Starting phenix.real_space_refine on Wed Jan 15 07:56:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8em2_28232/01_2025/8em2_28232.cif Found real_map, /net/cci-nas-00/data/ceres_data/8em2_28232/01_2025/8em2_28232.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.02 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8em2_28232/01_2025/8em2_28232.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8em2_28232/01_2025/8em2_28232.map" model { file = "/net/cci-nas-00/data/ceres_data/8em2_28232/01_2025/8em2_28232.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8em2_28232/01_2025/8em2_28232.cif" } resolution = 3.02 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= 0.026 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 25 5.16 5 C 5120 2.51 5 N 1431 2.21 5 O 1446 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 8022 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 502, 4004 Classifications: {'peptide': 502} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 24, 'TRANS': 477} Chain breaks: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 3990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 500, 3990 Classifications: {'peptide': 500} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 24, 'TRANS': 475} Chain breaks: 1 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 9 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 5.55, per 1000 atoms: 0.69 Number of scatterers: 8022 At special positions: 0 Unit cell: (81, 146.88, 81, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 25 16.00 O 1446 8.00 N 1431 7.00 C 5120 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 393 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 393 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 801 " - " ASN A 157 " Time building additional restraints: 2.03 Conformation dependent library (CDL) restraints added in 945.1 milliseconds 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1866 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 9 sheets defined 41.4% alpha, 16.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.92 Creating SS restraints... Processing helix chain 'A' and resid 35 through 41 Processing helix chain 'A' and resid 41 through 54 removed outlier: 3.598A pdb=" N GLU A 53 " --> pdb=" O LEU A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 83 Processing helix chain 'A' and resid 92 through 106 Processing helix chain 'A' and resid 114 through 132 removed outlier: 3.993A pdb=" N GLN A 118 " --> pdb=" O ALA A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 159 removed outlier: 3.559A pdb=" N ALA A 153 " --> pdb=" O TYR A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 192 removed outlier: 3.519A pdb=" N ALA A 183 " --> pdb=" O ASP A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 208 Processing helix chain 'A' and resid 210 through 212 No H-bonds generated for 'chain 'A' and resid 210 through 212' Processing helix chain 'A' and resid 213 through 220 Processing helix chain 'A' and resid 230 through 232 No H-bonds generated for 'chain 'A' and resid 230 through 232' Processing helix chain 'A' and resid 257 through 263 removed outlier: 4.104A pdb=" N ARG A 261 " --> pdb=" O TYR A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 276 Processing helix chain 'A' and resid 286 through 299 removed outlier: 3.785A pdb=" N LEU A 290 " --> pdb=" O ALA A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 324 removed outlier: 4.248A pdb=" N GLU A 318 " --> pdb=" O GLN A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 386 removed outlier: 3.607A pdb=" N HIS A 385 " --> pdb=" O SER A 382 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N TRP A 386 " --> pdb=" O GLU A 383 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 382 through 386' Processing helix chain 'A' and resid 456 through 468 removed outlier: 3.619A pdb=" N VAL A 460 " --> pdb=" O ASP A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 471 No H-bonds generated for 'chain 'A' and resid 469 through 471' Processing helix chain 'A' and resid 475 through 493 Proline residue: A 488 - end of helix Processing helix chain 'A' and resid 503 through 507 removed outlier: 3.603A pdb=" N GLU A 506 " --> pdb=" O GLY A 503 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ASN A 507 " --> pdb=" O GLY A 504 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 503 through 507' Processing helix chain 'B' and resid 35 through 41 removed outlier: 4.404A pdb=" N LYS B 39 " --> pdb=" O GLY B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 53 Processing helix chain 'B' and resid 69 through 83 Processing helix chain 'B' and resid 91 through 105 removed outlier: 3.511A pdb=" N GLU B 97 " --> pdb=" O SER B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 131 Processing helix chain 'B' and resid 145 through 149 Processing helix chain 'B' and resid 150 through 159 removed outlier: 3.952A pdb=" N SER B 159 " --> pdb=" O ASN B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 191 Processing helix chain 'B' and resid 203 through 207 removed outlier: 3.956A pdb=" N LEU B 206 " --> pdb=" O ASP B 203 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N GLY B 207 " --> pdb=" O HIS B 204 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 203 through 207' Processing helix chain 'B' and resid 210 through 212 No H-bonds generated for 'chain 'B' and resid 210 through 212' Processing helix