Starting phenix.real_space_refine on Sat Aug 3 12:42:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8em2_28232/08_2024/8em2_28232.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8em2_28232/08_2024/8em2_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8em2_28232/08_2024/8em2_28232.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8em2_28232/08_2024/8em2_28232.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8em2_28232/08_2024/8em2_28232.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8em2_28232/08_2024/8em2_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 Residue "A GLU 196": "OE1" <-> "OE2" Residue "A GLU 270": "OE1" <-> "OE2" Residue "A GLU 278": "OE1" <-> "OE2" Residue "A GLU 514": "OE1" <-> "OE2" Residue "B GLU 115": "OE1" <-> "OE2" Residue "B GLU 491": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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: 5.13, per 1000 atoms: 0.64 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 801 " - " ASN A 157 " Time building additional restraints: 2.96 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 1.03 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: 2.45 Time building geometry restraints manager: 3.26 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: 96.38 - 103.97: 115 103.97 - 111.56: 3444 111.56 - 119.15: 3145 119.15 - 126.73: 4306 126.73 - 134.32: 144 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: 1.840 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: 0.330 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 25.660 Find NCS groups from input model: 0.320 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:2.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.860 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 4 poor density : 113 time to evaluate : 0.897 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: 0.1994 time to fit residues: 31.6101 Evaluate side-chains 97 residues out of total 845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 95 time to evaluate : 0.917 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6624 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 fitting. rotamer outliers: 18 poor density : 95 time to evaluate : 0.921 Fit side-chains revert: symmetry clash REVERT: A 77 MET cc_start: 0.6621 (OUTLIER) cc_final: 0.6202 (tmm) REVERT: A 115 GLU cc_start: 0.8368 (pm20) cc_final: 0.8043 (pm20) REVERT: A 120 LEU cc_start: 0.8066 (mp) cc_final: 0.7666 (mp) REVERT: A 121 ASN cc_start: 0.6560 (m110) cc_final: 0.6313 (m110) REVERT: A 277 MET cc_start: 0.7275 (OUTLIER) cc_final: 0.7031 (ptm) REVERT: A 337 PHE cc_start: 0.6111 (OUTLIER) cc_final: 0.5810 (t80) REVERT: A 453 ARG cc_start: 0.7464 (ttp-110) cc_final: 0.7060 (mtm-85) REVERT: A 454 GLU cc_start: 0.7587 (mm-30) cc_final: 0.6985 (tp30) REVERT: A 469 ARG cc_start: 0.7297 (mtt90) cc_final: 0.6981 (mtt90) REVERT: B 77 MET cc_start: 0.6786 (ppp) cc_final: 0.5979 (tmm) REVERT: B 314 GLN cc_start: 0.7240 (tm-30) cc_final: 0.6158 (tm-30) REVERT: B 499 ARG cc_start: 0.5300 (OUTLIER) cc_final: 0.4831 (ttt180) outliers start: 18 outliers final: 9 residues processed: 106 average time/residue: 0.1987 time to fit residues: 29.3250 Evaluate side-chains 102 residues out of total 845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 89 time to evaluate : 0.914 ------------------------------------------------------------------------------- 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 277 MET 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 50 optimal weight: 3.9990 chunk 28 optimal weight: 5.9990 chunk 75 optimal weight: 0.2980 chunk 61 optimal weight: 0.9990 chunk 25 optimal weight: 0.7980 chunk 90 optimal weight: 0.6980 chunk 98 optimal weight: 3.9990 chunk 81 optimal weight: 0.8980 chunk 31 optimal weight: 4.9990 chunk 72 optimal weight: 1.9990 chunk 89 optimal weight: 4.