Starting phenix.real_space_refine on Thu Aug 6 11:14:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9no0_49590/08_2026/9no0_49590.cif Found real_map, /net/cci-nas-00/data/ceres_data/9no0_49590/08_2026/9no0_49590.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.08 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9no0_49590/08_2026/9no0_49590.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9no0_49590/08_2026/9no0_49590.map" model { file = "/net/cci-nas-00/data/ceres_data/9no0_49590/08_2026/9no0_49590.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9no0_49590/08_2026/9no0_49590.cif" } resolution = 2.08 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= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 8 5.49 5 S 60 5.16 5 C 9130 2.51 5 N 2474 2.21 5 O 2823 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14495 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 4788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 624, 4788 Classifications: {'peptide': 624} Link IDs: {'PTRANS': 31, 'TRANS': 592} Chain: "B" Number of atoms: 4788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 624, 4788 Classifications: {'peptide': 624} Link IDs: {'PTRANS': 31, 'TRANS': 592} Chain: "C" Number of atoms: 4779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 623, 4779 Classifications: {'peptide': 623} Link IDs: {'PTRANS': 31, 'TRANS': 591} Chain: "D" Number of atoms: 125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 125 Classifications: {'RNA': 6} Modifications used: {'5*END': 1, 'rna2p_pur': 2, 'rna3p_pur': 2, 'rna3p_pyr': 2} Link IDs: {'rna2p': 1, 'rna3p': 4} Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'PO4': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'PO4': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'PO4': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.38, per 1000 atoms: 0.23 Number of scatterers: 14495 At special positions: 0 Unit cell: (106.863, 108.573, 107.718, 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 60 16.00 P 8 15.00 O 2823 8.00 N 2474 7.00 C 9130 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: 1.10 Conformation dependent library (CDL) restraints added in 694.6 milliseconds 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3484 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 13 sheets defined 43.8% alpha, 22.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.59 Creating SS restraints... Processing helix chain 'A' and resid 124 through 139 Processing helix chain 'A' and resid 140 through 142 No H-bonds generated for 'chain 'A' and resid 140 through 142' Processing helix chain 'A' and resid 164 through 180 removed outlier: 4.156A pdb=" N LEU A 168 " --> pdb=" O GLU A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 210 Processing helix chain 'A' and resid 237 through 266 removed outlier: 3.669A pdb=" N GLN A 254 " --> pdb=" O LYS A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 300 removed outlier: 5.784A pdb=" N GLU A 293 " --> pdb=" O LYS A 289 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N ARG A 294 " --> pdb=" O LEU A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 328 Processing helix chain 'A' and resid 332 through 356 removed outlier: 3.702A pdb=" N VAL A 352 " --> pdb=" O PHE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 406 removed outlier: 3.921A pdb=" N ILE A 406 " --> pdb=" O GLU A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 435 Processing helix chain 'A' and resid 444 through 459 Processing helix chain 'A' and resid 460 through 462 No H-bonds generated for 'chain 'A' and resid 460 through 462' Processing helix chain 'A' and resid 482 through 499 Processing helix chain 'A' and resid 534 through 540 Processing helix chain 'A' and resid 567 through 593 removed outlier: 3.548A pdb=" N VAL A 571 " --> pdb=" O PRO A 567 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N THR A 592 " --> pdb=" O ILE A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 622 Processing helix chain 'A' and resid 625 through 636 Processing helix chain 'A' and resid 653 through 669 Processing helix chain 'B' and resid 115 through 122 Processing helix chain 'B' and resid 124 through 139 Processing helix chain 'B' and resid 140 through 142 No H-bonds generated for 'chain 'B' and resid 140 through 142' Processing helix chain 'B' and resid 164 through 180 removed outlier: 4.164A pdb=" N LEU B 168 " --> pdb=" O GLU B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 210 Processing helix chain 'B' and resid 237 through 267 removed outlier: 3.630A pdb=" N GLN B 254 " --> pdb=" O LYS B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 300 removed outlier: 5.696A pdb=" N GLU B 293 " --> pdb=" O LYS B 289 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N ARG B 294 " --> pdb=" O LEU B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 328 removed outlier: 3.530A pdb=" N GLN B 323 " --> pdb=" O ASP B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 356 removed outlier: 3.542A pdb=" N ILE B 337 " --> pdb=" O PRO B 333 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N VAL B 352 " --> pdb=" O PHE B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 407 removed outlier: 3.566A pdb=" N ILE B 406 " --> pdb=" O LEU B 402 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LYS B 407 " --> pdb=" O GLU B 403 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 402 through 407' Processing helix chain 'B' and resid 410 through 415 removed outlier: 3.704A pdb=" N ILE B 415 " --> pdb=" O VAL B 411 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 