Starting phenix.real_space_refine on Thu Jan 18 15:29:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oz1_13118/01_2024/7oz1_13118.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oz1_13118/01_2024/7oz1_13118.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oz1_13118/01_2024/7oz1_13118.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oz1_13118/01_2024/7oz1_13118.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oz1_13118/01_2024/7oz1_13118.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oz1_13118/01_2024/7oz1_13118.pdb" } resolution = 4.0 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= 0.002 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: 5 Type Number sf(0) Gaussians P 8 5.49 5 S 68 5.16 5 C 5864 2.51 5 N 1414 2.21 5 O 1588 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 165": "OD1" <-> "OD2" Residue "A TYR 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 323": "OD1" <-> "OD2" Residue "A ASP 335": "OD1" <-> "OD2" Residue "A ARG 399": "NH1" <-> "NH2" Residue "A ARG 406": "NH1" <-> "NH2" Residue "A GLU 468": "OE1" <-> "OE2" Residue "A GLU 475": "OE1" <-> "OE2" Residue "A TYR 481": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 575": "OD1" <-> "OD2" Residue "A ASP 612": "OD1" <-> "OD2" Residue "A ARG 627": "NH1" <-> "NH2" Residue "B ASP 165": "OD1" <-> "OD2" Residue "B TYR 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 323": "OD1" <-> "OD2" Residue "B ASP 335": "OD1" <-> "OD2" Residue "B ARG 399": "NH1" <-> "NH2" Residue "B ARG 406": "NH1" <-> "NH2" Residue "B GLU 468": "OE1" <-> "OE2" Residue "B GLU 475": "OE1" <-> "OE2" Residue "B TYR 481": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 575": "OD1" <-> "OD2" Residue "B ASP 612": "OD1" <-> "OD2" Residue "B ARG 627": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 8942 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 544, 4257 Classifications: {'peptide': 544} Link IDs: {'PTRANS': 19, 'TRANS': 524} Chain breaks: 2 Chain: "B" Number of atoms: 4257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 544, 4257 Classifications: {'peptide': 544} Link IDs: {'PTRANS': 19, 'TRANS': 524} Chain breaks: 2 Chain: "A" Number of atoms: 214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 214 Unusual residues: {'ATP': 1, 'PEE': 1, 'Y01': 4} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "B" Number of atoms: 214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 214 Unusual residues: {'ATP': 1, 'PEE': 1, 'Y01': 4} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Time building chain proxies: 5.19, per 1000 atoms: 0.58 Number of scatterers: 8942 At special positions: 0 Unit cell: (78.54, 104.94, 123.42, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 68 16.00 P 8 15.00 O 1588 8.00 N 1414 7.00 C 5864 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 611 " - pdb=" SG CYS A 617 " distance=2.04 Simple disulfide: pdb=" SG CYS B 611 " - pdb=" SG CYS B 617 " distance=2.04 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: 3.56 Conformation dependent library (CDL) restraints added in 1.6 seconds 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2012 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 8 sheets defined 60.5% alpha, 8.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.11 Creating SS restraints... Processing helix chain 'A' and resid 123 through 132 Processing helix chain 'A' and resid 154 through 157 Processing helix chain 'A' and resid 173 through 186 removed outlier: 3.748A pdb=" N LYS A 185 " --> pdb=" O SER A 181 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU A 186 " --> pdb=" O ALA A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 205 removed outlier: 3.924A pdb=" N GLU A 195 " --> pdb=" O GLU A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 211 removed outlier: 3.633A pdb=" N ALA A 210 " --> pdb=" O LEU A 207 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ASN A 211 " --> pdb=" O SER A 208 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 207 through 211' Processing helix chain 'A' and resid 218 through 232 removed outlier: 4.046A pdb=" N GLU A 230 " --> pdb=" O ALA A 226 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N VAL A 232 " --> pdb=" O ALA A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 264 Processing helix chain 'A' and resid 278 through 283 Processing helix chain 'A' and resid 303 through 310 removed outlier: 3.857A pdb=" N ASP A 310 " --> pdb=" O PRO A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 330 removed outlier: 3.607A pdb=" N SER A 330 " --> pdb=" O MET A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 344 removed outlier: 4.673A pdb=" N ARG A 342 " --> pdb=" O SER A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 406 Processing helix chain 'A' and resid 411 through 429 Processing helix chain 'A' and resid 439 through 475 removed outlier: 3.887A pdb=" N MET A 450 " --> pdb=" O LEU A 446 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ALA A 457 " --> pdb=" O LEU A 453 " (cutoff:3.500A) Proline residue: A 460 - end of helix Proline residue: A 466 - end of helix Processing helix chain 'A' and resid 482 through 513 removed outlier: 3.628A pdb=" N TYR A 486 " --> pdb=" O SER A 482 " (cutoff:3.500A) Proline residue: A 496 - end of helix Proline residue: A 502 - end of helix Processing helix chain 'A' and resid 518 