Starting phenix.real_space_refine on Fri Feb 14 11:16:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8orh_17125/02_2025/8orh_17125.cif Found real_map, /net/cci-nas-00/data/ceres_data/8orh_17125/02_2025/8orh_17125.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8orh_17125/02_2025/8orh_17125.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8orh_17125/02_2025/8orh_17125.map" model { file = "/net/cci-nas-00/data/ceres_data/8orh_17125/02_2025/8orh_17125.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8orh_17125/02_2025/8orh_17125.cif" } resolution = 4.2 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= 0.001 sd= 0.003 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 4 5.49 5 S 32 5.16 5 C 6434 2.51 5 N 1742 2.21 5 O 1912 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 10124 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 649, 5009 Classifications: {'peptide': 649} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 39, 'TRANS': 609} Chain: "B" Number of atoms: 5009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 649, 5009 Classifications: {'peptide': 649} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 39, 'TRANS': 609} Chain: "A" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 53 Unusual residues: {'FAD': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 53 Unusual residues: {'FAD': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.12, per 1000 atoms: 0.70 Number of scatterers: 10124 At special positions: 0 Unit cell: (98.8169, 90.1297, 112.934, 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 32 16.00 P 4 15.00 O 1912 8.00 N 1742 7.00 C 6434 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.43 Conformation dependent library (CDL) restraints added in 1.3 seconds 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2360 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 15 sheets defined 39.1% alpha, 20.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.01 Creating SS restraints... Processing helix chain 'A' and resid 67 through 78 removed outlier: 3.788A pdb=" N PHE A 78 " --> pdb=" O TYR A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 100 Processing helix chain 'A' and resid 101 through 106 removed outlier: 3.512A pdb=" N PHE A 104 " --> pdb=" O PRO A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 154 Processing helix chain 'A' and resid 164 through 171 removed outlier: 3.658A pdb=" N TRP A 171 " --> pdb=" O PHE A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 179 Processing helix chain 'A' and resid 180 through 192 removed outlier: 3.626A pdb=" N ARG A 186 " --> pdb=" O ASN A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 221 removed outlier: 4.190A pdb=" N SER A 204 " --> pdb=" O ALA A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 287 Processing helix chain 'A' and resid 299 through 303 Processing helix chain 'A' and resid 352 through 360 Processing helix chain 'A' and resid 364 through 372 Processing helix chain 'A' and resid 402 through 410 Processing helix chain 'A' and resid 460 through 468 Processing helix chain 'A' and resid 520 through 532 removed outlier: 3.515A pdb=" N GLN A 524 " --> pdb=" O PRO A 520 " (cutoff:3.500A) Proline residue: A 526 - end of helix Processing helix chain 'A' and resid 532 through 560 removed outlier: 3.976A pdb=" N GLN A 554 " --> pdb=" O ILE A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 586 removed outlier: 3.546A pdb=" N ILE A 575 " --> pdb=" O LEU A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 599 removed outlier: 4.500A pdb=" N TRP A 590 " --> pdb=" O ALA A 587 " (cutoff:3.500A) Proline residue: A 595 - end of helix removed outlier: 3.817A pdb=" N GLY A 599 " --> pdb=" O THR A 596 " (cutoff:3.500A) Processing helix chain 'A' and resid 602 through 616 Processing helix chain 'A' and resid 617 through 622 removed outlier: 3.587A pdb=" N VAL A 621 " --> pdb=" O TYR A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 659 Processing helix chain 'A' and resid 667 through 684 removed outlier: 3.958A pdb=" N ALA A 671 " --> pdb=" O THR A 667 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER A 672 " --> pdb=" O TRP A 668 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ASP A 680 " --> pdb=" O ALA A 676 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 691 Processing helix chain 'B' and resid 67 through 78 Processing helix chain 'B' and resid 95 through 100 Processing helix chain 'B' and resid 101 through 106 Processing helix chain 'B' and resid 110 through 114 removed outlier: 4.217A pdb=" N ASN B 114 " --> pdb=" O PRO B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 120 Processing helix chain 'B' and resid 149 through 154 removed outlier: 3.549A pdb=" N MET B 153 " --> pdb=" O GLY B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 170 Processing helix chain 'B' and resid 176 through 179 Processing helix chain 'B' and resid 180 through 192 Processing helix chain 'B' and resid 201 through 221 removed outlier: 3.687A pdb=" N VAL B 205 " --> pdb=" O SER B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 