435 Processing helix chain 'B' and resid 444 through 459 Processing helix chain 'B' and resid 460 through 462 No H-bonds generated for 'chain 'B' and resid 460 through 462' Processing helix chain 'B' and resid 482 through 499 Processing helix chain 'B' and resid 534 through 540 Processing helix chain 'B' and resid 567 through 593 removed outlier: 3.650A pdb=" N THR B 592 " --> pdb=" O ILE B 588 " (cutoff:3.500A) Processing helix chain 'B' and resid 613 through 622 removed outlier: 4.277A pdb=" N ALA B 618 " --> pdb=" O LEU B 614 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N LYS B 619 " --> pdb=" O SER B 615 " (cutoff:3.500A) Processing helix chain 'B' and resid 625 through 635 Processing helix chain 'B' and resid 653 through 669 Processing helix chain 'C' and resid 117 through 122 Processing helix chain 'C' and resid 124 through 139 Processing helix chain 'C' and resid 140 through 142 No H-bonds generated for 'chain 'C' and resid 140 through 142' Processing helix chain 'C' and resid 164 through 180 removed outlier: 4.190A pdb=" N LEU C 168 " --> pdb=" O GLU C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 205 through 211 removed outlier: 3.816A pdb=" N SER C 211 " --> pdb=" O LYS C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 237 through 267 removed outlier: 3.637A pdb=" N GLN C 254 " --> pdb=" O LYS C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 301 removed outlier: 5.866A pdb=" N GLU C 293 " --> pdb=" O LYS C 289 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N ARG C 294 " --> pdb=" O LEU C 290 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 328 removed outlier: 3.719A pdb=" N LYS C 325 " --> pdb=" O GLU C 321 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLU C 326 " --> pdb=" O GLU C 322 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS C 327 " --> pdb=" O GLN C 323 " (cutoff:3.500A) Processing helix chain 'C' and resid 332 through 356 removed outlier: 3.759A pdb=" N VAL C 352 " --> pdb=" O PHE C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 401 through 406 removed outlier: 3.556A pdb=" N ILE C 406 " --> pdb=" O GLU C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 409 through 417 Processing helix chain 'C' and resid 430 through 435 Processing helix chain 'C' and resid 444 through 459 Processing helix chain 'C' and resid 460 through 462 No H-bonds generated for 'chain 'C' and resid 460 through 462' Processing helix chain 'C' and resid 482 through 498 Processing helix chain 'C' and resid 534 through 541 Processing helix chain 'C' and resid 567 through 593 removed outlier: 3.527A pdb=" N VAL C 571 " --> pdb=" O PRO C 567 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N THR C 592 " --> pdb=" O ILE C 588 " (cutoff:3.500A) Processing helix chain 'C' and resid 613 through 622 removed outlier: 4.198A pdb=" N ALA C 618 " --> pdb=" O LEU C 614 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N LYS C 619 " --> pdb=" O SER C 615 " (cutoff:3.500A) Processing helix chain 'C' and resid 625 through 635 Processing helix chain 'C' and resid 653 through 668 Processing sheet with id=AA1, first strand: chain 'A' and resid 47 through 51 removed outlier: 6.377A pdb=" N ALA A 79 " --> pdb=" O LEU A 157 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ARG A 103 " --> pdb=" O CYS A 154 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N LEU A 156 " --> pdb=" O ARG A 103 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 199 through 202 removed outlier: 3.968A pdb=" N ILE A 195 " --> pdb=" O LEU A 214 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N LEU A 214 " --> pdb=" O ILE A 195 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ASN A 215 " --> pdb=" O ALA A 231 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ALA A 231 " --> pdb=" O ASN A 215 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N VAL A 217 " --> pdb=" O LEU A 229 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N LEU A 229 " --> pdb=" O VAL A 217 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ALA A 219 " --> pdb=" O VAL A 227 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLN A 225 " --> pdb=" O ALA A 221 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N VAL A 227 " --> pdb=" O ILE A 561 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ILE A 561 " --> pdb=" O VAL A 227 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LEU A 229 " --> pdb=" O ALA A 559 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N THR A 555 " --> pdb=" O ALA A 233 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N MET A 543 " --> pdb=" O LEU A 513 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N LEU A 513 " --> pdb=" O MET A 543 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 370 through 374 removed outlier: 6.374A pdb=" N GLN A 392 " --> pdb=" O LEU A 477 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 606 through 611 Processing sheet with id=AA5, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.373A pdb=" N ALA B 79 " --> pdb=" O LEU B 157 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LEU B 156 " --> pdb=" O ARG B 103 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 199 through 202 removed outlier: 4.125A pdb=" N ILE B 195 " --> pdb=" O LEU B 214 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N LEU B 214 " --> pdb=" O ILE B 195 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ASN B 215 " --> pdb=" O ALA B 231 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ALA B 231 " --> pdb=" O ASN B 215 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N VAL B 217 " --> pdb=" O LEU B 229 