through 547 removed outlier: 4.322A pdb=" N PHE A 522 " --> pdb=" O ASP A 518 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL A 523 " --> pdb=" O ALA A 519 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA A 545 " --> pdb=" O LEU A 541 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 560 Proline residue: A 558 - end of helix Processing helix chain 'A' and resid 560 through 567 removed outlier: 4.139A pdb=" N VAL A 564 " --> pdb=" O THR A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 580 No H-bonds generated for 'chain 'A' and resid 578 through 580' Processing helix chain 'A' and resid 581 through 586 removed outlier: 3.697A pdb=" N SER A 585 " --> pdb=" O LEU A 581 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N TYR A 586 " --> pdb=" O GLN A 582 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 581 through 586' Processing helix chain 'A' and resid 588 through 602 removed outlier: 3.779A pdb=" N TYR A 592 " --> pdb=" O SER A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 622 through 629 Processing helix chain 'A' and resid 636 through 664 removed outlier: 3.740A pdb=" N PHE A 640 " --> pdb=" O LEU A 636 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 132 Processing helix chain 'B' and resid 154 through 157 Processing helix chain 'B' and resid 173 through 186 removed outlier: 3.748A pdb=" N LYS B 185 " --> pdb=" O SER B 181 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU B 186 " --> pdb=" O ALA B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 205 removed outlier: 3.924A pdb=" N GLU B 195 " --> pdb=" O GLU B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 211 removed outlier: 3.632A pdb=" N ALA B 210 " --> pdb=" O LEU B 207 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ASN B 211 " --> pdb=" O SER B 208 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 207 through 211' Processing helix chain 'B' and resid 218 through 232 removed outlier: 4.046A pdb=" N GLU B 230 " --> pdb=" O ALA B 226 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N VAL B 232 " --> pdb=" O ALA B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 264 Processing helix chain 'B' and resid 278 through 283 Processing helix chain 'B' and resid 303 through 310 removed outlier: 3.857A pdb=" N ASP B 310 " --> pdb=" O PRO B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 320 through 330 removed outlier: 3.607A pdb=" N SER B 330 " --> pdb=" O MET B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 344 removed outlier: 4.673A pdb=" N ARG B 342 " --> pdb=" O SER B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 388 through 406 Processing helix chain 'B' and resid 411 through 429 Processing helix chain 'B' and resid 439 through 475 removed outlier: 3.887A pdb=" N MET B 450 " --> pdb=" O LEU B 446 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ALA B 457 " --> pdb=" O LEU B 453 " (cutoff:3.500A) Proline residue: B 460 - end of helix Proline residue: B 466 - end of helix Processing helix chain 'B' and resid 482 through 513 removed outlier: 3.628A pdb=" N TYR B 486 " --> pdb=" O SER B 482 " (cutoff:3.500A) Proline residue: B 496 - end of helix Proline residue: B 502 - end of helix Processing helix chain 'B' and resid 518 through 547 removed outlier: 4.322A pdb=" N PHE B 522 " --> pdb=" O ASP B 518 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N VAL B 523 " --> pdb=" O ALA B 519 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA B 545 " --> pdb=" O LEU B 541 " (cutoff:3.500A) Processing helix chain 'B' and resid 552 through 560 Proline residue: B 558 - end of helix Processing helix chain 'B' and resid 560 through 567 removed outlier: 4.139A pdb=" N VAL B 564 " --> pdb=" O THR B 560 " (cutoff:3.500A) Processing helix chain 'B' and resid 578 through 580 No H-bonds generated for 'chain 'B' and resid 578 through 580' Processing helix chain 'B' and resid 581 through 586 removed outlier: 3.696A pdb=" N SER B 585 " --> pdb=" O LEU B 581 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N TYR B 586 " --> pdb=" O GLN B 582 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 581 through 586' Processing helix chain 'B' and resid 588 through 602 removed outlier: 3.779A pdb=" N TYR B 592 " --> pdb=" O SER B 588 " (cutoff:3.500A) Processing helix chain 'B' and resid 622 through 629 Processing helix chain 'B' and resid 636 through 664 removed outlier: 3.741A pdb=" N PHE B 640 " --> pdb=" O LEU B 636 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 98 through 99 removed outlier: 5.219A pdb=" N ILE A 104 " --> pdb=" O ASP A 81 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 98 through 99 removed outlier: 4.209A pdb=" N LEU A 82 " --> pdb=" O LYS A 140 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N LYS A 140 " --> pdb=" O LEU A 82 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 159 through 161 removed outlier: 6.752A pdb=" N CYS A 160 " --> pdb=" O PHE A 239 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N GLN A 286 " --> pdb=" O LEU A 113 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 289 through 291 removed outlier: 7.006A pdb=" N VAL A 289 " --> pdb=" O VAL A 296 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 98 through 99 removed outlier: 5.219A pdb=" N ILE B 104 " --> pdb=" O ASP B 81 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 98 through 99 removed outlier: 4.209A pdb=" N LEU B 82 " --> pdb=" O LYS B 140 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N LYS B 140 " --> pdb=" O LEU B 82 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 159 through 161 removed outlier: 6.751A pdb=" N CYS B 160 " --> pdb=" O PHE B 239 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N GLN B 286 " --> pdb=" O LEU B 113 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 289 through 291 removed outlier: 7.007A pdb=" N VAL B 289 " --> pdb=" O VAL B 296 " (cutoff:3.500A) 458 hydrogen bonds defined for protein. 