Starting phenix.real_space_refine on Thu Jul 2 20:48:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7ptv_13641/07_2026/7ptv_13641.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ptv_13641/07_2026/7ptv_13641.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7ptv_13641/07_2026/7ptv_13641.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ptv_13641/07_2026/7ptv_13641.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ptv_13641/07_2026/7ptv_13641.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ptv_13641/07_2026/7ptv_13641.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7ptv_13641/07_2026/7ptv_13641.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7ptv_13641/07_2026/7ptv_13641.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.003 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 30 5.16 5 C 6374 2.51 5 N 1678 2.21 5 O 1910 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 52 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9996 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 645, 4945 Classifications: {'peptide': 645} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 39, 'TRANS': 603} Chain: "A" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 53 Unusual residues: {'FAD': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: B Time building chain proxies: 3.10, per 1000 atoms: 0.31 Number of scatterers: 9996 At special positions: 0 Unit cell: (88.29, 98.1, 110.09, 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 30 16.00 P 4 15.00 O 1910 8.00 N 1678 7.00 C 6374 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: 1.06 Conformation dependent library (CDL) restraints added in 273.7 milliseconds 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2344 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 16 sheets defined 38.4% alpha, 20.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'A' and resid 69 through 80 removed outlier: 3.707A pdb=" N PHE A 80 " --> pdb=" O TYR A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 102 Processing helix chain 'A' and resid 103 through 108 Processing helix chain 'A' and resid 112 through 116 removed outlier: 4.295A pdb=" N ASN A 116 " --> pdb=" O PRO A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 122 Processing helix chain 'A' and resid 151 through 156 Processing helix chain 'A' and resid 165 through 173 removed outlier: 4.442A pdb=" N PHE A 169 " --> pdb=" O GLY A 165 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N TRP A 173 " --> pdb=" O PHE A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 181 Processing helix chain 'A' and resid 182 through 194 Processing helix chain 'A' and resid 202 through 221 removed outlier: 3.764A pdb=" N ASN A 206 " --> pdb=" O VAL A 202 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLN A 218 " --> pdb=" O VAL A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 288 Processing helix chain 'A' and resid 301 through 305 Processing helix chain 'A' and resid 354 through 363 Processing helix chain 'A' and resid 366 through 374 Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.929A pdb=" N GLY A 442 " --> pdb=" O SER A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 468 Processing helix chain 'A' and resid 520 through 523 Processing helix chain 'A' and resid 524 through 558 removed outlier: 3.725A pdb=" N ALA A 528 " --> pdb=" O GLN A 524 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N LYS A 530 " --> pdb=" O PRO A 526 " (cutoff:3.500A) Proline residue: A 534 - end of helix removed outlier: 3.914A pdb=" N ILE A 548 " --> pdb=" O ALA A 544 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N VAL A 549 " --> pdb=" O ILE A 545 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N GLN A 550 " --> pdb=" O TYR A 546 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N GLN A 551 " --> pdb=" O GLN A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 586 removed outlier: 3.652A pdb=" N LEU A 578 " --> pdb=" O LEU A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 593 removed outlier: 4.677A pdb=" N TRP A 590 " --> pdb=" O ILE A 587 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 599 removed outlier: 3.970A pdb=" N VAL A 598 " --> pdb=" O VAL A 594 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N ASN A 599 " --> pdb=" O PRO A 595 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 594 through 599' Processing helix chain 'A' and resid 602 through 616 Processing helix chain 'A' and resid 616 through 622 removed outlier: 4.237A pdb=" N ARG A 620 " --> pdb=" O SER A 616 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 659 Processing helix chain 'A' and resid 668 through 684 removed outlier: 3.650A pdb=" N ASP A 680 " --> pdb=" O ALA A 676 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 691 removed outlier: 3.524A pdb=" N ASN A 690 " --> pdb=" O LEU A 687 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 80 removed outlier: 3.707A pdb=" N PHE B 80 " --> pdb=" O TYR B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 102 Processing helix chain 'B' and resid 103 through 108 Processing helix chain 'B' and resid 112 through 116 removed outlier: 4.295A pdb=" N ASN B 116 " --> pdb=" O PRO B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 122 Processing helix chain 'B' and resid 151 through 156 Processing helix chain 'B' and resid 165 through 173 removed outlier: 4.442A pdb=" N PHE B 169 " --> pdb=" O GLY B 165 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N TRP B 173 " --> pdb=" O PHE B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 181 Processing helix chain 'B' and resid 182 through 194 Processing helix chain 'B' and resid 202 through 221 removed outlier: 3.764A pdb=" N ASN B 206 " --> pdb=" O VAL B 202 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLN B 218 " --> pdb=" O VAL B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 288 Processing helix chain 'B' and resid 301 through 305 Processing helix chain 'B' and resid 354 through 363 Processing helix chain 'B' and resid 366 through 374 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.930A pdb=" N GLY B 442 " --> pdb=" O SER B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 460 through 468 Processing helix chain 'B' and resid 520 through 523 Processing helix chain 'B' and resid 524 through 558 removed outlier: 3.723A pdb=" N ALA B 528 " --> pdb=" O GLN B 524 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N