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N LEU B 229 " --> pdb=" O VAL B 217 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ALA B 219 " --> pdb=" O VAL B 227 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLN B 225 " --> pdb=" O ALA B 221 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N VAL B 227 " --> pdb=" O ILE B 561 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ILE B 561 " --> pdb=" O VAL B 227 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU B 229 " --> pdb=" O ALA B 559 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N THR B 555 " --> pdb=" O ALA B 233 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N MET B 543 " --> pdb=" O LEU B 513 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N LEU B 513 " --> pdb=" O MET B 543 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N ALA B 510 " --> pdb=" O THR B 531 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N THR B 531 " --> pdb=" O ALA B 510 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N GLY B 512 " --> pdb=" O LEU B 529 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N LEU B 529 " --> pdb=" O GLY B 512 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N VAL B 514 " --> pdb=" O TYR B 527 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N TYR B 527 " --> pdb=" O VAL B 514 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N LYS B 516 " --> pdb=" O GLU B 525 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 370 through 374 removed outlier: 6.260A pdb=" N GLN B 392 " --> pdb=" O LEU B 477 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 606 through 611 Processing sheet with id=AA9, first strand: chain 'C' and resid 47 through 51 removed outlier: 6.412A pdb=" N ALA C 79 " --> pdb=" O LEU C 157 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N LEU C 156 " --> pdb=" O ARG C 103 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 106 through 107 Processing sheet with id=AB2, first strand: chain 'C' and resid 199 through 202 removed outlier: 3.999A pdb=" N ILE C 195 " --> pdb=" O LEU C 214 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N LEU C 214 " --> pdb=" O ILE C 195 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ASN C 215 " --> pdb=" O ALA C 231 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N ALA C 231 " --> pdb=" O ASN C 215 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N VAL C 217 " --> pdb=" O LEU C 229 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N LEU C 229 " --> pdb=" O VAL C 217 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ALA C 219 " --> pdb=" O VAL C 227 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N VAL C 227 " --> pdb=" O ILE C 561 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ILE C 561 " --> pdb=" O VAL C 227 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU C 229 " --> pdb=" O ALA C 559 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N THR C 555 " --> pdb=" O ALA C 233 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N MET C 543 " --> pdb=" O LEU C 513 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N LEU C 513 " --> pdb=" O MET C 543 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASP C 526 " --> pdb=" O LYS C 516 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 370 through 371 removed outlier: 3.533A pdb=" N GLY C 382 " --> pdb=" O VAL C 397 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N GLN C 392 " --> pdb=" O LEU C 477 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 606 through 611 859 hydrogen bonds defined for protein. 2427 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.87 Time building geometry restraints manager: 1.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3882 1.33 - 1.45: 2275 1.45 - 1.57: 8475 1.57 - 1.69: 10 1.69 - 1.81: 99 Bond restraints: 14741 Sorted by residual: bond pdb=" C ARG C 139 " pdb=" O ARG C 139 " ideal model delta sigma weight residual 1.244 1.208 0.035 9.80e-03 1.04e+04 1.30e+01 bond pdb=" O4 PO4 C 901 " pdb=" P PO4 C 901 " ideal model delta sigma weight residual 1.568 1.505 0.063 2.00e-02 2.50e+03 1.00e+01 bond pdb=" O3 PO4 C 901 " pdb=" P PO4 C 901 " ideal model delta sigma weight residual 1.569 1.506 0.063 2.00e-02 2.50e+03 9.86e+00 bond pdb=" O2 PO4 C 901 " pdb=" P PO4 C 901 " ideal model delta sigma weight residual 1.567 1.504 0.063 2.00e-02 2.50e+03 9.80e+00 bond pdb=" O1 PO4 C 901 " pdb=" P PO4 C 901 " ideal model delta sigma weight residual 1.565 1.508 0.057 2.00e-02 2.50e+03 8.19e+00 ... (remaining 14736 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.13: 19696 2.13 - 4.26: 248 4.26 - 6.39: 37 6.39 - 8.53: 8 8.53 - 10.66: 1 Bond angle restraints: 19990 Sorted by residual: angle pdb=" O4' U D 5 " pdb=" C1' U D 5 " pdb=" N1 U D 5 " ideal model delta sigma weight residual 108.50 112.86 -4.36 7.00e-01 2.04e+00 3.87e+01 angle pdb=" O4' C D 3 " pdb=" C1' C D 3 " pdb=" N1 C D 3 " ideal model delta sigma weight residual 108.50 112.26 -3.76 7.00e-01 2.04e+00 2.89e+01 angle pdb=" C4' A D 7 " pdb=" O4' A D 7 " pdb=" C1' A D 7 " ideal model delta sigma weight residual 109.70 106.16 3.54 7.00e-01 2.04e+00 2.56e+01 angle pdb=" C1' C D 3 " pdb=" N1 C D 3 " pdb=" C2 C D 3 " ideal model delta sigma weight residual 118.80 123.93 -5.13 1.10e+00 8.26e-01 2.18e+01 angle pdb=" CA ARG C 139 " pdb=" CB ARG C 139 " pdb=" CG ARG C 139 " ideal model delta sigma weight residual 114.10 121.23 -7.13 2.00e+00 2.50e-01 1.27e+01 ... (remaining 19985 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.42: 8792 35.42 - 70.84: 246 70.84 - 106.27: 26 106.27 - 141.69: 0 141.69 - 177.11: 2 Dihedral