Starting phenix.real_space_refine on Fri Oct 11 03:08:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y91_39066/10_2024/8y91_39066.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y91_39066/10_2024/8y91_39066.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.13 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y91_39066/10_2024/8y91_39066.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y91_39066/10_2024/8y91_39066.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y91_39066/10_2024/8y91_39066.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y91_39066/10_2024/8y91_39066.cif" } resolution = 3.13 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.057 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians S 40 5.16 5 Cl 2 4.86 5 Na 2 4.78 5 C 6084 2.51 5 N 1416 2.21 5 O 1528 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/chem_data/mon_lib" Total number of atoms: 9072 Number of models: 1 Model: "" Number of chains: 4 Chain: "D" Number of atoms: 4516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 565, 4516 Classifications: {'peptide': 565} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 544} Chain: "A" Number of atoms: 4516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 565, 4516 Classifications: {'peptide': 565} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 544} Chain: "D" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 20 Unusual residues: {' CL': 1, ' NA': 1, 'A1LX5': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 20 Unusual residues: {' CL': 1, ' NA': 1, 'A1LX5': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 6.31, per 1000 atoms: 0.70 Number of scatterers: 9072 At special positions: 0 Unit cell: (78.11, 120.45, 89.79, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 2 17.00 S 40 16.00 Na 2 11.00 O 1528 8.00 N 1416 7.00 C 6084 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: 2.57 Conformation dependent library (CDL) restraints added in 1.1 seconds 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2076 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 0 sheets defined 78.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.97 Creating SS restraints... Processing helix chain 'D' and resid 61 through 74 removed outlier: 3.669A pdb=" N PHE D 65 " --> pdb=" O LYS D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 75 through 81 removed outlier: 3.621A pdb=" N VAL D 79 " --> pdb=" O ASP D 75 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 89 Processing helix chain 'D' and resid 90 through 93 Processing helix chain 'D' and resid 94 through 107 removed outlier: 3.905A pdb=" N LEU D 100 " --> pdb=" O ILE D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 107 through 120 Processing helix chain 'D' and resid 124 through 133 removed outlier: 3.835A pdb=" N VAL D 127 " --> pdb=" O ALA D 124 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N TRP D 128 " --> pdb=" O ALA D 125 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N LYS D 129 " --> pdb=" O THR D 126 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N ILE D 130 " --> pdb=" O VAL D 127 " (cutoff:3.500A) Proline residue: D 132 - end of helix Processing helix chain 'D' and resid 134 through 151 removed outlier: 3.761A pdb=" N ILE D 142 " --> pdb=" O GLY D 138 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLY D 149 " --> pdb=" O ALA D 145 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N TYR D 151 " --> pdb=" O TYR D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 151 through 166 removed outlier: 3.641A pdb=" N ILE D 156 " --> pdb=" O TYR D 152 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N TYR D 162 " --> pdb=" O TRP D 158 " (cutoff:3.500A) Processing helix chain 'D' and resid 208 through 219 removed outlier: 4.013A pdb=" N TYR D 214 " --> pdb=" O ALA D 210 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLU D 215 " --> pdb=" O ALA D 211 " (cutoff:3.500A) Processing helix chain 'D' and resid 220 through 224 Processing helix chain 'D' and resid 234 through 253 Processing helix chain 'D' and resid 255 through 267 removed outlier: 3.769A pdb=" N SER D 259 " --> pdb=" O GLY D 255 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N LYS D 261 " --> pdb=" O LYS D 257 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N TRP D 264 " --> pdb=" O GLY D 260 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N ILE D 265 " --> pdb=" O LYS D 261 " (cutoff:3.500A) Processing helix chain 'D' and resid 268 through 283 removed outlier: 3.554A pdb=" N PHE D 272 " --> pdb=" O THR D 268 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N THR D 283 " --> pdb=" O VAL D 279 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 295 removed outlier: 3.652A pdb=" N GLY D 290 " --> pdb=" O GLY D 286 " (cutoff:3.500A) Processing helix chain 'D' and resid 303 through 320 removed outlier: 4.838A pdb=" N ILE D 309 " --> pdb=" O ALA D 305 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N ASP D 310 " --> pdb=" O THR D 306 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLY D 320 " --> pdb=" O PHE D 316 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 331 Processing helix chain 'D' and resid 338 through 372 removed outlier: 3.610A pdb=" N ASP D 342 " --> pdb=" O ASN D 338 " (cutoff:3.500A) Processing helix chain 'D' and resid 375 through 380 removed outlier: 3.930A pdb=" N VAL D 379 " --> pdb=" O ASN D 375 " (cutoff:3.500A) Processing helix chain 'D' and resid 383 through 389 removed outlier: 3.730A pdb=" N VAL D 387 " --> pdb=" O GLY D 383 " (cutoff:3.500A) Processing helix chain 'D' and resid 390 through 398 removed outlier: 3.684A pdb=" N THR D 397 " --> pdb=" O GLU D 393 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU D 398 " --> pdb=" O ALA D 394 " (cutoff:3.500A) Processing helix chain 'D' and resid 400 through 435 removed outlier: 3.704A pdb=" N TRP D 404 " --> pdb=" O