Starting phenix.real_space_refine on Sat Aug 3 22:25:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y91_39066/08_2024/8y91_39066.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y91_39066/08_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_39066/08_2024/8y91_39066.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y91_39066/08_2024/8y91_39066.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y91_39066/08_2024/8y91_39066.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y91_39066/08_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 Residue "D ARG 81": "NH1" <-> "NH2" Residue "D GLU 223": "OE1" <-> "OE2" Residue "D GLU 377": "OE1" <-> "OE2" Residue "A ARG 81": "NH1" <-> "NH2" Residue "A GLU 223": "OE1" <-> "OE2" Residue "A GLU 377": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 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: 5.56, per 1000 atoms: 0.61 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.15 Conformation dependent library (CDL) restraints added in 2.2 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: 0.93 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: 2.68 Time building geometry restraints manager: 5.46 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: 100.65 - 107.33: 314 107.33 - 114.01: 5180 114.01 - 120.69: 4195 120.69 - 127.36: 2952 127.36 - 134.04: 141 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: 4876 14.97 - 29.93: 238 29.93 - 44.90: 93 44.90 - 59.86: 19 59.86 - 74.83: 8 Dihedral angle restraints: 5234 sinusoidal: 1970 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 5231 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: 3.100 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: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 30.910 Find NCS groups from input model: 0.410 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:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.680 ------------------------------------------------------------------------------- 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 : 11.488 74.830 3158 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 : 1.019 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: 0.1997 time to fit residues: 86.9403 Evaluate side-chains 174 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 160 time to evaluate : 0.976 ------------------------------------------------------------------------------- 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: 0.6561 moved from start: 0.2697 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 : 0.577 8.413 12782 Z= 0.290 Chirality : 0.039 0.153 1420 Planarity : 0.004 0.047 1556 Dihedral : 6.395 50.106 1268 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 3.89 % Allowed : 14.08 % 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 (0.19), residues: 764 sheet: None (None), residues: 0 loop : -1.01 (0.34), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 128 HIS 0.008 0.001 HIS A 370 PHE 0.021 0.002 PHE A 94 TYR 0.016 0.002 TYR D 575 ARG 0.005 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 234 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 197 time to evaluate : 0.977 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 250 PHE cc_start: 0.7491 (m-10) cc_final: 0.7215 (m-80) REVERT: D 264 TRP cc_start: 0.6110 (m100) cc_final: 0.5270 (m-10) REVERT: D 376 ILE cc_start: 0.8013 (OUTLIER) cc_final: 0.7540 (mt) REVERT: D 585 TRP cc_start: 0.5913 (m100) cc_final: 0.5572 (m100) REVERT: A 250 PHE cc_start: 0.7484 (m-10) cc_final: 0.7203 (m-80) REVERT: A 264 TRP cc_start: 0.6122 (m100) cc_final: 0.5295 (m-10) REVERT: A 376 ILE cc_start: 0.8034 (OUTLIER) cc_final: 0.7594 (mt) REVERT: A 585 TRP cc_start: 0.5918 (m100) cc_final: 0.5589 (m100) outliers start: 37 outliers final: 19 residues processed: 222 average time/residue: 0.1857 time to fit residues: 58.7404 Evaluate side-chains 183 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 162 time to evaluate : 0.949 ------------------------------------------------------------------------------- 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: 3.9990 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: 0.0060 chunk 90 optimal weight: 6.9990 chunk 