chain 'B' and resid 213 through 221 Processing helix chain 'B' and resid 221 through 226 removed outlier: 3.598A pdb=" N ASP B 226 " --> pdb=" O ARG B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 256 removed outlier: 4.465A pdb=" N GLU B 256 " --> pdb=" O SER B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 257 through 263 removed outlier: 4.090A pdb=" N ARG B 261 " --> pdb=" O TYR B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 277 Processing helix chain 'B' and resid 282 through 286 removed outlier: 3.648A pdb=" N SER B 285 " --> pdb=" O ASN B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 293 Processing helix chain 'B' and resid 293 through 299 removed outlier: 3.691A pdb=" N PHE B 297 " --> pdb=" O LYS B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 306 No H-bonds generated for 'chain 'B' and resid 304 through 306' Processing helix chain 'B' and resid 315 through 324 Processing helix chain 'B' and resid 382 through 386 removed outlier: 3.797A pdb=" N TRP B 386 " --> pdb=" O GLU B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 444 through 446 No H-bonds generated for 'chain 'B' and resid 444 through 446' Processing helix chain 'B' and resid 456 through 468 Processing helix chain 'B' and resid 475 through 482 removed outlier: 3.537A pdb=" N LEU B 480 " --> pdb=" O THR B 476 " (cutoff:3.500A) Processing helix chain 'B' and resid 486 through 493 Processing sheet with id=AA1, first strand: chain 'A' and resid 107 through 110 removed outlier: 8.397A pdb=" N GLN A 107 " --> pdb=" O PHE A 60 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N PHE A 62 " --> pdb=" O GLN A 107 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N ARG A 109 " --> pdb=" O PHE A 62 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N GLY A 64 " --> pdb=" O ARG A 109 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER A 61 " --> pdb=" O VAL A 26 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N HIS A 25 " --> pdb=" O GLU A 135 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLY A 137 " --> pdb=" O HIS A 25 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N VAL A 171 " --> pdb=" O ARG A 138 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N PHE A 140 " --> pdb=" O VAL A 171 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N VAL A 170 " --> pdb=" O TYR A 200 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N VAL A 202 " --> pdb=" O VAL A 170 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N LEU A 172 " --> pdb=" O VAL A 202 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ARG A 201 " --> pdb=" O ILE A 474 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 427 through 429 removed outlier: 6.065A pdb=" N GLN A 397 " --> pdb=" O SER A 415 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N GLY A 367 " --> pdb=" O ILE A 402 " (cutoff:3.500A) removed outlier: 8.701A pdb=" N ILE A 355 " --> pdb=" O GLU A 235 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N VAL A 237 " --> pdb=" O ILE A 355 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N MET A 357 " --> pdb=" O VAL A 237 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N ILE A 239 " --> pdb=" O MET A 357 " (cutoff:3.500A) removed outlier: 8.184A pdb=" N GLY A 359 " --> pdb=" O ILE A 239 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N MET A 241 " --> pdb=" O GLY A 359 " (cutoff:3.500A) removed outlier: 9.636A pdb=" N ARG A 499 " --> pdb=" O ALA A 308 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N VAL A 310 " --> pdb=" O ARG A 499 " (cutoff:3.500A) removed outlier: 7.970A pdb=" N TYR A 501 " --> pdb=" O VAL A 310 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N GLN A 312 " --> pdb=" O TYR A 501 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 377 through 378 removed outlier: 3.705A pdb=" N PHE B 513 " --> pdb=" O CYS A 378 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 437 through 438 Processing sheet with id=AA5, first strand: chain 'A' and resid 519 through 522 Processing sheet with id=AA6, first strand: chain 'B' and resid 106 through 110 removed outlier: 9.295A pdb=" N GLN B 107 " --> pdb=" O PHE B 60 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N PHE B 62 " --> pdb=" O GLN B 107 " (cutoff:3.500A) removed outlier: 7.880A pdb=" N ARG B 109 " --> pdb=" O PHE B 62 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N GLY B 64 " --> pdb=" O ARG B 109 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N TYR B 200 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N VAL B 170 " --> pdb=" O TYR B 200 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 411 through 414 removed outlier: 6.529A pdb=" N GLN B 397 " --> pdb=" O PHE B 373 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N PHE B 373 " --> pdb=" O GLN B 397 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N VAL B 399 " --> pdb=" O ILE B 371 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N ILE B 371 " --> pdb=" O VAL B 399 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N HIS B 401 " --> pdb=" O ALA B 369 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N ALA B 369 " --> pdb=" O HIS B 401 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLY B 359 " --> pdb=" O MET B 241 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 427 through 429 Processing sheet with id=AA9, first strand: chain 'B' and resid 437 through 438 323 hydrogen bonds defined for protein. 