233 removed outlier: 3.753A pdb=" N THR B 232 " --> pdb=" O ASN B 229 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLY B 233 " --> pdb=" O LYS B 230 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 229 through 233' Processing helix chain 'B' and resid 281 through 287 Processing helix chain 'B' and resid 299 through 303 Processing helix chain 'B' and resid 351 through 361 removed outlier: 4.215A pdb=" N THR B 355 " --> pdb=" O PHE B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 372 Processing helix chain 'B' and resid 402 through 410 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.975A pdb=" N ASN B 442 " --> pdb=" O ALA B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 460 through 468 Processing helix chain 'B' and resid 520 through 532 Proline residue: B 526 - end of helix Processing helix chain 'B' and resid 532 through 560 removed outlier: 3.832A pdb=" N GLN B 554 " --> pdb=" O ILE B 550 " (cutoff:3.500A) Processing helix chain 'B' and resid 571 through 586 Processing helix chain 'B' and resid 587 through 593 removed outlier: 4.653A pdb=" N TRP B 590 " --> pdb=" O ALA B 587 " (cutoff:3.500A) Processing helix chain 'B' and resid 594 through 599 removed outlier: 3.750A pdb=" N GLY B 599 " --> pdb=" O PRO B 595 " (cutoff:3.500A) Processing helix chain 'B' and resid 602 through 616 removed outlier: 3.501A pdb=" N SER B 616 " --> pdb=" O LEU B 612 " (cutoff:3.500A) Processing helix chain 'B' and resid 616 through 622 removed outlier: 4.236A pdb=" N ARG B 620 " --> pdb=" O SER B 616 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N VAL B 621 " --> pdb=" O TYR B 617 " (cutoff:3.500A) Processing helix chain 'B' and resid 655 through 659 Processing helix chain 'B' and resid 667 through 684 removed outlier: 3.703A pdb=" N ASP B 680 " --> pdb=" O ALA B 676 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 305 through 308 removed outlier: 6.121A pdb=" N ILE A 83 " --> pdb=" O ARG A 306 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N VAL A 308 " --> pdb=" O ILE A 83 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N LEU A 85 " --> pdb=" O VAL A 308 " (cutoff:3.500A) removed outlier: 11.348A pdb=" N THR A 56 " --> pdb=" O ASN A 341 " (cutoff:3.500A) removed outlier: 10.980A pdb=" N GLU A 343 " --> pdb=" O THR A 56 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N ASP A 58 " --> pdb=" O GLU A 343 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N VAL A 345 " --> pdb=" O ASP A 58 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N VAL A 60 " --> pdb=" O VAL A 345 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL A 340 " --> pdb=" O VAL A 324 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N VAL A 324 " --> pdb=" O VAL A 340 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N ILE A 317 " --> pdb=" O VAL A 324 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N VAL A 326 " --> pdb=" O ARG A 315 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N ARG A 315 " --> pdb=" O VAL A 326 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N TYR A 328 " --> pdb=" O VAL A 313 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N VAL A 313 " --> pdb=" O TYR A 328 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 305 through 308 removed outlier: 6.121A pdb=" N ILE A 83 " --> pdb=" O ARG A 306 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N VAL A 308 " --> pdb=" O ILE A 83 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N LEU A 85 " --> pdb=" O VAL A 308 " (cutoff:3.500A) removed outlier: 11.348A pdb=" N THR A 56 " --> pdb=" O ASN A 341 " (cutoff:3.500A) removed outlier: 10.980A pdb=" N GLU A 343 " --> pdb=" O THR A 56 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N ASP A 58 " --> pdb=" O GLU A 343 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N VAL A 345 " --> pdb=" O ASP A 58 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N VAL A 60 " --> pdb=" O VAL A 345 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 124 through 128 removed outlier: 3.689A pdb=" N HIS A 144 " --> pdb=" O TRP A 125 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ILE A 142 " --> pdb=" O GLY A 127 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 269 through 271 Processing sheet with id=AA5, first strand: chain 'A' and resid 385 through 387 removed outlier: 5.754A pdb=" N GLY A 490 " --> pdb=" O GLY A 386 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 426 through 428 removed outlier: 3.845A pdb=" N ALA A 426 " --> pdb=" O LEU A 451 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ALA A 481 " --> pdb=" O PRO A 393 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N TYR A 391 " --> pdb=" O ASP A 483 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 426 through 428 removed outlier: 3.845A pdb=" N ALA A 426 " --> pdb=" O LEU A 451 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ALA A 481 " --> pdb=" O PRO A 393 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N TYR A 391 " --> pdb=" O ASP A 483 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N SER A 392 " --> pdb=" O HIS