34 optimal weight: 0.7980 chunk 81 optimal weight: 0.9990 chunk 100 optimal weight: 0.9990 overall best weight: 0.7400 ------------------------------------------------------------------------------- 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: 0.6642 moved from start: 0.3315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9366 Z= 0.195 Angle : 0.577 9.133 12782 Z= 0.289 Chirality : 0.039 0.135 1420 Planarity : 0.004 0.061 1556 Dihedral : 6.158 47.660 1264 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 3.78 % Allowed : 14.71 % Favored : 81.51 % 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: 0.27 (0.25), residues: 1126 helix: 0.69 (0.19), residues: 762 sheet: None (None), residues: 0 loop : -0.76 (0.35), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 80 HIS 0.005 0.001 HIS A 370 PHE 0.020 0.002 PHE A 540 TYR 0.016 0.001 TYR A 152 ARG 0.005 0.000 ARG A 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 209 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 173 time to evaluate : 0.995 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 264 TRP cc_start: 0.6065 (m100) cc_final: 0.5224 (m-10) REVERT: D 298 ASP cc_start: 0.7354 (t70) cc_final: 0.6864 (t0) REVERT: D 309 ILE cc_start: 0.6811 (OUTLIER) cc_final: 0.6423 (mp) REVERT: D 376 ILE cc_start: 0.8079 (OUTLIER) cc_final: 0.7520 (mt) REVERT: D 585 TRP cc_start: 0.5859 (m100) cc_final: 0.5603 (m100) REVERT: A 264 TRP cc_start: 0.6095 (m100) cc_final: 0.5254 (m-10) REVERT: A 298 ASP cc_start: 0.7396 (t70) cc_final: 0.6866 (t0) REVERT: A 376 ILE cc_start: 0.8093 (OUTLIER) cc_final: 0.7577 (mt) REVERT: A 585 TRP cc_start: 0.5875 (m100) cc_final: 0.5607 (m100) outliers start: 36 outliers final: 18 residues processed: 199 average time/residue: 0.1933 time to fit residues: 54.7218 Evaluate side-chains 175 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 154 time to evaluate : 0.992 ------------------------------------------------------------------------------- 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 247 VAL Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain D residue 364 ILE Chi-restraints excluded: chain D residue 376 ILE 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 173 TRP 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 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 437 VAL 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: 1.9990 chunk 52 optimal weight: 0.6980 chunk 11 optimal weight: 2.9990 chunk 48 optimal weight: 0.6980 chunk 68 optimal weight: 3.9990 chunk 102 optimal weight: 1.9990 chunk 108 optimal weight: 0.7980 chunk 53 optimal weight: 6.9990 chunk 96 optimal weight: 0.8980 chunk 29 optimal weight: 0.8980 chunk 90 optimal weight: 5.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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: 0.6683 moved from start: 0.3769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9366 Z= 0.198 Angle : 0.563 8.139 12782 Z= 0.285 Chirality : 0.039 0.137 1420 Planarity : 0.004 0.037 1556 Dihedral : 5.958 45.538 1260 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 3.68 % Allowed : 15.13 % Favored : 81.20 % 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: 0.39 (0.26), residues: 1126 helix: 0.80 (0.19), residues: 764 sheet: None (None), residues: 0 loop : -0.78 (0.34), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 80 HIS 0.008 0.001 HIS A 372 PHE 0.018 0.002 PHE D 540 TYR 0.016 0.001 TYR A 152 ARG 0.005 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 211 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 176 time to evaluate : 1.001 Fit side-chains revert: symmetry clash REVERT: D 264 TRP cc_start: 0.6084 (m100) cc_final: 0.5234 (m-10) REVERT: D 309 ILE cc_start: 0.6853 (OUTLIER) cc_final: 0.6507 (mp) REVERT: D 376 ILE cc_start: 0.8100 (OUTLIER) cc_final: 0.7519 (mt) REVERT: D 585 TRP cc_start: 0.5874 (m100) cc_final: 0.5592 (m100) REVERT: A 264 TRP cc_start: 0.6088 (m100) cc_final: 0.5212 (m-10) REVERT: A 341 ARG cc_start: 0.7365 (ttp-110) cc_final: 0.7161 (ttp80) REVERT: A 376 ILE cc_start: 0.8064 (OUTLIER) cc_final: 0.7583 (mt) REVERT: A 585 TRP cc_start: 0.5892 (m100) cc_final: 0.5590 (m100) outliers start: 35 outliers final: 