909 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: 2.04 Time building geometry restraints manager: 2.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2624 1.34 - 1.46: 1630 1.46 - 1.58: 3944 1.58 - 1.69: 0 1.69 - 1.81: 38 Bond restraints: 8236 Sorted by residual: bond pdb=" C LYS B 174 " pdb=" N PRO B 175 " ideal model delta sigma weight residual 1.331 1.388 -0.057 1.20e-02 6.94e+03 2.23e+01 bond pdb=" C1 NAG B 801 " pdb=" O5 NAG B 801 " ideal model delta sigma weight residual 1.406 1.466 -0.060 2.00e-02 2.50e+03 8.87e+00 bond pdb=" C LYS A 174 " pdb=" N PRO A 175 " ideal model delta sigma weight residual 1.334 1.382 -0.048 2.34e-02 1.83e+03 4.21e+00 bond pdb=" C SER A 441 " pdb=" N PRO A 442 " ideal model delta sigma weight residual 1.332 1.356 -0.024 1.34e-02 5.57e+03 3.25e+00 bond pdb=" CA LEU A 46 " pdb=" C LEU A 46 " ideal model delta sigma weight residual 1.523 1.500 0.023 1.30e-02 5.92e+03 3.09e+00 ... (remaining 8231 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.15: 10867 2.15 - 4.29: 232 4.29 - 6.44: 36 6.44 - 8.58: 16 8.58 - 10.73: 3 Bond angle restraints: 11154 Sorted by residual: angle pdb=" N LEU B 206 " pdb=" CA LEU B 206 " pdb=" C LEU B 206 " ideal model delta sigma weight residual 113.72 104.30 9.42 1.30e+00 5.92e-01 5.25e+01 angle pdb=" C ASP A 219 " pdb=" N GLN A 220 " pdb=" CA GLN A 220 " ideal model delta sigma weight residual 122.56 115.27 7.29 1.72e+00 3.38e-01 1.80e+01 angle pdb=" CB GLU B 491 " pdb=" CG GLU B 491 " pdb=" CD GLU B 491 " ideal model delta sigma weight residual 112.60 118.88 -6.28 1.70e+00 3.46e-01 1.37e+01 angle pdb=" CA MET B 77 " pdb=" CB MET B 77 " pdb=" CG MET B 77 " ideal model delta sigma weight residual 114.10 121.37 -7.27 2.00e+00 2.50e-01 1.32e+01 angle pdb=" CB MET A 357 " pdb=" CG MET A 357 " pdb=" SD MET A 357 " ideal model delta sigma weight residual 112.70 123.43 -10.73 3.00e+00 1.11e-01 1.28e+01 ... (remaining 11149 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.14: 4418 24.14 - 48.27: 415 48.27 - 72.40: 51 72.40 - 96.54: 11 96.54 - 120.67: 3 Dihedral angle restraints: 4898 sinusoidal: 2002 harmonic: 2896 Sorted by residual: dihedral pdb=" CA TYR A 446 " pdb=" C TYR A 446 " pdb=" N TYR A 447 " pdb=" CA TYR A 447 " ideal model delta harmonic sigma weight residual 180.00 152.11 27.89 0 5.00e+00 4.00e-02 3.11e+01 dihedral pdb=" CA GLY B 403 " pdb=" C GLY B 403 " pdb=" N HIS B 404 " pdb=" CA HIS B 404 " ideal model delta harmonic sigma weight residual 180.00 153.85 26.15 0 5.00e+00 4.00e-02 2.73e+01 dihedral pdb=" CA TYR A 41 " pdb=" C TYR A 41 " pdb=" N LEU A 42 " pdb=" CA LEU A 42 " ideal model delta harmonic sigma weight residual -180.00 -159.13 -20.87 0 5.00e+00 4.00e-02 1.74e+01 ... (remaining 4895 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 778 0.043 - 0.085: 291 0.085 - 0.128: 80 0.128 - 0.170: 25 0.170 - 0.213: 5 Chirality restraints: 1179 Sorted by residual: chirality pdb=" CB VAL A 237 " pdb=" CA VAL A 237 " pdb=" CG1 VAL A 237 " pdb=" CG2 VAL A 237 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" CB VAL A 271 " pdb=" CA VAL A 271 " pdb=" CG1 VAL A 271 " pdb=" CG2 VAL A 271 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.18 2.00e-01 2.50e+01 8.52e-01 chirality pdb=" CB THR A 188 " pdb=" CA THR A 188 " pdb=" OG1 THR A 188 " pdb=" CG2 THR A 188 " both_signs ideal model delta sigma weight residual False 2.55 2.37 0.18 2.00e-01 2.50e+01 8.49e-01 ... (remaining 1176 not shown) Planarity restraints: 1463 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 144 " -0.044 5.00e-02 4.00e+02 6.71e-02 7.21e+00 pdb=" N PRO A 145 " 0.116 5.00e-02 4.00e+02 pdb=" CA PRO A 145 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 145 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 130 " -0.015 2.00e-02 2.50e+03 2.16e-02 7.00e+00 pdb=" CG HIS A 130 " 0.045 2.00e-02 2.50e+03 pdb=" ND1 HIS A 130 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 HIS A 130 " -0.017 2.00e-02 2.50e+03 pdb=" CE1 HIS A 130 " 0.000 2.00e-02 2.50e+03 pdb=" NE2 HIS A 130 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 50 " 0.013 2.00e-02 2.50e+03 1.87e-02 7.00e+00 pdb=" CG TYR B 50 " -0.045 2.00e-02 2.50e+03 pdb=" CD1 TYR B 50 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 TYR B 50 " 0.017 2.00e-02 2.50e+03 pdb=" CE1 TYR B 50 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR B 50 " -0.000 2.00e-02 2.50e+03 pdb=" CZ TYR B 50 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR B 50 " -0.001 2.00e-02 2.50e+03 ... (remaining 1460 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 1343 2.77 - 3.30: 7117 3.30 - 3.83: 13549 3.83 - 4.37: 15564 4.37 - 4.90: 27142 Nonbonded interactions: 64715 Sorted by model distance: nonbonded pdb=" O TRP A 483 " pdb=" OG1 THR A 487 " model vdw 2.233 3.040 nonbonded pdb=" OE2 GLU A 514 " pdb=" OG SER A 523 " model vdw 2.270 3.040 nonbonded pdb=" OG SER B 252 " pdb=" OE1 GLU B 323 " model vdw 2.278 3.040 nonbonded pdb=" O LEU A 264 " pdb=" OG1 THR A 269 " model vdw 2.283 3.040 nonbonded pdb=" O TRP B 483 " pdb=" OG1 THR B 487 " model vdw 2.286 3.040 ... (remaining 64710 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' and (resid 24 through 55 or resid 58 through 70 or (resid 71 and (nam \ e N or name CA or name C or name O or name CB )) or resid 72 through 81 or (resi \ d 82 and (name N or name CA or name C or name O or name CB )) or resid 83 throug \ h 149 or (resid 150 and (name N or name CA or name C or name O or name CB )) or \ resid 151 through 525 or resid 801)) selection = (chain 'B' and (resid 24 through 67 or (resid 68 through 69 and (name N or name \ CA or name C or name O or name CB )) or resid 70 through 88 or resid 91 through \ 99 or (resid 100 and (name N or name CA or name C or name O or name CB )) or res \ id 101 through 128 or (resid 129 and (name N or name CA or name C or name O or n \ ame CB )) or resid 130 through 132 or (resid 133 and (name N or name CA or name \ C or name O or name CB )) or resid 134 through 299 or (resid 300 and (name N or \ name CA or name C or name O or name CB )) or resid 301 through 525 or resid 801) \ ) } 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: 2.