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6619 moved from start: 0.1514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8236 Z= 0.183 Angle : 0.563 7.088 11154 Z= 0.285 Chirality : 0.042 0.151 1179 Planarity : 0.004 0.052 1462 Dihedral : 5.445 59.185 1140 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 3.35 % Allowed : 22.16 % 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: -0.45 (0.27), residues: 994 helix: 0.11 (0.28), residues: 356 sheet: 0.12 (0.45), residues: 152 loop : -0.66 (0.29), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 483 HIS 0.004 0.001 HIS B 98 PHE 0.018 0.002 PHE A 147 TYR 0.013 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 118 residues out of total 845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 90 time to evaluate : 0.911 Fit side-chains revert: symmetry clash REVERT: A 77 MET cc_start: 0.6706 (OUTLIER) cc_final: 0.6313 (tmm) REVERT: A 115 GLU cc_start: 0.8378 (pm20) cc_final: 0.8165 (pm20) REVERT: A 220 GLN cc_start: 0.6559 (OUTLIER) cc_final: 0.5280 (mm-40) REVERT: A 255 GLU cc_start: 0.6659 (OUTLIER) cc_final: 0.5322 (tm-30) REVERT: A 277 MET cc_start: 0.7278 (OUTLIER) cc_final: 0.7045 (ptm) REVERT: A 337 PHE cc_start: 0.6103 (OUTLIER) cc_final: 0.5807 (t80) REVERT: A 453 ARG cc_start: 0.7495 (ttp-110) cc_final: 0.7054 (mtm-85) REVERT: A 454 GLU cc_start: 0.7632 (mm-30) cc_final: 0.7034 (tp30) REVERT: A 469 ARG cc_start: 0.7332 (mtt90) cc_final: 0.7016 (mtt90) REVERT: B 77 MET cc_start: 0.6554 (ppp) cc_final: 0.5966 (tmm) REVERT: B 95 CYS cc_start: 0.2969 (OUTLIER) cc_final: 0.1808 (m) REVERT: B 129 GLN cc_start: 0.7829 (pt0) cc_final: 0.7621 (pp30) REVERT: B 314 GLN cc_start: 0.7290 (tm-30) cc_final: 0.6232 (tm-30) REVERT: B 392 GLN cc_start: 0.8009 (OUTLIER) cc_final: 0.5942 (mm-40) REVERT: B 510 LEU cc_start: 0.7946 (OUTLIER) cc_final: 0.7737 (mt) outliers start: 28 outliers final: 12 residues processed: 111 average time/residue: 0.1820 time to fit residues: 28.4982 Evaluate side-chains 102 residues out of total 845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 82 time to evaluate : 0.899 ------------------------------------------------------------------------------- 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 277 MET 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 68 optimal weight: 0.9990 chunk 47 optimal weight: 0.6980 chunk 10 optimal weight: 0.0030 chunk 43 optimal weight: 0.9980 chunk 61 optimal weight: 5.9990 chunk 91 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 80 optimal weight: 0.0770 chunk 54 optimal weight: 9.9990 overall best weight: 0.5550 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6605 moved from start: 0.1680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8236 Z= 0.155 Angle : 0.540 6.949 11154 Z= 0.274 Chirality : 0.041 0.144 1179 Planarity : 0.004 0.050 1462 Dihedral : 5.262 58.556 1140 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 2.99 % Allowed : 22.16 % Favored : 74.85 % 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: 0.47 (0.29), residues: 353 sheet: 0.21 (0.46), residues: 152 loop : -0.62 (0.29), residues: 489 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 0.012 0.001 PHE A 194 TYR 0.015 0.001 TYR B 41 ARG 0.006 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 112 residues out of total 845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 87 time to evaluate : 0.911 Fit side-chains revert: symmetry clash REVERT: A 77 MET cc_start: 0.6439 (OUTLIER) cc_final: 0.6153 (tmm) REVERT: A 115 GLU cc_start: 0.8355 (pm20) cc_final: 0.8143 (pm20) REVERT: A 220 GLN cc_start: 0.6469 (OUTLIER) cc_final: 0.5775 (tp-100) REVERT: A 255 GLU cc_start: 0.6679 (OUTLIER) cc_final: 0.5307 (tm-30) REVERT: A 277 MET cc_start: 0.7214 (OUTLIER) cc_final: 0.6956 (ptm) REVERT: A 454 GLU cc_start: 0.7647 (mm-30) cc_final: 0.7118 (tp30) REVERT: A 469 ARG cc_start: 0.7383 (mtt90) cc_final: 0.7063 (mtt90) REVERT: B 77 MET cc_start: 0.6507 (ppp) cc_final: 0.5919 (tmm) REVERT: B 95 CYS cc_start: 0.2944 (OUTLIER) cc_final: 0.1827 (m) REVERT: B 265 GLN cc_start: 0.7290 (OUTLIER) cc_final: 0.6479 (tp40) REVERT: B 392 GLN cc_start: 0.7993 (OUTLIER) cc_final: 0.5918 (mm-40) outliers start: 25 outliers final: 12 residues processed: 105 average time/residue: 0.1882 time to fit residues: 27.8366 Evaluate