25 residues processed: 202 average time/residue: 0.1980 time to fit residues: 56.7215 Evaluate side-chains 180 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 152 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 173 TRP 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 309 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 598 HIS 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 80 optimal weight: 9.9990 chunk 44 optimal weight: 1.9990 chunk 92 optimal weight: 0.8980 chunk 74 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 55 optimal weight: 9.9990 chunk 97 optimal weight: 2.9990 chunk 27 optimal weight: 0.5980 chunk 36 optimal weight: 0.7980 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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: 0.6750 moved from start: 0.4222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9366 Z= 0.234 Angle : 0.588 8.595 12782 Z= 0.299 Chirality : 0.040 0.139 1420 Planarity : 0.004 0.038 1556 Dihedral : 6.036 42.878 1260 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 3.89 % Allowed : 15.55 % Favored : 80.57 % 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: 0.52 (0.26), residues: 1126 helix: 0.96 (0.19), residues: 746 sheet: None (None), residues: 0 loop : -0.79 (0.33), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 80 HIS 0.005 0.001 HIS A 220 PHE 0.021 0.002 PHE A 213 TYR 0.017 0.001 TYR A 152 ARG 0.005 0.000 ARG A 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 186 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 149 time to evaluate : 1.054 Fit side-chains REVERT: D 264 TRP cc_start: 0.6129 (m100) cc_final: 0.5168 (m-10) REVERT: D 298 ASP cc_start: 0.7305 (t70) cc_final: 0.6680 (t0) REVERT: D 309 ILE cc_start: 0.6816 (OUTLIER) cc_final: 0.6589 (mp) REVERT: D 376 ILE cc_start: 0.8135 (OUTLIER) cc_final: 0.7495 (mt) REVERT: D 585 TRP cc_start: 0.5894 (m100) cc_final: 0.5596 (m100) REVERT: A 173 TRP cc_start: 0.6062 (OUTLIER) cc_final: 0.5655 (m-90) REVERT: A 264 TRP cc_start: 0.6136 (m100) cc_final: 0.5167 (m-10) REVERT: A 298 ASP cc_start: 0.7306 (t70) cc_final: 0.6651 (t0) REVERT: A 309 ILE cc_start: 0.6829 (OUTLIER) cc_final: 0.6555 (mp) REVERT: A 341 ARG cc_start: 0.7154 (ttp-110) cc_final: 0.6583 (ttm-80) REVERT: A 376 ILE cc_start: 0.8113 (OUTLIER) cc_final: 0.7567 (mt) REVERT: A 585 TRP cc_start: 0.5962 (m100) cc_final: 0.5632 (m100) outliers start: 37 outliers final: 28 residues processed: 175 average time/residue: 0.1976 time to fit residues: 48.9509 Evaluate side-chains 181 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 148 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 227 ILE Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 309 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 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 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 437 VAL Chi-restraints excluded: chain A residue 479 THR 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 2.9990 chunk 21 optimal weight: 0.2980 chunk 63 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 chunk 89 optimal weight: 5.9990 chunk 50 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 56 optimal weight: 10.0000 chunk 104 optimal weight: 4.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- 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: 0.6827 moved from start: 0.4706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 9366 Z= 0.311 Angle : 0.646 9.453 12782 Z= 0.329 Chirality : 0.043 0.165 1420 Planarity : 0.005 0.044 1556 Dihedral : 6.247 40.788 1260 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 5.04 % Allowed : 15.34 % Favored : 79.62 % 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: 0.26 (0.25), residues: 1126 helix: 0.69 (0.19), residues: 762 sheet: None (None), residues: 0 loop : -0.79 (0.33), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 80 HIS 0.006 0.001 HIS A 220 PHE 0.025 0.002 PHE A 409 TYR 0.020 0.002 TYR A 111 ARG 0.004 0.001 ARG D 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 201 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 153 time to evaluate : 1.054 Fit side-chains REVERT: D 133 PHE cc_start: 0.8451 (OUTLIER) cc_final: 0.7532 (m-80) REVERT: D 173 TRP cc_start: 0.6203 (OUTLIER) cc_final: 0.5458 (m-90) REVERT: D 264 TRP cc_start: 0.6188 (m100) cc_final: 0.5172 (m-10) REVERT: D 309 ILE cc_start: 0.6913 (OUTLIER) cc_final: 0.6540 (mp) REVERT: D 376 ILE cc_start: 0.8192 (OUTLIER) cc_final: 0.7553 (mt) REVERT: A 133 PHE cc_start: 0.8429 (OUTLIER) cc_final: 0.7542 (m-80) REVERT: A 173 TRP cc_start: 0.6221 (OUTLIER) cc_final: 0.5610 (m-90) REVERT: A 264 TRP cc_start: 0.6163 (m100) cc_final: 0.5915 (t60) REVERT: A 341 ARG cc_start: 0.7143 (ttp-110) cc_final: 0.6486 (ttm-80) REVERT: A 376 ILE cc_start: 0.8142 (OUTLIER) cc_final: 0.7621 (mt) outliers start: 48 outliers final: 32 residues processed: 184 average time/residue: 0.1928 time to fit residues: 50.9185 Evaluate side-chains 183 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 144 time to evaluate : 1.102 ------------------------------------------------------------------------------- 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 133 PHE 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 309 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 544 THR Chi-restraints excluded: chain D residue 598 HIS Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 173 TRP Chi-restraints excluded: chain A residue 191 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 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 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: 0.8980 chunk 61 optimal weight: 0.6980 chunk 79 optimal weight: 3.9990 chunk 91 optimal weight: 0.9990 chunk 60 optimal weight: 0.2980 chunk 107 optimal weight: 0.9990 chunk 67 optimal weight: 4.9990 chunk 65 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 66 optimal weight: 0.6980 chunk 43 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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: 0.6746 moved from start: 0.4563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 9366 Z= 0.200 Angle : 0.596 12.606 12782 Z= 0.295 Chirality : 0.039 0.143 1420 Planarity : 0.004 0.038 1556 Dihedral : 5.826 40.087 1256 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 3.99 % Allowed : 17.02 % Favored : 78.99 % 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: 0.52 (0.26), residues: 1126 helix: 0.91 (0.19), residues: 750 sheet: None (None), residues: 0 loop : -0.70 (0.33), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 80 HIS 0.004 0.001 HIS D 220 PHE 0.018 0.002 PHE D 316 TYR 0.015 0.001 TYR D 152 ARG 0.004 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 192 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 154 time to evaluate : 1.090 Fit side-chains REVERT: D 173 TRP cc_start: 0.6082 (OUTLIER) cc_final: 0.5266 (m-90) REVERT: D 309 ILE cc_start: 0.6889 (OUTLIER) cc_final: 0.6510 (mp) REVERT: D 376 ILE cc_start: 0.8142 (OUTLIER) cc_final: 0.7470 (mt) REVERT: A 122 GLU cc_start: 0.6350 (tp30) cc_final: 0.5932 (tp30) REVERT: A 173 TRP cc_start: 0.6059 (OUTLIER) cc_final: 0.5243 (m-90) REVERT: A 264 TRP cc_start: 0.6092 (m100) cc_final: 0.5877 (t60) REVERT: A 298 ASP cc_start: 0.7388 (t70) cc_final: 0.6661 (t0) REVERT: A 376 ILE cc_start: 0.8085 (OUTLIER) cc_final: 0.7544 (mt) outliers start: 38 outliers final: 31 residues processed: 174 average time/residue: 0.1870 time to fit residues: 46.3071 Evaluate side-chains 187 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 151 time to evaluate : 0.923 ------------------------------------------------------------------------------- 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 190 LEU Chi-restraints excluded: chain D residue 191 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 309 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 173 TRP Chi-restraints excluded: chain A residue 191 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 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 544 THR 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: 7.9990 chunk 21 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 68 optimal weight: 0.4980 chunk 73 optimal weight: 0.0270 chunk 53 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 chunk 84 optimal weight: 2.9990 chunk 98 optimal weight: 0.5980 chunk 103 optimal weight: 0.2980 overall best weight: 