Starting phenix.real_space_refine on Thu Mar 13 10:07:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8phe_17659/03_2025/8phe_17659.cif Found real_map, /net/cci-nas-00/data/ceres_data/8phe_17659/03_2025/8phe_17659.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8phe_17659/03_2025/8phe_17659.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8phe_17659/03_2025/8phe_17659.map" model { file = "/net/cci-nas-00/data/ceres_data/8phe_17659/03_2025/8phe_17659.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8phe_17659/03_2025/8phe_17659.cif" } resolution = 3.1 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= 0.004 sd= 0.119 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 46 5.16 5 C 5656 2.51 5 N 1498 2.21 5 O 1714 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 8914 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 551, 4304 Classifications: {'peptide': 551} Link IDs: {'PTRANS': 15, 'TRANS': 535} Chain breaks: 1 Chain: "B" Number of atoms: 4304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 551, 4304 Classifications: {'peptide': 551} Link IDs: {'PTRANS': 15, 'TRANS': 535} Chain breaks: 1 Chain: "C" Number of atoms: 134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 134 Classifications: {'peptide': 15} Link IDs: {'PTRANS': 2, 'TRANS': 12} Chain: "D" Number of atoms: 134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 134 Classifications: {'peptide': 15} Link IDs: {'PTRANS': 2, 'TRANS': 12} Chain: "A" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 19 Classifications: {'water': 19} Link IDs: {None: 18} Chain: "B" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 19 Classifications: {'water': 19} Link IDs: {None: 18} Time building chain proxies: 6.17, per 1000 atoms: 0.69 Number of scatterers: 8914 At special positions: 0 Unit cell: (91.797, 121.569, 76.084, 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 46 16.00 O 1714 8.00 N 1498 7.00 C 5656 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: 2.69 Conformation dependent library (CDL) restraints added in 1.1 seconds 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2088 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 5 sheets defined 62.6% alpha, 9.4% 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 39 through 44 removed outlier: 3.537A pdb=" N PHE A 44 " --> pdb=" O ALA A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 71 Processing helix chain 'A' and resid 74 through 81 Processing helix chain 'A' and resid 83 through 91 Processing helix chain 'A' and resid 94 through 105 Processing helix chain 'A' and resid 112 through 116 Processing helix chain 'A' and resid 121 through 133 removed outlier: 3.526A pdb=" N SER A 126 " --> pdb=" O ASN A 122 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ARG A 127 " --> pdb=" O THR A 123 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU A 128 " --> pdb=" O MET A 124 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLU A 130 " --> pdb=" O SER A 126 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ILE A 131 " --> pdb=" O ARG A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 147 removed outlier: 3.719A pdb=" N THR A 141 " --> pdb=" O SER A 137 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ALA A 143 " --> pdb=" O THR A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 157 Processing helix chain 'A' and resid 158 through 171 removed outlier: 3.654A pdb=" N LYS A 164 " --> pdb=" O GLU A 160 " (cutoff:3.500A) Proline residue: A 167 - end of helix removed outlier: 3.508A pdb=" N SER A 171 " --> pdb=" O PRO A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 252 No H-bonds generated for 'chain 'A' and resid 250 through 252' Processing helix chain 'A' and resid 292 through 303 removed outlier: 3.820A pdb=" N GLY A 303 " --> pdb=" O ILE A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 328 removed outlier: 3.785A pdb=" N ARG A 317 " --> pdb=" O GLY A 313 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLU A 320 " --> pdb=" O LYS A 316 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ALA A 323 " --> pdb=" O ILE A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 338 Processing helix chain 'A' and resid 339 through 368 removed outlier: 3.994A pdb=" N LYS A 345 " --> pdb=" O LEU A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 401 removed outlier: 3.976A pdb=" N ALA A 379 " --> pdb=" O CYS A 375 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU A 401 " --> pdb=" O ALA A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 405 Processing helix chain 'A' and resid 412 through 419 Processing helix chain 'A' and resid 420 through 424 Processing helix chain 'A' and resid 428 through 453 removed outlier: 3.711A pdb=" N MET A 434 " --> pdb=" O GLU A 430 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N HIS A 443 " --> pdb=" O THR A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 491 through 493 No H-bonds generated for 'chain 'A' and resid 491 through 493' Processing helix chain 'A' and resid 494 through 520 removed outlier: 3.748A pdb=" N ALA A 498 " --> pdb=" O LEU A 494 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASN A 499 " --> pdb=" O ALA A 495 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N LYS A 500 " --> pdb=" O ASP A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 521 through 525 Processing helix chain 'A' and resid 526 through 557 removed outlier: 3.584A pdb=" N LEU A 530 " --> pdb=" O GLU A 526 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 585 removed outlier: 3.918A pdb=" N GLU A 564 " --> pdb=" O ASN A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 