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 21.220 Find NCS groups from input model: 0.330 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:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6566 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 0.060 8236 Z= 0.293 Angle : 0.819 10.728 11154 Z= 0.439 Chirality : 0.050 0.213 1179 Planarity : 0.006 0.067 1462 Dihedral : 17.865 120.674 3026 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 0.48 % Allowed : 22.16 % Favored : 77.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.92 (0.24), residues: 994 helix: -1.69 (0.23), residues: 348 sheet: -0.18 (0.44), residues: 161 loop : -1.24 (0.26), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 229 HIS 0.028 0.002 HIS A 130 PHE 0.041 0.003 PHE A 147 TYR 0.045 0.003 TYR B 50 ARG 0.003 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 113 time to evaluate : 0.911 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 MET cc_start: 0.6204 (OUTLIER) cc_final: 0.5879 (tmm) REVERT: A 115 GLU cc_start: 0.8228 (pm20) cc_final: 0.7954 (pm20) REVERT: A 120 LEU cc_start: 0.8191 (mp) cc_final: 0.7986 (mt) REVERT: A 223 LYS cc_start: 0.7336 (mppt) cc_final: 0.7092 (tptt) REVERT: A 277 MET cc_start: 0.7205 (ttt) cc_final: 0.6949 (ptm) REVERT: A 453 ARG cc_start: 0.7606 (ttp-110) cc_final: 0.7107 (tmm-80) REVERT: A 454 GLU cc_start: 0.7352 (mm-30) cc_final: 0.6800 (tp30) REVERT: A 469 ARG cc_start: 0.7303 (mtt90) cc_final: 0.6939 (mtt90) REVERT: B 77 MET cc_start: 0.6930 (ppp) cc_final: 0.5900 (tmm) outliers start: 4 outliers final: 1 residues processed: 115 average time/residue: 0.1974 time to fit residues: 31.5619 Evaluate side-chains 97 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 95 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 MET Chi-restraints excluded: chain A residue 94 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 84 optimal weight: 4.9990 chunk 75 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 51 optimal weight: 10.0000 chunk 40 optimal weight: 0.9980 chunk 78 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 47 optimal weight: 0.0570 chunk 58 optimal weight: 1.9990 chunk 90 optimal weight: 0.0370 overall best weight: 1.0180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 GLN A 110 GLN ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 184 GLN A 314 GLN A 478 ASN A 524 GLN B 107 GLN B 110 GLN ** B 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 221 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4555 r_free = 0.4555 target = 0.189750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.159264 restraints weight = 11621.033| |-----------------------------------------------------------------------------| r_work (start): 0.4213 rms_B_bonded: 2.45 r_work: 0.4083 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.4083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6828 moved from start: 0.1220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8236 Z= 0.226 Angle : 0.632 9.839 11154 Z= 0.321 Chirality : 0.043 0.152 1179 Planarity : 0.005 0.056 1462 Dihedral : 6.996 74.803 1140 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 2.16 % Allowed : 21.56 % Favored : 76.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.26), residues: 994 helix: -0.39 (0.27), residues: 354 sheet: -0.12 (0.44), residues: 158 loop : -0.83 (0.28), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B 349 HIS 0.007 0.001 HIS A 130 PHE 0.024 0.002 PHE A 253 TYR 0.015 0.002 TYR A 446 ARG 0.005 0.000 ARG A 455 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 95 time to evaluate : 0.941 Fit side-chains revert: symmetry clash REVERT: A 77 MET cc_start: 0.6741 (OUTLIER) cc_final: 0.6296 (tmm) REVERT: A 115 GLU cc_start: 0.7878 (pm20) cc_final: 0.7677 (pm20) REVERT: A 120 LEU cc_start: 0.8075 (mp) cc_final: 0.7825 (mp) REVERT: A 337 PHE cc_start: 0.6438 (OUTLIER) cc_final: 0.6167 (t80) REVERT: A 453 ARG cc_start: 0.7774 (ttp-110) cc_final: 0.7432 (mtm-85) REVERT: A 454 GLU cc_start: 0.7444 (mm-30) cc_final: 0.6950 (tp30) REVERT: A 469 ARG cc_start: 0.7530 (mtt90) cc_final: 0.7227 (mtt90) REVERT: B 77 MET cc_start: 0.6729 (ppp) cc_final: 0.5873 (tmm) REVERT: B 314 GLN cc_start: 0.7425 (tm-30) cc_final: 0.6458 (tm-30) REVERT: B 499 ARG cc_start: 0.5176 (OUTLIER) cc_final: 0.4791 (ttt180) outliers start: 18 outliers final: 9 residues processed: 106 average time/residue: 0.1976 time to fit residues: 29.2687 Evaluate side-chains 100 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 88 time to evaluate : 0.