A 624 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N HIS A 624 " --> pdb=" O SER A 392 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 305 through 308 removed outlier: 6.286A pdb=" N ILE B 83 " --> pdb=" O ARG B 306 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N VAL B 308 " --> pdb=" O ILE B 83 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N LEU B 85 " --> pdb=" O VAL B 308 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N ILE B 84 " --> pdb=" O GLY B 57 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ILE B 59 " --> pdb=" O ILE B 84 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N LEU B 86 " --> pdb=" O ILE B 59 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ILE B 61 " --> pdb=" O LEU B 86 " (cutoff:3.500A) removed outlier: 11.622A pdb=" N THR B 56 " --> pdb=" O ASN B 341 " (cutoff:3.500A) removed outlier: 11.030A pdb=" N GLU B 343 " --> pdb=" O THR B 56 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N ASP B 58 " --> pdb=" O GLU B 343 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N VAL B 345 " --> pdb=" O ASP B 58 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N VAL B 60 " --> pdb=" O VAL B 345 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N VAL B 324 " --> pdb=" O VAL B 340 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ILE B 317 " --> pdb=" O VAL B 324 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N VAL B 326 " --> pdb=" O ARG B 315 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N ARG B 315 " --> pdb=" O VAL B 326 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N TYR B 328 " --> pdb=" O VAL B 313 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N VAL B 313 " --> pdb=" O TYR B 328 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 305 through 308 removed outlier: 6.286A pdb=" N ILE B 83 " --> pdb=" O ARG B 306 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N VAL B 308 " --> pdb=" O ILE B 83 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N LEU B 85 " --> pdb=" O VAL B 308 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N ILE B 84 " --> pdb=" O GLY B 57 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ILE B 59 " --> pdb=" O ILE B 84 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N LEU B 86 " --> pdb=" O ILE B 59 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ILE B 61 " --> pdb=" O LEU B 86 " (cutoff:3.500A) removed outlier: 11.622A pdb=" N THR B 56 " --> pdb=" O ASN B 341 " (cutoff:3.500A) removed outlier: 11.030A pdb=" N GLU B 343 " --> pdb=" O THR B 56 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N ASP B 58 " --> pdb=" O GLU B 343 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N VAL B 345 " --> pdb=" O ASP B 58 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N VAL B 60 " --> pdb=" O VAL B 345 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 124 through 128 removed outlier: 3.609A pdb=" N HIS B 144 " --> pdb=" O TRP B 125 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 269 through 271 Processing sheet with id=AB3, first strand: chain 'B' and resid 362 through 363 Processing sheet with id=AB4, first strand: chain 'B' and resid 385 through 387 removed outlier: 5.301A pdb=" N GLY B 490 " --> pdb=" O GLY B 386 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 426 through 428 removed outlier: 3.624A pdb=" N ALA B 426 " --> pdb=" O LEU B 451 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ALA B 481 " --> pdb=" O PRO B 393 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N TYR B 391 " --> pdb=" O ASP B 483 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ARG B 398 " --> pdb=" O GLU B 566 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 426 through 428 removed outlier: 3.624A pdb=" N ALA B 426 " --> pdb=" O LEU B 451 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ALA B 481 " --> pdb=" O PRO B 393 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N TYR B 391 " --> pdb=" O ASP B 483 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N SER B 392 " --> pdb=" O HIS B 624 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N HIS B 624 " --> pdb=" O SER B 392 " (cutoff:3.500A) 391 hydrogen bonds defined for protein. 1044 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: 4.41 Time building geometry restraints manager: 2.82 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: 3331 1.34 - 1.46: 1969 1.46 - 1.57: 5016 1.57 - 1.69: 4 1.69 - 1.81: 60 Bond restraints: 10380 Sorted by residual: bond pdb=" O3P FAD A 901 " pdb=" P FAD A 901 " ideal model delta sigma weight residual 1.660 1.577 0.083 2.00e-02 2.50e+03 1.72e+01 bond pdb=" O3P FAD B 901 " pdb=" P FAD B 901 " ideal model delta sigma weight residual 1.660 1.577 0.083 2.00e-02 2.50e+03 1.71e+01 bond pdb=" O5B FAD A 901 " pdb=" PA FAD A 901 " ideal model delta sigma weight residual 1.634 1.565 0.069 2.00e-02 2.50e+03 1.21e+01 bond pdb=" O5' FAD B 901 " pdb=" P FAD B 901 " ideal model delta sigma weight residual 1.637 1.572 0.065 2.00e-02 2.50e+03 1.06e+01 bond pdb=" O5' FAD A 901 " pdb=" P FAD A 901 " ideal model delta sigma weight