Starting phenix.real_space_refine on Thu Feb 13 07:54:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8phe_17659/02_2025/8phe_17659.cif Found real_map, /net/cci-nas-00/data/ceres_data/8phe_17659/02_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_17659/02_2025/8phe_17659.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8phe_17659/02_2025/8phe_17659.map" model { file = "/net/cci-nas-00/data/ceres_data/8phe_17659/02_2025/8phe_17659.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8phe_17659/02_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-5592/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: 5.23, per 1000 atoms: 0.59 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: 2.14 Conformation dependent library (CDL) restraints added in 1.0 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: 0.97 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: 2.58 Time building geometry restraints manager: 2.48 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: 0.05 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: 1.390 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: 0.000 Extract box with map and model: 0.320 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 22.090 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.100 ------------------------------------------------------------------------------- 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 : 1.124 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: 0.3106 time to fit residues: 56.6316 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 : 1.004 ------------------------------------------------------------------------------- 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 = 52)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.118425 restraints weight = 8863.492| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 1.95 r_work: 0.3064 rms_B_bonded: 2.93 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 : 1.015 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: 0.8608 (mppt) cc_final: 0.7850 (mtmm) REVERT: A 599 LYS cc_start: 0.7834 (mtmt) cc_final: 0.7405 (mttm) REVERT: B 65 ASN cc_start: 0.7900 (m-40) cc_final: 0.7314 (m110) REVERT: B 272 GLU cc_start: 0.8833 (pt0) cc_final: 0.8605 (tt0) REVERT: B 522 THR cc_start: 0.8695 (t) cc_final: 0.8228 (p) REVERT: B 551 SER cc_start: 0.8728 (t) cc_final: 0.8320 (m) REVERT: B 599 LYS cc_start: 0.7847 (mttp) cc_final: 0.7550 (mttp) outliers start: 10 outliers final: 8 residues processed: 126 average time/residue: 0.3121 time to fit residues: 50.6136 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 : 1.001 ------------------------------------------------------------------------------- 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: 7.9990 chunk 65 optimal weight: 0.9990 chunk 102 optimal weight: 0.9980 chunk 46 optimal weight: 0.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- 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 = 0.154078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.120831 restraints weight = 8948.180| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 1.95 r_work: 0.3151 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.1518 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 10.306 12174 Z= 0.261 Chirality : 0.040 0.145 1380 Planarity : 0.005 0.063 1562 Dihedral : 3.943 17.736 1214 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 1.46 % Allowed : 11.46 % Favored : 87.08 % 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 : 1.021 Fit side-chains revert: symmetry clash REVERT: A 521 LYS cc_start: 0.8577 (mppt) cc_final: 0.7789 (mtmm) REVERT: A 555 ARG cc_start: 0.7974 (ttp-110) cc_final: 0.7513 (ttp-110) REVERT: A 596 GLU cc_start: 0.7488 (mp0) cc_final: 0.7119 (mp0) REVERT: B 65 ASN cc_start: 0.7809 (m-40) cc_final: 0.7292 (m110) REVERT: B 272 GLU cc_start: 0.8786 (pt0) cc_final: 0.8458 (tt0) REVERT: B 522 THR cc_start: 0.8611 (t) cc_final: 0.8132 (p) REVERT: B 551 SER cc_start: 0.8699 (t) cc_final: 0.8282 (m) REVERT: B 599 LYS cc_start: 0.7821 (mttp) cc_final: 0.7577 (mttm) outliers start: 14 outliers final: 10 residues processed: 124 average time/residue: 0.2848 time to fit residues: 45.7315 Evaluate side-chains 119 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 109 time to evaluate : 1.040 ------------------------------------------------------------------------------- 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: 0.9980 chunk 96 optimal weight: 8.9990 chunk 60 optimal weight: 0.6980 chunk 39 optimal weight: 0.9980 chunk 48 optimal weight: 6.9990 chunk 14 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 66 optimal weight: 6.