angle restraints: 9066 sinusoidal: 3663 harmonic: 5403 Sorted by residual: dihedral pdb=" O4' U D 5 " pdb=" C1' U D 5 " pdb=" N1 U D 5 " pdb=" C2 U D 5 " ideal model delta sinusoidal sigma weight residual 200.00 22.89 177.11 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' C D 3 " pdb=" C1' C D 3 " pdb=" N1 C D 3 " pdb=" C2 C D 3 " ideal model delta sinusoidal sigma weight residual -160.00 16.86 -176.86 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" C5' A D 7 " pdb=" C4' A D 7 " pdb=" C3' A D 7 " pdb=" O3' A D 7 " ideal model delta sinusoidal sigma weight residual 147.00 103.53 43.47 1 8.00e+00 1.56e-02 4.11e+01 ... (remaining 9063 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.097: 2206 0.097 - 0.193: 132 0.193 - 0.290: 1 0.290 - 0.386: 2 0.386 - 0.483: 3 Chirality restraints: 2344 Sorted by residual: chirality pdb=" P C D 3 " pdb=" OP1 C D 3 " pdb=" OP2 C D 3 " pdb=" O5' C D 3 " both_signs ideal model delta sigma weight residual True 2.41 -2.89 -0.48 2.00e-01 2.50e+01 5.83e+00 chirality pdb=" P A D 6 " pdb=" OP1 A D 6 " pdb=" OP2 A D 6 " pdb=" O5' A D 6 " both_signs ideal model delta sigma weight residual True 2.41 -2.88 -0.47 2.00e-01 2.50e+01 5.43e+00 chirality pdb=" P U D 5 " pdb=" OP1 U D 5 " pdb=" OP2 U D 5 " pdb=" O5' U D 5 " both_signs ideal model delta sigma weight residual True 2.41 -2.84 -0.43 2.00e-01 2.50e+01 4.71e+00 ... (remaining 2341 not shown) Planarity restraints: 2567 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 132 " 0.778 9.50e-02 1.11e+02 3.49e-01 7.42e+01 pdb=" NE ARG C 132 " -0.045 2.00e-02 2.50e+03 pdb=" CZ ARG C 132 " -0.016 2.00e-02 2.50e+03 pdb=" NH1 ARG C 132 " 0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG C 132 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 446 " -0.700 9.50e-02 1.11e+02 3.14e-01 6.03e+01 pdb=" NE ARG C 446 " 0.040 2.00e-02 2.50e+03 pdb=" CZ ARG C 446 " 0.014 2.00e-02 2.50e+03 pdb=" NH1 ARG C 446 " 0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG C 446 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 139 " 0.391 9.50e-02 1.11e+02 1.75e-01 1.89e+01 pdb=" NE ARG C 139 " -0.024 2.00e-02 2.50e+03 pdb=" CZ ARG C 139 " -0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG C 139 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG C 139 " 0.013 2.00e-02 2.50e+03 ... (remaining 2564 not shown) Histogram of nonbonded interaction distances: 2.44 - 2.93: 6201 2.93 - 3.42: 14424 3.42 - 3.91: 25126 3.91 - 4.41: 29323 4.41 - 4.90: 47079 Nonbonded interactions: 122153 Sorted by model distance: nonbonded pdb=" O ILE B 196 " pdb=" OD1 ASP B 197 " model vdw 2.437 3.040 nonbonded pdb=" O ARG B 464 " pdb=" OD1 ASP B 465 " model vdw 2.455 3.040 nonbonded pdb=" N GLU A 330 " pdb=" OE1 GLU A 330 " model vdw 2.461 3.120 nonbonded pdb=" N GLU C 330 " pdb=" OE1 GLU C 330 " model vdw 2.461 3.120 nonbonded pdb=" N GLU C 293 " pdb=" OE1 GLU C 293 " model vdw 2.512 3.120 ... (remaining 122148 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 46 through 668 or resid 901)) selection = (chain 'B' and (resid 46 through 668 or resid 901)) selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.470 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: 0.020 Extract box with map and model: 0.270 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.730 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:9.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9235 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 0.063 14741 Z= 0.342 Angle : 0.629 10.658 19990 Z= 0.348 Chirality : 0.052 0.483 2344 Planarity : 0.011 0.349 2567 Dihedral : 16.179 177.108 5582 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.45 % Allowed : 15.36 % Favored : 83.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.27 (0.19), residues: 1865 helix: 1.05 (0.18), residues: 740 sheet: 1.55 (0.25), residues: 426 loop : 0.30 (0.24), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 661 TYR 0.018 0.002 TYR B 427 PHE 0.016 0.002 PHE C 545 TRP 0.004 0.002 TRP C 184 HIS 0.004 0.001 HIS B 658 Details of bonding type rmsd/Z covalent geometry : bond 0.00752 / 0.34 (14741) covalent geometry : angle 0.62878 / 0.35 (19990) hydrogen bonds : bond 0.19972 / 13.29 ( 859) hydrogen bonds : angle 7.54553 / 5.47 ( 2427) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 97 time to evaluate : 0.671 Fit side-chains revert: symmetry clash REVERT: A 103 ARG cc_start: 0.8497 (mmm-85) cc_final: 0.8080 (mmm160) REVERT: A 376 MET cc_start: 0.8254 (mmm) cc_final: 0.7553 (mmm) REVERT: A 424 MET cc_start: 0.9262 (ptp) cc_final: 0.8635 (ppp) REVERT: A 616 LYS cc_start: 0.9091 (OUTLIER) cc_final: 0.8781 (mmmt) REVERT: A 643 ASP cc_start: 0.8537 (m-30) cc_final: 0.8245 (m-30) REVERT: B 54 ARG cc_start: 0.8752 (OUTLIER) cc_final: 0.8028 (mmt90) REVERT: B 118 ARG cc_start: 0.6897 (tpt170) cc_final: 0.6455 (tpp-160) REVERT: B 125 ASP cc_start: 0.8575 (m-30) cc_final: 0.8372 (m-30) REVERT: B 230 GLU cc_start: 0.8958 (OUTLIER) cc_final: 0.8433 (tp30) REVERT: B 645 GLU cc_start: 0.8495 (mm-30) cc_final: 0.7933 (tm-30) REVERT: B 664 ILE cc_start: 0.8551 (pp) cc_final: 0.8180 (pp) REVERT: C 54 ARG cc_start: 0.8776 (OUTLIER) cc_final: 0.8504 (mmt90) REVERT: C 103 ARG cc_start: 0.8777 (OUTLIER) cc_final: 0.8198 (mtp85) REVERT: C 418 ILE cc_start: 0.8805 (tt) cc_final: 0.8579 (pp) REVERT: C 436 GLU cc_start: 0.8188 (OUTLIER) cc_final: 0.7419 (mp0) REVERT: C 616 LYS cc_start: 0.9130 (tppp) cc_final: 0.8780 (mmmm) REVERT: C 617 ARG cc_start: 0.9138 (OUTLIER) cc_final: 0.8694 (tpt-90) outliers start: 23 outliers final: 12 residues processed: 111 average