Starting phenix.real_space_refine on Mon Jul 28 22:49:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xr6_33408/07_2025/7xr6_33408.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xr6_33408/07_2025/7xr6_33408.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7xr6_33408/07_2025/7xr6_33408.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xr6_33408/07_2025/7xr6_33408.map" model { file = "/net/cci-nas-00/data/ceres_data/7xr6_33408/07_2025/7xr6_33408.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xr6_33408/07_2025/7xr6_33408.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.090 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Br 3 7.06 5 S 75 5.16 5 C 6860 2.51 5 N 1545 2.21 5 O 1710 1.98 5 F 6 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 10199 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 424, 3179 Classifications: {'peptide': 424} Link IDs: {'PTRANS': 14, 'TRANS': 409} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 3180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 424, 3180 Classifications: {'peptide': 424} Link IDs: {'PTRANS': 14, 'TRANS': 409} Chain breaks: 2 Chain: "C" Number of atoms: 3180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 424, 3180 Classifications: {'peptide': 424} Link IDs: {'PTRANS': 14, 'TRANS': 409} Chain breaks: 2 Chain: "A" Number of atoms: 220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 220 Unusual residues: {'GJ0': 1, 'PC1': 10, 'XKJ': 1, 'Y01': 1} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 404 Unresolved non-hydrogen angles: 494 Unresolved non-hydrogen dihedrals: 374 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'PC1:plan-2': 10, 'PC1:plan-1': 10} Unresolved non-hydrogen planarities: 62 Chain: "B" Number of atoms: 220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 220 Unusual residues: {'GJ0': 1, 'PC1': 10, 'XKJ': 1, 'Y01': 1} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 404 Unresolved non-hydrogen angles: 494 Unresolved non-hydrogen dihedrals: 374 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'PC1:plan-2': 10, 'PC1:plan-1': 10} Unresolved non-hydrogen planarities: 62 Chain: "C" Number of atoms: 220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 220 Unusual residues: {'GJ0': 1, 'PC1': 10, 'XKJ': 1, 'Y01': 1} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 404 Unresolved non-hydrogen angles: 494 Unresolved non-hydrogen dihedrals: 374 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'PC1:plan-2': 10, 'PC1:plan-1': 10} Unresolved non-hydrogen planarities: 62 Time building chain proxies: 6.82, per 1000 atoms: 0.67 Number of scatterers: 10199 At special positions: 0 Unit cell: (117.52, 117.52, 84.24, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Br 3 34.99 S 75 16.00 F 6 9.00 O 1710 8.00 N 1545 7.00 C 6860 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.68 Conformation dependent library (CDL) restraints added in 1.3 seconds 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2304 Finding SS restraints... Secondary structure from input PDB file: 67 helices and 3 sheets defined 84.9% alpha, 1.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.04 Creating SS restraints... Processing helix chain 'A' and resid 37 through 42 Processing helix chain 'A' and resid 44 through 66 Processing helix chain 'A' and resid 71 through 79 Processing helix chain 'A' and resid 79 through 107 removed outlier: 4.484A pdb=" N LEU A 94 " --> pdb=" O LYS A 90 " (cutoff:3.500A) Proline residue: A 95 - end of helix removed outlier: 4.118A pdb=" N LEU A 101 " --> pdb=" O ILE A 97 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ILE A 102 " --> pdb=" O ILE A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 113 removed outlier: 3.975A pdb=" N SER A 113 " --> pdb=" O ALA A 110 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 110 through 113' Processing helix chain 'A' and resid 114 through 143 removed outlier: 3.581A pdb=" N THR A 118 " --> pdb=" O GLY A 114 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N TYR A 123 " --> pdb=" O ARG A 119 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ILE A 129 " --> pdb=" O MET A 125 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLY A 135 " --> pdb=" O ALA A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 176 Processing helix chain 'A' and resid 181 through 185 removed outlier: 3.731A pdb=" N PHE A 185 " --> pdb=" O GLN A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 260 removed outlier: 3.573A pdb=" N GLY A 260 " --> pdb=" O MET A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 286 removed outlier: 3.818A pdb=" N PHE A 269 " --> pdb=" O LEU A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 302 Processing helix chain 'A' and resid 305 through 330 removed outlier: 3.694A pdb=" N VAL A 309 " --> pdb=" O ASP A 305 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ARG A 311 " --> pdb=" O GLU A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 340 Processing helix chain 'A' and resid 343 through 351 Processing helix chain 'A' and resid 351 through 362 Processing helix chain 'A' and resid 363 through 378 Proline residue: A 369 - end of helix Processing helix chain 'A' and resid 382 through 397 Proline residue: A 391 - end of helix removed outlier: 4.128A pdb=" N THR A 395 " --> pdb=" O PRO A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 416 removed outlier: 3.825A pdb=" N ALA A 402 " --> pdb=" O MET A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 437 removed outlier: 3.931A