side-chains 101 residues out of total 845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 82 time to evaluate : 0.896 ------------------------------------------------------------------------------- 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 238 GLU Chi-restraints excluded: chain A residue 255 GLU Chi-restraints excluded: chain A residue 277 MET Chi-restraints excluded: chain A residue 315 SER Chi-restraints excluded: chain A residue 336 THR 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 1 optimal weight: 7.9990 chunk 71 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 82 optimal weight: 0.1980 chunk 66 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 chunk 49 optimal weight: 0.7980 chunk 86 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 32 optimal weight: 0.0370 chunk 87 optimal weight: 0.5980 overall best weight: 0.4858 ------------------------------------------------------------------------------- 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 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6598 moved from start: 0.1833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 8236 Z= 0.147 Angle : 0.545 12.485 11154 Z= 0.269 Chirality : 0.041 0.164 1179 Planarity : 0.004 0.049 1462 Dihedral : 5.097 57.794 1140 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % 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: -0.07 (0.28), residues: 994 helix: 0.63 (0.29), residues: 353 sheet: 0.26 (0.46), residues: 152 loop : -0.59 (0.30), residues: 489 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 0.012 0.001 PHE A 194 TYR 0.010 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 117 residues out of total 845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 91 time to evaluate : 0.974 Fit side-chains revert: symmetry clash REVERT: A 255 GLU cc_start: 0.6698 (OUTLIER) cc_final: 0.5290 (tm-30) REVERT: A 453 ARG cc_start: 0.7422 (ttp-110) cc_final: 0.7014 (tmm-80) REVERT: A 454 GLU cc_start: 0.7645 (mm-30) cc_final: 0.7101 (tp30) REVERT: A 469 ARG cc_start: 0.7327 (mtt90) cc_final: 0.7006 (mtt90) REVERT: B 95 CYS cc_start: 0.2953 (OUTLIER) cc_final: 0.1839 (m) REVERT: B 265 GLN cc_start: 0.7244 (OUTLIER) cc_final: 0.6430 (tp40) REVERT: B 392 GLN cc_start: 0.7930 (OUTLIER) cc_final: 0.5882 (mm-40) REVERT: B 499 ARG cc_start: 0.5193 (OUTLIER) cc_final: 0.4947 (ttm-80) outliers start: 26 outliers final: 14 residues processed: 111 average time/residue: 0.2109 time to fit residues: 32.7002 Evaluate side-chains 105 residues out of total 845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 86 time to evaluate : 0.957 ------------------------------------------------------------------------------- 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 394 LEU Chi-restraints excluded: chain A residue 398 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 499 ARG 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 19 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 96 optimal weight: 0.9990 chunk 80 optimal weight: 6.9990 chunk 44 optimal weight: 1.9990 chunk 8 optimal weight: 4.9990 chunk 32 optimal weight: 0.8980 chunk 50 optimal weight: 4.9990 chunk 93 optimal weight: 0.9990 chunk 10 optimal weight: 6.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6678 moved from start: 0.2144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 8236 Z= 0.285 Angle : 0.641 16.185 11154 Z= 0.319 Chirality : 0.044 0.155 1179 Planarity : 0.004 0.047 1462 Dihedral : 5.201 47.967 1137 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 3.59 % Allowed : 21.44 % 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: -0.36 (0.27), residues: 994 helix: 0.46 (0.29), residues: 348 sheet: 0.05 (0.45), residues: 153 loop : -0.79 (0.29), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 486 HIS 0.005 0.001 HIS A 232 PHE 0.029 0.002 PHE A 253 TYR 0.019 0.002 TYR A 446 ARG 0.004 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 fitting. rotamer outliers: 30 poor density : 86 time to evaluate : 0.890 Fit side-chains revert: symmetry clash REVERT: A 23 GLN cc_start: 0.6665 (tp40) cc_final: 0.6407 (mm-40) REVERT: A 220 GLN cc_start: 0.6768 (mp10) cc_final: 0.5630 (tp-100) REVERT: A 255 GLU cc_start: 0.6735 (OUTLIER) cc_final: 0.5312 (tm-30) REVERT: A 454 GLU cc_start: 0.7779 (mm-30) cc_final: 0.7569 (mm-30) REVERT: A 514 GLU cc_start: 0.5648 (OUTLIER) cc_final: 0.4710 (mp0) REVERT: B 95 CYS cc_start: 0.2958 (OUTLIER) cc_final: 0.1831 (m) REVERT: B 265 GLN cc_start: 0.7708 (OUTLIER) cc_final: 0.6924 (tp40) REVERT: B 314 GLN cc_start: 0.7211 (tm-30) cc_final: 0.6144 (tm-30) REVERT: B 392 GLN cc_start: 0.8088 (OUTLIER) cc_final: 0.6085 (mm-40) outliers start: 30 outliers final: 17 residues processed: 112 average time/residue: 0.1934 time to fit residues: 30.2444 Evaluate side-chains 105 residues out of total 845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 83 time to evaluate : 0.957 ------------------------------------------------------------------------------- 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 255 GLU Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 279 LEU 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 129 GLN 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 55 optimal weight: 5.9990 chunk 70 optimal weight: 0.8980 chunk 54 optimal weight: 4.9990 chunk 81 optimal weight: 4.9990 chunk 96 optimal weight: 0.6980 chunk 60 optimal weight: 9.9990 chunk 58 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 chunk 38 optimal weight: 0.0040 chunk 57 optimal weight: 0.8980 overall best weight: 0.6792 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6635 moved from start: 0.2167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8236 Z= 0.181 Angle : 0.596 15.263 11154 Z= 0.293 Chirality : 0.042 0.147 1179 Planarity : 0.004 0.049 1462 Dihedral : 4.946 48.437 1137 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 3.35 % Allowed : 22.04 % 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: -0.23 (0.28), residues: 994 helix: 0.56 (0.29), residues: 348 sheet: 0.25 (0.46), residues: 146 loop : -0.74 (0.29), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 43 HIS 0.005 0.001 HIS B 98 PHE 0.020 0.001 PHE A 253 TYR 0.013 0.001 TYR B 50 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 114 residues out of total 845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 86 time to evaluate : 0.970 Fit side-chains REVERT: A 77 MET cc_start: 0.6814 (ppp) cc_final: 0.6180 (tmm) REVERT: A 220 GLN cc_start: 0.6723 (mp10) cc_final: 0.5590 (tp-100) REVERT: A 255 GLU cc_start: 0.6674 (OUTLIER) cc_final: 0.5192 (tm-30) REVERT: A 453 ARG cc_start: 0.7539 (ttp-110) cc_final: 0.7007 (mtm-85) REVERT: A 454 GLU cc_start: 0.7758 (mm-30) cc_final: 0.7456 (mm-30) REVERT: A 514 GLU cc_start: 0.5583 (OUTLIER) cc_final: 0.4679 (mp0) REVERT: B 77 MET cc_start: 0.7203 (ppp) cc_final: 0.5964 (ppp) REVERT: B 265 GLN cc_start: 0.7573 (OUTLIER) cc_final: 0.6727 (tp40) REVERT: B 314 GLN cc_start: 0.7306 (tm-30) cc_final: 0.6288 (tm-30) REVERT: B 392 GLN cc_start: 0.7998 (OUTLIER) cc_final: 0.5930 (mm-40) outliers start: 28 outliers final: 20 residues processed: 110 average time/residue: 0.1984 time to fit residues: 30.6033 Evaluate side-chains 106 residues out of total 845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 82 time to evaluate : 0.940 ------------------------------------------------------------------------------- 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 129 GLN 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 29 optimal weight: 3.9990 chunk 18 optimal weight: 0.0870 chunk 61 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 chunk 8 optimal weight: 0.8980 chunk 75 optimal weight: 0.6980 chunk 87 optimal weight: 0.8980 chunk 92 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 overall best weight: 0.6958 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6636 moved from start: 0.2231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8236 Z= 0.181 Angle : 0.587 14.991 11154 Z= 0.289 Chirality : 0.042 0.177 1179 Planarity : 0.004 0.049 1462 Dihedral : 4.897 49.219 1137 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 9.42 