LYS B 530 " --> pdb=" O PRO B 526 " (cutoff:3.500A) Proline residue: B 534 - end of helix removed outlier: 3.915A pdb=" N ILE B 548 " --> pdb=" O ALA B 544 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N VAL B 549 " --> pdb=" O ILE B 545 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N GLN B 550 " --> pdb=" O TYR B 546 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N GLN B 551 " --> pdb=" O GLN B 547 " (cutoff:3.500A) Processing helix chain 'B' and resid 571 through 586 removed outlier: 3.651A pdb=" N LEU B 578 " --> pdb=" O LEU B 574 " (cutoff:3.500A) Processing helix chain 'B' and resid 587 through 593 removed outlier: 4.677A pdb=" N TRP B 590 " --> pdb=" O ILE B 587 " (cutoff:3.500A) Processing helix chain 'B' and resid 594 through 599 removed outlier: 3.969A pdb=" N VAL B 598 " --> pdb=" O VAL B 594 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N ASN B 599 " --> pdb=" O PRO B 595 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 594 through 599' Processing helix chain 'B' and resid 602 through 616 Processing helix chain 'B' and resid 616 through 622 removed outlier: 4.237A pdb=" N ARG B 620 " --> pdb=" O SER B 616 " (cutoff:3.500A) Processing helix chain 'B' and resid 655 through 659 Processing helix chain 'B' and resid 668 through 684 removed outlier: 3.650A pdb=" N ASP B 680 " --> pdb=" O ALA B 676 " (cutoff:3.500A) Processing helix chain 'B' and resid 687 through 691 removed outlier: 3.524A pdb=" N ASN B 690 " --> pdb=" O LEU B 687 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 307 through 310 removed outlier: 6.304A pdb=" N ILE A 85 " --> pdb=" O ARG A 308 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N ILE A 310 " --> pdb=" O ILE A 85 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N LEU A 87 " --> pdb=" O ILE A 310 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N ASP A 60 " --> pdb=" O GLU A 345 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N GLU A 347 " --> pdb=" O ASP A 60 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N VAL A 62 " --> pdb=" O GLU A 347 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N VAL A 326 " --> pdb=" O VAL A 342 " (cutoff:3.500A) removed outlier: 9.968A pdb=" N LYS A 344 " --> pdb=" O ARG A 324 " (cutoff:3.500A) removed outlier: 9.713A pdb=" N ARG A 324 " --> pdb=" O LYS A 344 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N ALA A 325 " --> pdb=" O GLU A 321 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N GLU A 321 " --> pdb=" O ALA A 325 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N THR A 329 " --> pdb=" O ARG A 317 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ARG A 317 " --> pdb=" O THR A 329 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ILE A 331 " --> pdb=" O VAL A 315 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N VAL A 315 " --> pdb=" O ILE A 331 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 307 through 310 removed outlier: 6.304A pdb=" N ILE A 85 " --> pdb=" O ARG A 308 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N ILE A 310 " --> pdb=" O ILE A 85 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N LEU A 87 " --> pdb=" O ILE A 310 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N ASP A 60 " --> pdb=" O GLU A 345 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N GLU A 347 " --> pdb=" O ASP A 60 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N VAL A 62 " --> pdb=" O GLU A 347 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N ARG A 652 " --> pdb=" O LYS A 344 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N VAL A 346 " --> pdb=" O ARG A 652 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 126 through 127 Processing sheet with id=AA4, first strand: chain 'A' and resid 262 through 263 removed outlier: 3.623A pdb=" N GLY A 426 " --> pdb=" O LEU A 451 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ALA A 481 " --> pdb=" O PRO A 395 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N TYR A 393 " --> pdb=" O ASP A 483 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N GLN A 398 " --> pdb=" O ALA A 568 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 262 through 263 removed outlier: 3.623A pdb=" N GLY A 426 " --> pdb=" O LEU A 451 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ALA A 481 " --> pdb=" O PRO A 395 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N TYR A 393 " --> pdb=" O ASP A 483 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 271 through 273 Processing sheet with id=AA7, first strand: chain 'A' and resid 364 through 365 Processing sheet with id=AA8, first strand: chain 'A' and resid 491 through 493 Processing sheet with id=AA9, first strand: chain 'B' and resid 307 through 310 removed outlier: 6.304A pdb=" N ILE B 85 " --> pdb=" O ARG B 308 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N ILE B 310 " --> pdb=" O ILE B 85 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N LEU B 87 " --> pdb=" O ILE B 310 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N ASP B 60 " --> pdb=" O GLU B 345 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N GLU B 347 " --> pdb=" O ASP B 60 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N VAL B 62 " --> pdb=" O GLU B 347 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N VAL B 326 " --> pdb=" O VAL B 342 " (cutoff:3.500A) removed outlier: 9.967A pdb=" N LYS B 344 " --> pdb=" O ARG B 324 " (cutoff:3.500A) removed outlier: 9.714A pdb=" N ARG B 324 " --> pdb=" O LYS B 344 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N ALA B 325 " --> pdb=" O GLU B 321 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N GLU B 321 " --> pdb=" O ALA B 325 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N THR B 329 " --> pdb=" O ARG B 317 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N ARG B 317 " --> pdb=" O THR B 329 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ILE B 331 " --> pdb=" O VAL B 315 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N VAL B 315 " --> pdb=" O ILE B 331 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 307 through 310 removed outlier: 6.304A pdb=" N ILE B 85 " --> pdb=" O ARG B 308 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N ILE B 310 " --> pdb=" O ILE B 85 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N LEU B 87 " --> pdb=" O ILE B 310 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N