0.4840 ------------------------------------------------------------------------------- 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: 0.6702 moved from start: 0.4547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9366 Z= 0.176 Angle : 0.587 12.338 12782 Z= 0.285 Chirality : 0.038 0.126 1420 Planarity : 0.004 0.034 1556 Dihedral : 5.653 40.067 1256 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 3.26 % Allowed : 18.38 % Favored : 78.36 % 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: 1.13 (0.19), residues: 748 sheet: None (None), residues: 0 loop : -0.61 (0.33), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 404 HIS 0.003 0.001 HIS A 220 PHE 0.016 0.001 PHE D 511 TYR 0.014 0.001 TYR A 111 ARG 0.005 0.000 ARG A 341 *********************** 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 201 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 170 time to evaluate : 0.975 Fit side-chains REVERT: D 111 TYR cc_start: 0.7856 (t80) cc_final: 0.7582 (t80) REVERT: D 173 TRP cc_start: 0.6119 (OUTLIER) cc_final: 0.5314 (m-90) REVERT: D 298 ASP cc_start: 0.7247 (t70) cc_final: 0.6512 (t0) REVERT: D 309 ILE cc_start: 0.6716 (OUTLIER) cc_final: 0.6491 (mp) REVERT: D 376 ILE cc_start: 0.8115 (OUTLIER) cc_final: 0.7452 (mt) REVERT: A 111 TYR cc_start: 0.7888 (t80) cc_final: 0.7584 (t80) REVERT: A 173 TRP cc_start: 0.6115 (OUTLIER) cc_final: 0.5300 (m-90) REVERT: A 264 TRP cc_start: 0.6054 (m100) cc_final: 0.5836 (t60) REVERT: A 298 ASP cc_start: 0.7305 (t70) cc_final: 0.6599 (t0) REVERT: A 376 ILE cc_start: 0.8040 (OUTLIER) cc_final: 0.7507 (mt) outliers start: 31 outliers final: 23 residues processed: 186 average time/residue: 0.1869 time to fit residues: 49.9563 Evaluate side-chains 188 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 160 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 191 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 309 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.9990 chunk 100 optimal weight: 0.0770 chunk 103 optimal weight: 0.9980 chunk 60 optimal weight: 0.4980 chunk 43 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 90 optimal weight: 0.7980 chunk 95 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 chunk 106 optimal weight: 2.9990 overall best weight: 0.6538 ------------------------------------------------------------------------------- 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: 0.6715 moved from start: 0.4594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9366 Z= 0.190 Angle : 0.598 13.051 12782 Z= 0.293 Chirality : 0.039 0.132 1420 Planarity : 0.004 0.033 1556 Dihedral : 5.666 39.743 1256 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 3.47 % Allowed : 18.17 % Favored : 78.36 % 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: 0.86 (0.26), residues: 1126 helix: 1.20 (0.19), residues: 748 sheet: None (None), residues: 0 loop : -0.61 (0.33), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 80 HIS 0.004 0.001 HIS D 220 PHE 0.015 0.001 PHE D 511 TYR 0.015 0.001 TYR A 152 ARG 0.004 0.000 ARG A 341 *********************** 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 192 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 159 time to evaluate : 1.020 Fit side-chains REVERT: D 111 TYR cc_start: 0.7864 (t80) cc_final: 0.7581 (t80) REVERT: D 298 ASP cc_start: 0.7269 (t70) cc_final: 0.6541 (t0) REVERT: D 309 ILE cc_start: 0.6743 (OUTLIER) cc_final: 0.6514 (mp) REVERT: D 376 ILE cc_start: 0.8108 (OUTLIER) cc_final: 0.7478 (mt) REVERT: A 111 TYR cc_start: 0.7875 (t80) cc_final: 0.7536 (t80) REVERT: A 264 TRP cc_start: 0.6078 (m100) cc_final: 0.5859 (t60) REVERT: A 298 ASP cc_start: 0.7286 (t70) cc_final: 0.6572 (t0) REVERT: A 376 ILE cc_start: 0.8027 (OUTLIER) cc_final: 0.7487 (mt) outliers start: 33 outliers final: 27 residues processed: 177 average time/residue: 0.1840 time to fit residues: 47.0772 Evaluate side-chains 182 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 152 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 191 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 309 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 191 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 247 