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- 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 = 0.3617 r_free = 0.3617 target = 0.151898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.118777 restraints weight = 8892.104| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 1.93 r_work: 0.3074 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2908 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.1686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 9030 Z= 0.267 Angle : 0.523 10.899 12174 Z= 0.270 Chirality : 0.041 0.153 1380 Planarity : 0.005 0.063 1562 Dihedral : 4.003 17.557 1214 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 2.08 % Allowed : 12.29 % Favored : 85.62 % 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: 0.97 (0.26), residues: 1120 helix: 1.05 (0.21), residues: 644 sheet: -0.30 (0.52), residues: 76 loop : 0.40 (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 204 PHE 0.012 0.001 PHE A 571 TYR 0.017 0.002 TYR A 506 ARG 0.007 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 132 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 112 time to evaluate : 1.040 Fit side-chains REVERT: A 65 ASN cc_start: 0.7827 (m110) cc_final: 0.7158 (m110) REVERT: A 193 ARG cc_start: 0.7855 (mtm-85) cc_final: 0.7598 (mpp-170) REVERT: A 521 LYS cc_start: 0.8628 (mppt) cc_final: 0.7781 (mtmm) REVERT: B 65 ASN cc_start: 0.7945 (m-40) cc_final: 0.7451 (m110) REVERT: B 272 GLU cc_start: 0.8764 (pt0) cc_final: 0.8372 (tt0) REVERT: B 522 THR cc_start: 0.8634 (t) cc_final: 0.8165 (p) REVERT: B 551 SER cc_start: 0.8709 (t) cc_final: 0.8314 (m) REVERT: B 599 LYS cc_start: 0.7830 (mttp) cc_final: 0.7584 (mttm) outliers start: 20 outliers final: 16 residues processed: 125 average time/residue: 0.2994 time to fit residues: 48.5758 Evaluate side-chains 124 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 108 time to evaluate : 0.906 ------------------------------------------------------------------------------- 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 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: 6.9990 chunk 95 optimal weight: 1.9990 chunk 111 optimal weight: 7.9990 chunk 109 optimal weight: 5.9990 chunk 101 optimal weight: 0.8980 chunk 39 optimal weight: 0.8980 chunk 29 optimal weight: 0.8980 chunk 91 optimal weight: 3.9990 chunk 59 optimal weight: 0.2980 chunk 44 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 = 0.3649 r_free = 0.3649 target = 0.154897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.121717 restraints weight = 8847.744| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 1.94 r_work: 0.3122 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2954 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.1721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9030 Z= 0.197 Angle : 0.479 9.623 12174 Z= 0.250 Chirality : 0.039 0.133 1380 Planarity : 0.004 0.062 1562 Dihedral : 3.845 17.122 1214 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 1.88 % Allowed : 14.38 % 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: 1.22 (0.26), residues: 1120 helix: 1.27 (0.21), residues: 644 sheet: -0.17 (0.52), residues: 76 loop : 0.46 (0.35), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 213 HIS 0.003 0.001 HIS A 561 PHE 0.009 0.001 PHE A 54 TYR 0.016 0.001 TYR A 361 ARG 0.009 0.001 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 133 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 115 time to evaluate : 0.991 Fit