residual 1.637 1.573 0.064 2.00e-02 2.50e+03 1.04e+01 ... (remaining 10375 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.53: 13866 1.53 - 3.06: 252 3.06 - 4.59: 41 4.59 - 6.12: 11 6.12 - 7.66: 8 Bond angle restraints: 14178 Sorted by residual: angle pdb=" N ALA B 487 " pdb=" CA ALA B 487 " pdb=" C ALA B 487 " ideal model delta sigma weight residual 109.81 116.02 -6.21 2.21e+00 2.05e-01 7.89e+00 angle pdb=" O1P FAD A 901 " pdb=" P FAD A 901 " pdb=" O2P FAD A 901 " ideal model delta sigma weight residual 122.50 114.84 7.66 3.00e+00 1.11e-01 6.51e+00 angle pdb=" C MET B 567 " pdb=" N VAL B 568 " pdb=" CA VAL B 568 " ideal model delta sigma weight residual 123.16 120.46 2.70 1.06e+00 8.90e-01 6.49e+00 angle pdb=" N ALA A 487 " pdb=" CA ALA A 487 " pdb=" C ALA A 487 " ideal model delta sigma weight residual 109.81 115.42 -5.61 2.21e+00 2.05e-01 6.44e+00 angle pdb=" O1A FAD B 901 " pdb=" PA FAD B 901 " pdb=" O2A FAD B 901 " ideal model delta sigma weight residual 121.20 113.91 7.29 3.00e+00 1.11e-01 5.91e+00 ... (remaining 14173 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.52: 5571 17.52 - 35.05: 464 35.05 - 52.57: 84 52.57 - 70.09: 21 70.09 - 87.62: 6 Dihedral angle restraints: 6146 sinusoidal: 2426 harmonic: 3720 Sorted by residual: dihedral pdb=" CA ASN B 666 " pdb=" C ASN B 666 " pdb=" N THR B 667 " pdb=" CA THR B 667 " ideal model delta harmonic sigma weight residual -180.00 -161.85 -18.15 0 5.00e+00 4.00e-02 1.32e+01 dihedral pdb=" CA ASN A 666 " pdb=" C ASN A 666 " pdb=" N THR A 667 " pdb=" CA THR A 667 " ideal model delta harmonic sigma weight residual -180.00 -162.17 -17.83 0 5.00e+00 4.00e-02 1.27e+01 dihedral pdb=" CA VAL A 503 " pdb=" C VAL A 503 " pdb=" N PRO A 504 " pdb=" CA PRO A 504 " ideal model delta harmonic sigma weight residual 180.00 162.55 17.45 0 5.00e+00 4.00e-02 1.22e+01 ... (remaining 6143 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 913 0.031 - 0.063: 399 0.063 - 0.094: 145 0.094 - 0.125: 98 0.125 - 0.157: 17 Chirality restraints: 1572 Sorted by residual: chirality pdb=" CA ILE B 459 " pdb=" N ILE B 459 " pdb=" C ILE B 459 " pdb=" CB ILE B 459 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.14e-01 chirality pdb=" C2B FAD A 901 " pdb=" C1B FAD A 901 " pdb=" C3B FAD A 901 " pdb=" O2B FAD A 901 " both_signs ideal model delta sigma weight residual False -2.53 -2.69 0.15 2.00e-01 2.50e+01 5.84e-01 chirality pdb=" C2B FAD B 901 " pdb=" C1B FAD B 901 " pdb=" C3B FAD B 901 " pdb=" O2B FAD B 901 " both_signs ideal model delta sigma weight residual False -2.53 -2.68 0.14 2.00e-01 2.50e+01 5.19e-01 ... (remaining 1569 not shown) Planarity restraints: 1844 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU B 402 " -0.040 5.00e-02 4.00e+02 6.06e-02 5.88e+00 pdb=" N PRO B 403 " 0.105 5.00e-02 4.00e+02 pdb=" CA PRO B 403 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 403 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR B 569 " -0.030 5.00e-02 4.00e+02 4.55e-02 3.31e+00 pdb=" N PRO B 570 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO B 570 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 570 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A 569 " -0.028 5.00e-02 4.00e+02 4.29e-02 2.94e+00 pdb=" N PRO A 570 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO A 570 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 570 " -0.024 5.00e-02 4.00e+02 ... (remaining 1841 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 1747 2.77 - 3.30: 9368 3.30 - 3.83: 16573 3.83 - 4.37: 19676 4.37 - 4.90: 34634 Nonbonded interactions: 81998 Sorted by model distance: nonbonded pdb=" O TYR B 281 " pdb=" OG1 THR B 285 " model vdw 2.232 3.040 nonbonded pdb=" O GLY A 149 " pdb=" OG1 THR A 152 " model vdw 2.241 3.040 nonbonded pdb=" OE2 GLU B 87 " pdb=" O2B FAD B 901 " model vdw 2.251 3.040 nonbonded pdb=" O GLY A 174 " pdb=" NH2 ARG A 677 " model vdw 2.258 3.120 nonbonded pdb=" OE2 GLU A 87 " pdb=" O2B FAD A 901 " model vdw 2.263 3.040 ... (remaining 81993 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 5.080 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: 0.080 Check model and map are aligned: 0.060 Set scattering table: 0.100 Process input model: 28.300 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.060 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: 0.010 Load rotamer database and sin/cos tables:3.