time/residue: 0.6972 time to fit residues: 83.9378 Evaluate side-chains 113 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 94 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 416 ASN Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 611 GLN Chi-restraints excluded: chain A residue 616 LYS Chi-restraints excluded: chain B residue 54 ARG Chi-restraints excluded: chain B residue 230 GLU Chi-restraints excluded: chain B residue 400 ASP Chi-restraints excluded: chain C residue 54 ARG Chi-restraints excluded: chain C residue 103 ARG Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain C residue 289 LYS Chi-restraints excluded: chain C residue 371 SER Chi-restraints excluded: chain C residue 436 GLU Chi-restraints excluded: chain C residue 609 THR Chi-restraints excluded: chain C residue 617 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 2.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 632 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.089346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.064053 restraints weight = 22989.738| |-----------------------------------------------------------------------------| r_work (start): 0.2943 rms_B_bonded: 2.19 r_work: 0.2797 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2678 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9214 moved from start: 0.0722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 14741 Z= 0.188 Angle : 0.543 6.158 19990 Z= 0.303 Chirality : 0.045 0.143 2344 Planarity : 0.004 0.061 2567 Dihedral : 9.002 177.619 2128 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 2.39 % Allowed : 14.29 % Favored : 83.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 2.06 (0.19), residues: 1865 helix: 2.12 (0.18), residues: 733 sheet: 1.74 (0.25), residues: 430 loop : 0.39 (0.25), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 617 TYR 0.020 0.002 TYR C 334 PHE 0.017 0.001 PHE C 340 TRP 0.004 0.001 TRP C 184 HIS 0.002 0.000 HIS A 658 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.19 (14741) covalent geometry : angle 0.54318 / 0.30 (19990) hydrogen bonds : bond 0.07134 / 4.79 ( 859) hydrogen bonds : angle 5.62674 / 4.07 ( 2427) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 105 time to evaluate : 0.534 Fit side-chains revert: symmetry clash REVERT: A 103 ARG cc_start: 0.8529 (mmm-85) cc_final: 0.8107 (mmm160) REVERT: A 118 ARG cc_start: 0.6378 (mmt180) cc_final: 0.5037 (mmm160) REVERT: A 424 MET cc_start: 0.9167 (ptp) cc_final: 0.8593 (ppp) REVERT: A 616 LYS cc_start: 0.9036 (OUTLIER) cc_final: 0.8444 (mmmm) REVERT: A 643 ASP cc_start: 0.8535 (m-30) cc_final: 0.8227 (m-30) REVERT: B 118 ARG cc_start: 0.7130 (tpt170) cc_final: 0.6795 (tpp-160) REVERT: B 125 ASP cc_start: 0.8538 (m-30) cc_final: 0.8326 (m-30) REVERT: B 314 ASN cc_start: 0.9017 (OUTLIER) cc_final: 0.8584 (m110) REVERT: B 645 GLU cc_start: 0.8496 (mm-30) cc_final: 0.7939 (tm-30) REVERT: B 664 ILE cc_start: 0.8596 (pp) cc_final: 0.8235 (pp) REVERT: C 230 GLU cc_start: 0.8827 (OUTLIER) cc_final: 0.8450 (tp30) REVERT: C 418 ILE cc_start: 0.8771 (tt) cc_final: 0.8549 (pp) REVERT: C 436 GLU cc_start: 0.8184 (OUTLIER) cc_final: 0.7466 (mp0) REVERT: C 616 LYS cc_start: 0.9125 (tppp) cc_final: 0.8793 (mmmm) outliers start: 38 outliers final: 15 residues processed: 136 average time/residue: 0.6544 time to fit residues: 96.8365 Evaluate side-chains 119 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 100 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 416 ASN Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 616 LYS Chi-restraints excluded: chain B residue 116 TYR Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain B residue 371 SER Chi-restraints excluded: chain B residue 400 ASP Chi-restraints excluded: chain B residue 646 THR Chi-restraints excluded: chain C residue 125 ASP Chi-restraints excluded: chain C residue 230 GLU Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain C residue 436 GLU Chi-restraints excluded: chain C residue 606 VAL Chi-restraints excluded: chain C residue 609 THR Chi-restraints excluded: chain C residue 637 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 73 optimal weight: 0.5980 chunk 44 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 132 optimal weight: 2.9990 chunk 176 optimal weight: 0.5980 chunk 77 optimal weight: 0.9990 chunk 154 optimal weight: 1.9990 chunk 130 optimal weight: 0.0370 chunk 175 optimal weight: 0.0870 chunk 8 optimal weight: 3.9990 chunk 103 optimal weight: 0.8980 overall best weight: 0.4436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 611 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.091737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.066541 restraints weight = 23072.541| |-----------------------------------------------------------------------------| r_work (start): 0.2998 rms_B_bonded: 2.20 r_work: 0.2855 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2737 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9176 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 : 0.003 0.039 14741 Z= 0.131 Angle : 0.489 5.843 19990 Z= 0.270 Chirality : 0.044 0.141 2344 Planarity : 0.004 0.048 2567 Dihedral : 8.225 174.937 2098 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 2.77 % Allowed : 14.73 % Favored : 82.