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 TYR Chi-restraints excluded: chain A residue 77 MET Chi-restraints excluded: chain A residue 94 HIS Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 205 TYR Chi-restraints excluded: chain A residue 315 SER Chi-restraints excluded: chain A residue 337 PHE Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 426 SER Chi-restraints excluded: chain B residue 95 CYS Chi-restraints excluded: chain B residue 345 ASP Chi-restraints excluded: chain B residue 499 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 46 optimal weight: 1.9990 chunk 98 optimal weight: 3.9990 chunk 74 optimal weight: 0.9980 chunk 70 optimal weight: 0.7980 chunk 62 optimal weight: 0.0870 chunk 83 optimal weight: 1.9990 chunk 13 optimal weight: 4.9990 chunk 73 optimal weight: 2.9990 chunk 37 optimal weight: 0.6980 chunk 55 optimal weight: 6.9990 chunk 85 optimal weight: 4.9990 overall best weight: 0.9160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 GLN ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 220 GLN B 157 ASN B 319 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4528 r_free = 0.4528 target = 0.188819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.158133 restraints weight = 11841.100| |-----------------------------------------------------------------------------| r_work (start): 0.4168 rms_B_bonded: 2.56 r_work: 0.4042 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.4042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6834 moved from start: 0.1613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8236 Z= 0.204 Angle : 0.579 7.596 11154 Z= 0.293 Chirality : 0.042 0.149 1179 Planarity : 0.004 0.052 1462 Dihedral : 5.471 59.771 1140 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 3.47 % Allowed : 22.04 % Favored : 74.49 % 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: -0.46 (0.27), residues: 994 helix: 0.12 (0.28), residues: 356 sheet: 0.08 (0.45), residues: 152 loop : -0.67 (0.29), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B 486 HIS 0.005 0.001 HIS B 98 PHE 0.019 0.002 PHE A 147 TYR 0.015 0.001 TYR A 446 ARG 0.005 0.000 ARG A 455 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 90 time to evaluate : 0.846 Fit side-chains revert: symmetry clash REVERT: A 77 MET cc_start: 0.6793 (OUTLIER) cc_final: 0.6402 (tmm) REVERT: A 220 GLN cc_start: 0.6475 (OUTLIER) cc_final: 0.5345 (mm-40) REVERT: A 255 GLU cc_start: 0.6748 (OUTLIER) cc_final: 0.5406 (tm-30) REVERT: A 337 PHE cc_start: 0.6225 (OUTLIER) cc_final: 0.5972 (t80) REVERT: A 453 ARG cc_start: 0.7878 (ttp-110) cc_final: 0.7449 (mtm-85) REVERT: A 454 GLU cc_start: 0.7538 (mm-30) cc_final: 0.7047 (tp30) REVERT: A 469 ARG cc_start: 0.7566 (mtt90) cc_final: 0.7269 (mtt90) REVERT: B 77 MET cc_start: 0.6495 (ppp) cc_final: 0.5849 (tmm) REVERT: B 95 CYS cc_start: 0.3397 (OUTLIER) cc_final: 0.2175 (m) REVERT: B 314 GLN cc_start: 0.7543 (tm-30) cc_final: 0.6571 (tm-30) REVERT: B 392 GLN cc_start: 0.8267 (OUTLIER) cc_final: 0.6283 (mm-40) REVERT: B 499 ARG cc_start: 0.5115 (OUTLIER) cc_final: 0.3267 (ttt-90) outliers start: 29 outliers final: 13 residues processed: 113 average time/residue: 0.1999 time to fit residues: 31.7372 Evaluate side-chains 102 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 82 time to evaluate : 1.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 TYR Chi-restraints excluded: chain A residue 77 MET Chi-restraints excluded: chain A residue 94 HIS Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 205 TYR Chi-restraints excluded: chain A residue 220 GLN Chi-restraints excluded: chain A residue 238 GLU Chi-restraints excluded: chain A residue 255 GLU Chi-restraints excluded: chain A residue 315 SER Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 337 PHE Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 426 SER Chi-restraints excluded: chain B residue 95 CYS Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 345 ASP Chi-restraints excluded: chain B residue 392 GLN Chi-restraints excluded: chain B residue 499 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 43 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 63 optimal weight: 0.9980 chunk 2 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 5 optimal weight: 7.9990 chunk 94 optimal weight: 0.4980 chunk 82 optimal weight: 2.9990 chunk 97 optimal weight: 0.9990 chunk 81 optimal weight: 2.9990 chunk 62 optimal weight: 6.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 204 HIS ** 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 = 0.4522 r_free = 0.4522 target = 0.188247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.157608 restraints weight = 11893.075| |-----------------------------------------------------------------------------| r_work (start): 0.4164 rms_B_bonded: 2.58 r_work: 0.4036 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.4036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6843 moved from start: 0.1793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8236 Z= 0.201 Angle : 0.567 6.303 11154 Z= 0.289 Chirality : 0.042 0.147 1179 Planarity : 0.004 0.050 1462 Dihedral : 5.396 57.695 1140 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 3.11 % Allowed : 22.28 % Favored : 74.61 % 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: -0.31 (0.28), residues: 994 helix: 0.38 (0.29), residues: 350 sheet: 0.08 (0.45), residues: 152 loop : -0.65 (0.29), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B 486 HIS 0.005 0.001 HIS B 98 PHE 0.022 0.002 PHE A 253 TYR 0.014 0.001 TYR