pdb=" N VAL A 426 " --> pdb=" O GLY A 422 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR A 427 " --> pdb=" O GLY A 423 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N THR A 433 " --> pdb=" O SER A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 457 removed outlier: 3.625A pdb=" N VAL A 457 " --> pdb=" O ILE A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 469 removed outlier: 3.646A pdb=" N LEU A 467 " --> pdb=" O ASP A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 496 removed outlier: 4.096A pdb=" N MET A 477 " --> pdb=" O LEU A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 507 removed outlier: 3.576A pdb=" N GLN A 507 " --> pdb=" O THR A 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 42 Processing helix chain 'B' and resid 44 through 66 Processing helix chain 'B' and resid 71 through 79 Processing helix chain 'B' and resid 79 through 107 removed outlier: 3.548A pdb=" N LEU B 92 " --> pdb=" O MET B 88 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N LEU B 94 " --> pdb=" O LYS B 90 " (cutoff:3.500A) Proline residue: B 95 - end of helix removed outlier: 4.125A pdb=" N LEU B 101 " --> pdb=" O ILE B 97 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ILE B 102 " --> pdb=" O ILE B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 113 removed outlier: 4.015A pdb=" N SER B 113 " --> pdb=" O ALA B 110 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 110 through 113' Processing helix chain 'B' and resid 114 through 143 removed outlier: 3.718A pdb=" N TYR B 123 " --> pdb=" O ARG B 119 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ILE B 129 " --> pdb=" O MET B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 176 Processing helix chain 'B' and resid 241 through 260 removed outlier: 3.562A pdb=" N GLY B 260 " --> pdb=" O MET B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 286 Processing helix chain 'B' and resid 287 through 300 Processing helix chain 'B' and resid 305 through 330 removed outlier: 3.715A pdb=" N VAL B 309 " --> pdb=" O ASP B 305 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ARG B 311 " --> pdb=" O GLU B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 340 Processing helix chain 'B' and resid 343 through 362 removed outlier: 3.534A pdb=" N PHE B 347 " --> pdb=" O ASN B 343 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N GLN B 353 " --> pdb=" O ALA B 349 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N ALA B 354 " --> pdb=" O GLY B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 363 through 378 Proline residue: B 369 - end of helix Processing helix chain 'B' and resid 382 through 397 Proline residue: B 391 - end of helix removed outlier: 4.140A pdb=" N THR B 395 " --> pdb=" O PRO B 391 " (cutoff:3.500A) Processing helix chain 'B' and resid 398 through 416 removed outlier: 3.818A pdb=" N ALA B 402 " --> pdb=" O MET B 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 421 through 437 removed outlier: 3.999A pdb=" N VAL B 426 " --> pdb=" O GLY B 422 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N THR B 427 " --> pdb=" O GLY B 423 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N THR B 433 " --> pdb=" O SER B 429 " (cutoff:3.500A) Processing helix chain 'B' and resid 445 through 457 removed outlier: 3.636A pdb=" N VAL B 457 " --> pdb=" O ILE B 453 " (cutoff:3.500A) Processing helix chain 'B' and resid 463 through 471 removed outlier: 3.813A pdb=" N LEU B 467 " --> pdb=" O ASP B 463 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL B 470 " --> pdb=" O LEU B 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 473 through 496 removed outlier: 4.193A pdb=" N MET B 477 " --> pdb=" O LEU B 473 " (cutoff:3.500A) Processing helix chain 'B' and resid 497 through 507 removed outlier: 3.580A pdb=" N GLN B 507 " --> pdb=" O THR B 503 " (cutoff:3.500A) Processing helix chain 'C' and resid 37 through 42 Processing helix chain 'C' and resid 44 through 66 Processing helix chain 'C' and resid 71 through 79 Processing helix chain 'C' and resid 79 through 107 removed outlier: 4.460A pdb=" N LEU C 94 " --> pdb=" O LYS C 90 " (cutoff:3.500A) Proline residue: C 95 - end of helix removed outlier: 4.130A pdb=" N LEU C 101 " --> pdb=" O ILE C 97 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ILE C 102 " --> pdb=" O ILE C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 112 No H-bonds generated for 'chain 'C' and resid 110 through 112' Processing helix chain 'C' and resid 113 through 143 removed outlier: 3.766A pdb=" N GLY C 117 " --> pdb=" O SER C 113 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N TYR C 123 " --> pdb=" O ARG C 119 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ILE C 129 " --> pdb=" O MET C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 163 through 176 Processing helix chain 'C' and resid 241 through 260 removed outlier: 3.555A pdb=" N GLY C 260 " --> pdb=" O MET C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 263 through 286 removed outlier: 3.668A pdb=" N PHE C 269 " --> pdb=" O LEU C 265 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 302 removed outlier: 3.815A pdb=" N ILE C 301 " --> pdb=" O CYS C 297 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ALA C 302 " --> pdb=" O GLY C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 330 removed outlier: 3.765A pdb=" N VAL C 309 " --> pdb=" O ASP C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 340 Processing helix chain 'C' and resid 343 through 351 removed outlier: 3.565A