side-chains REVERT: A 65 ASN cc_start: 0.7764 (m110) cc_final: 0.7115 (m110) REVERT: A 193 ARG cc_start: 0.7814 (mtm-85) cc_final: 0.7563 (mpp-170) REVERT: A 521 LYS cc_start: 0.8607 (mppt) cc_final: 0.7858 (mtmm) REVERT: A 555 ARG cc_start: 0.8011 (ttp-110) cc_final: 0.7542 (ttp-110) REVERT: B 65 ASN cc_start: 0.7883 (m-40) cc_final: 0.7411 (m110) REVERT: B 182 GLU cc_start: 0.8451 (OUTLIER) cc_final: 0.8164 (mt-10) REVERT: B 272 GLU cc_start: 0.8754 (pt0) cc_final: 0.8344 (tt0) REVERT: B 448 LEU cc_start: 0.7365 (mm) cc_final: 0.7127 (mt) REVERT: B 522 THR cc_start: 0.8613 (t) cc_final: 0.8142 (p) REVERT: B 551 SER cc_start: 0.8712 (t) cc_final: 0.8323 (m) REVERT: B 580 LEU cc_start: 0.8452 (OUTLIER) cc_final: 0.7992 (mp) REVERT: B 599 LYS cc_start: 0.7792 (mttp) cc_final: 0.7537 (mttm) outliers start: 18 outliers final: 12 residues processed: 125 average time/residue: 0.3209 time to fit residues: 51.4103 Evaluate side-chains 126 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 112 time to evaluate : 1.070 ------------------------------------------------------------------------------- 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 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 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 580 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 91 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 52 optimal weight: 3.9990 chunk 86 optimal weight: 0.6980 chunk 76 optimal weight: 5.9990 chunk 65 optimal weight: 0.5980 chunk 7 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- 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 = 0.3629 r_free = 0.3629 target = 0.152984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.120870 restraints weight = 8819.762| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 1.83 r_work: 0.3181 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3023 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.1802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9030 Z= 0.230 Angle : 0.501 10.114 12174 Z= 0.258 Chirality : 0.040 0.143 1380 Planarity : 0.004 0.062 1562 Dihedral : 3.864 16.555 1214 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 1.88 % Allowed : 14.48 % 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: 1.23 (0.26), residues: 1120 helix: 1.27 (0.21), residues: 644 sheet: -0.16 (0.52), residues: 76 loop : 0.48 (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 0.018 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 130 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 112 time to evaluate : 1.223 Fit side-chains REVERT: A 65 ASN cc_start: 0.7867 (m110) cc_final: 0.7216 (m110) REVERT: A 193 ARG cc_start: 0.7819 (mtm-85) cc_final: 0.7569 (mpp-170) REVERT: A 206 ILE cc_start: 0.8292 (mt) cc_final: 0.8071 (mm) REVERT: A 521 LYS cc_start: 0.8666 (mppt) cc_final: 0.7907 (mtmm) REVERT: A 555 ARG cc_start: 0.8017 (ttp-110) cc_final: 0.7534 (ttp-110) REVERT: B 65 ASN cc_start: 0.7978 (m-40) cc_final: 0.7516 (m110) REVERT: B 182 GLU cc_start: 0.8460 (OUTLIER) cc_final: 0.8198 (mt-10) REVERT: B 272 GLU cc_start: 0.8695 (pt0) cc_final: 0.8290 (tt0) REVERT: B 422 LEU cc_start: 0.9008 (OUTLIER) cc_final: 0.7897 (mp) REVERT: B 522 THR cc_start: 0.8664 (t) cc_final: 0.8192 (p) REVERT: B 551 SER cc_start: 0.8717 (t) cc_final: 0.8330 (m) REVERT: B 580 LEU cc_start: 0.8517 (OUTLIER) cc_final: 0.7988 (mp) REVERT: B 599 LYS cc_start: 0.7881 (mttp) cc_final: 0.7617 (mttm) outliers start: 18 outliers final: 10 residues processed: 125 average time/residue: 0.2954 time to fit residues: 47.8457 Evaluate side-chains 123 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 110 time to evaluate : 1.038 ------------------------------------------------------------------------------- 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 103 SER 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 8 optimal weight: 4.9990 chunk 31 optimal weight: 0.7980 chunk 3 optimal weight: 0.7980 chunk 97 optimal weight: 0.9980 chunk 29 optimal weight: 0.6980 chunk 47 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 