B 41 ARG 0.005 0.000 ARG A 455 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 88 time to evaluate : 0.917 Fit side-chains revert: symmetry clash REVERT: A 77 MET cc_start: 0.6534 (OUTLIER) cc_final: 0.6253 (tmm) REVERT: A 220 GLN cc_start: 0.6684 (OUTLIER) cc_final: 0.5965 (tp-100) REVERT: A 255 GLU cc_start: 0.6781 (OUTLIER) cc_final: 0.5357 (tm-30) REVERT: A 337 PHE cc_start: 0.6245 (OUTLIER) cc_final: 0.5969 (t80) REVERT: A 454 GLU cc_start: 0.7603 (mm-30) cc_final: 0.7190 (tp30) REVERT: A 469 ARG cc_start: 0.7549 (mtt90) cc_final: 0.7235 (mtt90) REVERT: B 95 CYS cc_start: 0.3393 (OUTLIER) cc_final: 0.2199 (m) REVERT: B 265 GLN cc_start: 0.7654 (OUTLIER) cc_final: 0.6786 (tp40) REVERT: B 314 GLN cc_start: 0.7495 (tm-30) cc_final: 0.6538 (tm-30) REVERT: B 392 GLN cc_start: 0.8281 (OUTLIER) cc_final: 0.6287 (mm-40) outliers start: 26 outliers final: 12 residues processed: 109 average time/residue: 0.1915 time to fit residues: 29.2940 Evaluate side-chains 104 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 85 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 MET Chi-restraints excluded: chain A residue 94 HIS Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 205 TYR Chi-restraints excluded: chain A residue 220 GLN Chi-restraints excluded: chain A residue 255 GLU Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 315 SER Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 337 PHE Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain B residue 95 CYS Chi-restraints excluded: chain B residue 252 SER Chi-restraints excluded: chain B residue 265 GLN Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 345 ASP Chi-restraints excluded: chain B residue 392 GLN Chi-restraints excluded: chain B residue 510 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 32 optimal weight: 0.8980 chunk 53 optimal weight: 6.9990 chunk 41 optimal weight: 0.5980 chunk 57 optimal weight: 0.9990 chunk 28 optimal weight: 5.9990 chunk 80 optimal weight: 7.9990 chunk 79 optimal weight: 0.8980 chunk 48 optimal weight: 0.9990 chunk 30 optimal weight: 0.1980 chunk 16 optimal weight: 0.9990 chunk 1 optimal weight: 7.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 346 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4526 r_free = 0.4526 target = 0.188804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.158304 restraints weight = 11698.077| |-----------------------------------------------------------------------------| r_work (start): 0.4164 rms_B_bonded: 2.54 r_work: 0.4037 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.4037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6830 moved from start: 0.1923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8236 Z= 0.177 Angle : 0.572 13.127 11154 Z= 0.283 Chirality : 0.042 0.147 1179 Planarity : 0.004 0.050 1462 Dihedral : 5.257 57.030 1140 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 3.59 % Allowed : 21.80 % Favored : 74.61 % 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: -0.17 (0.28), residues: 994 helix: 0.59 (0.29), residues: 347 sheet: 0.29 (0.46), residues: 145 loop : -0.68 (0.29), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 229 HIS 0.005 0.001 HIS B 98 PHE 0.015 0.001 PHE A 253 TYR 0.012 0.001 TYR A 446 ARG 0.004 0.000 ARG A 455 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 88 time to evaluate : 0.850 Fit side-chains revert: symmetry clash REVERT: A 23 GLN cc_start: 0.6687 (tp40) cc_final: 0.6362 (mm-40) REVERT: A 220 GLN cc_start: 0.6617 (mp10) cc_final: 0.5630 (tp-100) REVERT: A 255 GLU cc_start: 0.6782 (OUTLIER) cc_final: 0.5322 (tm-30) REVERT: A 337 PHE cc_start: 0.6128 (OUTLIER) cc_final: 0.5918 (t80) REVERT: A 453 ARG cc_start: 0.7868 (ttp-110) cc_final: 0.7595 (tmm-80) REVERT: A 454 GLU cc_start: 0.7588 (mm-30) cc_final: 0.7229 (tp30) REVERT: A 514 GLU cc_start: 0.5204 (OUTLIER) cc_final: 0.4243 (mp0) REVERT: B 95 CYS cc_start: 0.3380 (OUTLIER) cc_final: 0.2178 (m) REVERT: B 265 GLN cc_start: 0.7490 (OUTLIER) cc_final: 0.6646 (tp40) REVERT: B 314 GLN cc_start: 0.7445 (tm-30) cc_final: 0.6462 (tm-30) REVERT: B 392 GLN cc_start: 0.8264 (OUTLIER) cc_final: 0.6234 (mm-40) outliers start: 30 outliers final: 16 residues processed: 112 average time/residue: 0.2076 time to fit residues: 32.1168 Evaluate side-chains 108 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 86 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 HIS Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 205 TYR Chi-restraints excluded: chain A residue 238 GLU Chi-restraints excluded: chain A residue 255 GLU Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 315 SER Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 337 PHE Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 514 GLU Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 95 CYS Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 252 SER Chi-restraints excluded: chain B residue 265 GLN Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 345 ASP Chi-restraints excluded: chain B residue 392 GLN Chi-restraints excluded: chain B residue 510 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 35 optimal weight: 5.9990 chunk 81 optimal weight: 3.9990 chunk 5 optimal weight: 6.9990 chunk 40 optimal weight: 0.0980 chunk 21 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 68 optimal weight: 0.3980 chunk 14 optimal weight: 3.9990 chunk 91 optimal weight: 0.8980 chunk 24 optimal weight: 0.