ASP B 60 " --> pdb=" O GLU B 345 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N GLU B 347 " --> pdb=" O ASP B 60 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N VAL B 62 " --> pdb=" O GLU B 347 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N ARG B 652 " --> pdb=" O LYS B 344 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N VAL B 346 " --> pdb=" O ARG B 652 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 126 through 127 Processing sheet with id=AB3, first strand: chain 'B' and resid 262 through 263 removed outlier: 3.623A pdb=" N GLY B 426 " --> pdb=" O LEU B 451 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ALA B 481 " --> pdb=" O PRO B 395 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N TYR B 393 " --> pdb=" O ASP B 483 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N GLN B 398 " --> pdb=" O ALA B 568 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 262 through 263 removed outlier: 3.623A pdb=" N GLY B 426 " --> pdb=" O LEU B 451 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ALA B 481 " --> pdb=" O PRO B 395 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N TYR B 393 " --> pdb=" O ASP B 483 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 271 through 273 Processing sheet with id=AB6, first strand: chain 'B' and resid 364 through 365 Processing sheet with id=AB7, first strand: chain 'B' and resid 491 through 493 386 hydrogen bonds defined for protein. 984 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: 1.56 Time building geometry restraints manager: 1.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3225 1.34 - 1.45: 1512 1.45 - 1.57: 5465 1.57 - 1.68: 10 1.68 - 1.80: 48 Bond restraints: 10260 Sorted by residual: bond pdb=" O3P FAD B 901 " pdb=" P FAD B 901 " ideal model delta sigma weight residual 1.660 1.571 0.089 2.00e-02 2.50e+03 1.96e+01 bond pdb=" O3P FAD A 901 " pdb=" P FAD A 901 " ideal model delta sigma weight residual 1.660 1.572 0.088 2.00e-02 2.50e+03 1.94e+01 bond pdb=" O5B FAD A 901 " pdb=" PA FAD A 901 " ideal model delta sigma weight residual 1.634 1.559 0.075 2.00e-02 2.50e+03 1.41e+01 bond pdb=" O5B FAD B 901 " pdb=" PA FAD B 901 " ideal model delta sigma weight residual 1.634 1.559 0.075 2.00e-02 2.50e+03 1.40e+01 bond pdb=" O5' FAD A 901 " pdb=" P FAD A 901 " ideal model delta sigma weight residual 1.637 1.572 0.065 2.00e-02 2.50e+03 1.05e+01 ... (remaining 10255 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.85: 13514 1.85 - 3.71: 440 3.71 - 5.56: 52 5.56 - 7.41: 14 7.41 - 9.27: 12 Bond angle restraints: 14032 Sorted by residual: angle pdb=" CA GLN A 551 " pdb=" CB GLN A 551 " pdb=" CG GLN A 551 " ideal model delta sigma weight residual 114.10 121.61 -7.51 2.00e+00 2.50e-01 1.41e+01 angle pdb=" CA GLN B 551 " pdb=" CB GLN B 551 " pdb=" CG GLN B 551 " ideal model delta sigma weight residual 114.10 121.61 -7.51 2.00e+00 2.50e-01 1.41e+01 angle pdb=" CB GLN B 551 " pdb=" CG GLN B 551 " pdb=" CD GLN B 551 " ideal model delta sigma weight residual 112.60 118.43 -5.83 1.70e+00 3.46e-01 1.17e+01 angle pdb=" CB GLN A 551 " pdb=" CG GLN A 551 " pdb=" CD GLN A 551 " ideal model delta sigma weight residual 112.60 118.41 -5.81 1.70e+00 3.46e-01 1.17e+01 angle pdb=" CA LYS A 303 " pdb=" CB LYS A 303 " pdb=" CG LYS A 303 " ideal model delta sigma weight residual 114.10 120.45 -6.35 2.00e+00 2.50e-01 1.01e+01 ... (remaining 14027 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.71: 5384 16.71 - 33.42: 441 33.42 - 50.13: 97 50.13 - 66.84: 30 66.84 - 83.55: 6 Dihedral angle restraints: 5958 sinusoidal: 2256 harmonic: 3702 Sorted by residual: dihedral pdb=" CA HIS B 319 " pdb=" C HIS B 319 " pdb=" N PHE B 320 " pdb=" CA PHE B 320 " ideal model delta harmonic sigma weight residual -180.00 -143.51 -36.49 0 5.00e+00 4.00e-02 5.33e+01 dihedral pdb=" CA HIS A 319 " pdb=" C HIS A 319 " pdb=" N PHE A 320 " pdb=" CA PHE A 320 " ideal model delta harmonic sigma weight residual -180.00 -143.52 -36.48 0 5.00e+00 4.00e-02 5.32e+01 dihedral pdb=" CA VAL B 144 " pdb=" C VAL B 144 " pdb=" N ALA B 145 " pdb=" CA ALA B 145 " ideal model delta harmonic sigma weight residual -180.00 -159.30 -20.70 0 5.00e+00 4.00e-02 1.71e+01 ... (remaining 5955 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 874 0.041 - 0.082: 471 0.082 - 0.122: 177 0.122 - 0.163: 38 0.163 - 0.204: 4 Chirality restraints: 1564 Sorted by residual: chirality pdb=" CA TYR A 161 " pdb=" N TYR A 161 " pdb=" C TYR A 161 " pdb=" CB TYR A 161 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" CA TYR B 161 " pdb=" N TYR B 161 " pdb=" C TYR B 161 " pdb=" CB TYR B 161 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.03e+00 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 -2.72 0.18 2.00e-01 2.50e+01 8.12e-01 ... (remaining 1561 not shown) Planarity restraints: 1812 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN A 128 " 0.042 5.00e-02 4.00e+02 6.29e-02 6.32e+00 pdb=" N PRO A 129 " -0.109 5.00e-02 4.00e+02 pdb=" CA PRO A 129 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 129 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN B 128 " 0.041 5.00e-02 4.00e+02 6.24e-02 6.23e+00 pdb=" N PRO B 129 " -0.108 5.00e-02 4.00e+02 pdb=" CA PRO B 129 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 129 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP B 525 " 0.033 5.00e-02 4.00e+02 5.01e-02 4.01e+00 pdb=" N PRO B 526 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO B 526 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 526 " 0.028 5.00e-02 4.00e+02 ... (remaining 1809 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 2574 2.79 - 3.32: 9064 3.32 - 3.84: 16491 3.84 - 4.37: 20057 4.37 - 4.90: 33931 Nonbonded interactions: 82117 Sorted by model distance: nonbonded pdb=" O ASN A 157 " pdb=" NH2 ARG A 281 " model vdw 2.259 3.120 nonbonded pdb=" O ASN B 157 " pdb=" NH2 ARG B 281 " model vdw 2.260 3.120 nonbonded pdb=" NH2 ARG A 213 " pdb=" O GLU A 241 " model vdw 2.304 3.120 nonbonded pdb=" NH2 ARG B 213 " pdb=" O GLU B 241 " model vdw 2.305 3.120 nonbonded pdb=" OD2 ASP B 192 " pdb=" OH TYR B 288 " model vdw 2.312 3.040 ... (remaining 82112 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: 0.02 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.540 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: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 11.310 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 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:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 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 : 0.008 0.089 10260 Z= 0.321 Angle : 0.803 9.268 14032 Z= 0.422 Chirality : 0.055 0.204 1564 Planarity : 0.005 0.063 1812 Dihedral : 13.728 83.554 3614 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.40 % Favored : 91.60 % Rotamer: Outliers : 2.05 % Allowed : 1.12 % Favored : 96.