pdb=" N PHE C 347 " --> pdb=" O ASN C 343 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 362 Processing helix chain 'C' and resid 363 through 378 Proline residue: C 369 - end of helix Processing helix chain 'C' and resid 382 through 397 Proline residue: C 391 - end of helix removed outlier: 4.293A pdb=" N THR C 395 " --> pdb=" O PRO C 391 " (cutoff:3.500A) Processing helix chain 'C' and resid 398 through 416 removed outlier: 3.740A pdb=" N ALA C 402 " --> pdb=" O MET C 398 " (cutoff:3.500A) Processing helix chain 'C' and resid 421 through 437 removed outlier: 4.050A pdb=" N VAL C 426 " --> pdb=" O GLY C 422 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N THR C 427 " --> pdb=" O GLY C 423 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N THR C 433 " --> pdb=" O SER C 429 " (cutoff:3.500A) Processing helix chain 'C' and resid 437 through 442 removed outlier: 4.183A pdb=" N SER C 441 " --> pdb=" O VAL C 437 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE C 442 " --> pdb=" O GLY C 438 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 437 through 442' Processing helix chain 'C' and resid 445 through 457 removed outlier: 3.599A pdb=" N VAL C 457 " --> pdb=" O ILE C 453 " (cutoff:3.500A) Processing helix chain 'C' and resid 463 through 471 removed outlier: 3.718A pdb=" N LEU C 467 " --> pdb=" O ASP C 463 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL C 470 " --> pdb=" O LEU C 466 " (cutoff:3.500A) Processing helix chain 'C' and resid 473 through 496 removed outlier: 4.050A pdb=" N MET C 477 " --> pdb=" O LEU C 473 " (cutoff:3.500A) Processing helix chain 'C' and resid 497 through 507 removed outlier: 3.560A pdb=" N GLN C 507 " --> pdb=" O THR C 503 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 188 through 191 Processing sheet with id=AA2, first strand: chain 'B' and resid 188 through 191 Processing sheet with id=AA3, first strand: chain 'C' and resid 188 through 191 732 hydrogen bonds defined for protein. 2184 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: 3.38 Time building geometry restraints manager: 3.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.33: 2665 1.33 - 1.49: 2594 1.49 - 1.64: 4934 1.64 - 1.79: 33 1.79 - 1.94: 102 Bond restraints: 10328 Sorted by residual: bond pdb=" CAX Y01 B 602 " pdb=" OAH Y01 B 602 " ideal model delta sigma weight residual 1.248 1.342 -0.094 2.00e-02 2.50e+03 2.22e+01 bond pdb=" CAX Y01 A 602 " pdb=" OAH Y01 A 602 " ideal model delta sigma weight residual 1.248 1.342 -0.094 2.00e-02 2.50e+03 2.21e+01 bond pdb=" CAX Y01 C 603 " pdb=" OAH Y01 C 603 " ideal model delta sigma weight residual 1.248 1.342 -0.094 2.00e-02 2.50e+03 2.19e+01 bond pdb=" C13 GJ0 C 602 " pdb=" N12 GJ0 C 602 " ideal model delta sigma weight residual 1.363 1.452 -0.089 2.00e-02 2.50e+03 1.97e+01 bond pdb=" C13 GJ0 A 601 " pdb=" N12 GJ0 A 601 " ideal model delta sigma weight residual 1.363 1.452 -0.089 2.00e-02 2.50e+03 1.97e+01 ... (remaining 10323 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.91: 13126 1.91 - 3.81: 443 3.81 - 5.72: 260 5.72 - 7.63: 14 7.63 - 9.54: 9 Bond angle restraints: 13852 Sorted by residual: angle pdb=" N ILE A 230 " pdb=" CA ILE A 230 " pdb=" C ILE A 230 " ideal model delta sigma weight residual 113.53 109.14 4.39 9.80e-01 1.04e+00 2.01e+01 angle pdb=" C11 GJ0 C 602 " pdb=" N12 GJ0 C 602 " pdb=" C13 GJ0 C 602 " ideal model delta sigma weight residual 129.20 119.66 9.54 3.00e+00 1.11e-01 1.01e+01 angle pdb=" C11 GJ0 A 601 " pdb=" N12 GJ0 A 601 " pdb=" C13 GJ0 A 601 " ideal model delta sigma weight residual 129.20 119.73 9.47 3.00e+00 1.11e-01 9.97e+00 angle pdb=" N VAL A 308 " pdb=" CA VAL A 308 " pdb=" C VAL A 308 " ideal model delta sigma weight residual 112.96 109.83 3.13 1.00e+00 1.00e+00 9.78e+00 angle pdb=" C11 GJ0 B 601 " pdb=" N12 GJ0 B 601 " pdb=" C13 GJ0 B 601 " ideal model delta sigma weight residual 129.20 120.10 9.10 3.00e+00 1.11e-01 9.19e+00 ... (remaining 13847 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.10: 6024 25.10 - 50.20: 339 50.20 - 75.30: 37 75.30 - 100.41: 32 100.41 - 125.51: 6 Dihedral angle restraints: 6438 sinusoidal: 2850 harmonic: 3588 Sorted by residual: dihedral pdb=" CBC Y01 B 602 " pdb=" CAR Y01 B 602 " pdb=" CAT Y01 B 602 " pdb=" CBH Y01 B 602 " ideal model delta sinusoidal sigma weight residual -57.13 68.38 -125.51 1 3.00e+01 1.11e-03 1.69e+01 dihedral pdb=" CBC Y01 C 603 " pdb=" CAR Y01 C 603 " pdb=" CAT Y01 C 603 " pdb=" CBH Y01 C 603 " ideal model delta sinusoidal sigma weight residual -57.13 68.25 -125.38 1 3.00e+01 1.11e-03 1.68e+01 dihedral pdb=" CBC Y01 A 602 " pdb=" CAR Y01 A 602 " pdb=" CAT Y01 A 602 " pdb=" CBH Y01 A 602 " ideal model delta sinusoidal sigma weight residual -57.13 68.04 -125.17 1 3.00e+01 1.11e-03 1.68e+01 ... (remaining 6435 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 1633 0.095 - 0.190: 67 0.190 - 0.284: 3 0.284 - 0.379: 3 0.379 - 0.474: 3 Chirality restraints: 1709 Sorted by residual: chirality pdb=" CBG Y01 A 602 " pdb=" CAQ Y01 A 602 " pdb=" CBD Y01 A 602 " pdb=" CBI Y01 A 602 " both_signs ideal model delta sigma weight residual False -2.33 -2.81 0.47 2.00e-01 2.50e+01 5.62e+00 chirality pdb=" CBG Y01 C 603 " pdb=" CAQ Y01 C 603 " pdb=" CBD Y01 C 603 " pdb=" CBI Y01 C 603 " both_signs ideal model delta sigma weight residual False -2.33 -2.80 0.47 2.00e-01 2.50e+01 5.49e+00 chirality pdb=" CBG Y01 B 602 " pdb=" CAQ Y01 B 602 " pdb=" CBD Y01 B 602 " pdb=" CBI Y01 B 602 " both_signs ideal model delta sigma weight residual False -2.33 -2.80 0.47 2.00e-01 2.50e+01 5.45e+00 ... (remaining 1706 not shown) Planarity restraints: 1617 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY C 135 " -0.007 2.00e-02 2.50e+03 1.41e-02 1.99e+00 pdb=" C GLY C 135 " 0.024 2.00e-02 2.50e+03 pdb=" O GLY C 135 " -0.009 2.00e-02 2.50e+03 pdb=" N VAL C 136 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY B 135 " -0.006 2.00e-02 2.50e+03 1.28e-02 1.65e+00 pdb=" C GLY B 135 " 0.022 2.00e-02 2.50e+03 pdb=" O GLY B 135 " -0.008 2.00e-02 2.50e+03 pdb=" N VAL B 136 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 135 " 0.006 2.00e-02 2.50e+03 1.27e-02 1.61e+00 pdb=" C GLY A 135 " -0.022 2.00e-02 2.50e+03 pdb=" O GLY A 135 " 0.008 2.00e-02 2.50e+03 pdb=" N VAL A 136 " 0.007 2.00e-02 2.50e+03 ... (remaining 1614 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1576 2.76 - 3.29: 10203 3.29 - 3.83: 16811 3.83 - 4.36: 19845 4.36 - 4.90: 34593 Nonbonded interactions: 83028 Sorted by model distance: nonbonded pdb=" O HIS B 143 " pdb=" ND1 HIS B 143 " model vdw 2.220 3.120 nonbonded pdb=" NZ LYS B 90 " pdb=" OG1 THR B 461 " model vdw 2.311 3.120 nonbonded pdb=" O ASN A 343 " pdb=" OG SER A 346 " model vdw 2.321 3.040 nonbonded pdb=" OD1 ASP B 170 " pdb=" OG1 THR B 190 " model vdw 2.325 3.040 nonbonded pdb=" NZ LYS A 90 " pdb=" OG1 THR A 461 " model vdw 2.327 3.120 ... (remaining 83023 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 36 through 507 or resid 604 or (resid 607 and (name C21 or \ name C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name C2 \ 8 or name C29 or name C2A or name C2B or name C2C or name C2D or name C2E)) or r \ esid 608 through 609 or (resid 610 and (name C21 or name C22 or name C23 or name \ C24 or name C25 or name C26 or name C27 or name C28 or name C29 or name C2A or \ name C2B or name C2C or name C2D)) or resid 611)) selection = (chain 'B' and (resid 36 through 126 or (resid 127 and (name N or name CA or nam \ e C or name O or name CB or name OG1)) or resid 128 through 507 or resid 604 or \ (resid 607 and (name C21 or name C22 or name C23 or name C24 or name C25 or name \ C26 or name C27 or name C28 or name C29 or name C2A or name C2B or name C2C or \ name C2D or name C2E)) or resid 608 through 609 or (resid 610 and (name C21 or n \ ame C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name C28 \ or name C29 or name C2A or name C2B or name C2C or name C2D)) or resid 611)) selection = (chain 'C' and (resid 36 through 126 or (resid 127 and (name N or name CA or nam \ e C or name O or name CB or name OG1)) or resid 128 through 507 or (resid 604 an \ d (name C21 or name C22 or name C23 or name C24 or name C25 or name C26 or name \ C27 or name C28 or name C29)) or resid 607 or (resid 608 and (name C21 or name C \ 22 or name C23 or name C24 or name C25 or name C26 or name C27 or name C28 or na \ me C29 or name C2A or name C2B or name C2C or name C2D or name C2E or name C2F o \ r name C2G)) or (resid 609 through 610 and (name C21 or name C22 or name C23 or \ name C24 or name C25 or name C26 or name C27 or name C28 or name C29 or name C2A \ or name C2B or name C2C or name C2D)) or (resid 611 and (name C21 or name C22 o \ r name C23 or name C24 or name C25 or name C26 or name C27 or name C28)))) } 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: 0.760 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: 0.020 Extract box with map and model: 0.410 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 27.500 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 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 : 0.005 0.094 10328 Z= 0.246 Angle : 0.974 9.535 13852 Z= 0.405 Chirality : 0.050 0.474 1709 Planarity : 0.004 0.029 1617 Dihedral : 16.903 125.508 4134 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.25), residues: 1254 helix: 0.79 (0.17), residues: 987 sheet: -1.71 (0.81), residues: 48 loop : -1.16 (0.50), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 472 HIS 0.005 0.002 HIS A 495 PHE 0.020 0.002 PHE C 249 TYR 0.008 0.001 TYR B 316 ARG 0.005 0.000 ARG A 387 Details of bonding type rmsd hydrogen bonds : bond 0.13025 ( 732) hydrogen bonds : angle 6.58280 ( 2184) covalent geometry : bond 0.00532 (10328) covalent geometry : angle 0.97405 (13852) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 179 time to evaluate : 1.147 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 179 average time/residue: 0.2038 time to fit residues: 52.8650 Evaluate side-chains 152 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 152 time to evaluate : 1.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 106 optimal weight: 2.9990 chunk 95 optimal weight: 0.4980 chunk 52 optimal weight: 0.3980 chunk 32 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 98 optimal weight: 5.9990 chunk 38 optimal weight: 0.9990 chunk 60 optimal weight: 0.8980 chunk 73 optimal weight: 0.6980 chunk 114 optimal weight: 3.