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 204 HIS ** 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 = 0.4529 r_free = 0.4529 target = 0.189156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.158549 restraints weight = 11764.445| |-----------------------------------------------------------------------------| r_work (start): 0.4167 rms_B_bonded: 2.55 r_work: 0.4042 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.4042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6825 moved from start: 0.2033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8236 Z= 0.173 Angle : 0.563 16.047 11154 Z= 0.278 Chirality : 0.041 0.146 1179 Planarity : 0.004 0.049 1462 Dihedral : 4.891 48.198 1137 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 3.47 % Allowed : 21.56 % Favored : 74.97 % 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: 994 helix: 0.65 (0.29), residues: 347 sheet: 0.29 (0.46), residues: 146 loop : -0.68 (0.29), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 43 HIS 0.004 0.001 HIS B 98 PHE 0.012 0.001 PHE A 515 TYR 0.014 0.001 TYR B 41 ARG 0.003 0.000 ARG A 455 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 87 time to evaluate : 0.932 Fit side-chains REVERT: A 220 GLN cc_start: 0.6591 (mp10) cc_final: 0.5675 (tp-100) REVERT: A 255 GLU cc_start: 0.6777 (OUTLIER) cc_final: 0.5295 (tm-30) REVERT: A 337 PHE cc_start: 0.6467 (OUTLIER) cc_final: 0.6239 (t80) REVERT: A 454 GLU cc_start: 0.7661 (mm-30) cc_final: 0.7444 (mm-30) REVERT: A 514 GLU cc_start: 0.5189 (OUTLIER) cc_final: 0.4225 (mp0) REVERT: B 265 GLN cc_start: 0.7480 (OUTLIER) cc_final: 0.6642 (tp40) REVERT: B 392 GLN cc_start: 0.8247 (OUTLIER) cc_final: 0.6275 (mm-40) outliers start: 29 outliers final: 19 residues processed: 113 average time/residue: 0.1877 time to fit residues: 29.9921 Evaluate side-chains 109 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 85 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 94 HIS Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 205 TYR Chi-restraints excluded: chain A residue 238 GLU Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 255 GLU Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 315 SER Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 337 PHE Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 514 GLU Chi-restraints excluded: chain B residue 95 CYS Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 252 SER Chi-restraints excluded: chain B residue 265 GLN Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 337 PHE Chi-restraints excluded: chain B residue 345 ASP Chi-restraints excluded: chain B residue 392 GLN Chi-restraints excluded: chain B residue 510 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 82 optimal weight: 0.3980 chunk 16 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 93 optimal weight: 0.9980 chunk 27 optimal weight: 0.5980 chunk 47 optimal weight: 0.4980 chunk 67 optimal weight: 0.9990 chunk 1 optimal weight: 9.9990 chunk 43 optimal weight: 0.0970 chunk 29 optimal weight: 0.9990 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 204 HIS ** 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 = 0.4551 r_free = 0.4551 target = 0.189424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.159189 restraints weight = 11613.421| |-----------------------------------------------------------------------------| r_work (start): 0.4214 rms_B_bonded: 2.42 r_work: 0.4091 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.4091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6818 moved from start: 0.2113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 8236 Z= 0.153 Angle : 0.557 15.268 11154 Z= 0.274 Chirality : 0.041 0.150 1179 Planarity : 0.004 0.049 1462 Dihedral : 4.762 49.090 1137 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 3.83 % Allowed : 21.20 % Favored : 74.97 % 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: -0.04 (0.28), residues: 994 helix: 0.73 (0.29), residues: 348 sheet: 0.30 (0.46), residues: 145 loop : -0.61 (0.30), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 43 HIS 0.003 0.001 HIS B 98 PHE 0.031 0.001 PHE A 253 TYR 0.010 0.001 TYR B 316 ARG 0.003 0.000 ARG A 455 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 90 time to evaluate : 0.972 Fit side-chains REVERT: A 23 GLN cc_start: 0.6630 (tp40) cc_final: 0.6331 (mm-40) REVERT: A 77 MET cc_start: 0.6610 (ppp) cc_final: 0.6044 (tmm) REVERT: A 220 GLN cc_start: 0.6447 (mp10) cc_final: 0.5477 (tp-100) REVERT: A 255 GLU cc_start: 0.6729 (OUTLIER) cc_final: 0.5258 (tm-30) REVERT: A 453 ARG cc_start: 0.7806 (ttp-110) cc_final: 0.7389 (mtm-85) REVERT: A 454 GLU cc_start: 0.7599 (mm-30) cc_final: 0.7336 (mm-30) REVERT: A 514 GLU cc_start: 0.5082 (OUTLIER) cc_final: 0.4134 (mp0) REVERT: B 265 GLN cc_start: 0.7449 (OUTLIER) cc_final: 0.6632 (tp40) REVERT: B 392 GLN cc_start: 0.8180 (OUTLIER) cc_final: 0.6187 (mm-40) outliers start: 32 outliers final: 19 residues processed: 117 average time/residue: 0.1970 time to fit residues: 32.9011 Evaluate side-chains 108 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 85 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 94 HIS Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 205 TYR Chi-restraints excluded: chain A residue 238 GLU Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 255 GLU Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 