GLY D 400 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER D 419 " --> pdb=" O LEU D 415 " (cutoff:3.500A) Processing helix chain 'D' and resid 435 through 441 removed outlier: 3.812A pdb=" N LYS D 439 " --> pdb=" O PHE D 435 " (cutoff:3.500A) Processing helix chain 'D' and resid 441 through 456 Processing helix chain 'D' and resid 464 through 494 removed outlier: 3.866A pdb=" N VAL D 468 " --> pdb=" O GLY D 464 " (cutoff:3.500A) Processing helix chain 'D' and resid 497 through 509 Processing helix chain 'D' and resid 514 through 523 removed outlier: 3.505A pdb=" N ARG D 518 " --> pdb=" O GLY D 514 " (cutoff:3.500A) Processing helix chain 'D' and resid 524 through 529 Processing helix chain 'D' and resid 530 through 539 Processing helix chain 'D' and resid 551 through 579 removed outlier: 3.811A pdb=" N ASN D 555 " --> pdb=" O PRO D 551 " (cutoff:3.500A) Proline residue: D 570 - end of helix Processing helix chain 'D' and resid 583 through 589 Processing helix chain 'D' and resid 598 through 604 removed outlier: 3.929A pdb=" N ALA D 602 " --> pdb=" O HIS D 598 " (cutoff:3.500A) Processing helix chain 'D' and resid 610 through 615 removed outlier: 4.030A pdb=" N TRP D 614 " --> pdb=" O GLN D 610 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 74 removed outlier: 3.661A pdb=" N PHE A 65 " --> pdb=" O LYS A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 81 removed outlier: 3.632A pdb=" N VAL A 79 " --> pdb=" O ASP A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 89 Processing helix chain 'A' and resid 90 through 93 Processing helix chain 'A' and resid 94 through 107 removed outlier: 3.914A pdb=" N LEU A 100 " --> pdb=" O ILE A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 120 Processing helix chain 'A' and resid 124 through 128 removed outlier: 3.824A pdb=" N VAL A 127 " --> pdb=" O ALA A 124 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N TRP A 128 " --> pdb=" O ALA A 125 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 124 through 128' Processing helix chain 'A' and resid 131 through 133 No H-bonds generated for 'chain 'A' and resid 131 through 133' Processing helix chain 'A' and resid 134 through 151 removed outlier: 3.764A pdb=" N ILE A 142 " --> pdb=" O GLY A 138 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLY A 149 " --> pdb=" O ALA A 145 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N TYR A 151 " --> pdb=" O TYR A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 166 removed outlier: 3.640A pdb=" N ILE A 156 " --> pdb=" O TYR A 152 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N TYR A 162 " --> pdb=" O TRP A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 219 removed outlier: 4.012A pdb=" N TYR A 214 " --> pdb=" O ALA A 210 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLU A 215 " --> pdb=" O ALA A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 224 Processing helix chain 'A' and resid 234 through 253 Processing helix chain 'A' and resid 255 through 267 removed outlier: 3.762A pdb=" N SER A 259 " --> pdb=" O GLY A 255 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N LYS A 261 " --> pdb=" O LYS A 257 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N TRP A 264 " --> pdb=" O GLY A 260 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ILE A 265 " --> pdb=" O LYS A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 283 removed outlier: 3.557A pdb=" N PHE A 272 " --> pdb=" O THR A 268 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N THR A 283 " --> pdb=" O VAL A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 295 removed outlier: 3.653A pdb=" N GLY A 290 " --> pdb=" O GLY A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 320 removed outlier: 3.511A pdb=" N VAL A 307 " --> pdb=" O LYS A 303 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N ILE A 309 " --> pdb=" O ALA A 305 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N ASP A 310 " --> pdb=" O THR A 306 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLY A 320 " --> pdb=" O PHE A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 331 Processing helix chain 'A' and resid 338 through 372 removed outlier: 3.617A pdb=" N ASP A 342 " --> pdb=" O ASN A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 380 removed outlier: 3.932A pdb=" N VAL A 379 " --> pdb=" O ASN A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 389 removed outlier: 3.722A pdb=" N VAL A 387 " --> pdb=" O GLY A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 398 removed outlier: 3.684A pdb=" N THR A 397 " --> pdb=" O GLU A 393 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU A 398 " --> pdb=" O ALA A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 435 removed outlier: 3.707A pdb=" N TRP A 404 " --> pdb=" O GLY A 400 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N SER A 419 " --> pdb=" O LEU A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 441 removed outlier: 3.816A pdb=" N LYS A 439 " --> pdb=" O PHE A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 456 Processing helix chain 'A' and resid 464 through 494 removed outlier: 3.864A pdb=" N VAL A 468 " --> pdb=" O GLY A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 509 Processing helix chain 'A' and resid 514 through 523 removed outlier: 3.527A pdb=" N ARG A 518 " --> pdb=" O GLY A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 539 Processing helix chain 'A' and resid 551 through 579 removed outlier: 3.809A pdb=" N ASN A 555 " --> pdb=" O PRO A 551 " (cutoff:3.500A) Proline residue: A 570 - end of helix Processing helix chain 'A' and resid 583 through 589 Processing helix chain 'A' and resid 598 through 604 removed outlier: 3.924A pdb=" N ALA A 602 " --> pdb=" O HIS A 598 " (cutoff:3.500A) Processing helix chain 'A' and resid 610 through 615 removed outlier: 4.036A pdb=" N TRP A 614 " --> pdb=" O GLN A 610 " (cutoff:3.500A) 546 hydrogen bonds defined for protein. 