VAL Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 368 MET 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 chunk 73 optimal weight: 0.7980 chunk 111 optimal weight: 8.9990 chunk 102 optimal weight: 0.6980 chunk 88 optimal weight: 5.9990 chunk 9 optimal weight: 1.9990 chunk 68 optimal weight: 0.3980 chunk 54 optimal weight: 0.6980 chunk 70 optimal weight: 0.7980 chunk 94 optimal weight: 1.9990 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: 0.6716 moved from start: 0.4642 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= 0.192 Angle : 0.598 13.045 12782 Z= 0.292 Chirality : 0.039 0.131 1420 Planarity : 0.004 0.033 1556 Dihedral : 5.435 39.516 1252 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 3.47 % Allowed : 17.86 % Favored : 78.68 % 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: 0.88 (0.26), residues: 1126 helix: 1.20 (0.19), residues: 752 sheet: None (None), residues: 0 loop : -0.59 (0.34), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 80 HIS 0.004 0.001 HIS A 220 PHE 0.017 0.001 PHE D 511 TYR 0.015 0.001 TYR D 205 ARG 0.004 0.000 ARG A 341 ********************** 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 188 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 155 time to evaluate : 0.909 Fit side-chains REVERT: D 111 TYR cc_start: 0.7871 (t80) cc_final: 0.7591 (t80) REVERT: D 298 ASP cc_start: 0.7265 (t70) cc_final: 0.6544 (t0) REVERT: D 309 ILE cc_start: 0.6765 (OUTLIER) cc_final: 0.6536 (mp) REVERT: D 316 PHE cc_start: 0.7458 (t80) cc_final: 0.6529 (m-10) REVERT: D 376 ILE cc_start: 0.8123 (OUTLIER) cc_final: 0.7530 (mt) REVERT: A 111 TYR cc_start: 0.7890 (t80) cc_final: 0.7561 (t80) REVERT: A 264 TRP cc_start: 0.6067 (m100) cc_final: 0.5851 (t60) REVERT: A 298 ASP cc_start: 0.7290 (t70) cc_final: 0.6570 (t0) REVERT: A 376 ILE cc_start: 0.8023 (OUTLIER) cc_final: 0.7496 (mt) outliers start: 33 outliers final: 29 residues processed: 171 average time/residue: 0.1846 time to fit residues: 45.0923 Evaluate side-chains 182 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 150 time to evaluate : 0.903 ------------------------------------------------------------------------------- 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 191 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 309 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 190 LEU Chi-restraints excluded: chain A residue 191 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 0.8980 chunk 81 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 chunk 24 optimal weight: 0.9990 chunk 88 optimal weight: 7.9990 chunk 37 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 11 optimal weight: 0.0470 chunk 16 optimal weight: 0.6980 chunk 78 optimal weight: 2.9990 chunk 5 optimal weight: 0.4980 overall best weight: 0.6280 ------------------------------------------------------------------------------- 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 = 0.4059 r_free = 0.4059 target = 0.181922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.156313 restraints weight = 11184.570| |-----------------------------------------------------------------------------| r_work (start): 0.3798 rms_B_bonded: 1.63 r_work: 0.3700 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3575 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.4649 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= 0.188 Angle : 0.598 13.213 12782 Z= 0.292 Chirality : 0.039 0.129 1420 Planarity : 0.004 0.033 1556 Dihedral : 5.423 39.860 1252 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 3.36 % Allowed : 18.07 % Favored : 78.57 % 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: 0.92 (0.26), residues: 1126 helix: 1.24 (0.19), residues: 752 sheet: None (None), residues: 0 loop : -0.60 (0.34), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 80 HIS 0.005 0.001 HIS D 220 PHE 0.029 0.002 PHE A 540 TYR 0.014 0.001 TYR D 152 ARG 0.004 0.000 ARG A 341 Origin is already at (0, 0, 0), no shifts will be applied Model does not fit in PDB format. =============================================================================== Job complete usr+sys time: 2204.73 seconds wall clock time: 39 minutes 35.83 seconds (2375.83 seconds total)