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.53 (0.22), residues: 1286 helix: -0.54 (0.24), residues: 420 sheet: -0.23 (0.37), residues: 172 loop : -1.52 (0.23), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 188 TYR 0.034 0.002 TYR B 161 PHE 0.019 0.002 PHE A 367 TRP 0.013 0.002 TRP A 668 HIS 0.008 0.001 HIS A 343 Details of bonding type rmsd/Z covalent geometry : bond 0.00758 / 0.32 (10260) covalent geometry : angle 0.80259 / 0.42 (14032) hydrogen bonds : bond 0.17016 / 11.76 ( 348) hydrogen bonds : angle 6.15883 / 4.26 ( 984) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 141 time to evaluate : 0.331 Fit side-chains REVERT: A 343 HIS cc_start: 0.8284 (m-70) cc_final: 0.8078 (m170) REVERT: A 398 GLN cc_start: 0.6857 (pp30) cc_final: 0.6620 (pp30) REVERT: A 551 GLN cc_start: 0.7896 (OUTLIER) cc_final: 0.7384 (mp10) REVERT: A 641 THR cc_start: 0.8911 (OUTLIER) cc_final: 0.8638 (p) REVERT: B 518 THR cc_start: 0.8851 (p) cc_final: 0.8585 (t) outliers start: 22 outliers final: 1 residues processed: 145 average time/residue: 0.0763 time to fit residues: 16.3414 Evaluate side-chains 112 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 109 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 551 GLN Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 641 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 chunk 35 optimal weight: 0.0980 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 343 HIS B 142 ASN B 206 ASN B 387 GLN B 440 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.074227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2652 r_free = 0.2652 target = 0.064874 restraints weight = 20284.283| |-----------------------------------------------------------------------------| r_work (start): 0.2644 rms_B_bonded: 1.96 r_work: 0.2550 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2436 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8905 moved from start: 0.1161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10260 Z= 0.136 Angle : 0.619 7.465 14032 Z= 0.323 Chirality : 0.049 0.134 1564 Planarity : 0.005 0.050 1812 Dihedral : 6.529 83.010 1412 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 1.68 % Allowed : 7.64 % Favored : 90.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.28 (0.23), residues: 1286 helix: -0.10 (0.26), residues: 400 sheet: -0.41 (0.37), residues: 160 loop : -1.40 (0.22), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 677 TYR 0.015 0.001 TYR B 75 PHE 0.015 0.001 PHE A 228 TRP 0.009 0.001 TRP A 127 HIS 0.003 0.001 HIS A 319 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.14 (10260) covalent geometry : angle 0.61898 / 0.32 (14032) hydrogen bonds : bond 0.05287 / 3.45 ( 348) hydrogen bonds : angle 4.97703 / 3.46 ( 984) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 113 time to evaluate : 0.294 Fit side-chains REVERT: A 161 TYR cc_start: 0.8197 (OUTLIER) cc_final: 0.7960 (m-10) REVERT: A 398 GLN cc_start: 0.7713 (pp30) cc_final: 0.7452 (pp30) REVERT: A 523 GLN cc_start: 0.8764 (pt0) cc_final: 0.8197 (pp30) REVERT: A 641 THR cc_start: 0.9313 (OUTLIER) cc_final: 0.9045 (p) REVERT: B 329 THR cc_start: 0.8972 (p) cc_final: 0.8761 (p) REVERT: B 387 GLN cc_start: 0.8426 (mm-40) cc_final: 0.8174 (mm110) REVERT: B 518 THR cc_start: 0.8867 (p) cc_final: 0.8531 (t) outliers start: 18 outliers final: 11 residues processed: 119 average time/residue: 0.0748 time to fit residues: 13.6307 Evaluate side-chains 117 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 104 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 TYR Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 439 SER Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 641 THR Chi-restraints excluded: chain B residue 142 ASN Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 203 ASN Chi-restraints excluded: chain B residue 227 ASP Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 420 MET Chi-restraints excluded: chain B residue 552 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 93 optimal weight: 0.4980 chunk 31 optimal weight: 4.9990 chunk 78 optimal weight: 0.8980 chunk 37 optimal weight: 3.9990 chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 0.9990 chunk 124 optimal weight: 0.7980 chunk 120 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 63 optimal weight: 6.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 319 HIS A 343 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.073892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2643 r_free = 0.2643 target = 0.064540 restraints weight = 20429.634| |-----------------------------------------------------------------------------| r_work (start): 0.2642 rms_B_bonded: 1.94 r_work: 0.2552 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2442 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8914 moved from start: 0.1404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 10260 Z= 0.150 Angle : 0.604 7.180 14032 Z= 0.313 Chirality : 0.049 0.144 1564 Planarity : 0.005 0.049 1812 Dihedral : 5.855 50.522 1409 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 1.68 % Allowed : 9.78 % Favored : 88.