1617 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: 2.56 Time building geometry restraints manager: 2.85 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: 2671 1.34 - 1.46: 2605 1.46 - 1.58: 4026 1.58 - 1.70: 2 1.70 - 1.81: 62 Bond restraints: 9366 Sorted by residual: bond pdb=" C01 A1LX5 D 703 " pdb=" N02 A1LX5 D 703 " ideal model delta sigma weight residual 1.444 1.290 0.154 2.00e-02 2.50e+03 5.93e+01 bond pdb=" C01 A1LX5 A 701 " pdb=" N02 A1LX5 A 701 " ideal model delta sigma weight residual 1.444 1.291 0.153 2.00e-02 2.50e+03 5.84e+01 bond pdb=" C07 A1LX5 A 701 " pdb=" N02 A1LX5 A 701 " ideal model delta sigma weight residual 1.444 1.375 0.069 2.00e-02 2.50e+03 1.19e+01 bond pdb=" C07 A1LX5 D 703 " pdb=" N02 A1LX5 D 703 " ideal model delta sigma weight residual 1.444 1.376 0.068 2.00e-02 2.50e+03 1.16e+01 bond pdb=" C05 A1LX5 D 703 " pdb=" C06 A1LX5 D 703 " ideal model delta sigma weight residual 1.391 1.325 0.066 2.00e-02 2.50e+03 1.10e+01 ... (remaining 9361 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.64: 12521 1.64 - 3.27: 222 3.27 - 4.91: 29 4.91 - 6.54: 8 6.54 - 8.18: 2 Bond angle restraints: 12782 Sorted by residual: angle pdb=" C GLY D 106 " pdb=" N MET D 107 " pdb=" CA MET D 107 " ideal model delta sigma weight residual 121.80 113.62 8.18 2.44e+00 1.68e-01 1.12e+01 angle pdb=" C GLY A 106 " pdb=" N MET A 107 " pdb=" CA MET A 107 " ideal model delta sigma weight residual 121.80 113.65 8.15 2.44e+00 1.68e-01 1.12e+01 angle pdb=" N ASP D 546 " pdb=" CA ASP D 546 " pdb=" C ASP D 546 " ideal model delta sigma weight residual 111.11 107.54 3.57 1.20e+00 6.94e-01 8.85e+00 angle pdb=" N ASP A 546 " pdb=" CA ASP A 546 " pdb=" C ASP A 546 " ideal model delta sigma weight residual 111.11 107.59 3.52 1.20e+00 6.94e-01 8.63e+00 angle pdb=" C ASP D 546 " pdb=" CA ASP D 546 " pdb=" CB ASP D 546 " ideal model delta sigma weight residual 110.81 115.42 -4.61 1.60e+00 3.91e-01 8.30e+00 ... (remaining 12777 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.97: 4884 14.97 - 29.93: 238 29.93 - 44.90: 93 44.90 - 59.86: 19 59.86 - 74.83: 8 Dihedral angle restraints: 5242 sinusoidal: 1978 harmonic: 3264 Sorted by residual: dihedral pdb=" CA THR A 179 " pdb=" C THR A 179 " pdb=" N TRP A 180 " pdb=" CA TRP A 180 " ideal model delta harmonic sigma weight residual -180.00 -129.07 -50.93 0 5.00e+00 4.00e-02 1.04e+02 dihedral pdb=" CA THR D 179 " pdb=" C THR D 179 " pdb=" N TRP D 180 " pdb=" CA TRP D 180 " ideal model delta harmonic sigma weight residual 180.00 -129.08 -50.92 0 5.00e+00 4.00e-02 1.04e+02 dihedral pdb=" CA HIS A 178 " pdb=" C HIS A 178 " pdb=" N THR A 179 " pdb=" CA THR A 179 " ideal model delta harmonic sigma weight residual 180.00 149.81 30.19 0 5.00e+00 4.00e-02 3.65e+01 ... (remaining 5239 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 1392 0.093 - 0.185: 26 0.185 - 0.278: 0 0.278 - 0.371: 0 0.371 - 0.464: 2 Chirality restraints: 1420 Sorted by residual: chirality pdb=" C04 A1LX5 D 703 " pdb=" C03 A1LX5 D 703 " pdb=" C05 A1LX5 D 703 " pdb=" C13 A1LX5 D 703 " both_signs ideal model delta sigma weight residual False 2.49 2.96 -0.46 2.00e-01 2.50e+01 5.37e+00 chirality pdb=" C04 A1LX5 A 701 " pdb=" C03 A1LX5 A 701 " pdb=" C05 A1LX5 A 701 " pdb=" C13 A1LX5 A 701 " both_signs ideal model delta sigma weight residual False 2.49 2.95 -0.46 2.00e-01 2.50e+01 5.30e+00 chirality pdb=" CA MET A 107 " pdb=" N MET A 107 " pdb=" C MET A 107 " pdb=" CB MET A 107 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.88e-01 ... (remaining 1417 not shown) Planarity restraints: 1556 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE D 104 " 0.011 2.00e-02 2.50e+03 2.22e-02 4.94e+00 pdb=" C ILE D 104 " -0.038 2.00e-02 2.50e+03 pdb=" O ILE D 104 " 0.014 2.00e-02 2.50e+03 pdb=" N ALA D 105 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 104 " -0.011 2.00e-02 2.50e+03 2.11e-02 4.45e+00 pdb=" C ILE A 104 " 0.036 2.00e-02 2.50e+03 pdb=" O ILE A 104 " -0.014 2.00e-02 2.50e+03 pdb=" N ALA A 105 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 103 " -0.010 2.00e-02 2.50e+03 1.94e-02 3.77e+00 pdb=" C ILE A 103 " 0.034 2.00e-02 2.50e+03 pdb=" O ILE A 103 " -0.013 2.00e-02 2.50e+03 pdb=" N ILE A 104 " -0.011 2.00e-02 2.50e+03 ... (remaining 1553 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 44 2.53 - 3.12: 7168 3.12 - 3.72: 14844 3.72 - 4.31: 20964 4.31 - 4.90: 34263 Nonbonded interactions: 77283 Sorted by model distance: nonbonded pdb=" O GLY A 71 " pdb="NA NA A 702 " model vdw 1.938 2.470 nonbonded pdb=" O GLY D 71 " pdb="NA NA D 701 " model vdw 2.046 2.470 nonbonded pdb=" O ALA A 476 " pdb=" OG SER A 480 " model vdw 2.224 3.040 nonbonded pdb=" O ALA D 476 " pdb=" OG SER D 480 " model vdw 2.228 3.040 nonbonded pdb=" O TRP D 264 " pdb=" OG1 THR D 268 " model vdw 2.267 3.040 ... (remaining 77278 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 53 through 617) selection = (chain 'D' and resid 53 through 617) } 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: 6.120 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: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 23.570 Find NCS groups from input model: 0.380 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6260 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.154 9366 Z= 0.257 Angle : 0.553 8.181 12782 Z= 0.332 Chirality : 0.039 0.464 1420 Planarity : 0.004 0.035 1556 Dihedral : 11.479 74.830 3166 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 5.04 % Allowed : 6.93 % Favored : 88.