26 optimal weight: 4.9990 chunk 4 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 46 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3656 r_free = 0.3656 target = 0.155781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.122492 restraints weight = 8832.309| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 1.94 r_work: 0.3299 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.1835 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= 0.172 Angle : 0.474 8.895 12174 Z= 0.244 Chirality : 0.039 0.131 1380 Planarity : 0.004 0.061 1562 Dihedral : 3.724 15.470 1214 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 1.25 % Allowed : 14.79 % 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: 1.44 (0.26), residues: 1120 helix: 1.49 (0.21), residues: 642 sheet: -0.09 (0.53), residues: 76 loop : 0.48 (0.35), residues: 402 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 0.016 0.001 TYR B 361 ARG 0.009 0.000 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 125 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 113 time to evaluate : 1.109 Fit side-chains REVERT: A 65 ASN cc_start: 0.7825 (m110) cc_final: 0.7156 (m110) REVERT: A 193 ARG cc_start: 0.7690 (mtm-85) cc_final: 0.7418 (mpp-170) REVERT: A 206 ILE cc_start: 0.8239 (mt) cc_final: 0.8011 (mm) REVERT: A 521 LYS cc_start: 0.8692 (mppt) cc_final: 0.7944 (mtmm) REVERT: A 555 ARG cc_start: 0.7860 (ttp-110) cc_final: 0.7361 (ttp-110) REVERT: B 65 ASN cc_start: 0.7883 (m-40) cc_final: 0.7442 (m110) REVERT: B 182 GLU cc_start: 0.8359 (OUTLIER) cc_final: 0.8116 (mt-10) REVERT: B 272 GLU cc_start: 0.8517 (pt0) cc_final: 0.8165 (tt0) REVERT: B 422 LEU cc_start: 0.8903 (OUTLIER) cc_final: 0.7888 (mp) REVERT: B 522 THR cc_start: 0.8656 (t) cc_final: 0.8185 (p) REVERT: B 551 SER cc_start: 0.8630 (t) cc_final: 0.8256 (m) REVERT: B 599 LYS cc_start: 0.7780 (mttp) cc_final: 0.7524 (mttm) outliers start: 12 outliers final: 8 residues processed: 123 average time/residue: 0.3022 time to fit residues: 48.0273 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 : 0.956 ------------------------------------------------------------------------------- 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 580 LEU 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 422 LEU Chi-restraints excluded: chain B residue 490 VAL Chi-restraints excluded: chain B residue 514 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 71 optimal weight: 8.9990 chunk 60 optimal weight: 0.6980 chunk 91 optimal weight: 4.9990 chunk 101 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 2 optimal weight: 0.0050 chunk 76 optimal weight: 4.9990 chunk 7 optimal weight: 0.0870 chunk 16 optimal weight: 9.9990 chunk 74 optimal weight: 10.0000 chunk 106 optimal weight: 2.9990 overall best weight: 0.7576 ------------------------------------------------------------------------------- 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 = 0.3694 r_free = 0.3694 target = 0.158578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.126607 restraints weight = 8910.243| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 1.84 r_work: 0.3249 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3092 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.1883 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= 0.169 Angle : 0.461 8.554 12174 Z= 0.240 Chirality : 0.039 0.135 1380 Planarity : 0.004 0.061 1562 Dihedral : 3.656 15.128 1214 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 1.46 % Allowed : 14.79 % 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: 1.53 (0.26), residues: 1120 helix: 1.58 (0.21), residues: 644 sheet: -0.06 (0.53), residues: 76 loop : 0.46 (0.36), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 213 HIS 0.004 0.001 HIS A 204 PHE 0.008 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: 14 poor density : 114 time to evaluate : 0.963 Fit side-chains REVERT: A 42 GLU cc_start: 0.8199 (mp0) cc_final: 0.7988 (mp0) REVERT: A 65 ASN cc_start: 0.7861 (m110) cc_final: 0.7206 (m110) REVERT: A 193 ARG cc_start: 0.7738 (mtm-85) cc_final: 0.7465 (mpp-170) REVERT: A 521 LYS cc_start: 0.8708 (mppt) cc_final: 0.7916 (mtmm) REVERT: A 555 ARG cc_start: 0.8009 (ttp-110) cc_final: 0.7525 (ttp-110) REVERT: B 65 ASN cc_start: 0.7927 (m-40) cc_final: 0.7480 (m110) REVERT: B 272 GLU cc_start: 0.8623 (pt0) cc_final: 0.8342 (tt0) REVERT: B 413 GLU cc_start: 0.7674 (OUTLIER) cc_final: 0.7368 (tt0) REVERT: B 422 LEU cc_start: 0.8975 (OUTLIER) cc_final: 0.7998 (mp) REVERT: B 522 THR cc_start: 0.8659 (t) cc_final: 0.8181 (p) REVERT: B 551 SER cc_start: 0.8700 (t) cc_final: 0.8398 (m) REVERT: B 555 ARG cc_start: 0.7954 (ttp-110) cc_final: 0.7497 (ttp-110) REVERT: B 580 LEU cc_start: 0.8455 (OUTLIER) cc_final: 0.8025 (mp) REVERT: B 599 LYS cc_start: 0.7842 (mttp) cc_final: 0.7583 (mttm) outliers start: 14 outliers final: 9 residues processed: 124 average time/residue: 0.3071 time to fit residues: 48.6469 Evaluate side-chains 120 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 108 time to evaluate : 1.081 ------------------------------------------------------------------------------- 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 580 LEU Chi-restraints excluded: chain B residue 103 SER 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: 6.9990 chunk 56 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 chunk 44 optimal weight: 3.9990 chunk 71 optimal weight: 10.0000 chunk 97 optimal weight: 6.9990 chunk 12 optimal weight: 0.9980 chunk 74 optimal weight: 8.9990 chunk 27 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 overall best weight: 1.7986 ------------------------------------------------------------------------------- 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 = 0.3641 r_free = 0.3641 target = 0.153817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.121769 restraints weight = 8876.235| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 1.81 r_work: 0.3264 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3106 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.1955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 9030 Z= 0.303 Angle : 0.554 11.183 12174 Z= 0.283 Chirality : 0.042 0.171 1380 Planarity : 0.005 0.061 1562 Dihedral : 3.950 17.705 1214 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 1.98 % Allowed : 14.58 % Favored : 83.44 % 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: 1.21 (0.26), residues: 1120 helix: 1.24 (0.21), residues: 644 sheet: -0.17 (0.53), residues: 76 loop : 0.48 (0.35), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 213 HIS 0.004 0.001 HIS A 561 PHE 0.015 0.002 PHE A 54 TYR 0.020 0.001 TYR A 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 122 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 103 time to evaluate : 0.998 Fit side-chains REVERT: A 42 GLU cc_start: 0.8250 (mp0) cc_final: 0.8000 (mp0) REVERT: A 64 LEU cc_start: 0.8161 (tp) cc_final: 0.7956 (tp) REVERT: A 521 LYS cc_start: 0.8719 (mppt) cc_final: 0.7921 (mtmm) REVERT: B 65 ASN cc_start: 0.8025 (m-40) cc_final: 0.7546 (m110) REVERT: B 272 GLU cc_start: 0.8635 (pt0) cc_final: 0.8264 (tt0) REVERT: B 422 LEU cc_start: 0.9043 (OUTLIER) cc_final: 0.7834 (mp) REVERT: B 522 THR cc_start: 0.8683 (t) cc_final: 0.8206 (p) REVERT: B 551 SER cc_start: 0.8718 (t) cc_final: 0.8329 (m) REVERT: B 580 LEU cc_start: 0.8583 (OUTLIER) cc_final: 0.8017 (mp) REVERT: B 599 LYS cc_start: 0.7950 (mttp) cc_final: 0.7680 (mttm) outliers start: 19 outliers final: 12 residues processed: 119 average time/residue: 0.2932 time to fit residues: 45.2613 Evaluate side-chains 114 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 100 time to evaluate : 1.