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 44 ASN A 143 HIS A 416 ASN A 507 GLN B 507 GLN C 44 ASN C 143 HIS C 507 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.145823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.112709 restraints weight = 10151.025| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 1.26 r_work: 0.3017 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2873 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.1226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 10328 Z= 0.126 Angle : 0.602 8.871 13852 Z= 0.290 Chirality : 0.040 0.156 1709 Planarity : 0.004 0.035 1617 Dihedral : 11.591 85.827 1992 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 0.86 % Allowed : 9.87 % Favored : 89.27 % 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: 1.34 (0.25), residues: 1254 helix: 1.47 (0.17), residues: 999 sheet: -2.11 (0.74), residues: 48 loop : -1.01 (0.52), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 355 HIS 0.016 0.003 HIS C 143 PHE 0.018 0.002 PHE C 249 TYR 0.012 0.002 TYR A 287 ARG 0.003 0.000 ARG B 373 Details of bonding type rmsd hydrogen bonds : bond 0.03825 ( 732) hydrogen bonds : angle 4.39058 ( 2184) covalent geometry : bond 0.00287 (10328) covalent geometry : angle 0.60165 (13852) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 159 time to evaluate : 1.915 Fit side-chains REVERT: A 290 LEU cc_start: 0.8991 (tt) cc_final: 0.8690 (tp) REVERT: B 290 LEU cc_start: 0.8981 (tt) cc_final: 0.8752 (tp) REVERT: C 304 LYS cc_start: 0.8093 (mmtt) cc_final: 0.7798 (tptt) outliers start: 9 outliers final: 2 residues processed: 165 average time/residue: 0.2608 time to fit residues: 63.9542 Evaluate side-chains 151 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 149 time to evaluate : 1.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 127 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 0 optimal weight: 20.0000 chunk 124 optimal weight: 2.9990 chunk 102 optimal weight: 0.6980 chunk 41 optimal weight: 5.9990 chunk 10 optimal weight: 0.6980 chunk 70 optimal weight: 0.1980 chunk 33 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 3 optimal weight: 6.9990 chunk 98 optimal weight: 6.9990 chunk 29 optimal weight: 3.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 143 HIS C 143 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.142967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.109539 restraints weight = 10248.446| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 1.29 r_work: 0.2976 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2832 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.1354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 10328 Z= 0.157 Angle : 0.579 7.698 13852 Z= 0.287 Chirality : 0.040 0.148 1709 Planarity : 0.004 0.037 1617 Dihedral : 10.170 85.089 1992 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.25 % Allowed : 12.64 % Favored : 86.11 % 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: 1.36 (0.25), residues: 1254 helix: 1.49 (0.17), residues: 1008 sheet: -2.36 (0.72), residues: 48 loop : -1.07 (0.52), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 286 HIS 0.017 0.003 HIS C 143 PHE 0.019 0.002 PHE A 249 TYR 0.010 0.002 TYR A 404 ARG 0.002 0.000 ARG A 387 Details of bonding type rmsd hydrogen bonds : bond 0.03936 ( 732) hydrogen bonds : angle 4.30426 ( 2184) covalent geometry : bond 0.00382 (10328) covalent geometry : angle 0.57863 (13852) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 158 time to evaluate : 1.045 Fit side-chains REVERT: C 188 ILE cc_start: 0.9317 (OUTLIER) cc_final: 0.8982 (tt) REVERT: C 304 LYS cc_start: 0.8159 (mmtt) cc_final: 0.7890 (tptt) outliers start: 13 outliers final: 10 residues processed: 167 average time/residue: 0.2206 time to fit residues: 53.9531 Evaluate side-chains 168 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 157 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 126 SER Chi-restraints excluded: chain C residue 188 ILE Chi-restraints excluded: chain C residue 395 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 108 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 chunk 104 optimal weight: 0.9990 chunk 112 optimal weight: 0.6980 chunk 90 optimal weight: 1.9990 chunk 11 optimal weight: 0.5980 chunk 113 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 81 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 HIS B 143 HIS ** C 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.143318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.109754 restraints weight = 9983.269| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 1.29 r_work: 0.2980 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2833 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.1498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 10328 Z= 0.149 Angle : 0.569 7.783 13852 Z= 0.282 Chirality : 0.040 0.149 1709 Planarity : 0.004 0.038 1617 Dihedral : 9.634 86.233 1992 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.53 % Allowed : 13.70 % Favored : 84.77 % 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: 1.44 (0.25), residues: 1254 helix: 1.55 (0.17), residues: 1011 sheet: -2.56 (0.71), residues: 48 loop : -1.06 (0.52), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 286 HIS 0.018 0.003 HIS C 143 PHE 0.017 0.002 PHE C 249 TYR 0.010 0.002 TYR A 404 ARG 0.002 0.000 ARG A 387 Details of bonding type rmsd hydrogen bonds : bond 0.03814 ( 732) hydrogen bonds : angle 4.19043 ( 2184) covalent geometry : bond 0.00361 (10328) covalent geometry : angle 0.56948 (13852) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 155 time to evaluate : 1.228 Fit side-chains REVERT: A 387 ARG cc_start: 0.8426 (tmm-80) cc_final: 0.8167 (ttm-80) REVERT: C 304 LYS cc_start: 0.8181 (mmtt) cc_final: 0.7896 (tptt) outliers start: 16 outliers final: 12 residues processed: 167 average time/residue: 0.2667 time to fit residues: 66.3447 Evaluate side-chains 160 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 148 time to evaluate : 1.