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.37 % 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 (0.24), residues: 1126 helix: -0.80 (0.17), residues: 746 sheet: None (None), residues: 0 loop : -1.42 (0.33), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 553 HIS 0.001 0.000 HIS D 222 PHE 0.012 0.001 PHE A 362 TYR 0.013 0.001 TYR D 98 ARG 0.001 0.000 ARG D 216 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 278 time to evaluate : 0.899 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 119 TYR cc_start: 0.7341 (t80) cc_final: 0.6938 (t80) REVERT: D 264 TRP cc_start: 0.5833 (m100) cc_final: 0.5394 (m-10) REVERT: D 303 LYS cc_start: 0.7237 (OUTLIER) cc_final: 0.6993 (ptmt) REVERT: D 341 ARG cc_start: 0.7259 (ttp-110) cc_final: 0.6742 (ttm-80) REVERT: D 344 LEU cc_start: 0.7082 (mt) cc_final: 0.6835 (mp) REVERT: D 376 ILE cc_start: 0.8364 (OUTLIER) cc_final: 0.7933 (mt) REVERT: D 507 GLN cc_start: 0.8029 (tt0) cc_final: 0.7709 (tt0) REVERT: D 544 THR cc_start: 0.7020 (p) cc_final: 0.6751 (t) REVERT: D 545 TYR cc_start: 0.6371 (t80) cc_final: 0.5415 (t80) REVERT: A 119 TYR cc_start: 0.7339 (t80) cc_final: 0.6934 (t80) REVERT: A 264 TRP cc_start: 0.5841 (m100) cc_final: 0.5385 (m-10) REVERT: A 341 ARG cc_start: 0.7264 (ttp-110) cc_final: 0.6753 (ttm-80) REVERT: A 344 LEU cc_start: 0.7073 (mt) cc_final: 0.6825 (mp) REVERT: A 376 ILE cc_start: 0.8353 (OUTLIER) cc_final: 0.7951 (mt) REVERT: A 507 GLN cc_start: 0.8028 (tt0) cc_final: 0.7703 (tt0) REVERT: A 544 THR cc_start: 0.7022 (p) cc_final: 0.6769 (t) REVERT: A 545 TYR cc_start: 0.6360 (t80) cc_final: 0.5450 (t80) outliers start: 48 outliers final: 11 residues processed: 313 average time/residue: 0.2008 time to fit residues: 88.0004 Evaluate side-chains 174 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 160 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 173 TRP Chi-restraints excluded: chain D residue 227 ILE Chi-restraints excluded: chain D residue 303 LYS Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain D residue 315 ILE Chi-restraints excluded: chain D residue 376 ILE Chi-restraints excluded: chain D residue 598 HIS Chi-restraints excluded: chain A residue 173 TRP Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 376 ILE Chi-restraints excluded: chain A residue 528 PHE Chi-restraints excluded: chain A residue 598 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.9990 chunk 84 optimal weight: 6.9990 chunk 47 optimal weight: 0.8980 chunk 28 optimal weight: 4.9990 chunk 57 optimal weight: 0.7980 chunk 45 optimal weight: 3.9990 chunk 87 optimal weight: 0.1980 chunk 33 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 chunk 65 optimal weight: 0.8980 chunk 101 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6564 moved from start: 0.2715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9366 Z= 0.192 Angle : 0.581 8.610 12782 Z= 0.292 Chirality : 0.039 0.152 1420 Planarity : 0.004 0.047 1556 Dihedral : 6.437 50.009 1276 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 4.10 % Allowed : 13.87 % Favored : 82.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.37 % 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: -0.24 (0.25), residues: 1126 helix: 0.32 (0.18), residues: 764 sheet: None (None), residues: 0 loop : -1.00 (0.34), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 128 HIS 0.008 0.001 HIS A 370 PHE 0.023 0.002 PHE A 408 TYR 0.016 0.002 TYR D 575 ARG 0.006 0.001 ARG D 81 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 198 time to evaluate : 0.880 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 250 PHE cc_start: 0.7493 (m-10) cc_final: 0.7217 (m-80) REVERT: D 264 TRP cc_start: 0.6114 (m100) cc_final: 0.5270 (m-10) REVERT: D 376 ILE cc_start: 0.8026 (OUTLIER) cc_final: 0.7536 (mt) REVERT: D 585 TRP cc_start: 0.5915 (m100) cc_final: 0.5574 (m100) REVERT: A 250 PHE cc_start: 0.7480 (m-10) cc_final: 0.7198 (m-80) REVERT: A 264 TRP cc_start: 0.6123 (m100) cc_final: 0.5294 (m-10) REVERT: A 376 ILE cc_start: 0.8047 (OUTLIER) cc_final: 0.7600 (mt) REVERT: A 585 TRP cc_start: 0.5920 (m100) cc_final: 0.5590 (m100) outliers start: 39 outliers final: 19 residues processed: 225 average time/residue: 0.1837 time to fit residues: 58.9623 Evaluate side-chains 183 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 162 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 173 TRP Chi-restraints excluded: chain D residue 227 ILE Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain D residue 315 ILE Chi-restraints excluded: chain D residue 364 ILE Chi-restraints excluded: chain D residue 376 ILE Chi-restraints excluded: chain D residue 378 ASP Chi-restraints excluded: chain D residue 437 VAL Chi-restraints excluded: chain D residue 598 HIS Chi-restraints excluded: chain A residue 173 TRP Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 376 ILE Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 528 PHE Chi-restraints excluded: chain A residue 598 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 56 optimal weight: 10.0000 chunk 31 optimal weight: 0.9980 chunk 84 optimal weight: 7.9990 chunk 69 optimal weight: 8.9990 chunk 28 optimal weight: 4.9990 chunk 101 optimal weight: 0.8980 chunk 110 optimal weight: 2.9990 chunk 90 optimal weight: 6.9990 chunk 34 optimal weight: 7.9990 chunk 81 optimal weight: 6.9990 chunk 100 optimal weight: 0.8980 overall best weight: 2.