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.18 (0.23), residues: 1286 helix: -0.05 (0.26), residues: 412 sheet: -0.17 (0.37), residues: 172 loop : -1.41 (0.23), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 141 TYR 0.017 0.001 TYR B 75 PHE 0.014 0.001 PHE A 228 TRP 0.010 0.001 TRP B 127 HIS 0.005 0.001 HIS A 319 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.15 (10260) covalent geometry : angle 0.60449 / 0.31 (14032) hydrogen bonds : bond 0.05068 / 3.31 ( 348) hydrogen bonds : angle 4.79399 / 3.34 ( 984) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 111 time to evaluate : 0.465 Fit side-chains revert: symmetry clash REVERT: A 212 MET cc_start: 0.9116 (mmm) cc_final: 0.8889 (mmm) REVERT: A 226 VAL cc_start: 0.8704 (OUTLIER) cc_final: 0.8491 (t) REVERT: A 398 GLN cc_start: 0.7734 (pp30) cc_final: 0.7481 (pp30) REVERT: A 551 GLN cc_start: 0.7753 (mp10) cc_final: 0.7510 (mp10) REVERT: A 641 THR cc_start: 0.9292 (OUTLIER) cc_final: 0.9012 (p) REVERT: B 161 TYR cc_start: 0.8231 (OUTLIER) cc_final: 0.7926 (m-10) outliers start: 18 outliers final: 13 residues processed: 122 average time/residue: 0.0837 time to fit residues: 15.3369 Evaluate side-chains 117 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 101 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 439 SER Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 594 VAL Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 641 THR Chi-restraints excluded: chain B residue 161 TYR Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 227 ASP Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 420 MET Chi-restraints excluded: chain B residue 552 MET Chi-restraints excluded: chain B residue 594 VAL Chi-restraints excluded: chain B residue 648 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 15 optimal weight: 0.5980 chunk 85 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 86 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 119 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 chunk 65 optimal weight: 5.9990 chunk 83 optimal weight: 0.0670 chunk 87 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 overall best weight: 0.8520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 343 HIS ** A 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 142 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.074166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2646 r_free = 0.2646 target = 0.064740 restraints weight = 20411.989| |-----------------------------------------------------------------------------| r_work (start): 0.2653 rms_B_bonded: 1.95 r_work: 0.2560 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2447 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8905 moved from start: 0.1621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10260 Z= 0.133 Angle : 0.577 6.182 14032 Z= 0.300 Chirality : 0.048 0.244 1564 Planarity : 0.004 0.045 1812 Dihedral : 5.638 49.543 1409 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 2.42 % Allowed : 11.08 % Favored : 86.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.08 (0.23), residues: 1286 helix: 0.09 (0.26), residues: 412 sheet: -0.21 (0.36), residues: 188 loop : -1.38 (0.23), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 188 TYR 0.018 0.001 TYR B 75 PHE 0.013 0.001 PHE A 228 TRP 0.014 0.001 TRP A 668 HIS 0.006 0.001 HIS A 319 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.13 (10260) covalent geometry : angle 0.57716 / 0.30 (14032) hydrogen bonds : bond 0.04661 / 3.04 ( 348) hydrogen bonds : angle 4.64643 / 3.24 ( 984) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 104 time to evaluate : 0.385 Fit side-chains revert: symmetry clash REVERT: A 226 VAL cc_start: 0.8655 (OUTLIER) cc_final: 0.8419 (t) REVERT: A 398 GLN cc_start: 0.7822 (pp30) cc_final: 0.7567 (pp30) REVERT: A 641 THR cc_start: 0.9328 (OUTLIER) cc_final: 0.9039 (p) REVERT: B 161 TYR cc_start: 0.8322 (OUTLIER) cc_final: 0.7896 (m-10) REVERT: B 227 ASP cc_start: 0.8439 (OUTLIER) cc_final: 0.8234 (t70) outliers start: 26 outliers final: 18 residues processed: 121 average time/residue: 0.0827 time to fit residues: 15.0606 Evaluate side-chains 122 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 100 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 ASN Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 439 SER Chi-restraints excluded: chain A residue 594 VAL Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 641 THR Chi-restraints excluded: chain B residue 142 ASN Chi-restraints excluded: chain B residue 161 TYR Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 203 ASN Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 227 ASP Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 320 PHE Chi-restraints excluded: chain B residue 420 MET Chi-restraints excluded: chain B residue 552 MET Chi-restraints excluded: chain B residue 564 THR Chi-restraints excluded: chain B residue 594 VAL Chi-restraints excluded: chain B residue 648 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 106 optimal weight: 4.9990 chunk 71 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 67 optimal weight: 6.9990 chunk 39 optimal weight: 1.9990 chunk 108 optimal weight: 0.7980 chunk 88 optimal weight: 6.9990 chunk 51 optimal weight: 0.9990 chunk 89 optimal weight: 0.6980 chunk 98 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.2815 r_free = 0.2815 target = 0.073432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2632 r_free = 0.2632 target = 0.064069 restraints weight = 20171.697| |-----------------------------------------------------------------------------| r_work (start): 0.2626 rms_B_bonded: 1.96 r_work: 0.2533 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2420 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8926 moved from start: 0.1693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10260 Z= 0.168 Angle : 0.612 8.930 14032 Z= 0.316 Chirality : 0.049 0.238 1564 Planarity : 0.005 0.049 1812 Dihedral : 5.619 49.179 1409 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 3.17 % Allowed : 12.01 % Favored : 84.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.98 (0.23), residues: 1286 helix: 0.17 (0.26), residues: 412 sheet: -0.21 (0.36), residues: 188 loop : -1.29 (0.23), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 281 TYR 0.019 0.001 TYR B 75 PHE 0.014 0.001 PHE A 228 TRP 0.011 0.001 TRP B 127 HIS 0.005 0.001 HIS A 319 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.17 (10260) covalent geometry : angle 0.61207 / 0.32 (14032) hydrogen bonds : bond 0.04963 / 3.24 ( 348) hydrogen bonds : angle 4.67440 / 3.25 ( 984) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 103 time to evaluate : 0.304 Fit side-chains revert: symmetry clash REVERT: A 551 GLN cc_start: 0.7926 (mp10) cc_final: 0.7702 (mp10) REVERT: B 161 TYR cc_start: 0.8274 (OUTLIER) cc_final: 0.7795 (m-10) outliers start: 34 outliers final: 24 residues processed: 125 average time/residue: 0.0730 time to fit residues: 14.1038 Evaluate side-chains 126 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 101 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 