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 126 SER Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 126 SER Chi-restraints excluded: chain C residue 395 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 30 optimal weight: 0.9980 chunk 88 optimal weight: 0.9990 chunk 50 optimal weight: 5.9990 chunk 9 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 63 optimal weight: 0.9980 chunk 125 optimal weight: 0.9990 chunk 67 optimal weight: 0.7980 chunk 69 optimal weight: 4.9990 chunk 97 optimal weight: 2.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 143 HIS B 416 ASN ** C 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.144237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.113545 restraints weight = 10000.833| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 1.22 r_work: 0.3023 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2880 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.1582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10328 Z= 0.141 Angle : 0.561 7.236 13852 Z= 0.277 Chirality : 0.039 0.147 1709 Planarity : 0.004 0.037 1617 Dihedral : 9.362 89.206 1992 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.92 % Allowed : 14.66 % Favored : 83.43 % 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: 1.53 (0.25), residues: 1254 helix: 1.64 (0.17), residues: 1008 sheet: -2.65 (0.70), residues: 48 loop : -1.11 (0.51), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 286 HIS 0.012 0.002 HIS B 143 PHE 0.017 0.002 PHE A 249 TYR 0.009 0.002 TYR A 404 ARG 0.002 0.000 ARG A 387 Details of bonding type rmsd hydrogen bonds : bond 0.03692 ( 732) hydrogen bonds : angle 4.11339 ( 2184) covalent geometry : bond 0.00340 (10328) covalent geometry : angle 0.56062 (13852) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 156 time to evaluate : 1.112 Fit side-chains REVERT: C 304 LYS cc_start: 0.8152 (mmtt) cc_final: 0.7918 (tptt) REVERT: C 372 PHE cc_start: 0.7916 (OUTLIER) cc_final: 0.7681 (m-80) REVERT: C 470 VAL cc_start: 0.9089 (OUTLIER) cc_final: 0.8860 (t) outliers start: 20 outliers final: 14 residues processed: 171 average time/residue: 0.1947 time to fit residues: 49.2449 Evaluate side-chains 167 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 151 time to evaluate : 1.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 126 SER Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 126 SER Chi-restraints excluded: chain C residue 372 PHE Chi-restraints excluded: chain C residue 395 THR Chi-restraints excluded: chain C residue 470 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 43 optimal weight: 0.8980 chunk 14 optimal weight: 7.9990 chunk 48 optimal weight: 0.3980 chunk 9 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 75 optimal weight: 0.9980 chunk 50 optimal weight: 3.9990 chunk 62 optimal weight: 0.9990 chunk 29 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 88 optimal weight: 0.7980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 143 HIS ** C 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.144878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.111490 restraints weight = 10096.101| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 1.29 r_work: 0.3003 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2857 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.1716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10328 Z= 0.129 Angle : 0.552 9.490 13852 Z= 0.272 Chirality : 0.039 0.152 1709 Planarity : 0.003 0.037 1617 Dihedral : 9.048 85.598 1992 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.01 % Allowed : 15.90 % Favored : 82.09 % 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: 1.63 (0.25), residues: 1254 helix: 1.72 (0.17), residues: 1008 sheet: -2.70 (0.70), residues: 48 loop : -1.13 (0.51), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 286 HIS 0.011 0.002 HIS B 143 PHE 0.016 0.002 PHE B 249 TYR 0.009 0.002 TYR A 404 ARG 0.003 0.000 ARG A 387 Details of bonding type rmsd hydrogen bonds : bond 0.03556 ( 732) hydrogen bonds : angle 4.02889 ( 2184) covalent geometry : bond 0.00308 (10328) covalent geometry : angle 0.55218 (13852) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 156 time to evaluate : 1.090 Fit side-chains REVERT: A 387 ARG cc_start: 0.8454 (tmm-80) cc_final: 0.8208 (ttm-80) REVERT: C 304 LYS cc_start: 0.8183 (mmtt) cc_final: 0.7842 (tptt) REVERT: C 372 PHE cc_start: 0.7880 (OUTLIER) cc_final: 0.7642 (m-80) outliers start: 21 outliers final: 16 residues processed: 169 average time/residue: 0.1920 time to fit residues: 47.9776 Evaluate side-chains 168 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 151 time to evaluate : 1.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 415 MET Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 126 SER Chi-restraints excluded: chain C residue 188 ILE Chi-restraints excluded: chain C residue 372 PHE Chi-restraints excluded: chain C residue 395 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 34 optimal weight: 0.5980 chunk 36 optimal weight: 0.9980 chunk 4 optimal weight: 0.9990 chunk 16 optimal weight: 0.7980 chunk 83 optimal weight: 5.9990 chunk 124 optimal weight: 0.7980 chunk 75 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 21 optimal weight: 0.7980 chunk 57 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 GLN ** C 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.145160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.114587 restraints weight = 10076.545| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 1.24 r_work: 0.3049 