1338 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: 2.72 Time building geometry restraints manager: 3.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1397 1.32 - 1.45: 2380 1.45 - 1.57: 5245 1.57 - 1.70: 14 1.70 - 1.83: 110 Bond restraints: 9146 Sorted by residual: bond pdb=" C4 ATP A 701 " pdb=" C5 ATP A 701 " ideal model delta sigma weight residual 1.388 1.471 -0.083 1.00e-02 1.00e+04 6.90e+01 bond pdb=" C4 ATP B 701 " pdb=" C5 ATP B 701 " ideal model delta sigma weight residual 1.388 1.471 -0.083 1.00e-02 1.00e+04 6.89e+01 bond pdb=" C5 ATP A 701 " pdb=" C6 ATP A 701 " ideal model delta sigma weight residual 1.409 1.481 -0.072 1.00e-02 1.00e+04 5.14e+01 bond pdb=" C5 ATP B 701 " pdb=" C6 ATP B 701 " ideal model delta sigma weight residual 1.409 1.480 -0.071 1.00e-02 1.00e+04 5.06e+01 bond pdb=" C8 ATP A 701 " pdb=" N7 ATP A 701 " ideal model delta sigma weight residual 1.310 1.357 -0.047 1.00e-02 1.00e+04 2.20e+01 ... (remaining 9141 not shown) Histogram of bond angle deviations from ideal: 94.16 - 102.50: 72 102.50 - 110.84: 3203 110.84 - 119.19: 4458 119.19 - 127.53: 4605 127.53 - 135.88: 70 Bond angle restraints: 12408 Sorted by residual: angle pdb=" PB ATP A 701 " pdb=" O3B ATP A 701 " pdb=" PG ATP A 701 " ideal model delta sigma weight residual 139.87 123.04 16.83 1.00e+00 1.00e+00 2.83e+02 angle pdb=" PB ATP B 701 " pdb=" O3B ATP B 701 " pdb=" PG ATP B 701 " ideal model delta sigma weight residual 139.87 123.04 16.83 1.00e+00 1.00e+00 2.83e+02 angle pdb=" PA ATP B 701 " pdb=" O3A ATP B 701 " pdb=" PB ATP B 701 " ideal model delta sigma weight residual 136.83 120.56 16.27 1.00e+00 1.00e+00 2.65e+02 angle pdb=" PA ATP A 701 " pdb=" O3A ATP A 701 " pdb=" PB ATP A 701 " ideal model delta sigma weight residual 136.83 120.59 16.24 1.00e+00 1.00e+00 2.64e+02 angle pdb=" N PRO A 276 " pdb=" CA PRO A 276 " pdb=" C PRO A 276 " ideal model delta sigma weight residual 112.47 94.16 18.31 2.06e+00 2.36e-01 7.90e+01 ... (remaining 12403 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.15: 5712 34.15 - 68.30: 156 68.30 - 102.46: 14 102.46 - 136.61: 0 136.61 - 170.76: 6 Dihedral angle restraints: 5888 sinusoidal: 2746 harmonic: 3142 Sorted by residual: dihedral pdb=" CB CYS A 611 " pdb=" SG CYS A 611 " pdb=" SG CYS A 617 " pdb=" CB CYS A 617 " ideal model delta sinusoidal sigma weight residual -86.00 -45.47 -40.53 1 1.00e+01 1.00e-02 2.30e+01 dihedral pdb=" CB CYS B 611 " pdb=" SG CYS B 611 " pdb=" SG CYS B 617 " pdb=" CB CYS B 617 " ideal model delta sinusoidal sigma weight residual -86.00 -45.49 -40.51 1 1.00e+01 1.00e-02 2.30e+01 dihedral pdb=" C4 PEE B 706 " pdb=" O4P PEE B 706 " pdb=" P PEE B 706 " pdb=" O2P PEE B 706 " ideal model delta sinusoidal sigma weight residual 284.22 113.46 170.76 1 3.00e+01 1.11e-03 2.12e+01 ... (remaining 5885 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 1238 0.070 - 0.140: 167 0.140 - 0.210: 19 0.210 - 0.280: 4 0.280 - 0.350: 2 Chirality restraints: 1430 Sorted by residual: chirality pdb=" CA PRO A 276 " pdb=" N PRO A 276 " pdb=" C PRO A 276 " pdb=" CB PRO A 276 " both_signs ideal model delta sigma weight residual False 2.72 3.07 -0.35 2.00e-01 2.50e+01 3.07e+00 chirality pdb=" CA PRO B 276 " pdb=" N PRO B 276 " pdb=" C PRO B 276 " pdb=" CB PRO B 276 " both_signs ideal model delta sigma weight residual False 2.72 3.07 -0.35 2.00e-01 2.50e+01 3.05e+00 chirality pdb=" CBE Y01 B 702 " pdb=" CAP Y01 B 702 " pdb=" CBB Y01 B 702 " pdb=" CBI Y01 B 702 " both_signs ideal model delta sigma weight residual False 2.57 2.29 0.27 2.00e-01 2.50e+01 1.86e+00 ... (remaining 1427 not shown) Planarity restraints: 1490 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER B 277 " 0.017 2.00e-02 2.50e+03 3.51e-02 1.23e+01 pdb=" C SER B 277 " -0.061 2.00e-02 2.50e+03 pdb=" O SER B 277 " 0.022 2.00e-02 2.50e+03 pdb=" N ALA B 278 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 277 " -0.017 2.00e-02 2.50e+03 3.49e-02 1.22e+01 pdb=" C SER A 277 " 0.060 2.00e-02 2.50e+03 pdb=" O SER A 277 " -0.022 2.00e-02 2.50e+03 pdb=" N ALA A 278 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET A 459 " 0.034 5.00e-02 4.00e+02 5.05e-02 4.09e+00 pdb=" N PRO A 460 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO A 460 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 460 " 0.029 5.00e-02 4.00e+02 ... (remaining 1487 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 119 2.67 - 3.23: 8739 3.23 - 3.78: 13178 3.78 - 4.34: 17986 4.34 - 4.90: 28954 Nonbonded interactions: 68976 Sorted by model distance: nonbonded pdb=" OG SER B 125 " pdb=" O1B ATP B 701 " model vdw 2.109 2.440 nonbonded pdb=" OG SER A 125 " pdb=" O1B ATP A 701 " model vdw 2.131 2.440 nonbonded pdb=" OH TYR B 297 " pdb=" O LYS B 300 " model vdw 2.160 2.440 nonbonded pdb=" OH TYR A 297 " pdb=" O LYS A 300 " model vdw 2.160 2.440 nonbonded pdb=" O LEU B 550 " pdb=" OG1 THR B 554 " model vdw 2.251 2.440 ... (remaining 68971 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 74 through 664 or resid 701 through 704)) selection = (chain 'B' and (resid 74 through 664 or resid 701 through 704)) } 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 group one per residue 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: 2.