ASN Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 227 ASP Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 439 SER Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain A residue 502 ASP Chi-restraints excluded: chain A residue 594 VAL Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 653 VAL Chi-restraints excluded: chain B residue 161 TYR Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 203 ASN Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 320 PHE Chi-restraints excluded: chain B residue 352 SER Chi-restraints excluded: chain B residue 420 MET Chi-restraints excluded: chain B residue 552 MET Chi-restraints excluded: chain B residue 564 THR Chi-restraints excluded: chain B residue 594 VAL Chi-restraints excluded: chain B residue 648 VAL Chi-restraints excluded: chain B residue 653 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 2 optimal weight: 0.0050 chunk 14 optimal weight: 3.9990 chunk 57 optimal weight: 8.9990 chunk 116 optimal weight: 0.9980 chunk 121 optimal weight: 5.9990 chunk 42 optimal weight: 1.9990 chunk 108 optimal weight: 0.8980 chunk 8 optimal weight: 0.5980 chunk 24 optimal weight: 0.9980 chunk 89 optimal weight: 5.9990 chunk 118 optimal weight: 0.0010 overall best weight: 0.5000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 343 HIS ** A 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 523 GLN ** 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 = 0.2862 r_free = 0.2862 target = 0.075969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2681 r_free = 0.2681 target = 0.066539 restraints weight = 20395.549| |-----------------------------------------------------------------------------| r_work (start): 0.2681 rms_B_bonded: 1.99 r_work: 0.2586 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2472 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8887 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 10260 Z= 0.108 Angle : 0.549 10.689 14032 Z= 0.284 Chirality : 0.046 0.138 1564 Planarity : 0.004 0.048 1812 Dihedral : 5.356 50.706 1408 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 2.33 % Allowed : 13.31 % Favored : 84.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.81 (0.23), residues: 1286 helix: 0.36 (0.27), residues: 400 sheet: -0.19 (0.36), residues: 188 loop : -1.17 (0.23), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 188 TYR 0.021 0.001 TYR B 75 PHE 0.012 0.001 PHE A 228 TRP 0.009 0.001 TRP A 127 HIS 0.003 0.000 HIS A 319 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 (10260) covalent geometry : angle 0.54894 / 0.28 (14032) hydrogen bonds : bond 0.04108 / 2.68 ( 348) hydrogen bonds : angle 4.47126 / 3.12 ( 984) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 109 time to evaluate : 0.365 Fit side-chains revert: symmetry clash REVERT: B 161 TYR cc_start: 0.8259 (OUTLIER) cc_final: 0.7803 (m-10) REVERT: B 226 VAL cc_start: 0.8318 (OUTLIER) cc_final: 0.7916 (t) REVERT: B 499 PHE cc_start: 0.8133 (p90) cc_final: 0.7920 (p90) outliers start: 25 outliers final: 16 residues processed: 126 average time/residue: 0.0724 time to fit residues: 14.0386 Evaluate side-chains 117 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 99 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 ASN Chi-restraints excluded: chain A residue 227 ASP Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 320 PHE Chi-restraints excluded: chain A residue 594 VAL Chi-restraints excluded: chain A residue 601 ASP Chi-restraints excluded: chain A residue 653 VAL Chi-restraints excluded: chain B residue 161 TYR Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 203 ASN Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 320 PHE Chi-restraints excluded: chain B residue 420 MET Chi-restraints excluded: chain B residue 552 MET Chi-restraints excluded: chain B residue 564 THR Chi-restraints excluded: chain B residue 594 VAL Chi-restraints excluded: chain B residue 648 VAL Chi-restraints excluded: chain B residue 653 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 106 optimal weight: 1.9990 chunk 25 optimal weight: 5.9990 chunk 37 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 118 optimal weight: 0.9980 chunk 65 optimal weight: 5.9990 chunk 15 optimal weight: 0.7980 chunk 104 optimal weight: 0.8980 chunk 21 optimal weight: 0.9990 chunk 90 optimal weight: 4.9990 chunk 82 optimal weight: 6.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 343 HIS ** A 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 523 GLN ** 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 = 0.2826 r_free = 0.2826 target = 0.073898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2650 r_free = 0.2650 target = 0.064877 restraints weight = 20431.797| |-----------------------------------------------------------------------------| r_work (start): 0.2651 rms_B_bonded: 1.93 r_work: 0.2561 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2451 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8938 moved from start: 0.1942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10260 Z= 0.157 Angle : 0.612 12.193 14032 Z= 0.311 Chirality : 0.049 0.220 1564 Planarity : 0.005 0.047 1812 Dihedral : 5.207 48.015 1406 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 2.61 % Allowed : 13.87 % Favored : 83.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.81 (0.24), residues: 1286 helix: 0.28 (0.27), residues: 412 sheet: -0.05 (0.37), residues: 188 loop : -1.19 (0.24), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 281 TYR 0.020 0.001 TYR B 75 PHE 0.014 0.001 PHE A 699 TRP 0.011 0.001 TRP A 127 HIS 0.005 0.001 HIS A 628 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.16 (10260) covalent geometry : angle 0.61155 / 0.31 (14032) hydrogen bonds : bond 0.04713 / 3.08 ( 348) hydrogen bonds : angle 4.53972 / 3.16 ( 984) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 103 time to evaluate : 0.279 Fit side-chains revert: symmetry clash REVERT: A 583 ASN cc_start: 0.8175 (p0) cc_final: 0.7940 (p0) REVERT: B 161 TYR cc_start: 0.8293 (OUTLIER) cc_final: 0.7781 (m-10) REVERT: B 226 VAL cc_start: 0.8491 (OUTLIER) cc_final: 0.8083 (t) outliers start: 28 outliers final: 23 residues processed: 125 average time/residue: 0.0719 time to fit residues: 13.8617 Evaluate side-chains 129 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 104 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 ASN Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 