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2909 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.1778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 10328 Z= 0.128 Angle : 0.548 8.507 13852 Z= 0.270 Chirality : 0.039 0.169 1709 Planarity : 0.004 0.037 1617 Dihedral : 8.776 82.569 1992 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 2.20 % Allowed : 16.86 % Favored : 80.94 % 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: 1.84 (0.25), residues: 1254 helix: 1.92 (0.17), residues: 990 sheet: -2.66 (0.70), residues: 48 loop : -1.11 (0.48), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 286 HIS 0.009 0.001 HIS C 143 PHE 0.016 0.002 PHE A 249 TYR 0.009 0.002 TYR A 404 ARG 0.003 0.000 ARG A 387 Details of bonding type rmsd hydrogen bonds : bond 0.03528 ( 732) hydrogen bonds : angle 3.99517 ( 2184) covalent geometry : bond 0.00303 (10328) covalent geometry : angle 0.54776 (13852) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 155 time to evaluate : 1.133 Fit side-chains REVERT: A 387 ARG cc_start: 0.8417 (tmm-80) cc_final: 0.8192 (ttp-110) REVERT: C 304 LYS cc_start: 0.8152 (mmtt) cc_final: 0.7855 (tptt) REVERT: C 470 VAL cc_start: 0.9030 (OUTLIER) cc_final: 0.8805 (t) outliers start: 23 outliers final: 19 residues processed: 170 average time/residue: 0.1964 time to fit residues: 49.7067 Evaluate side-chains 172 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 152 time to evaluate : 1.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 399 ASP Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 76 MET Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 415 MET Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 126 SER Chi-restraints excluded: chain C residue 188 ILE Chi-restraints excluded: chain C residue 395 THR Chi-restraints excluded: chain C residue 399 ASP Chi-restraints excluded: chain C residue 470 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 11 optimal weight: 5.9990 chunk 30 optimal weight: 0.9980 chunk 92 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 40 optimal weight: 0.5980 chunk 41 optimal weight: 0.9980 chunk 68 optimal weight: 2.9990 chunk 75 optimal weight: 0.3980 chunk 80 optimal weight: 0.6980 chunk 121 optimal weight: 0.0060 chunk 0 optimal weight: 20.0000 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 312 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.147506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.116024 restraints weight = 10023.010| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 1.23 r_work: 0.3080 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2939 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.1953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 10328 Z= 0.109 Angle : 0.532 8.437 13852 Z= 0.261 Chirality : 0.038 0.153 1709 Planarity : 0.003 0.035 1617 Dihedral : 8.309 72.847 1992 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 2.30 % Allowed : 16.38 % Favored : 81.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.03 (0.25), residues: 1254 helix: 2.04 (0.17), residues: 993 sheet: -2.50 (0.72), residues: 48 loop : -1.05 (0.49), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 355 HIS 0.010 0.001 HIS C 143 PHE 0.017 0.001 PHE A 249 TYR 0.008 0.001 TYR A 404 ARG 0.002 0.000 ARG A 387 Details of bonding type rmsd hydrogen bonds : bond 0.03304 ( 732) hydrogen bonds : angle 3.88547 ( 2184) covalent geometry : bond 0.00247 (10328) covalent geometry : angle 0.53183 (13852) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 155 time to evaluate : 1.289 Fit side-chains REVERT: A 261 ASP cc_start: 0.8342 (t70) cc_final: 0.8097 (t0) REVERT: C 304 LYS cc_start: 0.8175 (mmtt) cc_final: 0.7888 (tptt) REVERT: C 470 VAL cc_start: 0.9079 (OUTLIER) cc_final: 0.8844 (t) outliers start: 24 outliers final: 20 residues processed: 171 average time/residue: 0.2590 time to fit residues: 64.3319 Evaluate side-chains 172 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 151 time to evaluate : 1.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 399 ASP Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 76 MET Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 415 MET Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 126 SER Chi-restraints excluded: chain C residue 188 ILE Chi-restraints excluded: chain C residue 395 THR Chi-restraints excluded: chain C residue 399 ASP Chi-restraints excluded: chain C residue 415 MET Chi-restraints excluded: chain C residue 470 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 117 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 65 optimal weight: 0.5980 chunk 71 optimal weight: 1.9990 chunk 94 optimal weight: 0.0870 chunk 114 optimal weight: 0.4980 chunk 39 optimal weight: 0.8980 chunk 86 optimal weight: 0.9990 chunk 27 optimal weight: 0.7980 chunk 51 optimal weight: 0.8980 chunk 90 optimal weight: 2.9990 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.147233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.115437 restraints weight = 10129.693| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 1.21 r_work: 0.3052 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2915 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.2035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10328 Z= 0.112 Angle : 0.535 8.131 13852 Z= 0.261 Chirality : 0.039 0.150 1709 Planarity : 0.003 0.035 1617 Dihedral : 8.126 65.020 1992 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 1.92 % Allowed : 17.24 % Favored : 80.