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 12.360 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 26.980 Find NCS groups from input model: 0.570 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:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 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 : 0.006 0.083 9146 Z= 0.401 Angle : 0.916 18.314 12408 Z= 0.584 Chirality : 0.051 0.350 1430 Planarity : 0.004 0.051 1490 Dihedral : 16.761 170.761 3870 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 14.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.62 % Favored : 92.38 % Rotamer: Outliers : 0.21 % Allowed : 7.51 % Favored : 92.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.23 (0.23), residues: 1076 helix: -1.39 (0.18), residues: 602 sheet: -1.84 (0.63), residues: 74 loop : -3.31 (0.30), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 480 HIS 0.002 0.001 HIS A 171 PHE 0.012 0.002 PHE B 646 TYR 0.009 0.001 TYR B 481 ARG 0.003 0.000 ARG A 224 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 199 time to evaluate : 1.060 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 179 MET cc_start: 0.8493 (tpp) cc_final: 0.8029 (tpt) REVERT: A 259 MET cc_start: 0.8671 (ttm) cc_final: 0.8359 (ttm) REVERT: A 492 MET cc_start: 0.7730 (mmm) cc_final: 0.7334 (mtp) REVERT: A 511 TRP cc_start: 0.8125 (m100) cc_final: 0.7833 (m-10) REVERT: A 609 LEU cc_start: 0.8598 (tp) cc_final: 0.8385 (tp) REVERT: B 179 MET cc_start: 0.8477 (tpp) cc_final: 0.7954 (tpt) REVERT: B 259 MET cc_start: 0.8654 (ttm) cc_final: 0.8327 (ttm) REVERT: B 492 MET cc_start: 0.7721 (mmm) cc_final: 0.7368 (mtp) REVERT: B 511 TRP cc_start: 0.8110 (m100) cc_final: 0.7852 (m-10) REVERT: B 609 LEU cc_start: 0.8582 (tp) cc_final: 0.8366 (tp) outliers start: 2 outliers final: 0 residues processed: 201 average time/residue: 0.2501 time to fit residues: 66.3997 Evaluate side-chains 142 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 142 time to evaluate : 1.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 1.9990 chunk 81 optimal weight: 0.7980 chunk 45 optimal weight: 4.9990 chunk 27 optimal weight: 0.9980 chunk 55 optimal weight: 2.9990 chunk 43 optimal weight: 0.5980 chunk 84 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 chunk 51 optimal weight: 0.4980 chunk 63 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 GLN A 418 HIS A 515 GLN B 175 GLN B 336 GLN B 418 HIS B 515 GLN B 633 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.1380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9146 Z= 0.175 Angle : 0.618 5.604 12408 Z= 0.304 Chirality : 0.041 0.165 1430 Planarity : 0.004 0.033 1490 Dihedral : 14.768 176.290 1896 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 1.18 % Allowed : 16.63 % Favored : 82.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.25), residues: 1076 helix: -0.06 (0.21), residues: 618 sheet: -1.69 (0.57), residues: 74 loop : -2.93 (0.31), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 480 HIS 0.003 0.001 HIS A 319 PHE 0.017 0.002 PHE B 281 TYR 0.007 0.001 TYR B 487 ARG 0.005 0.000 ARG A 345 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 147 time to evaluate : 0.998 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 178 MET cc_start: 0.7922 (mmm) cc_final: 0.7356 (mmm) REVERT: A 179 MET cc_start: 0.8578 (tpp) cc_final: 0.8132 (tpt) REVERT: A 277 SER cc_start: 0.8301 (OUTLIER) cc_final: 0.7925 (p) REVERT: A 298 ARG cc_start: 0.8101 (ttt180) cc_final: 0.7831 (tmm-80) REVERT: A 404 ILE cc_start: 0.8017 (tt) cc_final: 0.7671 (mt) REVERT: A 446 LEU cc_start: 0.8204 (tp) cc_final: 0.7885 (tp) REVERT: A 492 MET cc_start: 0.7750 (mmm) cc_final: 0.7249 (mtp) REVERT: A 511 TRP cc_start: 0.7995 (m100) cc_final: 0.7688 (m-10) REVERT: A 609 LEU cc_start: 0.8520 (tp) cc_final: 0.8236 (tp) REVERT: B 178 MET cc_start: 0.7905 (mmm) cc_final: 0.7300 (mmm) REVERT: B 179 MET cc_start: 0.8552 (tpp) cc_final: 0.7904 (tpt) REVERT: B 298 ARG cc_start: 0.8356 (tmm-80) cc_final: 0.8100 (ttt180) REVERT: B 404 ILE cc_start: 0.8033 (tt) cc_final: 0.7688 (mt) REVERT: B 446 LEU cc_start: 0.8183 (tp) cc_final: 0.7836 (tp) REVERT: B 454 MET cc_start: 0.8213 (ttp) cc_final: 0.8012 (tmm) REVERT: B 492 MET cc_start: 0.7760 (mmm) cc_final: 0.7282 (mtp) REVERT: B 511 TRP cc_start: 0.7959 (m100) cc_final: 0.7692 (m-10) REVERT: B 609 LEU cc_start: 0.8490 (tp) cc_final: 0.8208 (tp) outliers start: 11 outliers final: 6 residues processed: 156 average time/residue: 0.2023 time to fit residues: 45.4426 Evaluate side-chains 140 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 133 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 CYS Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain A residue 418 HIS Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain B residue 160 CYS Chi-restraints excluded: chain B residue 418 HIS Chi-restraints excluded: chain B residue 467 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 54 optimal weight: 6.9990 chunk 30 optimal weight: 4.9990 chunk 81 optimal weight: 5.9990 chunk 66 optimal weight: 5.9990 chunk 27 optimal weight: 4.9990 chunk 98 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 87 optimal weight: 0.7980 chunk 97 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 78 optimal weight: 0.