414 THR cc_start: 0.9139 (m) cc_final: 0.8569 (p) outliers start: 20 outliers final: 17 residues processed: 66 average time/residue: 0.1471 time to fit residues: 14.1151 Evaluate side-chains 66 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 46 time to evaluate : 0.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 MET Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 209 CYS Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 300 LYS Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 104 ARG Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 234 GLU Chi-restraints excluded: chain B residue 243 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 13 optimal weight: 1.9990 chunk 78 optimal weight: 0.0170 chunk 75 optimal weight: 4.9990 chunk 34 optimal weight: 0.0980 chunk 25 optimal weight: 5.9990 chunk 14 optimal weight: 0.9990 chunk 72 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 44 optimal weight: 0.7980 chunk 73 optimal weight: 4.9990 chunk 60 optimal weight: 1.9990 overall best weight: 0.5822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.089496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.064350 restraints weight = 15064.221| |-----------------------------------------------------------------------------| r_work (start): 0.2966 rms_B_bonded: 4.05 r_work: 0.2784 rms_B_bonded: 4.72 restraints_weight: 0.5000 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.1729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 6341 Z= 0.088 Angle : 0.470 8.919 8598 Z= 0.236 Chirality : 0.041 0.153 1036 Planarity : 0.003 0.032 1121 Dihedral : 5.075 35.554 966 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.36 % Allowed : 23.41 % Favored : 75.23 % 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: 2.02 (0.31), residues: 822 helix: 3.02 (0.27), residues: 392 sheet: 0.79 (0.45), residues: 136 loop : -0.79 (0.35), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 407 HIS 0.003 0.000 HIS A 226 PHE 0.005 0.001 PHE B 355 TYR 0.011 0.001 TYR B 119 ARG 0.002 0.000 ARG B 109 Details of bonding type rmsd hydrogen bonds : bond 0.02655 ( 346) hydrogen bonds : angle 3.92256 ( 999) covalent geometry : bond 0.00190 ( 6340) covalent geometry : angle 0.46960 ( 8598) Misc. bond : bond 0.00007 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 54 time to evaluate : 0.804 Fit side-chains REVERT: A 136 THR cc_start: 0.9110 (t) cc_final: 0.8906 (t) REVERT: A 190 MET cc_start: 0.8714 (mtm) cc_final: 0.8325 (mtp) REVERT: A 196 MET cc_start: 0.8553 (tmm) cc_final: 0.7903 (tmm) REVERT: A 265 ILE cc_start: 0.9218 (OUTLIER) cc_final: 0.8989 (tp) REVERT: A 360 ASP cc_start: 0.8770 (t0) cc_final: 0.8482 (t0) REVERT: B 186 GLU cc_start: 0.9288 (OUTLIER) cc_final: 0.9035 (tp30) REVERT: B 414 THR cc_start: 0.9189 (m) cc_final: 0.8606 (p) outliers start: 9 outliers final: 5 residues processed: 60 average time/residue: 0.1431 time to fit residues: 12.6306 Evaluate side-chains 59 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 52 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 MET Chi-restraints excluded: chain A residue 209 CYS Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 215 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/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-5711/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/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-5711/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/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-5711/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-5711/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-5711/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-5711/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-5711/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-5711/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-5711/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-5711/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/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-5711/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-5711/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-5711/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-5711/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: 72.0734 > 50: distance: 37 - 43: 34.507 distance: 43 - 44: 39.269 distance: 45 - 46: 39.032 distance: 45 - 54: 38.831 distance: 46 - 74: 37.953 distance: 47 - 48: 40.659 distance: 48 - 49: 39.264 distance: 50 - 51: 40.497 distance: 51 - 53: 40.564 distance: 56 - 57: 39.295 distance: 56 - 59: 40.691 distance: 57 - 80: 55.766 distance: 59 - 60: 39.760 distance: 60 - 61: 40.237 distance: 60 - 63: 57.509 distance: 62 - 89: 37.672 distance: 63 - 64: 38.949 distance: 64 - 65: 56.884 distance: 64 - 66: 40.873 distance: 67 - 68: 39.838 distance: 68 - 71: 38.691 distance: 69 - 74: 39.939 distance: 70 - 97: 56.132 distance: 71 - 72: 41.078 distance: 74 - 75: 57.601 distance: 76 - 77: 56.375 distance: 76 - 80: 56.378 distance: 77 - 105: 39.292 distance: 78 - 79: 39.562 distance: 81 - 82: 53.541 distance: 81 - 84: 39.539 distance: 82 - 83: 6.121 distance: 82 - 89: 35.967 distance: 83 - 116: 3.227 distance: 84 - 85: 41.488 distance: 85 - 86: 39.595 distance: 86 - 88: 39.262 distance: 89 - 90: 40.329 distance: 90 - 91: 38.899 distance: 91 - 92: 40.599 distance: 93 - 94: 39.799 distance: 94 - 95: 40.081 distance: 99 - 100: 39.869 distance: 101 - 102: 55.834 distance: 102 - 104: 41.221 distance: 105 - 106: 40.595 distance: 106 - 107: 40.269 distance: 107 - 116: 39.579 distance: 109 - 110: 56.840 distance: 112 - 113: 69.572 distance: 116 - 117: 40.583 distance: 117 - 118: 39.904 distance: 117 - 120: 39.978 distance: 118 - 124: 34.904