595 through 609 removed outlier: 3.832A pdb=" N LYS A 600 " --> pdb=" O GLU A 596 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 46 Processing helix chain 'B' and resid 60 through 81 Proline residue: B 73 - end of helix Processing helix chain 'B' and resid 83 through 91 Processing helix chain 'B' and resid 94 through 105 Processing helix chain 'B' and resid 106 through 109 removed outlier: 4.167A pdb=" N LEU B 109 " --> pdb=" O LEU B 106 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 106 through 109' Processing helix chain 'B' and resid 112 through 116 Processing helix chain 'B' and resid 121 through 133 removed outlier: 3.589A pdb=" N LEU B 128 " --> pdb=" O MET B 124 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLU B 130 " --> pdb=" O SER B 126 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ILE B 131 " --> pdb=" O ARG B 127 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SER B 133 " --> pdb=" O GLY B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 147 removed outlier: 3.570A pdb=" N THR B 141 " --> pdb=" O SER B 137 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA B 143 " --> pdb=" O THR B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 157 Processing helix chain 'B' and resid 158 through 171 removed outlier: 3.510A pdb=" N ALA B 163 " --> pdb=" O GLU B 159 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LYS B 164 " --> pdb=" O GLU B 160 " (cutoff:3.500A) Proline residue: B 167 - end of helix removed outlier: 3.502A pdb=" N SER B 171 " --> pdb=" O PRO B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 252 No H-bonds generated for 'chain 'B' and resid 250 through 252' Processing helix chain 'B' and resid 291 through 302 removed outlier: 4.274A pdb=" N VAL B 295 " --> pdb=" O ASP B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 327 removed outlier: 4.009A pdb=" N GLY B 308 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N SER B 309 " --> pdb=" O PHE B 305 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ARG B 317 " --> pdb=" O GLY B 313 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA B 323 " --> pdb=" O ILE B 319 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N GLU B 324 " --> pdb=" O GLU B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 368 removed outlier: 4.010A pdb=" N LYS B 345 " --> pdb=" O LEU B 341 " (cutoff:3.500A) Processing helix chain 'B' and resid 376 through 401 removed outlier: 3.646A pdb=" N LEU B 401 " --> pdb=" O ALA B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 405 Processing helix chain 'B' and resid 412 through 419 Processing helix chain 'B' and resid 420 through 424 Processing helix chain 'B' and resid 428 through 453 removed outlier: 3.867A pdb=" N MET B 434 " --> pdb=" O GLU B 430 " (cutoff:3.500A) Processing helix chain 'B' and resid 491 through 493 No H-bonds generated for 'chain 'B' and resid 491 through 493' Processing helix chain 'B' and resid 494 through 519 removed outlier: 3.730A pdb=" N ALA B 498 " --> pdb=" O LEU B 494 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ASN B 499 " --> pdb=" O ALA B 495 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N LYS B 500 " --> pdb=" O ASP B 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 520 through 525 removed outlier: 3.854A pdb=" N MET B 524 " --> pdb=" O LYS B 521 " (cutoff:3.500A) Processing helix chain 'B' and resid 526 through 557 removed outlier: 3.567A pdb=" N ARG B 532 " --> pdb=" O LEU B 528 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N LEU B 547 " --> pdb=" O MET B 543 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 585 removed outlier: 3.820A pdb=" N GLU B 564 " --> pdb=" O ASN B 560 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N PHE B 571 " --> pdb=" O LEU B 567 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLU B 574 " --> pdb=" O THR B 570 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLN B 585 " --> pdb=" O PHE B 581 " (cutoff:3.500A) Processing helix chain 'B' and resid 595 through 609 Processing helix chain 'C' and resid 321 through 327 Processing helix chain 'D' and resid 323 through 327 Processing sheet with id=AA1, first strand: chain 'A' and resid 176 through 179 removed outlier: 6.952A pdb=" N ALA A 177 " --> pdb=" O THR A 224 " (cutoff:3.500A) removed outlier: 8.201A pdb=" N PHE A 226 " --> pdb=" O ALA A 177 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N CYS A 179 " --> pdb=" O PHE A 226 " (cutoff:3.500A) removed outlier: 9.375A pdb=" N LYS A 228 " --> pdb=" O CYS A 179 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 195 through 198 removed outlier: 6.415A pdb=" N TYR A 205 " --> pdb=" O LYS A 279 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N LYS A 279 " --> pdb=" O TYR A 205 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N LEU A 207 " --> pdb=" O ASN A 277 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N TRP A 213 " --> pdb=" O CYS A 271 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N CYS A 271 " --> pdb=" O TRP A 213 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 176 through 179 removed outlier: 7.038A pdb=" N ALA B 177 " --> pdb=" O THR B 224 " (cutoff:3.500A) removed outlier: 8.254A pdb=" N PHE B 226 " --> pdb=" O ALA B 177 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N CYS B 179 " --> pdb=" O PHE B 226 " (cutoff:3.500A) removed outlier: 9.389A pdb=" N LYS B 228 " --> pdb=" O CYS B 179 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N GLU B 230 " --> pdb=" O ALA B 196 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N LEU B 198 " --> pdb=" O GLU B 