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 320 ASN A 418 HIS B 418 HIS B 582 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.1577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 9146 Z= 0.299 Angle : 0.641 6.363 12408 Z= 0.317 Chirality : 0.043 0.144 1430 Planarity : 0.004 0.036 1490 Dihedral : 14.059 174.274 1896 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.97 % Favored : 93.03 % Rotamer: Outliers : 2.47 % Allowed : 19.42 % Favored : 78.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.39 (0.26), residues: 1076 helix: 0.26 (0.21), residues: 624 sheet: -1.67 (0.57), residues: 74 loop : -2.79 (0.31), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 583 HIS 0.014 0.002 HIS B 418 PHE 0.032 0.002 PHE A 501 TYR 0.010 0.001 TYR B 288 ARG 0.003 0.000 ARG B 309 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 134 time to evaluate : 1.016 Fit side-chains REVERT: A 179 MET cc_start: 0.8562 (tpp) cc_final: 0.8044 (tpt) REVERT: A 404 ILE cc_start: 0.8085 (tt) cc_final: 0.7736 (mt) REVERT: A 407 ASP cc_start: 0.8245 (t0) cc_final: 0.7931 (t0) REVERT: A 492 MET cc_start: 0.7682 (mmm) cc_final: 0.7250 (mtp) REVERT: A 511 TRP cc_start: 0.8105 (m100) cc_final: 0.7766 (m-10) REVERT: B 179 MET cc_start: 0.8542 (tpp) cc_final: 0.7894 (tpt) REVERT: B 404 ILE cc_start: 0.8083 (tt) cc_final: 0.7731 (mt) REVERT: B 407 ASP cc_start: 0.8214 (t0) cc_final: 0.7912 (t0) REVERT: B 492 MET cc_start: 0.7730 (mmm) cc_final: 0.7310 (mtp) REVERT: B 511 TRP cc_start: 0.8043 (m100) cc_final: 0.7746 (m-10) outliers start: 23 outliers final: 19 residues processed: 151 average time/residue: 0.1790 time to fit residues: 39.4544 Evaluate side-chains 147 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 128 time to evaluate : 1.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 139 MET Chi-restraints excluded: chain A residue 160 CYS Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 418 HIS Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 657 VAL Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 160 CYS Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 418 HIS Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain B residue 543 ILE Chi-restraints excluded: chain B residue 590 VAL Chi-restraints excluded: chain B residue 657 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 97 optimal weight: 0.7980 chunk 73 optimal weight: 1.9990 chunk 50 optimal weight: 5.9990 chunk 10 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 98 optimal weight: 3.9990 chunk 104 optimal weight: 0.9980 chunk 51 optimal weight: 0.8980 chunk 93 optimal weight: 3.9990 chunk 28 optimal weight: 4.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 418 HIS B 418 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.1862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9146 Z= 0.207 Angle : 0.598 6.485 12408 Z= 0.292 Chirality : 0.041 0.140 1430 Planarity : 0.004 0.030 1490 Dihedral : 13.234 170.483 1896 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 2.90 % Allowed : 20.49 % Favored : 76.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.26), residues: 1076 helix: 0.62 (0.22), residues: 618 sheet: -1.60 (0.57), residues: 74 loop : -2.65 (0.30), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 583 HIS 0.006 0.001 HIS A 418 PHE 0.036 0.002 PHE B 501 TYR 0.007 0.001 TYR B 288 ARG 0.004 0.000 ARG B 298 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 139 time to evaluate : 1.014 Fit side-chains revert: symmetry clash REVERT: A 178 MET cc_start: 0.7949 (mmm) cc_final: 0.7363 (mmm) REVERT: A 179 MET cc_start: 0.8573 (tpp) cc_final: 0.8073 (tpt) REVERT: A 404 ILE cc_start: 0.8034 (tt) cc_final: 0.7684 (mt) REVERT: A 407 ASP cc_start: 0.8283 (t0) cc_final: 0.7944 (t0) REVERT: A 492 MET cc_start: 0.7619 (mmm) cc_final: 0.7212 (mtp) REVERT: A 511 TRP cc_start: 0.8017 (m100) cc_final: 0.7573 (m-10) REVERT: B 178 MET cc_start: 0.7924 (mmm) cc_final: 0.7295 (mmm) REVERT: B 179 MET cc_start: 0.8553 (tpp) cc_final: 0.8034 (tpt) REVERT: B 404 ILE cc_start: 0.8044 (tt) cc_final: 0.7733 (mt) REVERT: B 407 ASP cc_start: 0.8255 (t0) cc_final: 0.7932 (t0) REVERT: B 492 MET cc_start: 0.7687 (mmm) cc_final: 0.7266 (mtp) REVERT: B 511 TRP cc_start: 0.7983 (m100) cc_final: 0.7574 (m-10) outliers start: 27 outliers final: 20 residues processed: 157 average time/residue: 0.1678 time to fit residues: 39.0469 Evaluate side-chains 146 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 126 time to evaluate : 1.