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 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 0.083 10380 Z= 0.254 Angle : 0.557 7.656 14178 Z= 0.280 Chirality : 0.047 0.157 1572 Planarity : 0.005 0.061 1844 Dihedral : 13.568 87.616 3786 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % 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: -0.23 (0.24), residues: 1294 helix: 0.52 (0.26), residues: 414 sheet: 0.09 (0.40), residues: 202 loop : -0.59 (0.24), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 125 HIS 0.003 0.001 HIS B 144 PHE 0.023 0.001 PHE B 486 TYR 0.009 0.001 TYR B 618 ARG 0.006 0.000 ARG A 606 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 1.151 Fit side-chains revert: symmetry clash REVERT: A 216 GLN cc_start: 0.7637 (tm-30) cc_final: 0.7248 (tm-30) REVERT: B 216 GLN cc_start: 0.7497 (tt0) cc_final: 0.7270 (tp-100) outliers start: 0 outliers final: 0 residues processed: 60 average time/residue: 0.3141 time to fit residues: 25.6568 Evaluate side-chains 49 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 108 optimal weight: 2.9990 chunk 97 optimal weight: 9.9990 chunk 53 optimal weight: 5.9990 chunk 33 optimal weight: 9.9990 chunk 65 optimal weight: 1.9990 chunk 51 optimal weight: 10.0000 chunk 100 optimal weight: 10.0000 chunk 38 optimal weight: 0.0060 chunk 61 optimal weight: 0.3980 chunk 74 optimal weight: 2.9990 chunk 116 optimal weight: 0.9990 overall best weight: 1.2802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 666 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2466 r_free = 0.2466 target = 0.052535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2273 r_free = 0.2273 target = 0.044320 restraints weight = 26327.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2297 r_free = 0.2297 target = 0.045295 restraints weight = 17107.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2315 r_free = 0.2315 target = 0.046007 restraints weight = 12622.808| |-----------------------------------------------------------------------------| r_work (final): 0.2311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.0714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 10380 Z= 0.143 Angle : 0.515 5.664 14178 Z= 0.270 Chirality : 0.046 0.148 1572 Planarity : 0.005 0.049 1844 Dihedral : 6.023 74.348 1514 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % 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: -0.02 (0.24), residues: 1294 helix: 0.78 (0.26), residues: 404 sheet: 0.07 (0.40), residues: 198 loop : -0.46 (0.24), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 125 HIS 0.002 0.001 HIS B 73 PHE 0.017 0.001 PHE B 486 TYR 0.011 0.001 TYR B 592 ARG 0.004 0.000 ARG A 606 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 1.200 Fit side-chains REVERT: A 216 GLN cc_start: 0.7608 (tm-30) cc_final: 0.7226 (tm-30) outliers start: 0 outliers final: 0 residues processed: 59 average time/residue: 0.2887 time to fit residues: 23.8002 Evaluate side-chains 50 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 1.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 36 optimal weight: 6.9990 chunk 121 optimal weight: 7.9990 chunk 21 optimal weight: 0.3980 chunk 59 optimal weight: 0.0980 chunk 4 optimal weight: 5.9990 chunk 70 optimal weight: 9.9990 chunk 62 optimal weight: 10.0000 chunk 35 optimal weight: 2.9990 chunk 38 optimal weight: 0.6980 chunk 71 optimal weight: 7.9990 chunk 98 optimal weight: 10.0000 overall best weight: 2.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 524 GLN ** B 666 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2464 r_free = 0.2464 target = 0.052521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2271 r_free = 0.2271 target = 0.044202 restraints weight = 26453.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.2295 r_free = 0.2295 target = 0.045196 restraints weight = 17133.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2313 r_free = 0.2313 target = 0.045911 restraints weight = 12686.121| |-----------------------------------------------------------------------------| r_work (final): 0.2311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.0923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 10380 Z= 0.163 Angle : 0.513 5.554 14178 Z= 0.266 Chirality : 0.047 0.162 1572 Planarity : 0.005 0.050 1844 Dihedral : 5.628 73.265 1514 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % 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: 0.17 (0.24), residues: 1294 helix: 1.07 (0.27), residues: 390 sheet: 0.01 (0.39), residues: 198 loop : -0.35 (0.24), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 125 HIS 0.003 0.001 HIS B 73 PHE 0.018 0.001 PHE B 486 TYR 0.010 0.001 TYR B 491 ARG 0.006 0.000 ARG A 606 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 1.155 Fit side-chains REVERT: A 216 GLN cc_start: 0.7535 (tm-30) cc_final: 0.7165 (tm-30) outliers start: 0 outliers final: 0 residues processed: 59 average time/residue: 0.2822 time to fit residues: 23.6939 Evaluate side-chains 50 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 1.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 43 optimal weight: 20.0000 chunk 25 optimal weight: 10.0000 chunk 18 optimal weight: 20.0000 chunk 64 optimal weight: 20.0000 chunk 76 optimal weight: 7.9990 chunk 1 optimal weight: 0.0870 chunk 48 optimal weight: 2.9990 chunk 27 optimal weight: 6.9990 chunk 20 optimal weight: 10.0000 chunk 105 optimal weight: 10.0000 chunk 89 optimal weight: 20.0000 overall best weight: 5.6168 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 ASN ** A 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 666 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2417 r_free = 0.2417 target = 0.050437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2218 r_free = 0.2218 target = 0.042084 restraints weight = 26904.