230 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N TYR B 205 " --> pdb=" O LYS B 279 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N LYS B 279 " --> pdb=" O TYR B 205 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N LEU B 207 " --> pdb=" O ASN B 277 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N TRP B 213 " --> pdb=" O CYS B 271 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N CYS B 271 " --> pdb=" O TRP B 213 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 176 through 179 removed outlier: 7.038A pdb=" N ALA B 177 " --> pdb=" O THR B 224 " (cutoff:3.500A) removed outlier: 8.254A pdb=" N PHE B 226 " --> pdb=" O ALA B 177 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N CYS B 179 " --> pdb=" O PHE B 226 " (cutoff:3.500A) removed outlier: 9.389A pdb=" N LYS B 228 " --> pdb=" O CYS B 179 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N ALA B 244 " --> pdb=" O LEU B 286 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 330 through 331 493 hydrogen bonds defined for protein. 1401 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: 2.61 Time building geometry restraints manager: 3.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2917 1.34 - 1.46: 1777 1.46 - 1.58: 4262 1.58 - 1.69: 0 1.69 - 1.81: 74 Bond restraints: 9030 Sorted by residual: bond pdb=" C GLU B 182 " pdb=" N PRO B 183 " ideal model delta sigma weight residual 1.333 1.345 -0.012 1.17e-02 7.31e+03 1.14e+00 bond pdb=" CA GLY B 287 " pdb=" C GLY B 287 " ideal model delta sigma weight residual 1.514 1.529 -0.015 1.41e-02 5.03e+03 1.13e+00 bond pdb=" N ILE B 265 " pdb=" CA ILE B 265 " ideal model delta sigma weight residual 1.474 1.458 0.017 1.57e-02 4.06e+03 1.11e+00 bond pdb=" N GLY B 287 " pdb=" CA GLY B 287 " ideal model delta sigma weight residual 1.449 1.464 -0.015 1.45e-02 4.76e+03 1.02e+00 bond pdb=" CB MET A 381 " pdb=" CG MET A 381 " ideal model delta sigma weight residual 1.520 1.491 0.029 3.00e-02 1.11e+03 9.40e-01 ... (remaining 9025 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.41: 11915 1.41 - 2.82: 204 2.82 - 4.23: 43 4.23 - 5.64: 10 5.64 - 7.06: 2 Bond angle restraints: 12174 Sorted by residual: angle pdb=" N ILE B 265 " pdb=" CA ILE B 265 " pdb=" C ILE B 265 " ideal model delta sigma weight residual 106.21 109.98 -3.77 1.07e+00 8.73e-01 1.24e+01 angle pdb=" N ILE B 148 " pdb=" CA ILE B 148 " pdb=" C ILE B 148 " ideal model delta sigma weight residual 113.53 110.28 3.25 9.80e-01 1.04e+00 1.10e+01 angle pdb=" C LYS B 50 " pdb=" N LYS B 51 " pdb=" CA LYS B 51 " ideal model delta sigma weight residual 121.54 126.58 -5.04 1.91e+00 2.74e-01 6.95e+00 angle pdb=" C GLY B 303 " pdb=" N ARG B 304 " pdb=" CA ARG B 304 " ideal model delta sigma weight residual 121.54 126.51 -4.97 1.91e+00 2.74e-01 6.78e+00 angle pdb=" CA LYS B 51 " pdb=" CB LYS B 51 " pdb=" CG LYS B 51 " ideal model delta sigma weight residual 114.10 119.17 -5.07 2.00e+00 2.50e-01 6.41e+00 ... (remaining 12169 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.10: 4882 17.10 - 34.21: 449 34.21 - 51.31: 89 51.31 - 68.42: 21 68.42 - 85.52: 17 Dihedral angle restraints: 5458 sinusoidal: 2208 harmonic: 3250 Sorted by residual: dihedral pdb=" CB GLU B 592 " pdb=" CG GLU B 592 " pdb=" CD GLU B 592 " pdb=" OE1 GLU B 592 " ideal model delta sinusoidal sigma weight residual 0.00 85.52 -85.52 1 3.00e+01 1.11e-03 9.83e+00 dihedral pdb=" CB GLU A 58 " pdb=" CG GLU A 58 " pdb=" CD GLU A 58 " pdb=" OE1 GLU A 58 " ideal model delta sinusoidal sigma weight residual 0.00 -85.10 85.10 1 3.00e+01 1.11e-03 9.76e+00 dihedral pdb=" CB MET B 434 " pdb=" CG MET B 434 " pdb=" SD MET B 434 " pdb=" CE MET B 434 " ideal model delta sinusoidal sigma weight residual 60.00 116.47 -56.47 3 1.50e+01 4.44e-03 9.40e+00 ... (remaining 5455 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 822 0.028 - 0.056: 385 0.056 - 0.084: 109 0.084 - 0.112: 39 0.112 - 0.140: 25 Chirality restraints: 1380 Sorted by residual: chirality pdb=" CA VAL A 111 " pdb=" N VAL A 111 " pdb=" C VAL A 111 " pdb=" CB VAL A 111 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.91e-01 chirality pdb=" CA ILE A 280 " pdb=" N ILE A 280 " pdb=" C ILE A 280 " pdb=" CB ILE A 280 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.52e-01 chirality pdb=" CA ILE B 280 " pdb=" N ILE B 280 " pdb=" C ILE B 280 " pdb=" CB ILE B 280 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.41e-01 ... (remaining 1377 not shown) Planarity restraints: 1562 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS B 491 " 0.041 5.00e-02 4.00e+02 6.28e-02 6.31e+00 pdb=" N PRO B 492 " -0.109 5.00e-02 4.00e+02 pdb=" CA PRO B 492 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 492 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR D 320 " 0.029 5.00e-02 4.00e+02 4.32e-02 2.99e+00 pdb=" N PRO D 321 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO D 321 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO D 321 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG B 304 " 0.008 2.00e-02 2.50e+03 1.52e-02 2.31e+00 pdb=" C ARG B 304 " -0.026 2.00e-02 2.50e+03 pdb=" O ARG B 304 " 0.010 2.00e-02 2.50e+03 pdb=" N PHE B 305 " 0.009 2.00e-02 2.50e+03 ... (remaining 1559 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 170 2.70 - 3.25: 8802 3.25 - 3.80: 13747 3.80 - 4.35: 19172 4.35 - 4.90: 32373 Nonbonded interactions: 74264 Sorted by model distance: nonbonded pdb=" NH1 ARG A 193 " pdb=" O HOH A 701 " model vdw 2.148 3.120 nonbonded pdb=" OG1 THR A 363 " pdb=" OH TYR A 541 " model vdw 2.220 3.040 nonbonded pdb=" OD2 ASP B 88 " pdb=" NH2 ARG B 417 " model vdw 