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6842 moved from start: 0.4403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 9366 Z= 0.388 Angle : 0.737 10.843 12782 Z= 0.377 Chirality : 0.046 0.196 1420 Planarity : 0.005 0.052 1556 Dihedral : 6.988 43.542 1272 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 4.52 % Allowed : 13.87 % Favored : 81.62 % 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: -0.28 (0.25), residues: 1126 helix: 0.26 (0.19), residues: 758 sheet: None (None), residues: 0 loop : -0.94 (0.34), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D 80 HIS 0.005 0.001 HIS D 220 PHE 0.032 0.003 PHE D 409 TYR 0.019 0.002 TYR D 271 ARG 0.005 0.001 ARG D 81 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 169 time to evaluate : 0.994 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 133 PHE cc_start: 0.8394 (OUTLIER) cc_final: 0.7334 (m-80) REVERT: D 264 TRP cc_start: 0.6175 (m100) cc_final: 0.5282 (m-10) REVERT: D 298 ASP cc_start: 0.7412 (t70) cc_final: 0.6795 (t0) REVERT: D 376 ILE cc_start: 0.8215 (OUTLIER) cc_final: 0.7688 (mt) REVERT: D 418 ASP cc_start: 0.7554 (OUTLIER) cc_final: 0.7319 (m-30) REVERT: D 585 TRP cc_start: 0.5961 (m100) cc_final: 0.5656 (m100) REVERT: A 264 TRP cc_start: 0.6133 (m100) cc_final: 0.5250 (m-10) REVERT: A 298 ASP cc_start: 0.7423 (t70) cc_final: 0.6811 (t0) REVERT: A 309 ILE cc_start: 0.6839 (OUTLIER) cc_final: 0.6549 (mp) REVERT: A 316 PHE cc_start: 0.7627 (t80) cc_final: 0.7365 (t80) REVERT: A 376 ILE cc_start: 0.8216 (OUTLIER) cc_final: 0.7719 (mt) REVERT: A 418 ASP cc_start: 0.7525 (OUTLIER) cc_final: 0.7307 (m-30) REVERT: A 585 TRP cc_start: 0.5977 (m100) cc_final: 0.5653 (m100) outliers start: 43 outliers final: 25 residues processed: 200 average time/residue: 0.1976 time to fit residues: 58.0994 Evaluate side-chains 176 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 145 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 118 GLN Chi-restraints excluded: chain D residue 133 PHE Chi-restraints excluded: chain D residue 173 TRP Chi-restraints excluded: chain D residue 227 ILE Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 364 ILE Chi-restraints excluded: chain D residue 376 ILE Chi-restraints excluded: chain D residue 378 ASP Chi-restraints excluded: chain D residue 381 THR Chi-restraints excluded: chain D residue 386 LEU Chi-restraints excluded: chain D residue 418 ASP Chi-restraints excluded: chain D residue 437 VAL Chi-restraints excluded: chain D residue 481 ILE Chi-restraints excluded: chain D residue 598 HIS Chi-restraints excluded: chain A residue 118 GLN Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 173 TRP Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 376 ILE Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 418 ASP Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 528 PHE Chi-restraints excluded: chain A residue 598 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 5.9990 chunk 52 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 48 optimal weight: 0.9980 chunk 68 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 108 optimal weight: 0.9990 chunk 53 optimal weight: 6.9990 chunk 96 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6815 moved from start: 0.4478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 9366 Z= 0.277 Angle : 0.632 9.772 12782 Z= 0.326 Chirality : 0.042 0.166 1420 Planarity : 0.005 0.051 1556 Dihedral : 6.275 41.494 1264 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 3.99 % Allowed : 14.60 % Favored : 81.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: 0.02 (0.26), residues: 1126 helix: 0.49 (0.19), residues: 760 sheet: None (None), residues: 0 loop : -0.84 (0.34), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 80 HIS 0.006 0.001 HIS D 372 PHE 0.023 0.002 PHE D 316 TYR 0.017 0.002 TYR A 152 ARG 0.004 0.000 ARG A 81 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 150 time to evaluate : 1.031 Fit side-chains REVERT: D 173 TRP cc_start: 0.6123 (OUTLIER) cc_final: 0.5791 (m-90) REVERT: D 264 TRP cc_start: 0.6083 (m100) cc_final: 0.5134 (m-10) REVERT: D 376 ILE cc_start: 0.8180 (OUTLIER) cc_final: 0.7629 (mt) REVERT: D 585 TRP cc_start: 0.5927 (m100) cc_final: 0.5628 (m100) REVERT: A 133 PHE cc_start: 0.8400 (OUTLIER) cc_final: 0.7430 (m-80) REVERT: A 173 TRP cc_start: 0.6117 (OUTLIER) cc_final: 0.5784 (m-90) REVERT: A 264 TRP cc_start: 0.6098 (m100) cc_final: 0.5151 (m-10) REVERT: A 376 ILE cc_start: 0.8186 (OUTLIER) cc_final: 0.7673 (mt) REVERT: A 585 TRP cc_start: 0.5951 (m100) cc_final: 0.5623 (m100) outliers start: 38 outliers final: 26 residues processed: 176 average time/residue: 0.1875 time to fit residues: 47.8055 Evaluate side-chains 182 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 151 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 173 TRP Chi-restraints excluded: chain D residue 199 HIS Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 242 MET Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 291 ILE Chi-restraints excluded: chain D residue 364 ILE Chi-restraints excluded: chain D residue 376 ILE Chi-restraints excluded: chain D residue 381 THR Chi-restraints excluded: chain D residue 386 LEU Chi-restraints excluded: chain D residue 437 VAL Chi-restraints excluded: chain D residue 481 ILE Chi-restraints excluded: chain D residue 529 LEU Chi-restraints excluded: chain D residue 598 HIS Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 173 TRP Chi-restraints excluded: chain A residue 199 HIS Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 242 MET Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 376 ILE Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 598 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 0.6980 chunk 1 optimal weight: 0.7980 chunk 80 optimal weight: 8.9990 chunk 44 optimal weight: 2.9990 chunk 92 optimal weight: 0.5980 chunk 74 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 55 optimal weight: 0.1980 chunk 97 optimal weight: 0.9990 chunk 27 optimal weight: 0.5980 chunk 36 optimal weight: 0.8980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6730 moved from start: 0.4409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9366 Z= 0.182 Angle : 0.568 8.356 12782 Z= 0.287 Chirality : 0.039 0.154 1420 Planarity : 0.004 0.042 1556 Dihedral : 5.522 38.653 1258 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 3.89 % Allowed : 16.18 % Favored : 79.