227 ASP Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 320 PHE Chi-restraints excluded: chain A residue 439 SER Chi-restraints excluded: chain A residue 502 ASP Chi-restraints excluded: chain A residue 594 VAL Chi-restraints excluded: chain A residue 601 ASP Chi-restraints excluded: chain A residue 653 VAL Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain B residue 161 TYR Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 320 PHE Chi-restraints excluded: chain B residue 352 SER Chi-restraints excluded: chain B residue 420 MET Chi-restraints excluded: chain B residue 552 MET Chi-restraints excluded: chain B residue 564 THR Chi-restraints excluded: chain B residue 594 VAL Chi-restraints excluded: chain B residue 648 VAL Chi-restraints excluded: chain B residue 653 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 2 optimal weight: 0.8980 chunk 6 optimal weight: 0.5980 chunk 84 optimal weight: 3.9990 chunk 112 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 76 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 77 optimal weight: 0.5980 chunk 113 optimal weight: 0.8980 chunk 105 optimal weight: 4.9990 chunk 65 optimal weight: 5.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 343 HIS ** A 523 GLN ** 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 = 0.2849 r_free = 0.2849 target = 0.075042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2675 r_free = 0.2675 target = 0.066055 restraints weight = 20363.206| |-----------------------------------------------------------------------------| r_work (start): 0.2678 rms_B_bonded: 1.92 r_work: 0.2588 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2477 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8921 moved from start: 0.2050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10260 Z= 0.121 Angle : 0.573 11.562 14032 Z= 0.293 Chirality : 0.047 0.209 1564 Planarity : 0.004 0.048 1812 Dihedral : 5.160 48.646 1406 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 2.79 % Allowed : 13.59 % Favored : 83.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.75 (0.24), residues: 1286 helix: 0.35 (0.27), residues: 400 sheet: -0.03 (0.37), residues: 188 loop : -1.13 (0.24), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 188 TYR 0.019 0.001 TYR B 75 PHE 0.015 0.001 PHE A 699 TRP 0.010 0.001 TRP B 127 HIS 0.003 0.001 HIS A 628 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.12 (10260) covalent geometry : angle 0.57339 / 0.29 (14032) hydrogen bonds : bond 0.04278 / 2.79 ( 348) hydrogen bonds : angle 4.44326 / 3.09 ( 984) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 102 time to evaluate : 0.371 Fit side-chains revert: symmetry clash REVERT: A 161 TYR cc_start: 0.7926 (OUTLIER) cc_final: 0.6789 (m-10) REVERT: A 583 ASN cc_start: 0.8156 (p0) cc_final: 0.7922 (p0) REVERT: B 161 TYR cc_start: 0.8219 (OUTLIER) cc_final: 0.7727 (m-10) REVERT: B 226 VAL cc_start: 0.8448 (OUTLIER) cc_final: 0.8060 (t) outliers start: 30 outliers final: 21 residues processed: 124 average time/residue: 0.0679 time to fit residues: 13.0433 Evaluate side-chains 124 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 100 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 ASN Chi-restraints excluded: chain A residue 161 TYR Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 227 ASP Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 320 PHE Chi-restraints excluded: chain A residue 594 VAL Chi-restraints excluded: chain A residue 601 ASP Chi-restraints excluded: chain A residue 653 VAL Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain B residue 161 TYR Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 203 ASN Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 320 PHE Chi-restraints excluded: chain B residue 352 SER Chi-restraints excluded: chain B residue 420 MET Chi-restraints excluded: chain B residue 552 MET Chi-restraints excluded: chain B residue 564 THR Chi-restraints excluded: chain B residue 594 VAL Chi-restraints excluded: chain B residue 648 VAL Chi-restraints excluded: chain B residue 653 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 46 optimal weight: 0.9990 chunk 17 optimal weight: 0.0980 chunk 102 optimal weight: 0.0970 chunk 44 optimal weight: 0.6980 chunk 100 optimal weight: 0.8980 chunk 122 optimal weight: 3.9990 chunk 40 optimal weight: 0.8980 chunk 67 optimal weight: 4.9990 chunk 38 optimal weight: 0.4980 chunk 35 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 overall best weight: 0.4378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 343 HIS ** A 523 GLN ** 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 = 0.2877 r_free = 0.2877 target = 0.076547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2706 r_free = 0.2706 target = 0.067645 restraints weight = 20177.670| |-----------------------------------------------------------------------------| r_work (start): 0.2707 rms_B_bonded: 1.89 r_work: 0.2619 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2510 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8897 moved from start: 0.2159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 10260 Z= 0.105 Angle : 0.554 9.614 14032 Z= 0.283 Chirality : 0.047 0.204 1564 Planarity : 0.004 0.048 1812 Dihedral : 5.074 51.618 1406 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 2.42 % Allowed : 13.59 % Favored : 83.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.66 (0.24), residues: 1286 helix: 0.42 (0.27), residues: 400 sheet: 0.00 (0.38), residues: 188 loop : -1.07 (0.24), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 197 TYR 0.019 0.001 TYR B 75 PHE 0.020 0.001 PHE A 499 TRP 0.009 0.001 TRP B 127 HIS 0.002 0.001 HIS A 319 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.11 (10260) covalent geometry : angle 0.55444 / 0.28 (14032) hydrogen bonds : bond 0.03942 / 2.56 ( 348) hydrogen bonds : angle 4.31800 / 3.01 ( 984) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 103 time to evaluate : 0.276 Fit side-chains revert: symmetry clash REVERT: A 161 TYR cc_start: 0.7900 (OUTLIER) cc_final: 0.7002 (m-10) REVERT: A 551 GLN cc_start: 0.7976 (mp10) cc_final: 0.7450 (mp10) REVERT: A 583 ASN cc_start: 0.8087 (p0) cc_final: 0.7858 (p0) REVERT: B 161 TYR cc_start: 0.8152 (OUTLIER) cc_final: 0.7667 (m-10) REVERT: B 226 VAL cc_start: 0.8424 (OUTLIER) cc_final: 0.8045 (t) outliers start: 26 outliers final: 21 