315 SER Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 514 GLU Chi-restraints excluded: chain B residue 95 CYS Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 252 SER Chi-restraints excluded: chain B residue 265 GLN Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 337 PHE Chi-restraints excluded: chain B residue 345 ASP Chi-restraints excluded: chain B residue 392 GLN Chi-restraints excluded: chain B residue 510 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 92 optimal weight: 0.1980 chunk 37 optimal weight: 2.9990 chunk 29 optimal weight: 4.9990 chunk 60 optimal weight: 10.0000 chunk 93 optimal weight: 0.8980 chunk 59 optimal weight: 5.9990 chunk 24 optimal weight: 0.9980 chunk 54 optimal weight: 8.9990 chunk 3 optimal weight: 8.9990 chunk 83 optimal weight: 2.9990 chunk 73 optimal weight: 0.5980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 GLN ** A 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 204 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4528 r_free = 0.4528 target = 0.188444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.157965 restraints weight = 11817.767| |-----------------------------------------------------------------------------| r_work (start): 0.4170 rms_B_bonded: 2.42 r_work: 0.4048 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.4048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6889 moved from start: 0.2261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8236 Z= 0.242 Angle : 0.625 15.253 11154 Z= 0.306 Chirality : 0.043 0.162 1179 Planarity : 0.004 0.046 1462 Dihedral : 5.022 49.227 1137 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 3.71 % Allowed : 21.56 % Favored : 74.73 % 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 (0.28), residues: 994 helix: 0.68 (0.29), residues: 348 sheet: 0.17 (0.46), residues: 146 loop : -0.77 (0.29), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 486 HIS 0.004 0.001 HIS A 233 PHE 0.024 0.002 PHE A 253 TYR 0.016 0.002 TYR A 446 ARG 0.003 0.000 ARG A 218 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 89 time to evaluate : 0.945 Fit side-chains REVERT: A 23 GLN cc_start: 0.6654 (tp40) cc_final: 0.6407 (mm-40) REVERT: A 77 MET cc_start: 0.7113 (OUTLIER) cc_final: 0.6285 (tmm) REVERT: A 220 GLN cc_start: 0.6569 (mp10) cc_final: 0.5702 (tp-100) REVERT: A 255 GLU cc_start: 0.6799 (OUTLIER) cc_final: 0.5393 (tm-30) REVERT: A 454 GLU cc_start: 0.7676 (mm-30) cc_final: 0.7330 (mt-10) REVERT: A 514 GLU cc_start: 0.5162 (OUTLIER) cc_final: 0.4155 (mp0) REVERT: B 215 LEU cc_start: 0.7847 (OUTLIER) cc_final: 0.7622 (mp) REVERT: B 265 GLN cc_start: 0.7800 (OUTLIER) cc_final: 0.7074 (tp40) REVERT: B 314 GLN cc_start: 0.7451 (tm-30) cc_final: 0.6583 (tm-30) REVERT: B 392 GLN cc_start: 0.8264 (OUTLIER) cc_final: 0.6257 (mm-40) outliers start: 31 outliers final: 20 residues processed: 113 average time/residue: 0.1906 time to fit residues: 30.3083 Evaluate side-chains 111 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 85 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 77 MET Chi-restraints excluded: chain A residue 94 HIS Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 205 TYR Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 255 GLU Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 315 SER Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 514 GLU Chi-restraints excluded: chain B residue 95 CYS Chi-restraints excluded: chain B residue 129 GLN Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 252 SER Chi-restraints excluded: chain B residue 265 GLN Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 337 PHE Chi-restraints excluded: chain B residue 345 ASP Chi-restraints excluded: chain B residue 392 GLN Chi-restraints excluded: chain B residue 510 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 59.0734 > 50: distance: 41 - 42: 4.231 distance: 41 - 47: 4.916 distance: 42 - 43: 5.731 distance: 42 - 45: 3.441 distance: 43 - 44: 4.091 distance: 48 - 49: 3.530 distance: 49 - 50: 5.932 distance: 50 - 51: 5.501 distance: 50 - 52: 4.110 distance: 53 - 56: 3.268 distance: 54 - 55: 8.361 distance: 54 - 60: 3.880 distance: 60 - 61: 3.193 distance: 61 - 62: 3.868 distance: 61 - 64: 3.934 distance: 62 - 63: 3.183 distance: 62 - 71: 3.349 distance: 68 - 69: 5.276 distance: 68 - 70: 4.902 distance: 71 - 72: 4.436 distance: 71 - 97: 15.895 distance: 72 - 75: 3.297 distance: 73 - 74: 3.420 distance: 75 - 76: 3.342 distance: 76 - 77: 4.817 distance: 76 - 78: 8.616 distance: 79 - 80: 3.706 distance: 80 - 83: 3.377 distance: 83 - 84: 5.369 distance: 84 - 85: 3.089 distance: 84 - 86: 4.830 distance: 85 - 87: 5.860 distance: 86 - 88: 6.601 distance: 87 - 89: 4.883 distance: 88 - 89: 9.433 distance: 90 - 91: 5.692 distance: 91 - 92: 3.963 distance: 92 - 93: 4.439 distance: 92 - 94: 5.688 distance: 94 - 95: 5.758 distance: 95 - 96: 5.643 distance: 95 - 98: 7.626 distance: 96 - 97: 13.159 distance: 96 - 100: 7.111 distance: 98 - 99: 6.313 distance: 100 - 101: 10.207 distance: 100 - 106: 4.663 distance: 101 - 102: 8.527 distance: 101 - 104: 8.359 distance: 102 - 103: 31.195 distance: 102 - 107: 30.281 distance: 104 - 105: 8.973 distance: 105 - 106: 10.931 distance: 107 - 108: 14.928 distance: 108 - 109: 29.959 distance: 108 - 111: 3.736 distance: 109 - 110: 19.641 distance: 109 - 115: 9.647 distance: 111 - 112: 31.441 distance: 112 - 113: 8.007 distance: 112 - 114: 8.807