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.19 (0.20), residues: 1865 helix: 2.31 (0.18), residues: 736 sheet: 1.70 (0.25), residues: 434 loop : 0.42 (0.25), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 617 TYR 0.020 0.001 TYR B 334 PHE 0.016 0.001 PHE C 545 TRP 0.007 0.001 TRP B 184 HIS 0.002 0.000 HIS A 304 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.13 (14741) covalent geometry : angle 0.48863 / 0.27 (19990) hydrogen bonds : bond 0.05551 / 3.73 ( 859) hydrogen bonds : angle 5.05971 / 3.63 ( 2427) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 108 time to evaluate : 0.585 Fit side-chains revert: symmetry clash REVERT: A 103 ARG cc_start: 0.8488 (mmm-85) cc_final: 0.8265 (mmm-85) REVERT: A 424 MET cc_start: 0.9087 (ptp) cc_final: 0.8552 (ppp) REVERT: A 616 LYS cc_start: 0.9054 (tppp) cc_final: 0.8504 (mmmm) REVERT: A 643 ASP cc_start: 0.8512 (m-30) cc_final: 0.8193 (m-30) REVERT: A 645 GLU cc_start: 0.8201 (tp30) cc_final: 0.7780 (tp30) REVERT: A 657 MET cc_start: 0.8793 (tpp) cc_final: 0.8556 (tpt) REVERT: B 118 ARG cc_start: 0.7230 (tpt170) cc_final: 0.6826 (tpp-160) REVERT: B 125 ASP cc_start: 0.8524 (OUTLIER) cc_final: 0.8312 (m-30) REVERT: B 282 GLU cc_start: 0.8386 (pm20) cc_final: 0.8084 (pp20) REVERT: B 314 ASN cc_start: 0.8924 (OUTLIER) cc_final: 0.8608 (m-40) REVERT: B 400 ASP cc_start: 0.7750 (OUTLIER) cc_final: 0.7083 (p0) REVERT: B 645 GLU cc_start: 0.8495 (mm-30) cc_final: 0.7932 (tm-30) REVERT: B 664 ILE cc_start: 0.8569 (pp) cc_final: 0.8234 (pp) REVERT: C 230 GLU cc_start: 0.8772 (OUTLIER) cc_final: 0.8411 (tp30) REVERT: C 436 GLU cc_start: 0.8159 (OUTLIER) cc_final: 0.7464 (mp0) REVERT: C 616 LYS cc_start: 0.9153 (tppp) cc_final: 0.8834 (mmmm) REVERT: C 617 ARG cc_start: 0.9096 (OUTLIER) cc_final: 0.8724 (tpt-90) outliers start: 44 outliers final: 15 residues processed: 143 average time/residue: 0.6792 time to fit residues: 106.1015 Evaluate side-chains 124 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 103 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 416 ASN Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain B residue 116 TYR Chi-restraints excluded: chain B residue 125 ASP Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 371 SER Chi-restraints excluded: chain B residue 372 CYS Chi-restraints excluded: chain B residue 400 ASP Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 646 THR Chi-restraints excluded: chain C residue 125 ASP Chi-restraints excluded: chain C residue 230 GLU Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain C residue 289 LYS Chi-restraints excluded: chain C residue 436 GLU Chi-restraints excluded: chain C residue 606 VAL Chi-restraints excluded: chain C residue 617 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 73 optimal weight: 0.0070 chunk 88 optimal weight: 4.9990 chunk 127 optimal weight: 5.9990 chunk 133 optimal weight: 0.9980 chunk 28 optimal weight: 7.9990 chunk 38 optimal weight: 2.9990 chunk 122 optimal weight: 4.9990 chunk 11 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 117 optimal weight: 1.9990 overall best weight: 1.8004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 155 ASN A 611 GLN A 632 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.089417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.063944 restraints weight = 23171.523| |-----------------------------------------------------------------------------| r_work (start): 0.2942 rms_B_bonded: 2.20 r_work: 0.2798 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2679 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9214 moved from start: 0.0996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 14741 Z= 0.240 Angle : 0.544 5.568 19990 Z= 0.300 Chirality : 0.046 0.148 2344 Planarity : 0.004 0.051 2567 Dihedral : 8.274 173.043 2092 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.71 % Allowed : 14.47 % Favored : 82.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.19 (0.19), residues: 1865 helix: 2.35 (0.18), residues: 728 sheet: 1.78 (0.25), residues: 434 loop : 0.32 (0.24), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 617 TYR 0.018 0.002 TYR C 334 PHE 0.018 0.001 PHE C 340 TRP 0.005 0.001 TRP C 184 HIS 0.003 0.001 HIS C 243 Details of bonding type rmsd/Z covalent geometry : bond 0.00534 / 0.24 (14741) covalent geometry : angle 0.54433 / 0.30 (19990) hydrogen bonds : bond 0.06242 / 4.18 ( 859) hydrogen bonds : angle 5.19536 / 3.75 ( 2427) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 103 time to evaluate : 0.590 Fit side-chains revert: symmetry clash REVERT: A 103 ARG cc_start: 0.8531 (mmm-85) cc_final: 0.8108 (mmm160) REVERT: A 424 MET cc_start: 0.9146 (ptp) cc_final: 0.8646 (ppp) REVERT: A 616 LYS cc_start: 0.9079 (OUTLIER) cc_final: 0.8559 (mmmm) REVERT: A 643 ASP cc_start: 0.8506 (m-30) cc_final: 0.8197 (m-30) REVERT: A 645 GLU cc_start: 0.8163 (tp30) cc_final: 0.7697 (tp30) REVERT: A 657 MET cc_start: 0.8874 (tpp) cc_final: 0.8593 (tpt) REVERT: B 54 ARG cc_start: 0.8669 (OUTLIER) cc_final: 0.7773 (mmt90) REVERT: B 118 ARG cc_start: 0.7202 (tpt170) cc_final: 0.6782 (tpp-160) REVERT: B 125 ASP cc_start: 0.8548 (m-30) cc_final: 0.8340 (m-30) REVERT: B 230 GLU cc_start: 0.8825 (OUTLIER) cc_final: 0.8309 (tp30) REVERT: B 314 ASN cc_start: 0.8976 (OUTLIER) cc_final: 0.8600 (m110) REVERT: B 611 GLN cc_start: 0.9248 (tp40) cc_final: 0.8030 (tp40) REVERT: B 645 GLU cc_start: 0.8470 (mm-30) cc_final: 0.7839 (tm-30) REVERT: B 664 ILE cc_start: 0.8598 (pp) cc_final: 0.8227 (pp) REVERT: C 56 LEU cc_start: 0.9287 (OUTLIER) cc_final: 0.8956 (mp) REVERT: C 230 GLU cc_start: 0.8854 (OUTLIER) cc_final: 0.8475 (tp30) REVERT: C 436 GLU cc_start: 0.8203 (OUTLIER) cc_final: 0.7515 (mp0) REVERT: C 616 LYS cc_start: 0.9151 (tppp) cc_final: 0.8829 (mmmm) REVERT: C 617 ARG cc_start: 0.9133 (OUTLIER) cc_final: 0.8709 (tpt-90) outliers start: 43 outliers final: 