2.268 3.120 nonbonded pdb=" OD2 ASP A 88 " pdb=" NH2 ARG A 417 " model vdw 2.285 3.120 nonbonded pdb=" O ASP A 188 " pdb=" O HOH A 701 " model vdw 2.286 3.040 ... (remaining 74259 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } 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: 1.020 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: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 25.220 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 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 : 0.003 0.030 9030 Z= 0.164 Angle : 0.501 7.056 12174 Z= 0.282 Chirality : 0.039 0.140 1380 Planarity : 0.004 0.063 1562 Dihedral : 14.633 85.519 3370 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 0.00 % Allowed : 0.10 % Favored : 99.90 % 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: 0.27 (0.26), residues: 1120 helix: 0.33 (0.21), residues: 644 sheet: -0.69 (0.50), residues: 76 loop : 0.41 (0.36), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 391 HIS 0.003 0.001 HIS A 491 PHE 0.008 0.001 PHE A 54 TYR 0.016 0.001 TYR B 506 ARG 0.009 0.000 ARG B 408 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 143 time to evaluate : 0.901 Fit side-chains REVERT: A 47 LYS cc_start: 0.7592 (mmtm) cc_final: 0.7291 (ptmt) REVERT: A 521 LYS cc_start: 0.8577 (mppt) cc_final: 0.8310 (mptt) REVERT: A 555 ARG cc_start: 0.7612 (ttp-110) cc_final: 0.7076 (ttp-110) REVERT: B 65 ASN cc_start: 0.7728 (m-40) cc_final: 0.7403 (m110) outliers start: 0 outliers final: 0 residues processed: 143 average time/residue: 0.3029 time to fit residues: 55.2827 Evaluate side-chains 111 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 chunk 33 optimal weight: 0.0870 chunk 53 optimal weight: 2.9990 chunk 65 optimal weight: 4.9990 chunk 101 optimal weight: 1.9990 overall best weight: 2.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 146 GLN ** A 504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 146 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.151967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.118423 restraints weight = 8863.492| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 1.95 r_work: 0.3063 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2894 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.1396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 9030 Z= 0.338 Angle : 0.587 11.981 12174 Z= 0.304 Chirality : 0.043 0.184 1380 Planarity : 0.005 0.063 1562 Dihedral : 4.160 17.964 1214 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 1.04 % Allowed : 9.69 % 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: 0.60 (0.26), residues: 1120 helix: 0.70 (0.20), residues: 644 sheet: -0.41 (0.50), residues: 76 loop : 0.32 (0.34), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 213 HIS 0.004 0.001 HIS A 561 PHE 0.014 0.002 PHE A 571 TYR 0.017 0.002 TYR B 361 ARG 0.010 0.001 ARG B 408 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 119 time to evaluate : 0.934 Fit side-chains revert: symmetry clash REVERT: A 193 ARG cc_start: 0.7917 (mtm-85) cc_final: 0.7714 (mpp-170) REVERT: A 521 LYS cc_start: 0.8609 (mppt) cc_final: 0.7850 (mtmm) REVERT: A 599 LYS cc_start: 0.7837 (mtmt) cc_final: 0.7409 (mttm) REVERT: B 65 ASN cc_start: 0.7901 (m-40) cc_final: 0.7317 (m110) REVERT: B 272 GLU cc_start: 0.8835 (pt0) cc_final: 0.8606 (tt0) REVERT: B 522 THR cc_start: 0.8695 (t) cc_final: 0.8228 (p) REVERT: B 551 SER cc_start: 0.8726 (t) cc_final: 0.8319 (m) REVERT: B 599 LYS cc_start: 0.7848 (mttp) cc_final: 0.7551 (mttp) outliers start: 10 outliers final: 8 residues processed: 126 average time/residue: 0.2894 time to fit residues: 46.8907 Evaluate side-chains 116 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 108 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 GLN Chi-restraints excluded: chain A residue 100 LYS Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 607 GLU Chi-restraints excluded: chain B residue 182 GLU Chi-restraints excluded: chain B residue 490 VAL Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 607 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 59 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 90 optimal weight: 3.9990 chunk 81 optimal weight: 5.9990 chunk 2 optimal weight: 5.9990 chunk 53 optimal weight: 0.7980 chunk 87 optimal weight: 1.9990 chunk 71 optimal weight: 4.9990 chunk 65 optimal weight: 0.8980 chunk 102 optimal weight: 0.9980 chunk 46 optimal weight: 0.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.154146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.120913 restraints weight = 8944.053| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 1.95 r_work: 0.3151 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.1513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9030 Z= 0.221 Angle : 0.499 10.298 12174 Z= 0.261 Chirality : 0.040 0.144 1380 Planarity : 0.005 0.063 1562 Dihedral : 3.939 17.691 1214 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 1.46 % Allowed : 11.25 % Favored : 87.29 % 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: 0.96 (0.26), residues: 1120 helix: 1.05 (0.21), residues: 644 sheet: -0.30 (0.52), residues: 76 loop : 0.36 (0.35), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 213 HIS 0.003 0.001 HIS A 561 PHE 0.011 0.001 PHE A 54 TYR 0.017 0.001 TYR A 361 ARG 0.007 0.000 ARG A 408 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 116 time to evaluate : 0.930 Fit side-chains revert: symmetry clash REVERT: A 521 LYS cc_start: 0.8576 (mppt) cc_final: 0.7788 (mtmm) REVERT: A 555 ARG cc_start: 0.7977 (ttp-110) cc_final: 0.7517 (ttp-110) REVERT: A 596 GLU cc_start: 0.7484 (mp0) cc_final: 0.7118 (mp0) REVERT: B 65 ASN cc_start: 0.7814 (m-40) cc_final: 0.7297 (m110) REVERT: B 272 GLU cc_start: 0.8790 (pt0) cc_final: 0.8463 (tt0) REVERT: B 522 THR cc_start: 0.8609 (t) cc_final: 0.8130 (p) REVERT: B 551 SER cc_start: 0.8701 (t) cc_final: 0.8285 (m) REVERT: B 599 LYS cc_start: 0.7827 (mttp) cc_final: 0.7509 (mttp) outliers start: 14 outliers final: 10 residues processed: 124 average time/residue: 0.2859 time to fit residues: 45.9366 Evaluate side-chains 118 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 108 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 89 GLN Chi-restraints excluded: chain A residue 100 LYS Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain B residue 182 GLU Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 490 VAL Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 556 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 91 optimal weight: 4.9990 chunk 80 optimal weight: 7.9990 chunk 13 optimal weight: 7.9990 chunk 46 optimal weight: 0.7980 chunk 96 optimal weight: 7.9990 chunk 60 optimal weight: 0.2980 chunk 39 optimal weight: 0.9980 chunk 48 optimal weight: 6.9990 chunk 14 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 66 optimal weight: 6.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.152008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.118719 restraints weight = 8896.114| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 1.94 r_work: 0.3117 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2949 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.1689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 9030 Z= 0.278 Angle : 0.529 11.147 12174 Z= 0.273 Chirality : 0.041 0.157 1380 Planarity : 0.005 0.063 1562 Dihedral : 4.027 17.787 1214 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 2.19 % Allowed : 12.40 % Favored : 85.42 % 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: 0.94 (0.26), residues: 1120 helix: 1.02 (0.21), residues: 644 sheet: -0.31 (0.52), residues: 76 loop : 0.39 (0.35), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 213 HIS 0.003 0.001 HIS A 561 PHE 0.013 0.001 PHE A 54 TYR 0.017 0.002 TYR B 361 ARG 0.006 0.001 ARG B 408 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 110 time to evaluate : 0.939 Fit side-chains REVERT: A 65 ASN cc_start: 0.7747 (m110) cc_final: 0.7075 (m110) REVERT: A 193 ARG cc_start: 0.7853 (mtm-85) cc_final: 0.7603 (mpp-170) REVERT: A 521 LYS cc_start: 0.8584 (mppt) cc_final: 0.7746 (mtmm) REVERT: B 65 ASN cc_start: 0.7880 (m-40) cc_final: 0.7374 (m110) REVERT: B 272 GLU cc_start: 0.8762 (pt0) cc_final: 0.8353 (tt0) REVERT: B 522 THR cc_start: 0.8607 (t) cc_final: 0.8132 (p) REVERT: B 551 SER cc_start: 0.8697 (t) cc_final: 0.8279 (m) REVERT: B 599 LYS cc_start: 0.7778 (mttp) cc_final: 0.7527 (mttm) outliers start: 21 outliers final: 17 residues processed: 123 average time/residue: 0.2801 time to fit residues: 44.8688 Evaluate side-chains 124 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 107 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 89 GLN Chi-restraints excluded: chain A residue 100 LYS Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 375 CYS Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 607 GLU Chi-restraints excluded: chain B residue 83 ASP Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain B residue 182 GLU Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 490 VAL Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 556 ILE Chi-restraints excluded: chain B residue 607 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 5.9990 chunk 95 optimal weight: 2.9990 chunk 111 optimal weight: 6.9990 chunk 109 optimal weight: 5.9990 chunk 101 optimal weight: 0.9980 chunk 39 optimal weight: 0.6980 chunk 29 optimal weight: 0.9980 chunk 91 optimal weight: 3.9990 chunk 59 optimal weight: 0.0570 chunk 44 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 overall best weight: 0.7500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.156064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.122942 restraints weight = 8832.717| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 1.94 r_work: 0.3219 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3052 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.1707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9030 Z= 0.170 Angle : 0.463 8.917 12174 Z= 0.242 Chirality : 0.039 0.131 1380 Planarity : 0.004 0.062 1562 Dihedral : 3.782 16.550 1214 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 1.25 % Allowed : 14.69 % Favored : 84.06 % 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: 1.29 (0.26), residues: 1120 helix: 1.36 (0.21), residues: 642 sheet: -0.13 (0.53), residues: 76 loop : 0.42 (0.35), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 213 HIS 0.002 0.001 HIS A 561 PHE 0.008 0.001 PHE A 54 TYR 0.015 0.001 TYR A 361 ARG 0.008 0.000 ARG A 408 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 115 time to evaluate : 0.956 Fit side-chains revert: symmetry clash REVERT: A 193 ARG cc_start: 0.7782 (mtm-85) cc_final: 0.7522 (mpp-170) REVERT: A 521 LYS cc_start: 0.8570 (mppt) cc_final: 0.7813 (mtmm) REVERT: A 555 ARG cc_start: 0.7931 (ttp-110) cc_final: 0.7463 (ttp-110) REVERT: A 596 GLU cc_start: 0.7401 (mp0) cc_final: 0.7023 (mp0) REVERT: B 65 ASN cc_start: 0.7834 (m-40) cc_final: 0.7360 (m110) REVERT: B 182 GLU cc_start: 0.8422 (OUTLIER) cc_final: 0.8130 (mt-10) REVERT: B 272 GLU cc_start: 0.8747 (pt0) cc_final: 0.8356 (tt0) REVERT: B 448 LEU cc_start: 0.7270 (mm) cc_final: 0.7042 (mt) REVERT: B 522 THR cc_start: 0.8599 (t) cc_final: 0.8116 (p) REVERT: B 551 SER cc_start: 0.8681 (t) cc_final: 0.8315 (m) REVERT: B 555 ARG cc_start: 0.7904 (ttp-110) cc_final: 0.7467 (ttp-110) REVERT: B 599 LYS cc_start: 0.7741 (mttp) cc_final: 0.7487 (mttm) outliers start: 12 outliers final: 6 residues processed: 124 average time/residue: 0.2970 time to fit residues: 47.4420 Evaluate side-chains 124 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 117 time to evaluate : 1.