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.09 (0.25), residues: 1254 helix: 2.10 (0.17), residues: 993 sheet: -2.42 (0.74), residues: 48 loop : -1.09 (0.48), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 286 HIS 0.009 0.001 HIS C 143 PHE 0.018 0.001 PHE A 249 TYR 0.008 0.001 TYR A 404 ARG 0.004 0.000 ARG A 387 Details of bonding type rmsd hydrogen bonds : bond 0.03330 ( 732) hydrogen bonds : angle 3.87999 ( 2184) covalent geometry : bond 0.00255 (10328) covalent geometry : angle 0.53464 (13852) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 154 time to evaluate : 1.035 Fit side-chains REVERT: A 261 ASP cc_start: 0.8328 (t70) cc_final: 0.8097 (t0) REVERT: A 387 ARG cc_start: 0.8438 (tmm-80) cc_final: 0.8221 (ttp-110) REVERT: C 470 VAL cc_start: 0.9135 (OUTLIER) cc_final: 0.8858 (t) outliers start: 20 outliers final: 17 residues processed: 167 average time/residue: 0.1807 time to fit residues: 45.0464 Evaluate side-chains 171 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 153 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 399 ASP Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 76 MET Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain B residue 415 MET Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 188 ILE Chi-restraints excluded: chain C residue 395 THR Chi-restraints excluded: chain C residue 399 ASP Chi-restraints excluded: chain C residue 415 MET Chi-restraints excluded: chain C residue 470 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 46 optimal weight: 0.3980 chunk 122 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 96 optimal weight: 0.9990 chunk 47 optimal weight: 0.6980 chunk 100 optimal weight: 0.7980 chunk 102 optimal weight: 0.6980 chunk 6 optimal weight: 0.9990 chunk 118 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.146320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.114738 restraints weight = 10122.831| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 1.20 r_work: 0.3039 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2902 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.2038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10328 Z= 0.122 Angle : 0.550 7.969 13852 Z= 0.268 Chirality : 0.039 0.147 1709 Planarity : 0.003 0.034 1617 Dihedral : 8.108 60.202 1992 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.20 % Allowed : 17.05 % Favored : 80.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.05 (0.25), residues: 1254 helix: 2.07 (0.17), residues: 993 sheet: -2.43 (0.75), residues: 48 loop : -1.18 (0.48), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 286 HIS 0.009 0.001 HIS C 143 PHE 0.017 0.002 PHE B 249 TYR 0.009 0.002 TYR A 404 ARG 0.003 0.000 ARG A 387 Details of bonding type rmsd hydrogen bonds : bond 0.03415 ( 732) hydrogen bonds : angle 3.89953 ( 2184) covalent geometry : bond 0.00287 (10328) covalent geometry : angle 0.55001 (13852) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 156 time to evaluate : 1.233 Fit side-chains REVERT: A 259 MET cc_start: 0.8432 (ttm) cc_final: 0.8230 (mtp) REVERT: A 261 ASP cc_start: 0.8376 (t70) cc_final: 0.8138 (t0) REVERT: A 387 ARG cc_start: 0.8391 (tmm-80) cc_final: 0.8139 (tmm-80) REVERT: C 470 VAL cc_start: 0.9122 (OUTLIER) cc_final: 0.8859 (t) outliers start: 23 outliers final: 20 residues processed: 172 average time/residue: 0.2017 time to fit residues: 52.4061 Evaluate side-chains 176 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 155 time to evaluate : 1.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 399 ASP Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 76 MET Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 415 MET Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 188 ILE Chi-restraints excluded: chain C residue 395 THR Chi-restraints excluded: chain C residue 399 ASP Chi-restraints excluded: chain C residue 415 MET Chi-restraints excluded: chain C residue 470 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 42 optimal weight: 20.0000 chunk 1 optimal weight: 2.9990 chunk 60 optimal weight: 0.9990 chunk 97 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 62 optimal weight: 0.8980 chunk 5 optimal weight: 0.9990 chunk 92 optimal weight: 0.9980 chunk 14 optimal weight: 7.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.144879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.115194 restraints weight = 10166.105| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 1.17 r_work: 0.3027 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2894 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.1979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10328 Z= 0.142 Angle : 0.565 7.855 13852 Z= 0.276 Chirality : 0.040 0.146 1709 Planarity : 0.004 0.034 1617 Dihedral : 8.273 61.004 1992 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.11 % Allowed : 17.43 % Favored : 80.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.92 (0.25), residues: 1254 helix: 1.99 (0.17), residues: 993 sheet: -2.51 (0.74), residues: 48 loop : -1.24 (0.47), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 286 HIS 0.009 0.001 HIS C 143 PHE 0.017 0.002 PHE B 249 TYR 0.011 0.002 TYR A 404 ARG 0.003 0.000 ARG A 387 Details of bonding type rmsd hydrogen bonds : bond 0.03622 ( 732) hydrogen bonds : angle 3.98517 ( 2184) covalent geometry : bond 0.00346 (10328) covalent geometry : angle 0.56475 (13852) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5798.03 seconds wall clock time: 105 minutes 9.61 seconds (6309.61 seconds total)