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: 0.40 (0.26), residues: 1126 helix: 0.84 (0.19), residues: 752 sheet: None (None), residues: 0 loop : -0.80 (0.34), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 80 HIS 0.003 0.001 HIS D 220 PHE 0.017 0.001 PHE D 316 TYR 0.015 0.001 TYR D 152 ARG 0.004 0.000 ARG D 81 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 176 time to evaluate : 0.953 Fit side-chains REVERT: D 173 TRP cc_start: 0.5989 (OUTLIER) cc_final: 0.5135 (m-90) REVERT: D 264 TRP cc_start: 0.6095 (m100) cc_final: 0.5120 (m-10) REVERT: D 298 ASP cc_start: 0.7367 (t70) cc_final: 0.6724 (t0) REVERT: D 342 ASP cc_start: 0.7463 (OUTLIER) cc_final: 0.7200 (t70) REVERT: D 376 ILE cc_start: 0.8110 (OUTLIER) cc_final: 0.7496 (mt) REVERT: D 585 TRP cc_start: 0.5942 (m100) cc_final: 0.5623 (m100) REVERT: A 173 TRP cc_start: 0.5984 (OUTLIER) cc_final: 0.5130 (m-90) REVERT: A 264 TRP cc_start: 0.6066 (m100) cc_final: 0.5111 (m-10) REVERT: A 298 ASP cc_start: 0.7421 (t70) cc_final: 0.6760 (t0) REVERT: A 342 ASP cc_start: 0.7499 (OUTLIER) cc_final: 0.7240 (t70) REVERT: A 376 ILE cc_start: 0.8091 (OUTLIER) cc_final: 0.7589 (mt) REVERT: A 585 TRP cc_start: 0.5963 (m100) cc_final: 0.5617 (m100) outliers start: 37 outliers final: 23 residues processed: 196 average time/residue: 0.2056 time to fit residues: 56.8786 Evaluate side-chains 181 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 152 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 173 TRP Chi-restraints excluded: chain D residue 199 HIS Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 242 MET Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 342 ASP Chi-restraints excluded: chain D residue 376 ILE Chi-restraints excluded: chain D residue 381 THR Chi-restraints excluded: chain D residue 437 VAL Chi-restraints excluded: chain D residue 479 THR Chi-restraints excluded: chain D residue 481 ILE Chi-restraints excluded: chain D residue 529 LEU Chi-restraints excluded: chain D residue 598 HIS Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 173 TRP Chi-restraints excluded: chain A residue 199 HIS Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 342 ASP Chi-restraints excluded: chain A residue 376 ILE Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 598 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 26 optimal weight: 0.4980 chunk 108 optimal weight: 0.8980 chunk 89 optimal weight: 5.9990 chunk 50 optimal weight: 5.9990 chunk 9 optimal weight: 0.5980 chunk 35 optimal weight: 3.9990 chunk 56 optimal weight: 10.0000 chunk 104 optimal weight: 3.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6753 moved from start: 0.4552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9366 Z= 0.204 Angle : 0.580 10.425 12782 Z= 0.290 Chirality : 0.039 0.140 1420 Planarity : 0.004 0.041 1556 Dihedral : 5.515 38.933 1258 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 4.31 % Allowed : 16.39 % Favored : 79.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: 0.56 (0.26), residues: 1126 helix: 0.95 (0.19), residues: 752 sheet: None (None), residues: 0 loop : -0.70 (0.35), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 80 HIS 0.004 0.001 HIS D 220 PHE 0.015 0.001 PHE A 362 TYR 0.016 0.001 TYR D 152 ARG 0.003 0.000 ARG A 81 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 148 time to evaluate : 1.097 Fit side-chains revert: symmetry clash REVERT: D 118 GLN cc_start: 0.7603 (OUTLIER) cc_final: 0.7142 (tt0) REVERT: D 173 TRP cc_start: 0.6061 (OUTLIER) cc_final: 0.5234 (m-90) REVERT: D 264 TRP cc_start: 0.6090 (m100) cc_final: 0.5102 (m-10) REVERT: D 298 ASP cc_start: 0.7321 (t70) cc_final: 0.6711 (t0) REVERT: D 376 ILE cc_start: 0.8102 (OUTLIER) cc_final: 0.7503 (mt) REVERT: A 118 GLN cc_start: 0.7601 (OUTLIER) cc_final: 0.7250 (tt0) REVERT: A 173 TRP cc_start: 0.6048 (OUTLIER) cc_final: 0.5217 (m-90) REVERT: A 264 TRP cc_start: 0.6064 (m100) cc_final: 0.5854 (t60) REVERT: A 298 ASP cc_start: 0.7395 (t70) cc_final: 0.6754 (t0) REVERT: A 376 ILE cc_start: 0.8081 (OUTLIER) cc_final: 0.7480 (mt) REVERT: A 575 TYR cc_start: 0.7294 (t80) cc_final: 0.7075 (t80) outliers start: 41 outliers final: 31 residues processed: 171 average time/residue: 0.1964 time to fit residues: 48.3436 Evaluate side-chains 187 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 150 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 118 GLN Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 173 TRP Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 199 HIS Chi-restraints excluded: chain D residue 227 ILE Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 242 MET Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 265 ILE Chi-restraints excluded: chain D residue 364 ILE Chi-restraints excluded: chain D residue 376 ILE Chi-restraints excluded: chain D residue 381 THR Chi-restraints excluded: chain D residue 386 LEU Chi-restraints excluded: chain D residue 437 VAL Chi-restraints excluded: chain D residue 479 THR Chi-restraints excluded: chain D residue 481 ILE Chi-restraints excluded: chain D residue 529 LEU Chi-restraints excluded: chain D residue 598 HIS Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 118 GLN Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 173 TRP Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 199 HIS Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 242 MET Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 376 ILE Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 598 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 0.5980 chunk 61 optimal weight: 0.6980 chunk 79 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 60 optimal weight: 0.6980 chunk 107 optimal weight: 2.9990 chunk 67 optimal weight: 0.6980 chunk 65 optimal weight: 0.6980 chunk 49 optimal weight: 0.0970 chunk 66 optimal weight: 0.5980 chunk 43 optimal weight: 2.9990 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6713 moved from start: 0.4525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9366 Z= 0.174 Angle : 0.555 9.710 12782 Z= 0.276 Chirality : 0.038 0.150 1420 Planarity : 0.004 0.037 1556 Dihedral : 5.324 40.042 1258 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 3.89 % Allowed : 17.33 % Favored : 78.