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: -0.18 (0.28), residues: 994 helix: 0.58 (0.29), residues: 349 sheet: 0.28 (0.46), residues: 143 loop : -0.69 (0.29), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 43 HIS 0.004 0.001 HIS B 98 PHE 0.013 0.001 PHE B 515 TYR 0.015 0.001 TYR B 41 ARG 0.003 0.000 ARG A 455 *********************** 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 113 residues out of total 845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 83 time to evaluate : 1.141 Fit side-chains REVERT: A 77 MET cc_start: 0.6922 (OUTLIER) cc_final: 0.6276 (tmm) REVERT: A 220 GLN cc_start: 0.6739 (mp10) cc_final: 0.5591 (tp-100) REVERT: A 255 GLU cc_start: 0.6715 (OUTLIER) cc_final: 0.5311 (tm-30) REVERT: A 453 ARG cc_start: 0.7524 (ttp-110) cc_final: 0.7008 (mtm-85) REVERT: A 454 GLU cc_start: 0.7757 (mm-30) cc_final: 0.7453 (mm-30) REVERT: A 514 GLU cc_start: 0.5548 (OUTLIER) cc_final: 0.4662 (mp0) REVERT: B 265 GLN cc_start: 0.7542 (OUTLIER) cc_final: 0.6692 (tp40) REVERT: B 314 GLN cc_start: 0.7284 (tm-30) cc_final: 0.6255 (tm-30) REVERT: B 392 GLN cc_start: 0.7977 (OUTLIER) cc_final: 0.5871 (mm-40) REVERT: B 499 ARG cc_start: 0.5202 (OUTLIER) cc_final: 0.4739 (ttm-80) outliers start: 30 outliers final: 20 residues processed: 107 average time/residue: 0.1974 time to fit residues: 29.1988 Evaluate side-chains 107 residues out of total 845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 81 time to evaluate : 0.964 ------------------------------------------------------------------------------- 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 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 129 GLN 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 499 ARG 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-5409/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 70.4204 > 50: distance: 81 - 86: 21.889 distance: 86 - 87: 15.309 distance: 87 - 88: 47.533 distance: 87 - 90: 14.846 distance: 88 - 89: 38.645 distance: 88 - 92: 40.507 distance: 90 - 91: 34.838 distance: 92 - 93: 16.325 distance: 93 - 94: 18.674 distance: 93 - 96: 8.848 distance: 94 - 95: 14.046 distance: 94 - 103: 54.357 distance: 96 - 97: 32.821 distance: 97 - 98: 5.156 distance: 98 - 99: 6.126 distance: 99 - 100: 14.688 distance: 100 - 102: 17.393 distance: 103 - 104: 12.087 distance: 104 - 105: 24.323 distance: 104 - 107: 18.515 distance: 105 - 106: 15.147 distance: 105 - 111: 24.804 distance: 107 - 108: 20.699 distance: 108 - 109: 38.451 distance: 108 - 110: 31.525 distance: 111 - 112: 16.288 distance: 112 - 113: 51.781 distance: 112 - 115: 32.873 distance: 113 - 119: 33.631 distance: 115 - 116: 3.737 distance: 116 - 117: 36.336 distance: 116 - 118: 56.049 distance: 119 - 120: 6.510 distance: 120 - 121: 5.652 distance: 120 - 123: 35.318 distance: 121 - 122: 40.532 distance: 121 - 130: 31.632 distance: 123 - 124: 7.752 distance: 124 - 126: 6.034 distance: 125 - 127: 15.034 distance: 126 - 128: 29.933 distance: 127 - 129: 30.921 distance: 128 - 129: 35.879 distance: 130 - 131: 33.768 distance: 131 - 132: 60.206 distance: 131 - 134: 36.755 distance: 132 - 133: 17.088 distance: 132 - 141: 37.823 distance: 135 - 136: 6.914 distance: 136 - 137: 4.020 distance: 137 - 138: 47.688 distance: 138 - 139: 7.552 distance: 138 - 140: 33.904 distance: 141 - 142: 30.783 distance: 141 - 147: 41.342 distance: 142 - 145: 45.349 distance: 143 - 144: 10.960 distance: 143 - 148: 37.221 distance: 145 - 146: 7.671 distance: 146 - 147: 46.551 distance: 148 - 149: 10.105 distance: 149 - 150: 55.292 distance: 149 - 152: 42.014 distance: 150 - 151: 8.561 distance: 150 - 154: 49.800 distance: 152 - 153: 40.651 distance: 154 - 155: 42.705 distance: 155 - 156: 22.451 distance: 155 - 158: 40.861 distance: 156 - 157: 53.566 distance: 156 - 162: 42.121 distance: 158 - 159: 29.646 distance: 159 - 160: 44.092 distance: 159 - 161: 40.807 distance: 162 - 163: 45.362 distance: 162 - 168: 33.605 distance: 163 - 164: 41.336 distance: 163 - 166: 40.607 distance: 164 - 169: 34.462 distance: 166 - 167: 37.071 distance: 167 - 168: 35.795