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 GLN Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain B residue 182 GLU Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 490 VAL Chi-restraints excluded: chain B residue 514 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 91 optimal weight: 5.9990 chunk 34 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 24 optimal weight: 0.0670 chunk 52 optimal weight: 3.9990 chunk 86 optimal weight: 0.5980 chunk 76 optimal weight: 6.9990 chunk 65 optimal weight: 0.4980 chunk 7 optimal weight: 4.9990 chunk 74 optimal weight: 7.9990 overall best weight: 1.2322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.162491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.131512 restraints weight = 8697.108| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 1.76 r_work: 0.3221 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3066 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.1786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9030 Z= 0.226 Angle : 0.499 9.989 12174 Z= 0.257 Chirality : 0.040 0.141 1380 Planarity : 0.004 0.062 1562 Dihedral : 3.840 16.163 1214 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 1.77 % Allowed : 14.38 % Favored : 83.85 % 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: 1.28 (0.26), residues: 1120 helix: 1.32 (0.21), residues: 644 sheet: -0.16 (0.52), residues: 76 loop : 0.47 (0.35), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 213 HIS 0.003 0.001 HIS A 561 PHE 0.011 0.001 PHE A 571 TYR 0.017 0.001 TYR B 506 ARG 0.008 0.000 ARG B 446 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 114 time to evaluate : 0.977 Fit side-chains REVERT: A 65 ASN cc_start: 0.7904 (m110) cc_final: 0.7235 (m110) REVERT: A 193 ARG cc_start: 0.7817 (mtm-85) cc_final: 0.7565 (mpp-170) REVERT: A 206 ILE cc_start: 0.8308 (mt) cc_final: 0.8104 (mm) REVERT: A 521 LYS cc_start: 0.8681 (mppt) cc_final: 0.7934 (mtmm) REVERT: A 555 ARG cc_start: 0.8011 (ttp-110) cc_final: 0.7535 (ttp-110) REVERT: B 65 ASN cc_start: 0.7986 (m-40) cc_final: 0.7535 (m110) REVERT: B 182 GLU cc_start: 0.8445 (OUTLIER) cc_final: 0.8186 (mt-10) REVERT: B 272 GLU cc_start: 0.8685 (pt0) cc_final: 0.8292 (tt0) REVERT: B 422 LEU cc_start: 0.9006 (OUTLIER) cc_final: 0.7881 (mp) REVERT: B 522 THR cc_start: 0.8674 (t) cc_final: 0.8202 (p) REVERT: B 551 SER cc_start: 0.8723 (t) cc_final: 0.8349 (m) REVERT: B 580 LEU cc_start: 0.8526 (OUTLIER) cc_final: 0.8026 (mp) REVERT: B 599 LYS cc_start: 0.7920 (mttp) cc_final: 0.7657 (mttm) outliers start: 17 outliers final: 10 residues processed: 124 average time/residue: 0.2972 time to fit residues: 47.2910 Evaluate side-chains 124 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 111 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 GLN Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 188 ASP Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain B residue 182 GLU Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 490 VAL Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 556 ILE Chi-restraints excluded: chain B residue 580 LEU Chi-restraints excluded: chain B residue 607 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 8 optimal weight: 0.9980 chunk 31 optimal weight: 0.5980 chunk 3 optimal weight: 0.7980 chunk 97 optimal weight: 0.9990 chunk 29 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 4 optimal weight: 0.3980 chunk 21 optimal weight: 3.9990 chunk 46 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.158907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.127077 restraints weight = 8816.850| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 1.82 r_work: 0.3254 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3098 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.1819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9030 Z= 0.166 Angle : 0.467 8.579 12174 Z= 0.241 Chirality : 0.039 0.130 1380 Planarity : 0.004 0.061 1562 Dihedral : 3.692 15.251 1214 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 1.35 % Allowed : 14.58 % Favored : 84.06 % 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: 1.46 (0.27), residues: 1120 helix: 1.52 (0.21), residues: 644 sheet: -0.08 (0.53), residues: 76 loop : 0.45 (0.36), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 213 HIS 0.005 0.001 HIS A 204 PHE 0.008 0.001 PHE A 54 TYR 0.015 0.001 TYR B 361 ARG 0.009 0.001 ARG A 446 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 114 time to evaluate : 0.974 Fit side-chains REVERT: A 65 ASN cc_start: 0.7874 (m110) cc_final: 0.7224 (m110) REVERT: A 193 ARG cc_start: 0.7787 (mtm-85) cc_final: 0.7520 (mpp-170) REVERT: A 206 ILE cc_start: 0.8273 (mt) cc_final: 0.8060 (mm) REVERT: A 521 LYS cc_start: 0.8671 (mppt) cc_final: 0.7914 (mtmm) REVERT: A 555 ARG cc_start: 0.7981 (ttp-110) cc_final: 0.7503 (ttp-110) REVERT: B 65 ASN cc_start: 0.7921 (m-40) cc_final: 0.7474 (m110) REVERT: B 182 GLU cc_start: 0.8425 (OUTLIER) cc_final: 0.8171 (mt-10) REVERT: B 272 GLU cc_start: 0.8624 (pt0) cc_final: 0.8282 (tt0) REVERT: B 422 LEU cc_start: 0.8980 (OUTLIER) cc_final: 0.8013 (mp) REVERT: B 522 THR cc_start: 0.8662 (t) cc_final: 0.8185 (p) REVERT: B 551 SER cc_start: 0.8704 (t) cc_final: 0.8386 (m) REVERT: B 555 ARG cc_start: 0.7960 (ttp-110) cc_final: 0.7510 (ttp-110) REVERT: B 580 LEU cc_start: 0.8458 (OUTLIER) cc_final: 0.8033 (mp) REVERT: B 599 LYS cc_start: 0.7864 (mttp) cc_final: 0.7608 (mttm) outliers start: 13 outliers final: 7 residues processed: 123 average time/residue: 0.3238 time to fit residues: 50.9993 Evaluate side-chains 121 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 111 time to evaluate : 1.