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 GLN 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 103 SER 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 37 optimal weight: 0.0060 chunk 48 optimal weight: 1.9990 chunk 110 optimal weight: 0.8980 chunk 41 optimal weight: 4.9990 chunk 53 optimal weight: 0.8980 chunk 9 optimal weight: 0.9990 chunk 2 optimal weight: 0.9980 chunk 101 optimal weight: 0.6980 chunk 31 optimal weight: 0.6980 chunk 39 optimal weight: 0.7980 chunk 108 optimal weight: 0.9980 overall best weight: 0.6196 ------------------------------------------------------------------------------- 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 = 0.3695 r_free = 0.3695 target = 0.158892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.127119 restraints weight = 8789.002| |-----------------------------------------------------------------------------| r_work (start): 0.3501 rms_B_bonded: 1.82 r_work: 0.3332 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3176 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.1966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 9030 Z= 0.160 Angle : 0.475 8.292 12174 Z= 0.248 Chirality : 0.039 0.140 1380 Planarity : 0.004 0.061 1562 Dihedral : 3.703 15.856 1214 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 0.94 % Allowed : 15.52 % 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: 1.55 (0.26), residues: 1120 helix: 1.60 (0.21), residues: 642 sheet: -0.08 (0.54), residues: 76 loop : 0.49 (0.35), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 213 HIS 0.008 0.001 HIS A 204 PHE 0.023 0.001 PHE A 425 TYR 0.019 0.001 TYR A 506 ARG 0.010 0.001 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 116 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 107 time to evaluate : 1.080 Fit side-chains REVERT: A 42 GLU cc_start: 0.8203 (mp0) cc_final: 0.7988 (mp0) REVERT: A 65 ASN cc_start: 0.7947 (m110) cc_final: 0.7279 (m110) REVERT: A 521 LYS cc_start: 0.8678 (mppt) cc_final: 0.7893 (mtmm) REVERT: A 555 ARG cc_start: 0.7985 (ttp-110) cc_final: 0.7508 (ttp-110) REVERT: B 65 ASN cc_start: 0.7967 (m-40) cc_final: 0.7522 (m110) REVERT: B 272 GLU cc_start: 0.8604 (pt0) cc_final: 0.8223 (tt0) REVERT: B 422 LEU cc_start: 0.8991 (OUTLIER) cc_final: 0.7919 (mp) REVERT: B 522 THR cc_start: 0.8670 (t) cc_final: 0.8201 (p) REVERT: B 551 SER cc_start: 0.8737 (t) cc_final: 0.8415 (m) REVERT: B 555 ARG cc_start: 0.8009 (ttp-110) cc_final: 0.7567 (ttp-110) REVERT: B 580 LEU cc_start: 0.8461 (OUTLIER) cc_final: 0.8047 (mp) REVERT: B 599 LYS cc_start: 0.7868 (mttp) cc_final: 0.7605 (mttm) outliers start: 9 outliers final: 5 residues processed: 113 average time/residue: 0.3303 time to fit residues: 47.8181 Evaluate side-chains 113 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 106 time to evaluate : 1.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain B residue 103 SER 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: 1.9990 chunk 12 optimal weight: 0.0060 chunk 45 optimal weight: 0.9980 chunk 30 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 72 optimal weight: 0.7980 chunk 76 optimal weight: 0.6980 chunk 86 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 chunk 36 optimal weight: 3.9990 chunk 42 optimal weight: 0.8980 overall best weight: 0.6396 ------------------------------------------------------------------------------- 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 ** A 504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 256 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.157091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.123712 restraints weight = 8769.950| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 1.93 r_work: 0.3311 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.1996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 9030 Z= 0.160 Angle : 0.476 8.169 12174 Z= 0.246 Chirality : 0.039 0.139 1380 Planarity : 0.004 0.061 1562 Dihedral : 3.638 15.153 1214 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 1.04 % Allowed : 15.62 % Favored : 83.33 % 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: 1.65 (0.26), residues: 1120 helix: 1.68 (0.21), residues: 644 sheet: -0.07 (0.55), residues: 76 loop : 0.54 (0.36), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 213 HIS 0.007 0.001 HIS A 204 PHE 0.022 0.001 PHE A 425 TYR 0.019 0.001 TYR B 506 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: 4434.34 seconds wall clock time: 79 minutes 35.99 seconds (4775.99 seconds total)