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: 0.74 (0.26), residues: 1126 helix: 1.11 (0.19), residues: 752 sheet: None (None), residues: 0 loop : -0.68 (0.35), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 80 HIS 0.003 0.001 HIS A 220 PHE 0.024 0.001 PHE D 540 TYR 0.014 0.001 TYR D 152 ARG 0.003 0.000 ARG A 81 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 170 time to evaluate : 0.927 Fit side-chains REVERT: D 234 GLN cc_start: 0.6783 (tp40) cc_final: 0.6029 (tm-30) REVERT: D 264 TRP cc_start: 0.6074 (m100) cc_final: 0.5870 (t60) REVERT: D 298 ASP cc_start: 0.7298 (t70) cc_final: 0.6726 (t0) REVERT: D 376 ILE cc_start: 0.8082 (OUTLIER) cc_final: 0.7494 (mt) REVERT: A 376 ILE cc_start: 0.8036 (OUTLIER) cc_final: 0.7448 (mt) outliers start: 37 outliers final: 29 residues processed: 188 average time/residue: 0.1880 time to fit residues: 51.0312 Evaluate side-chains 192 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 161 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 199 HIS Chi-restraints excluded: chain D residue 227 ILE Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 265 ILE Chi-restraints excluded: chain D residue 364 ILE Chi-restraints excluded: chain D residue 376 ILE Chi-restraints excluded: chain D residue 381 THR Chi-restraints excluded: chain D residue 386 LEU Chi-restraints excluded: chain D residue 437 VAL Chi-restraints excluded: chain D residue 479 THR Chi-restraints excluded: chain D residue 481 ILE Chi-restraints excluded: chain D residue 529 LEU Chi-restraints excluded: chain D residue 598 HIS Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 199 HIS Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 242 MET Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 376 ILE Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 598 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 chunk 21 optimal weight: 0.2980 chunk 20 optimal weight: 5.9990 chunk 68 optimal weight: 3.9990 chunk 73 optimal weight: 0.7980 chunk 53 optimal weight: 3.9990 chunk 10 optimal weight: 0.5980 chunk 84 optimal weight: 6.9990 chunk 98 optimal weight: 0.7980 chunk 103 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6754 moved from start: 0.4710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9366 Z= 0.215 Angle : 0.596 8.442 12782 Z= 0.297 Chirality : 0.040 0.136 1420 Planarity : 0.004 0.039 1556 Dihedral : 5.221 39.437 1254 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 4.20 % Allowed : 17.54 % Favored : 78.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: 0.80 (0.26), residues: 1126 helix: 1.11 (0.19), residues: 752 sheet: None (None), residues: 0 loop : -0.56 (0.34), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 80 HIS 0.004 0.001 HIS D 220 PHE 0.030 0.002 PHE D 540 TYR 0.017 0.001 TYR A 111 ARG 0.003 0.000 ARG A 81 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 160 time to evaluate : 0.952 Fit side-chains REVERT: D 118 GLN cc_start: 0.7622 (OUTLIER) cc_final: 0.7136 (tt0) REVERT: D 119 TYR cc_start: 0.7436 (t80) cc_final: 0.7052 (t80) REVERT: D 264 TRP cc_start: 0.6066 (m100) cc_final: 0.5845 (t60) REVERT: D 298 ASP cc_start: 0.7316 (t70) cc_final: 0.6739 (t0) REVERT: D 376 ILE cc_start: 0.8106 (OUTLIER) cc_final: 0.7559 (mt) REVERT: A 122 GLU cc_start: 0.6539 (OUTLIER) cc_final: 0.6005 (tp30) REVERT: A 264 TRP cc_start: 0.6677 (t60) cc_final: 0.6472 (t60) REVERT: A 298 ASP cc_start: 0.7393 (t70) cc_final: 0.6649 (t0) REVERT: A 376 ILE cc_start: 0.8045 (OUTLIER) cc_final: 0.7482 (mt) outliers start: 40 outliers final: 30 residues processed: 177 average time/residue: 0.2000 time to fit residues: 50.6612 Evaluate side-chains 188 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 154 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 118 GLN Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 191 LEU Chi-restraints excluded: chain D residue 199 HIS Chi-restraints excluded: chain D residue 212 GLU Chi-restraints excluded: chain D residue 227 ILE Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 265 ILE Chi-restraints excluded: chain D residue 364 ILE Chi-restraints excluded: chain D residue 376 ILE Chi-restraints excluded: chain D residue 381 THR Chi-restraints excluded: chain D residue 386 LEU Chi-restraints excluded: chain D residue 437 VAL Chi-restraints excluded: chain D residue 479 THR Chi-restraints excluded: chain D residue 481 ILE Chi-restraints excluded: chain D residue 529 LEU Chi-restraints excluded: chain D residue 598 HIS Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 199 HIS Chi-restraints excluded: chain A residue 212 GLU Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 242 MET Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 376 ILE Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 598 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 2.9990 chunk 100 optimal weight: 0.9990 chunk 103 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 90 optimal weight: 0.7980 chunk 95 optimal weight: 0.5980 chunk 66 optimal weight: 0.8980 chunk 106 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6751 moved from start: 0.4740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9366 Z= 0.211 Angle : 0.598 8.542 12782 Z= 0.298 Chirality : 0.040 0.139 1420 Planarity : 0.004 0.038 1556 Dihedral : 5.259 39.343 1254 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 3.89 % Allowed : 17.65 % Favored : 78.