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 GLN Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 188 ASP Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain B residue 182 GLU Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 490 VAL Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 580 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 71 optimal weight: 6.9990 chunk 60 optimal weight: 0.6980 chunk 91 optimal weight: 4.9990 chunk 101 optimal weight: 0.8980 chunk 39 optimal weight: 0.9980 chunk 2 optimal weight: 0.0570 chunk 76 optimal weight: 5.9990 chunk 7 optimal weight: 2.9990 chunk 16 optimal weight: 10.0000 chunk 74 optimal weight: 4.9990 chunk 106 optimal weight: 2.9990 overall best weight: 1.1300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 256 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.156935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.124855 restraints weight = 8958.600| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 1.84 r_work: 0.3301 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3143 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.1864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9030 Z= 0.214 Angle : 0.488 9.803 12174 Z= 0.252 Chirality : 0.040 0.134 1380 Planarity : 0.004 0.061 1562 Dihedral : 3.752 15.753 1214 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 1.77 % Allowed : 14.48 % Favored : 83.75 % 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: 1.41 (0.26), residues: 1120 helix: 1.47 (0.21), residues: 642 sheet: -0.12 (0.53), residues: 76 loop : 0.46 (0.35), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 213 HIS 0.004 0.001 HIS A 204 PHE 0.011 0.001 PHE A 571 TYR 0.019 0.001 TYR B 506 ARG 0.009 0.000 ARG A 446 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 111 time to evaluate : 1.063 Fit side-chains REVERT: A 42 GLU cc_start: 0.8252 (mp0) cc_final: 0.8023 (mp0) REVERT: A 65 ASN cc_start: 0.7896 (m110) cc_final: 0.7240 (m110) REVERT: A 193 ARG cc_start: 0.7775 (mtm-85) cc_final: 0.7494 (mpp-170) REVERT: A 521 LYS cc_start: 0.8690 (mppt) cc_final: 0.7925 (mtmm) REVERT: A 555 ARG cc_start: 0.8050 (ttp-110) cc_final: 0.7554 (ttp-110) REVERT: B 65 ASN cc_start: 0.7981 (m-40) cc_final: 0.7535 (m110) REVERT: B 182 GLU cc_start: 0.8487 (OUTLIER) cc_final: 0.8246 (mt-10) REVERT: B 272 GLU cc_start: 0.8638 (pt0) cc_final: 0.8296 (tt0) REVERT: B 413 GLU cc_start: 0.7749 (OUTLIER) cc_final: 0.7479 (tt0) REVERT: B 422 LEU cc_start: 0.9012 (OUTLIER) cc_final: 0.7922 (mp) REVERT: B 522 THR cc_start: 0.8672 (t) cc_final: 0.8190 (p) REVERT: B 551 SER cc_start: 0.8737 (t) cc_final: 0.8375 (m) REVERT: B 580 LEU cc_start: 0.8514 (OUTLIER) cc_final: 0.8022 (mp) REVERT: B 599 LYS cc_start: 0.7881 (mttp) cc_final: 0.7617 (mttm) outliers start: 17 outliers final: 10 residues processed: 120 average time/residue: 0.2833 time to fit residues: 44.3145 Evaluate side-chains 124 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 110 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 GLN Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 188 ASP Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain B residue 182 GLU Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 413 GLU Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 490 VAL Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 580 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 41 optimal weight: 5.9990 chunk 56 optimal weight: 2.9990 chunk 29 optimal weight: 0.6980 chunk 44 optimal weight: 3.9990 chunk 71 optimal weight: 5.9990 chunk 97 optimal weight: 6.9990 chunk 12 optimal weight: 0.9990 chunk 74 optimal weight: 6.9990 chunk 27 optimal weight: 1.9990 chunk 99 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 256 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.156786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.124904 restraints weight = 8814.605| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 1.82 r_work: 0.3225 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3068 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.1879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9030 Z= 0.214 Angle : 0.496 9.524 12174 Z= 0.256 Chirality : 0.040 0.146 1380 Planarity : 0.004 0.061 1562 Dihedral : 3.746 15.929 1214 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 1.67 % Allowed : 14.38 % Favored : 83.96 % 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: 1.43 (0.26), residues: 1120 helix: 1.48 (0.21), residues: 642 sheet: -0.08 (0.53), residues: 76 loop : 0.47 (0.35), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 213 HIS 0.003 0.001 HIS A 561 PHE 0.011 0.001 PHE A 571 TYR 0.016 0.001 TYR B 361 ARG 0.010 0.001 ARG A 446 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 112 time to evaluate : 0.933 Fit side-chains REVERT: A 42 GLU cc_start: 0.8200 (mp0) cc_final: 0.7953 (mp0) REVERT: A 65 ASN cc_start: 0.7868 (m110) cc_final: 0.7203 (m110) REVERT: A 521 LYS cc_start: 0.8700 (mppt) cc_final: 0.7928 (mtmm) REVERT: A 555 ARG