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 139 MET Chi-restraints excluded: chain A residue 160 CYS Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 418 HIS Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 657 VAL Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 160 CYS Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 418 HIS Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain B residue 471 VAL Chi-restraints excluded: chain B residue 657 VAL Chi-restraints excluded: chain B residue 658 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 86 optimal weight: 0.5980 chunk 59 optimal weight: 0.2980 chunk 1 optimal weight: 3.9990 chunk 77 optimal weight: 9.9990 chunk 43 optimal weight: 0.9990 chunk 89 optimal weight: 6.9990 chunk 72 optimal weight: 0.2980 chunk 0 optimal weight: 5.9990 chunk 53 optimal weight: 3.9990 chunk 93 optimal weight: 0.1980 chunk 26 optimal weight: 10.0000 overall best weight: 0.4782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 264 GLN A 418 HIS A 618 HIS B 264 GLN B 418 HIS B 618 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.2150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9146 Z= 0.143 Angle : 0.561 7.422 12408 Z= 0.272 Chirality : 0.039 0.159 1430 Planarity : 0.003 0.030 1490 Dihedral : 12.545 167.843 1896 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 2.58 % Allowed : 22.53 % Favored : 74.89 % 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: -0.72 (0.26), residues: 1076 helix: 0.84 (0.22), residues: 632 sheet: -1.33 (0.58), residues: 74 loop : -2.67 (0.30), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 583 HIS 0.005 0.001 HIS B 418 PHE 0.041 0.001 PHE A 501 TYR 0.007 0.001 TYR A 134 ARG 0.001 0.000 ARG A 345 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 132 time to evaluate : 0.998 Fit side-chains REVERT: A 178 MET cc_start: 0.7993 (mmm) cc_final: 0.7375 (mmm) REVERT: A 179 MET cc_start: 0.8563 (tpp) cc_final: 0.8179 (tpt) REVERT: A 404 ILE cc_start: 0.7961 (tt) cc_final: 0.7673 (mt) REVERT: A 407 ASP cc_start: 0.8297 (t0) cc_final: 0.7956 (t0) REVERT: A 492 MET cc_start: 0.7544 (mmm) cc_final: 0.7178 (mtp) REVERT: A 511 TRP cc_start: 0.7912 (m100) cc_final: 0.7474 (m-10) REVERT: B 139 MET cc_start: 0.7007 (ppp) cc_final: 0.6806 (ptt) REVERT: B 178 MET cc_start: 0.7952 (mmm) cc_final: 0.7297 (mmm) REVERT: B 179 MET cc_start: 0.8549 (tpp) cc_final: 0.8079 (tpt) REVERT: B 277 SER cc_start: 0.8284 (OUTLIER) cc_final: 0.8036 (p) REVERT: B 404 ILE cc_start: 0.7980 (tt) cc_final: 0.7648 (mt) REVERT: B 407 ASP cc_start: 0.8277 (t0) cc_final: 0.7939 (t0) REVERT: B 492 MET cc_start: 0.7594 (mmm) cc_final: 0.7243 (mtp) REVERT: B 511 TRP cc_start: 0.7877 (m100) cc_final: 0.7452 (m-10) outliers start: 24 outliers final: 16 residues processed: 155 average time/residue: 0.1808 time to fit residues: 40.8654 Evaluate side-chains 144 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 127 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 160 CYS Chi-restraints excluded: chain A residue 418 HIS Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 625 ILE Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 160 CYS Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 418 HIS Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain B residue 590 VAL Chi-restraints excluded: chain B residue 609 LEU Chi-restraints excluded: chain B residue 658 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 35 optimal weight: 7.9990 chunk 94 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 chunk 61 optimal weight: 0.9980 chunk 25 optimal weight: 7.9990 chunk 104 optimal weight: 3.9990 chunk 86 optimal weight: 0.9980 chunk 48 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 54 optimal weight: 6.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 418 HIS ** B 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 418 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.2167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9146 Z= 0.281 Angle : 0.623 7.034 12408 Z= 0.304 Chirality : 0.042 0.140 1430 Planarity : 0.004 0.030 1490 Dihedral : 12.484 169.205 1896 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer: Outliers : 3.76 % Allowed : 22.10 % Favored : 74.14 % 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: -0.84 (0.26), residues: 1076 helix: 0.74 (0.21), residues: 634 sheet: -1.45 (0.57), residues: 74 loop : -2.74 (0.30), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 583 HIS 0.007 0.001 HIS A 418 PHE 0.035 0.002 PHE A 501 TYR 0.009 0.001 TYR B 487 ARG 0.005 0.000 ARG A 651 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 126 time to evaluate : 0.999 Fit side-chains REVERT: A 179 MET cc_start: 0.8554 (tpp) cc_final: 0.8059 (tpt) REVERT: A 404 ILE cc_start: 0.8015 (tt) cc_final: 0.7709 (mt) REVERT: A 407 ASP cc_start: 0.8296 (t0) cc_final: 0.7975 (t0) REVERT: A 492 MET cc_start: 0.7646 (mmm) cc_final: 0.7268 (mtp) REVERT: A 511 TRP cc_start: 0.8021 (m100) cc_final: 0.7664 (m-10) REVERT: B 179 MET cc_start: 0.8548 (tpp) cc_final: 0.7920 (tpt) REVERT: B 277 SER cc_start: 0.8371 (OUTLIER) cc_final: 0.8013 (p) REVERT: B 404 ILE cc_start: 0.8009 (tt) cc_final: 0.7709 (mt) REVERT: B 407 ASP cc_start: 0.8267 (t0) cc_final: 0.7963 (t0) REVERT: B 492 MET cc_start: 0.7658 (mmm) cc_final: 0.7287 (mtp) REVERT: B 511 TRP cc_start: 0.7990 (m100) cc_final: 0.7667 (m-10) outliers start: 35 outliers final: 24 residues processed: 155 average time/residue: 0.1723 time to fit residues: 39.4246 Evaluate side-chains 144 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 119 time to evaluate : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 109 ASN Chi-restraints excluded: chain A residue 160 CYS Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 418 HIS Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 625 ILE Chi-restraints