21 residues processed: 137 average time/residue: 0.6157 time to fit residues: 92.9240 Evaluate side-chains 130 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 101 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 416 ASN Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 616 LYS Chi-restraints excluded: chain B residue 54 ARG Chi-restraints excluded: chain B residue 116 TYR Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 230 GLU Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 371 SER Chi-restraints excluded: chain B residue 372 CYS Chi-restraints excluded: chain B residue 400 ASP Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 483 SER Chi-restraints excluded: chain B residue 533 ILE Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 646 THR Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 125 ASP Chi-restraints excluded: chain C residue 230 GLU Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain C residue 289 LYS Chi-restraints excluded: chain C residue 436 GLU Chi-restraints excluded: chain C residue 606 VAL Chi-restraints excluded: chain C residue 609 THR Chi-restraints excluded: chain C residue 617 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 36 optimal weight: 3.9990 chunk 47 optimal weight: 0.6980 chunk 109 optimal weight: 2.9990 chunk 157 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 145 optimal weight: 3.9990 chunk 119 optimal weight: 5.9990 chunk 23 optimal weight: 0.9980 chunk 169 optimal weight: 0.9990 chunk 40 optimal weight: 0.8980 chunk 25 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 611 GLN A 632 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.090995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.065298 restraints weight = 22916.572| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 2.22 r_work: 0.2829 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2710 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9193 moved from start: 0.1149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14741 Z= 0.151 Angle : 0.501 6.148 19990 Z= 0.275 Chirality : 0.044 0.149 2344 Planarity : 0.004 0.049 2567 Dihedral : 8.157 171.758 2092 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 2.58 % Allowed : 14.73 % Favored : 82.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.27 (0.20), residues: 1865 helix: 2.46 (0.18), residues: 730 sheet: 1.75 (0.25), residues: 435 loop : 0.37 (0.25), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 661 TYR 0.018 0.001 TYR B 334 PHE 0.016 0.001 PHE C 340 TRP 0.005 0.001 TRP B 184 HIS 0.001 0.000 HIS C 243 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.15 (14741) covalent geometry : angle 0.50067 / 0.27 (19990) hydrogen bonds : bond 0.05575 / 3.74 ( 859) hydrogen bonds : angle 4.98680 / 3.59 ( 2427) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 106 time to evaluate : 0.574 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 103 ARG cc_start: 0.8514 (mmm-85) cc_final: 0.8074 (mmm160) REVERT: A 424 MET cc_start: 0.9123 (ptp) cc_final: 0.8587 (ppp) REVERT: A 616 LYS cc_start: 0.9077 (OUTLIER) cc_final: 0.8567 (mmmm) REVERT: A 643 ASP cc_start: 0.8504 (m-30) cc_final: 0.8191 (m-30) REVERT: A 645 GLU cc_start: 0.8138 (tp30) cc_final: 0.7633 (tp30) REVERT: A 657 MET cc_start: 0.8869 (tpp) cc_final: 0.8561 (tpt) REVERT: B 125 ASP cc_start: 0.8536 (OUTLIER) cc_final: 0.8318 (m-30) REVERT: B 230 GLU cc_start: 0.8789 (OUTLIER) cc_final: 0.8270 (tp30) REVERT: B 314 ASN cc_start: 0.8936 (OUTLIER) cc_final: 0.8588 (m-40) REVERT: B 664 ILE cc_start: 0.8545 (pp) cc_final: 0.8212 (pp) REVERT: C 56 LEU cc_start: 0.9276 (OUTLIER) cc_final: 0.8956 (mp) REVERT: C 230 GLU cc_start: 0.8821 (OUTLIER) cc_final: 0.8430 (tp30) REVERT: C 436 GLU cc_start: 0.8184 (OUTLIER) cc_final: 0.7499 (mp0) REVERT: C 616 LYS cc_start: 0.9147 (tppp) cc_final: 0.8830 (mmmm) REVERT: C 617 ARG cc_start: 0.9107 (OUTLIER) cc_final: 0.8720 (tpt-90) outliers start: 41 outliers final: 21 residues processed: 136 average time/residue: 0.6097 time to fit residues: 91.6444 Evaluate side-chains 126 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 97 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 416 ASN Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 616 LYS Chi-restraints excluded: chain B residue 116 TYR Chi-restraints excluded: chain B residue 125 ASP Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 230 GLU Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 371 SER Chi-restraints excluded: chain B residue 372 CYS Chi-restraints excluded: chain B residue 400 ASP Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 483 SER Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 646 THR Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 230 GLU Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain C residue 289 LYS Chi-restraints excluded: chain C residue 406 ILE Chi-restraints excluded: chain C residue 436 GLU Chi-restraints excluded: chain C residue 606 VAL Chi-restraints excluded: chain C residue 609 THR Chi-restraints excluded: chain C residue 617 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 115 optimal weight: 3.9990 chunk 168 optimal weight: 6.9990 chunk 84 optimal weight: 2.9990 chunk 149 optimal weight: 2.9990 chunk 78 optimal weight: 0.6980 chunk 61 optimal weight: 6.9990 chunk 26 optimal weight: 4.9990 chunk 31 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 110 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 155 ASN A 611 GLN ** A 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.087874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.062561 restraints weight = 23252.276| |-----------------------------------------------------------------------------| r_work (start): 0.2924 rms_B_bonded: 2.18 r_work: 0.2780 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2661 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9238 moved from start: 0.0916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.059 14741 Z= 0.336 Angle : 0.611 6.313 19990 Z= 0.336 Chirality : 0.049 0.167 2344 Planarity : 0.005 0.064 2567 Dihedral : 8.412 170.792 2092 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 2.89 % Allowed : 14.35 % Favored : 82.