cc_start: 0.8029 (ttp-110) cc_final: 0.7543 (ttp-110) REVERT: B 65 ASN cc_start: 0.7961 (m-40) cc_final: 0.7509 (m110) REVERT: B 182 GLU cc_start: 0.8423 (OUTLIER) cc_final: 0.8191 (mt-10) REVERT: B 272 GLU cc_start: 0.8619 (pt0) cc_final: 0.8264 (tt0) REVERT: B 413 GLU cc_start: 0.7719 (OUTLIER) cc_final: 0.7452 (tt0) REVERT: B 422 LEU cc_start: 0.8993 (OUTLIER) cc_final: 0.7899 (mp) REVERT: B 522 THR cc_start: 0.8667 (t) cc_final: 0.8190 (p) REVERT: B 551 SER cc_start: 0.8722 (t) cc_final: 0.8356 (m) REVERT: B 580 LEU cc_start: 0.8506 (OUTLIER) cc_final: 0.7992 (mp) REVERT: B 599 LYS cc_start: 0.7841 (mttp) cc_final: 0.7571 (mttm) outliers start: 16 outliers final: 10 residues processed: 123 average time/residue: 0.2940 time to fit residues: 46.8936 Evaluate side-chains 124 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 110 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 188 ASP Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain B residue 182 GLU Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 256 ASN Chi-restraints excluded: chain B residue 413 GLU Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 490 VAL Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 580 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 37 optimal weight: 0.9980 chunk 48 optimal weight: 5.9990 chunk 110 optimal weight: 0.7980 chunk 41 optimal weight: 6.9990 chunk 53 optimal weight: 0.6980 chunk 9 optimal weight: 0.3980 chunk 2 optimal weight: 0.0170 chunk 101 optimal weight: 0.7980 chunk 31 optimal weight: 0.6980 chunk 39 optimal weight: 0.9990 chunk 108 optimal weight: 2.9990 overall best weight: 0.5218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 256 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.157595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.124239 restraints weight = 8798.949| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 1.95 r_work: 0.3321 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.1951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 9030 Z= 0.148 Angle : 0.463 8.046 12174 Z= 0.241 Chirality : 0.039 0.139 1380 Planarity : 0.004 0.061 1562 Dihedral : 3.601 14.988 1214 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 1.35 % Allowed : 15.10 % Favored : 83.54 % 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: 1.67 (0.27), residues: 1120 helix: 1.71 (0.21), residues: 644 sheet: 0.00 (0.55), residues: 76 loop : 0.51 (0.36), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 391 HIS 0.008 0.001 HIS A 204 PHE 0.007 0.001 PHE A 54 TYR 0.019 0.001 TYR A 506 ARG 0.010 0.000 ARG A 446 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 115 time to evaluate : 0.943 Fit side-chains REVERT: A 42 GLU cc_start: 0.8019 (mp0) cc_final: 0.7789 (mp0) REVERT: A 65 ASN cc_start: 0.7803 (m110) cc_final: 0.7144 (m110) REVERT: A 521 LYS cc_start: 0.8631 (mppt) cc_final: 0.7904 (mtmm) REVERT: A 555 ARG cc_start: 0.7858 (ttp-110) cc_final: 0.7360 (ttp-110) REVERT: A 607 GLU cc_start: 0.8042 (tm-30) cc_final: 0.7809 (tp30) REVERT: B 50 LYS cc_start: 0.7490 (pttp) cc_final: 0.7094 (mttm) REVERT: B 65 ASN cc_start: 0.7852 (m-40) cc_final: 0.7404 (m110) REVERT: B 272 GLU cc_start: 0.8479 (pt0) cc_final: 0.8232 (tt0) REVERT: B 422 LEU cc_start: 0.8817 (OUTLIER) cc_final: 0.7898 (mp) REVERT: B 551 SER cc_start: 0.8630 (t) cc_final: 0.8306 (m) REVERT: B 555 ARG cc_start: 0.7788 (ttp-110) cc_final: 0.7338 (ttp-110) REVERT: B 580 LEU cc_start: 0.8356 (OUTLIER) cc_final: 0.7943 (mp) REVERT: B 599 LYS cc_start: 0.7700 (mttp) cc_final: 0.7449 (mttm) outliers start: 13 outliers final: 7 residues processed: 125 average time/residue: 0.3293 time to fit residues: 53.2708 Evaluate side-chains 119 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 110 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 GLN Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 188 ASP Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain B residue 256 ASN Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 490 VAL Chi-restraints excluded: chain B residue 580 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 79 optimal weight: 0.9990 chunk 12 optimal weight: 0.9990 chunk 45 optimal weight: 3.9990 chunk 30 optimal weight: 0.5980 chunk 14 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 36 optimal weight: 5.9990 chunk 42 optimal weight: 0.0470 overall best weight: 0.7082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 256 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.159930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.128024 restraints weight = 8755.503| |-----------------------------------------------------------------------------| r_work (start): 0.3522 rms_B_bonded: 1.82 r_work: 0.3337 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3169 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.1970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9030 Z= 0.165 Angle : 0.469 8.118 12174 Z= 0.244 Chirality : 0.039 0.139 1380 Planarity : 0.004 0.061 1562 Dihedral : 3.584 14.867 1214 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 0.94 % Allowed : 15.42 % Favored : 83.65 % 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: 1.69 (0.26), residues: 1120 helix: 1.72 (0.21), residues: 644 sheet: -0.00 (0.55), residues: 76 loop : 0.52 (0.35), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 213 HIS 0.007 0.001 HIS A 204 PHE 0.011 0.001 PHE B 226 TYR 0.015 0.001 TYR B 361 ARG 0.009 0.000 ARG A 446 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4863.72 seconds wall clock time: 84 minutes 46.01 seconds (5086.01 seconds total)