excluded: chain A residue 657 VAL Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 109 ASN Chi-restraints excluded: chain B residue 160 CYS Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 418 HIS Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 590 VAL Chi-restraints excluded: chain B residue 609 LEU Chi-restraints excluded: chain B residue 625 ILE Chi-restraints excluded: chain B residue 657 VAL Chi-restraints excluded: chain B residue 658 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 100 optimal weight: 6.9990 chunk 11 optimal weight: 4.9990 chunk 59 optimal weight: 6.9990 chunk 76 optimal weight: 0.9990 chunk 87 optimal weight: 0.5980 chunk 58 optimal weight: 4.9990 chunk 104 optimal weight: 0.9980 chunk 65 optimal weight: 6.9990 chunk 63 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 418 HIS ** B 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 418 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.2274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 9146 Z= 0.267 Angle : 0.627 6.741 12408 Z= 0.303 Chirality : 0.041 0.140 1430 Planarity : 0.004 0.031 1490 Dihedral : 12.346 165.522 1896 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 3.76 % Allowed : 22.64 % Favored : 73.61 % 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: -0.80 (0.26), residues: 1076 helix: 0.77 (0.21), residues: 634 sheet: -1.53 (0.56), residues: 74 loop : -2.69 (0.30), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 583 HIS 0.005 0.001 HIS B 418 PHE 0.032 0.002 PHE A 501 TYR 0.008 0.001 TYR A 288 ARG 0.003 0.000 ARG A 651 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 127 time to evaluate : 0.915 Fit side-chains REVERT: A 178 MET cc_start: 0.7971 (mmm) cc_final: 0.7390 (mmm) REVERT: A 179 MET cc_start: 0.8572 (tpp) cc_final: 0.8063 (tpt) REVERT: A 404 ILE cc_start: 0.8017 (tt) cc_final: 0.7716 (mt) REVERT: A 407 ASP cc_start: 0.8304 (t0) cc_final: 0.7995 (t0) REVERT: A 492 MET cc_start: 0.7604 (mmm) cc_final: 0.7251 (mtp) REVERT: A 511 TRP cc_start: 0.8036 (m100) cc_final: 0.7707 (m-10) REVERT: B 179 MET cc_start: 0.8561 (tpp) cc_final: 0.8017 (tpt) REVERT: B 277 SER cc_start: 0.8343 (OUTLIER) cc_final: 0.8006 (p) REVERT: B 404 ILE cc_start: 0.8026 (tt) cc_final: 0.7726 (mt) REVERT: B 407 ASP cc_start: 0.8270 (t0) cc_final: 0.7982 (t0) REVERT: B 492 MET cc_start: 0.7656 (mmm) cc_final: 0.7298 (mtp) REVERT: B 511 TRP cc_start: 0.8001 (m100) cc_final: 0.7686 (m-10) outliers start: 35 outliers final: 26 residues processed: 155 average time/residue: 0.1721 time to fit residues: 39.7209 Evaluate side-chains 149 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 122 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 109 ASN Chi-restraints excluded: chain A residue 160 CYS Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 418 HIS Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 657 VAL Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 109 ASN Chi-restraints excluded: chain B residue 160 CYS Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 418 HIS Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 590 VAL Chi-restraints excluded: chain B residue 609 LEU Chi-restraints excluded: chain B residue 625 ILE Chi-restraints excluded: chain B residue 657 VAL Chi-restraints excluded: chain B residue 658 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 41 optimal weight: 0.6980 chunk 62 optimal weight: 4.9990 chunk 31 optimal weight: 0.9990 chunk 20 optimal weight: 0.6980 chunk 66 optimal weight: 0.9990 chunk 70 optimal weight: 0.0980 chunk 51 optimal weight: 5.9990 chunk 9 optimal weight: 4.9990 chunk 81 optimal weight: 1.9990 chunk 94 optimal weight: 0.9990 chunk 99 optimal weight: 2.9990 overall best weight: 0.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 418 HIS ** B 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 418 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.2455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9146 Z= 0.160 Angle : 0.579 7.976 12408 Z= 0.277 Chirality : 0.040 0.175 1430 Planarity : 0.003 0.031 1490 Dihedral : 11.985 156.947 1896 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 2.79 % Allowed : 23.82 % Favored : 73.39 % 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: -0.53 (0.26), residues: 1076 helix: 0.97 (0.22), residues: 636 sheet: -1.35 (0.57), residues: 74 loop : -2.58 (0.30), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 583 HIS 0.004 0.001 HIS B 418 PHE 0.041 0.002 PHE B 501 TYR 0.007 0.001 TYR B 487 ARG 0.002 0.000 ARG A 651 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 144 time to evaluate : 1.013 Fit side-chains REVERT: A 178 MET cc_start: 0.7963 (mmm) cc_final: 0.7411 (mmm) REVERT: A 179 MET cc_start: 0.8568 (tpp) cc_final: 0.8131 (tpt) REVERT: A 404 ILE cc_start: 0.7946 (tt) cc_final: 0.7667 (mt) REVERT: A 407 ASP cc_start: 0.8307 (t0) cc_final: 0.7989 (t0) REVERT: A 492 MET cc_start: 0.7581 (mmm) cc_final: 0.7265 (mtp) REVERT: A 511 TRP cc_start: 0.7931 (m100) cc_final: 0.7589 (m-10) REVERT: A 660 TYR cc_start: 0.7960 (t80) cc_final: 0.7528 (t80) REVERT: B 179 MET cc_start: 0.8552 (tpp) cc_final: 0.8091 (tpt) REVERT: B 277 SER cc_start: 0.8331 (OUTLIER) cc_final: 0.7956 (p) REVERT: B 404 ILE cc_start: 0.7971 (tt) cc_final: 0.7688 (mt) REVERT: B 407 ASP cc_start: 0.8288 (t0) cc_final: 0.7955 (t0) REVERT: B 