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2240 r_free = 0.2240 target = 0.043001 restraints weight = 17781.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2257 r_free = 0.2257 target = 0.043673 restraints weight = 13363.739| |-----------------------------------------------------------------------------| r_work (final): 0.2255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.0998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 10380 Z= 0.319 Angle : 0.602 7.574 14178 Z= 0.312 Chirality : 0.050 0.171 1572 Planarity : 0.005 0.050 1844 Dihedral : 5.820 73.999 1514 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % 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: -0.05 (0.24), residues: 1294 helix: 0.89 (0.27), residues: 390 sheet: 0.00 (0.39), residues: 192 loop : -0.52 (0.23), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 125 HIS 0.005 0.001 HIS A 336 PHE 0.021 0.002 PHE A 365 TYR 0.013 0.002 TYR A 491 ARG 0.005 0.000 ARG B 156 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 1.189 Fit side-chains REVERT: A 216 GLN cc_start: 0.7561 (tm-30) cc_final: 0.7219 (tm-30) outliers start: 0 outliers final: 0 residues processed: 56 average time/residue: 0.2591 time to fit residues: 21.0601 Evaluate side-chains 49 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 1.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 114 optimal weight: 9.9990 chunk 121 optimal weight: 4.9990 chunk 20 optimal weight: 0.9990 chunk 86 optimal weight: 7.9990 chunk 70 optimal weight: 0.0670 chunk 9 optimal weight: 9.9990 chunk 61 optimal weight: 8.9990 chunk 33 optimal weight: 2.9990 chunk 54 optimal weight: 10.0000 chunk 48 optimal weight: 2.9990 chunk 120 optimal weight: 5.9990 overall best weight: 2.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 379 ASN B 666 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2450 r_free = 0.2450 target = 0.051819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2254 r_free = 0.2254 target = 0.043496 restraints weight = 26542.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2278 r_free = 0.2278 target = 0.044467 restraints weight = 17225.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2294 r_free = 0.2294 target = 0.045126 restraints weight = 12827.421| |-----------------------------------------------------------------------------| r_work (final): 0.2291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.1065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10380 Z= 0.176 Angle : 0.525 6.619 14178 Z= 0.272 Chirality : 0.047 0.155 1572 Planarity : 0.004 0.047 1844 Dihedral : 5.564 74.966 1514 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 0.09 % Allowed : 2.03 % Favored : 97.87 % 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: 0.05 (0.24), residues: 1294 helix: 1.01 (0.27), residues: 390 sheet: 0.02 (0.39), residues: 192 loop : -0.46 (0.24), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 125 HIS 0.003 0.001 HIS B 73 PHE 0.013 0.001 PHE B 486 TYR 0.012 0.001 TYR B 491 ARG 0.004 0.000 ARG A 606 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 60 time to evaluate : 1.141 Fit side-chains REVERT: A 216 GLN cc_start: 0.7539 (tm-30) cc_final: 0.7186 (tm-30) REVERT: B 216 GLN cc_start: 0.7541 (tp-100) cc_final: 0.7279 (tt0) outliers start: 1 outliers final: 0 residues processed: 61 average time/residue: 0.2702 time to fit residues: 23.3742 Evaluate side-chains 47 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 1.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 88 optimal weight: 7.9990 chunk 43 optimal weight: 6.9990 chunk 102 optimal weight: 10.0000 chunk 101 optimal weight: 20.0000 chunk 23 optimal weight: 6.9990 chunk 29 optimal weight: 9.9990 chunk 22 optimal weight: 2.9990 chunk 48 optimal weight: 8.9990 chunk 105 optimal weight: 9.9990 chunk 17 optimal weight: 10.0000 chunk 14 optimal weight: 20.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 524 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2401 r_free = 0.2401 target = 0.049700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2211 r_free = 0.2211 target = 0.041859 restraints weight = 27357.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2230 r_free = 0.2230 target = 0.042622 restraints weight = 18946.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.2244 r_free = 0.2244 target = 0.043153 restraints weight = 14759.318| |-----------------------------------------------------------------------------| r_work (final): 0.2242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.1150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 10380 Z= 0.388 Angle : 0.644 8.326 14178 Z= 0.335 Chirality : 0.052 0.170 1572 Planarity : 0.005 0.047 1844 Dihedral : 6.058 76.639 1514 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % 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: -0.29 (0.23), residues: 1294 helix: 0.67 (0.26), residues: 396 sheet: -0.16 (0.39), residues: 192 loop : -0.67 (0.23), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 125 HIS 0.006 0.002 HIS A 336 PHE 0.026 0.002 PHE A 486 TYR 0.014 0.002 TYR A 465 ARG 0.005 0.001 ARG B 156 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 1.191 Fit side-chains REVERT: A 216 GLN cc_start: 0.7583 (tm-30) cc_final: 0.7269 (tm-30) outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.3109 time to fit residues: 23.2503 Evaluate side-chains 45 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 1.