residues processed: 122 average time/residue: 0.0695 time to fit residues: 13.0804 Evaluate side-chains 127 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 103 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 ASN Chi-restraints excluded: chain A residue 161 TYR Chi-restraints excluded: chain A residue 227 ASP Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 320 PHE Chi-restraints excluded: chain A residue 439 SER Chi-restraints excluded: chain A residue 502 ASP Chi-restraints excluded: chain A residue 594 VAL Chi-restraints excluded: chain A residue 601 ASP Chi-restraints excluded: chain A residue 653 VAL Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain B residue 161 TYR Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 203 ASN Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 320 PHE Chi-restraints excluded: chain B residue 352 SER Chi-restraints excluded: chain B residue 420 MET Chi-restraints excluded: chain B residue 552 MET Chi-restraints excluded: chain B residue 594 VAL Chi-restraints excluded: chain B residue 648 VAL Chi-restraints excluded: chain B residue 653 VAL 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 11 optimal weight: 0.3980 chunk 102 optimal weight: 0.9980 chunk 122 optimal weight: 0.7980 chunk 63 optimal weight: 0.0040 chunk 25 optimal weight: 5.9990 chunk 60 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 97 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 chunk 113 optimal weight: 1.9990 overall best weight: 0.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 343 HIS ** A 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 387 GLN B 398 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.076645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2705 r_free = 0.2705 target = 0.067667 restraints weight = 20119.114| |-----------------------------------------------------------------------------| r_work (start): 0.2703 rms_B_bonded: 1.92 r_work: 0.2614 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2502 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8899 moved from start: 0.2213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 10260 Z= 0.111 Angle : 0.557 9.534 14032 Z= 0.284 Chirality : 0.047 0.196 1564 Planarity : 0.004 0.047 1812 Dihedral : 5.062 51.484 1406 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 2.33 % Allowed : 13.59 % Favored : 84.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.24), residues: 1286 helix: 0.44 (0.27), residues: 400 sheet: -0.00 (0.38), residues: 188 loop : -1.05 (0.24), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 188 TYR 0.019 0.001 TYR B 75 PHE 0.019 0.001 PHE A 499 TRP 0.009 0.001 TRP B 127 HIS 0.009 0.001 HIS A 319 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.11 (10260) covalent geometry : angle 0.55736 / 0.28 (14032) hydrogen bonds : bond 0.03976 / 2.59 ( 348) hydrogen bonds : angle 4.28293 / 2.99 ( 984) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 106 time to evaluate : 0.237 Fit side-chains revert: symmetry clash REVERT: A 161 TYR cc_start: 0.7959 (OUTLIER) cc_final: 0.7221 (m-80) REVERT: A 551 GLN cc_start: 0.8011 (mp10) cc_final: 0.7483 (mp10) REVERT: A 583 ASN cc_start: 0.8067 (p0) cc_final: 0.7835 (p0) REVERT: B 161 TYR cc_start: 0.8170 (OUTLIER) cc_final: 0.7612 (m-10) REVERT: B 226 VAL cc_start: 0.8376 (OUTLIER) cc_final: 0.8083 (t) outliers start: 25 outliers final: 20 residues processed: 123 average time/residue: 0.0787 time to fit residues: 14.8475 Evaluate side-chains 126 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 103 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 ASN Chi-restraints excluded: chain A residue 161 TYR Chi-restraints excluded: chain A residue 227 ASP Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 320 PHE Chi-restraints excluded: chain A residue 439 SER Chi-restraints excluded: chain A residue 502 ASP Chi-restraints excluded: chain A residue 594 VAL Chi-restraints excluded: chain A residue 601 ASP Chi-restraints excluded: chain A residue 653 VAL Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain B residue 161 TYR Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 203 ASN Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 320 PHE Chi-restraints excluded: chain B residue 420 MET Chi-restraints excluded: chain B residue 552 MET Chi-restraints excluded: chain B residue 594 VAL Chi-restraints excluded: chain B residue 648 VAL Chi-restraints excluded: chain B residue 653 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 99 optimal weight: 5.9990 chunk 35 optimal weight: 4.9990 chunk 114 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 85 optimal weight: 3.9990 chunk 30 optimal weight: 0.5980 chunk 43 optimal weight: 2.9990 chunk 28 optimal weight: 0.6980 chunk 90 optimal weight: 0.9980 chunk 92 optimal weight: 4.9990 chunk 8 optimal weight: 0.3980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 343 HIS ** A 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 387 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.074370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2657 r_free = 0.2657 target = 0.065301 restraints weight = 20413.061| |-----------------------------------------------------------------------------| r_work (start): 0.2662 rms_B_bonded: 1.91 r_work: 0.2572 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2460 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8932 moved from start: 0.2126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 10260 Z= 0.154 Angle : 0.604 10.123 14032 Z= 0.308 Chirality : 0.049 0.263 1564 Planarity : 0.004 0.047 1812 Dihedral : 5.169 47.305 1406 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 2.51 % Allowed : 13.97 % Favored : 83.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.69 (0.24), residues: 1286 helix: 0.32 (0.26), residues: 412 sheet: 0.03 (0.38), residues: 188 loop : -1.08 (0.24), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 188 TYR 0.020 0.001 TYR B 75 PHE 0.019 0.001 PHE A 499 TRP 0.011 0.001 TRP B 127 HIS 0.006 0.001 HIS A 319 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.15 (10260) covalent geometry : angle 0.60423 / 0.31 (14032) hydrogen bonds : bond 0.04597 / 3.00 ( 348) hydrogen bonds : angle 4.39643 / 3.05 ( 984) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1803.34 seconds wall clock time: 31 minutes 48.47 seconds (1908.47 seconds total)