492 MET cc_start: 0.7601 (mmm) cc_final: 0.7275 (mtp) REVERT: B 511 TRP cc_start: 0.7892 (m100) cc_final: 0.7569 (m-10) outliers start: 26 outliers final: 20 residues processed: 167 average time/residue: 0.1683 time to fit residues: 41.9029 Evaluate side-chains 157 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 136 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 160 CYS Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 418 HIS Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 160 CYS Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 418 HIS Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 590 VAL Chi-restraints excluded: chain B residue 609 LEU Chi-restraints excluded: chain B residue 658 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 90 optimal weight: 0.9980 chunk 97 optimal weight: 0.0970 chunk 99 optimal weight: 2.9990 chunk 58 optimal weight: 5.9990 chunk 42 optimal weight: 0.5980 chunk 76 optimal weight: 1.9990 chunk 29 optimal weight: 6.9990 chunk 87 optimal weight: 0.9980 chunk 91 optimal weight: 2.9990 chunk 96 optimal weight: 3.9990 chunk 63 optimal weight: 4.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 418 HIS ** B 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 418 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.2532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9146 Z= 0.178 Angle : 0.577 7.810 12408 Z= 0.279 Chirality : 0.040 0.175 1430 Planarity : 0.003 0.032 1490 Dihedral : 11.844 150.806 1896 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 3.33 % Allowed : 23.18 % Favored : 73.50 % 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: -0.46 (0.26), residues: 1076 helix: 1.03 (0.21), residues: 644 sheet: -1.24 (0.57), residues: 74 loop : -2.64 (0.30), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 583 HIS 0.003 0.001 HIS B 418 PHE 0.038 0.002 PHE A 501 TYR 0.007 0.001 TYR A 487 ARG 0.002 0.000 ARG A 651 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 141 time to evaluate : 1.079 Fit side-chains REVERT: A 179 MET cc_start: 0.8546 (tpp) cc_final: 0.8099 (tpt) REVERT: A 404 ILE cc_start: 0.7932 (tt) cc_final: 0.7667 (mt) REVERT: A 405 MET cc_start: 0.8325 (tmm) cc_final: 0.7857 (tmm) REVERT: A 407 ASP cc_start: 0.8326 (t0) cc_final: 0.7978 (t0) REVERT: A 492 MET cc_start: 0.7583 (mmm) cc_final: 0.7277 (mtp) REVERT: A 511 TRP cc_start: 0.8050 (m100) cc_final: 0.7568 (m-10) REVERT: A 660 TYR cc_start: 0.7937 (t80) cc_final: 0.7517 (t80) REVERT: B 178 MET cc_start: 0.7998 (mmm) cc_final: 0.7369 (mmm) REVERT: B 179 MET cc_start: 0.8549 (tpp) cc_final: 0.8099 (tpt) REVERT: B 277 SER cc_start: 0.8326 (OUTLIER) cc_final: 0.7920 (p) REVERT: B 404 ILE cc_start: 0.7941 (tt) cc_final: 0.7679 (mt) REVERT: B 405 MET cc_start: 0.8362 (tmm) cc_final: 0.7877 (tmm) REVERT: B 407 ASP cc_start: 0.8291 (t0) cc_final: 0.7933 (t0) REVERT: B 492 MET cc_start: 0.7606 (mmm) cc_final: 0.7285 (mtp) REVERT: B 511 TRP cc_start: 0.8015 (m100) cc_final: 0.7588 (m-10) REVERT: B 660 TYR cc_start: 0.7924 (t80) cc_final: 0.7514 (t80) outliers start: 31 outliers final: 24 residues processed: 163 average time/residue: 0.1651 time to fit residues: 40.2239 Evaluate side-chains 159 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 134 time to evaluate : 1.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 109 ASN Chi-restraints excluded: chain A residue 160 CYS Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 418 HIS Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 625 ILE Chi-restraints excluded: chain A residue 657 VAL Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 109 ASN Chi-restraints excluded: chain B residue 160 CYS Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 418 HIS Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 590 VAL Chi-restraints excluded: chain B residue 609 LEU Chi-restraints excluded: chain B residue 657 VAL Chi-restraints excluded: chain B residue 658 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 71.457 > 50: distance: 88 - 90: 33.944 distance: 90 - 91: 39.654 distance: 91 - 92: 40.009 distance: 91 - 94: 68.011 distance: 92 - 101: 67.118 distance: 95 - 96: 38.799 distance: 95 - 97: 57.457 distance: 96 - 98: 40.515 distance: 97 - 99: 38.935 distance: 99 - 100: 40.651 distance: 101 - 102: 40.354 distance: 102 - 103: 39.865 distance: 103 - 104: 40.051 distance: 106 - 107: 40.569 distance: 109 - 111: 39.817 distance: 112 - 113: 38.580 distance: 113 - 114: 44.456 distance: 113 - 116: 57.603 distance: 114 - 115: 19.452 distance: 114 - 119: 44.638 distance: 116 - 117: 38.975 distance: 119 - 120: 39.071 distance: 120 - 121: 40.652 distance: 123 - 124: 40.501 distance: 126 - 127: 40.051 distance: 130 - 131: 56.976 distance: 130 - 132: 39.724 distance: 131 - 133: 40.993 distance: 132 - 134: 39.206 distance: 134 - 135: 40.213 distance: 136 - 137: 39.378 distance: 138 - 139: 56.613 distance: 138 - 144: 55.695 distance: 141 - 143: 39.588 distance: 148 - 149: 31.012 distance: 148 - 150: 39.317 distance: 151 - 152: 38.648 distance: 152 - 155: 40.722 distance: 153 - 154: 39.650 distance: 155 - 156: 40.070 distance: 155 - 157: 41.340 distance: 159 - 165: 40.041 distance: 160 - 161: 39.262 distance: 160 - 163: 39.751 distance: 166 - 167: 39.390 distance: 167 - 168: 39.827 distance: 167 - 170: 56.402 distance: 168 - 173: 35.747 distance: 170 - 172: 42.746