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 20 optimal weight: 9.9990 chunk 83 optimal weight: 9.9990 chunk 58 optimal weight: 0.4980 chunk 50 optimal weight: 10.0000 chunk 68 optimal weight: 5.9990 chunk 34 optimal weight: 10.0000 chunk 64 optimal weight: 10.0000 chunk 43 optimal weight: 4.9990 chunk 125 optimal weight: 10.0000 chunk 85 optimal weight: 10.0000 chunk 89 optimal weight: 5.9990 overall best weight: 5.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2413 r_free = 0.2413 target = 0.050179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2224 r_free = 0.2224 target = 0.042364 restraints weight = 27206.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2243 r_free = 0.2243 target = 0.043108 restraints weight = 18869.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2257 r_free = 0.2257 target = 0.043650 restraints weight = 14717.039| |-----------------------------------------------------------------------------| r_work (final): 0.2255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.1153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 10380 Z= 0.322 Angle : 0.614 7.870 14178 Z= 0.320 Chirality : 0.051 0.191 1572 Planarity : 0.005 0.052 1844 Dihedral : 6.017 78.218 1514 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % 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: -0.31 (0.23), residues: 1294 helix: 0.70 (0.26), residues: 396 sheet: -0.15 (0.39), residues: 192 loop : -0.71 (0.23), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 125 HIS 0.004 0.001 HIS A 336 PHE 0.025 0.002 PHE A 486 TYR 0.013 0.002 TYR A 491 ARG 0.008 0.001 ARG A 606 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 1.100 Fit side-chains REVERT: A 216 GLN cc_start: 0.7563 (tm-30) cc_final: 0.7249 (tm-30) REVERT: B 153 MET cc_start: 0.7735 (ttp) cc_final: 0.7449 (ttp) outliers start: 0 outliers final: 0 residues processed: 59 average time/residue: 0.2967 time to fit residues: 24.7882 Evaluate side-chains 49 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 1.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 104 optimal weight: 5.9990 chunk 26 optimal weight: 9.9990 chunk 1 optimal weight: 20.0000 chunk 57 optimal weight: 5.9990 chunk 22 optimal weight: 2.9990 chunk 61 optimal weight: 7.9990 chunk 66 optimal weight: 9.9990 chunk 13 optimal weight: 0.0570 chunk 12 optimal weight: 5.9990 chunk 52 optimal weight: 6.9990 chunk 124 optimal weight: 0.8980 overall best weight: 3.1904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2432 r_free = 0.2432 target = 0.051041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2232 r_free = 0.2232 target = 0.042637 restraints weight = 27292.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.2258 r_free = 0.2258 target = 0.043661 restraints weight = 17462.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2276 r_free = 0.2276 target = 0.044370 restraints weight = 12749.300| |-----------------------------------------------------------------------------| r_work (final): 0.2274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.1145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10380 Z= 0.219 Angle : 0.565 7.050 14178 Z= 0.294 Chirality : 0.048 0.174 1572 Planarity : 0.005 0.049 1844 Dihedral : 5.820 79.368 1514 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.24), residues: 1294 helix: 0.97 (0.27), residues: 382 sheet: -0.12 (0.39), residues: 192 loop : -0.52 (0.23), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 125 HIS 0.003 0.001 HIS B 73 PHE 0.021 0.001 PHE A 486 TYR 0.012 0.001 TYR B 491 ARG 0.007 0.000 ARG A 606 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 1.227 Fit side-chains REVERT: A 216 GLN cc_start: 0.7515 (tm-30) cc_final: 0.7167 (tm-30) outliers start: 0 outliers final: 0 residues processed: 59 average time/residue: 0.2647 time to fit residues: 22.5222 Evaluate side-chains 47 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 1.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 52 optimal weight: 10.0000 chunk 126 optimal weight: 7.9990 chunk 17 optimal weight: 10.0000 chunk 97 optimal weight: 10.0000 chunk 65 optimal weight: 9.9990 chunk 44 optimal weight: 8.9990 chunk 83 optimal weight: 0.0870 chunk 42 optimal weight: 9.9990 chunk 82 optimal weight: 0.0870 chunk 14 optimal weight: 6.9990 chunk 72 optimal weight: 2.9990 overall best weight: 3.6342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2433 r_free = 0.2433 target = 0.051039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2248 r_free = 0.2248 target = 0.043252 restraints weight = 26945.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2268 r_free = 0.2268 target = 0.044044 restraints weight = 18652.