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: 0.84 (0.26), residues: 1126 helix: 1.14 (0.19), residues: 754 sheet: None (None), residues: 0 loop : -0.53 (0.35), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 80 HIS 0.005 0.001 HIS D 220 PHE 0.024 0.002 PHE D 540 TYR 0.017 0.001 TYR A 111 ARG 0.003 0.000 ARG A 81 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 160 time to evaluate : 0.887 Fit side-chains REVERT: D 122 GLU cc_start: 0.6277 (tp30) cc_final: 0.5894 (tp30) REVERT: D 264 TRP cc_start: 0.6101 (m100) cc_final: 0.5891 (t60) REVERT: D 316 PHE cc_start: 0.7587 (t80) cc_final: 0.6386 (m-80) REVERT: D 376 ILE cc_start: 0.8091 (OUTLIER) cc_final: 0.7483 (mt) REVERT: A 122 GLU cc_start: 0.6289 (OUTLIER) cc_final: 0.5916 (tp30) REVERT: A 298 ASP cc_start: 0.7383 (t70) cc_final: 0.6651 (t0) REVERT: A 376 ILE cc_start: 0.8032 (OUTLIER) cc_final: 0.7473 (mt) outliers start: 37 outliers final: 29 residues processed: 178 average time/residue: 0.1957 time to fit residues: 49.5825 Evaluate side-chains 192 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 160 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 199 HIS Chi-restraints excluded: chain D residue 212 GLU Chi-restraints excluded: chain D residue 227 ILE Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 265 ILE Chi-restraints excluded: chain D residue 364 ILE Chi-restraints excluded: chain D residue 376 ILE Chi-restraints excluded: chain D residue 381 THR Chi-restraints excluded: chain D residue 386 LEU Chi-restraints excluded: chain D residue 437 VAL Chi-restraints excluded: chain D residue 479 THR Chi-restraints excluded: chain D residue 481 ILE Chi-restraints excluded: chain D residue 529 LEU Chi-restraints excluded: chain D residue 598 HIS Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 199 HIS Chi-restraints excluded: chain A residue 212 GLU Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 242 MET Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 376 ILE Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 598 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 0.9980 chunk 50 optimal weight: 0.8980 chunk 73 optimal weight: 1.9990 chunk 111 optimal weight: 3.9990 chunk 102 optimal weight: 0.7980 chunk 88 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 chunk 68 optimal weight: 0.9980 chunk 54 optimal weight: 0.3980 chunk 70 optimal weight: 0.0470 chunk 94 optimal weight: 0.9990 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6716 moved from start: 0.4722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9366 Z= 0.184 Angle : 0.582 8.608 12782 Z= 0.289 Chirality : 0.039 0.143 1420 Planarity : 0.004 0.035 1556 Dihedral : 5.117 39.249 1254 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 3.26 % Allowed : 18.28 % Favored : 78.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: 0.78 (0.26), residues: 1126 helix: 1.08 (0.19), residues: 768 sheet: None (None), residues: 0 loop : -0.58 (0.36), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 80 HIS 0.003 0.001 HIS D 220 PHE 0.021 0.001 PHE D 540 TYR 0.014 0.001 TYR D 152 ARG 0.003 0.000 ARG A 81 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 164 time to evaluate : 0.990 Fit side-chains REVERT: D 298 ASP cc_start: 0.7207 (t70) cc_final: 0.6505 (t0) REVERT: D 316 PHE cc_start: 0.7502 (t80) cc_final: 0.6537 (m-80) REVERT: D 376 ILE cc_start: 0.8022 (OUTLIER) cc_final: 0.7514 (mt) REVERT: A 119 TYR cc_start: 0.7402 (t80) cc_final: 0.7020 (t80) REVERT: A 298 ASP cc_start: 0.7303 (t70) cc_final: 0.6551 (t0) REVERT: A 376 ILE cc_start: 0.7988 (OUTLIER) cc_final: 0.7460 (mt) outliers start: 31 outliers final: 27 residues processed: 180 average time/residue: 0.1965 time to fit residues: 50.9095 Evaluate side-chains 176 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 147 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 199 HIS Chi-restraints excluded: chain D residue 227 ILE Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 265 ILE Chi-restraints excluded: chain D residue 364 ILE Chi-restraints excluded: chain D residue 376 ILE Chi-restraints excluded: chain D residue 381 THR Chi-restraints excluded: chain D residue 386 LEU Chi-restraints excluded: chain D residue 437 VAL Chi-restraints excluded: chain D residue 479 THR Chi-restraints excluded: chain D residue 481 ILE Chi-restraints excluded: chain D residue 529 LEU Chi-restraints excluded: chain D residue 598 HIS Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 199 HIS Chi-restraints excluded: chain A residue 212 GLU Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 376 ILE Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 598 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 0.9980 chunk 81 optimal weight: 0.9990 chunk 13 optimal weight: 9.9990 chunk 24 optimal weight: 8.9990 chunk 88 optimal weight: 5.9990 chunk 37 optimal weight: 0.9990 chunk 91 optimal weight: 0.5980 chunk 11 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.177469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.151307 restraints weight = 11284.313| |-----------------------------------------------------------------------------| r_work (start): 0.3738 rms_B_bonded: 1.64 r_work: 0.3636 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3512 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.4908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9366 Z= 0.244 Angle : 0.623 9.086 12782 Z= 0.312 Chirality : 0.041 0.159 1420 Planarity : 0.005 0.037 1556 Dihedral : 5.352 38.645 1254 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 3.78 % Allowed : 17.96 % Favored : 78.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: 0.81 (0.26), residues: 1126 helix: 1.12 (0.19), residues: 754 sheet: None (None), residues: 0 loop : -0.56 (0.35), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 80 HIS 0.005 0.001 HIS D 220 PHE 0.022 0.002 PHE D 540 TYR 0.017 0.001 TYR A 111 ARG 0.003 0.000 ARG A 81 Origin is already at (0, 0, 0), no shifts will be applied Model does not fit in PDB format. =============================================================================== Job complete usr+sys time: 2133.84 seconds wall clock time: 39 minutes 50.52 seconds (2390.52 seconds total)