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2282 r_free = 0.2282 target = 0.044611 restraints weight = 14414.167| |-----------------------------------------------------------------------------| r_work (final): 0.2279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.1150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 10380 Z= 0.233 Angle : 0.569 7.081 14178 Z= 0.296 Chirality : 0.049 0.169 1572 Planarity : 0.005 0.050 1844 Dihedral : 5.803 79.405 1514 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % 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: -0.02 (0.24), residues: 1294 helix: 1.01 (0.27), residues: 382 sheet: -0.09 (0.39), residues: 192 loop : -0.51 (0.23), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 125 HIS 0.003 0.001 HIS B 73 PHE 0.021 0.002 PHE A 486 TYR 0.013 0.001 TYR B 491 ARG 0.006 0.000 ARG A 606 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 1.220 Fit side-chains REVERT: A 216 GLN cc_start: 0.7526 (tm-30) cc_final: 0.7203 (tm-30) REVERT: B 153 MET cc_start: 0.7632 (ttp) cc_final: 0.7418 (ttp) outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.2576 time to fit residues: 20.4176 Evaluate side-chains 48 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 1.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 121 optimal weight: 6.9990 chunk 125 optimal weight: 8.9990 chunk 102 optimal weight: 8.9990 chunk 66 optimal weight: 10.0000 chunk 99 optimal weight: 10.0000 chunk 114 optimal weight: 9.9990 chunk 4 optimal weight: 4.9990 chunk 15 optimal weight: 10.0000 chunk 101 optimal weight: 0.0020 chunk 28 optimal weight: 10.0000 chunk 5 optimal weight: 0.6980 overall best weight: 4.3394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2424 r_free = 0.2424 target = 0.050654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2228 r_free = 0.2228 target = 0.042453 restraints weight = 27210.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2252 r_free = 0.2252 target = 0.043406 restraints weight = 17712.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2268 r_free = 0.2268 target = 0.044048 restraints weight = 13095.679| |-----------------------------------------------------------------------------| r_work (final): 0.2266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.1183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 10380 Z= 0.268 Angle : 0.592 7.356 14178 Z= 0.306 Chirality : 0.049 0.171 1572 Planarity : 0.005 0.051 1844 Dihedral : 5.866 79.634 1514 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % 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: -0.07 (0.23), residues: 1294 helix: 0.95 (0.27), residues: 382 sheet: -0.11 (0.39), residues: 192 loop : -0.53 (0.23), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 125 HIS 0.004 0.001 HIS B 73 PHE 0.022 0.002 PHE A 486 TYR 0.013 0.001 TYR B 491 ARG 0.006 0.000 ARG A 606 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 1.112 Fit side-chains REVERT: A 216 GLN cc_start: 0.7574 (tm-30) cc_final: 0.7226 (tm-30) REVERT: B 153 MET cc_start: 0.7656 (ttp) cc_final: 0.7448 (ttp) outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.2666 time to fit residues: 21.0593 Evaluate side-chains 47 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 1.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 51 optimal weight: 5.9990 chunk 30 optimal weight: 5.9990 chunk 35 optimal weight: 10.0000 chunk 50 optimal weight: 9.9990 chunk 37 optimal weight: 8.9990 chunk 72 optimal weight: 0.2980 chunk 48 optimal weight: 3.9990 chunk 34 optimal weight: 9.9990 chunk 75 optimal weight: 3.9990 chunk 106 optimal weight: 4.9990 chunk 23 optimal weight: 5.9990 overall best weight: 3.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2428 r_free = 0.2428 target = 0.050841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2230 r_free = 0.2230 target = 0.042619 restraints weight = 26978.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2254 r_free = 0.2254 target = 0.043550 restraints weight = 17510.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2271 r_free = 0.2271 target = 0.044249 restraints weight = 12978.168| |-----------------------------------------------------------------------------| r_work (final): 0.2269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.1180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 10380 Z= 0.244 Angle : 0.570 7.196 14178 Z= 0.296 Chirality : 0.049 0.168 1572 Planarity : 0.005 0.051 1844 Dihedral : 5.822 79.800 1514 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 0.00 % Allowed : 0.09 % Favored : 99.91 % 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: -0.04 (0.24), residues: 1294 helix: 1.00 (0.27), residues: 382 sheet: -0.12 (0.39), residues: 192 loop : -0.52 (0.23), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 125 HIS 0.003 0.001 HIS B 73 PHE 0.021 0.002 PHE A 486 TYR 0.013 0.001 TYR B 491 ARG 0.006 0.000 ARG A 606 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2338.49 seconds wall clock time: 43 minutes 42.26 seconds (2622.26 seconds total)