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 2.01 (0.19), residues: 1865 helix: 2.17 (0.18), residues: 734 sheet: 1.74 (0.25), residues: 433 loop : 0.22 (0.24), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 617 TYR 0.019 0.002 TYR C 334 PHE 0.018 0.002 PHE A 340 TRP 0.004 0.002 TRP A 184 HIS 0.004 0.001 HIS C 243 Details of bonding type rmsd/Z covalent geometry : bond 0.00762 / 0.34 (14741) covalent geometry : angle 0.61124 / 0.34 (19990) hydrogen bonds : bond 0.06834 / 4.58 ( 859) hydrogen bonds : angle 5.31951 / 3.85 ( 2427) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 103 time to evaluate : 0.591 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 103 ARG cc_start: 0.8512 (mmm-85) cc_final: 0.8102 (mmm160) REVERT: A 294 ARG cc_start: 0.9003 (OUTLIER) cc_final: 0.8491 (mtm-85) REVERT: A 424 MET cc_start: 0.9146 (ptp) cc_final: 0.8650 (ppp) REVERT: A 616 LYS cc_start: 0.9088 (OUTLIER) cc_final: 0.8574 (mmmm) REVERT: A 643 ASP cc_start: 0.8569 (m-30) cc_final: 0.8253 (m-30) REVERT: A 645 GLU cc_start: 0.8173 (tp30) cc_final: 0.7827 (tp30) REVERT: A 657 MET cc_start: 0.8930 (tpp) cc_final: 0.8614 (tpt) REVERT: B 54 ARG cc_start: 0.8739 (OUTLIER) cc_final: 0.7870 (mmt90) REVERT: B 125 ASP cc_start: 0.8566 (OUTLIER) cc_final: 0.8355 (m-30) REVERT: B 230 GLU cc_start: 0.8839 (OUTLIER) cc_final: 0.8325 (tp30) REVERT: B 664 ILE cc_start: 0.8591 (pp) cc_final: 0.8236 (pp) REVERT: C 56 LEU cc_start: 0.9317 (OUTLIER) cc_final: 0.8993 (mp) REVERT: C 230 GLU cc_start: 0.8899 (OUTLIER) cc_final: 0.8502 (tp30) REVERT: C 436 GLU cc_start: 0.8215 (OUTLIER) cc_final: 0.7475 (mp0) REVERT: C 616 LYS cc_start: 0.9149 (tppp) cc_final: 0.8831 (mmmm) REVERT: C 617 ARG cc_start: 0.9132 (OUTLIER) cc_final: 0.8687 (tpt-90) outliers start: 46 outliers final: 25 residues processed: 140 average time/residue: 0.6660 time to fit residues: 101.9965 Evaluate side-chains 135 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 101 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 294 ARG Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 416 ASN Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 616 LYS Chi-restraints excluded: chain B residue 54 ARG Chi-restraints excluded: chain B residue 116 TYR Chi-restraints excluded: chain B residue 125 ASP Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 230 GLU Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 371 SER Chi-restraints excluded: chain B residue 372 CYS Chi-restraints excluded: chain B residue 400 ASP Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 483 SER Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 646 THR Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 230 GLU Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain C residue 289 LYS Chi-restraints excluded: chain C residue 406 ILE Chi-restraints excluded: chain C residue 436 GLU Chi-restraints excluded: chain C residue 606 VAL Chi-restraints excluded: chain C residue 609 THR Chi-restraints excluded: chain C residue 617 ARG Chi-restraints excluded: chain C residue 637 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 64 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 167 optimal weight: 0.6980 chunk 129 optimal weight: 0.9990 chunk 47 optimal weight: 0.0020 chunk 86 optimal weight: 0.9980 chunk 183 optimal weight: 2.9990 chunk 19 optimal weight: 0.0980 chunk 164 optimal weight: 2.9990 chunk 140 optimal weight: 0.9980 chunk 97 optimal weight: 2.9990 overall best weight: 0.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 611 GLN A 632 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.090705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.065667 restraints weight = 22945.215| |-----------------------------------------------------------------------------| r_work (start): 0.2989 rms_B_bonded: 2.18 r_work: 0.2847 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2730 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9195 moved from start: 0.1192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14741 Z= 0.139 Angle : 0.522 7.359 19990 Z= 0.284 Chirality : 0.044 0.151 2344 Planarity : 0.004 0.055 2567 Dihedral : 8.098 169.624 2092 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.14 % Allowed : 15.54 % Favored : 82.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 2.26 (0.19), residues: 1865 helix: 2.48 (0.18), residues: 727 sheet: 1.71 (0.25), residues: 435 loop : 0.35 (0.25), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 661 TYR 0.020 0.001 TYR B 334 PHE 0.016 0.001 PHE C 545 TRP 0.007 0.001 TRP B 184 HIS 0.002 0.001 HIS C 426 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.14 (14741) covalent geometry : angle 0.52207 / 0.28 (19990) hydrogen bonds : bond 0.05447 / 3.65 ( 859) hydrogen bonds : angle 4.94497 / 3.55 ( 2427) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 107 time to evaluate : 0.595 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 GLN cc_start: 0.7968 (mm-40) cc_final: 0.7418 (mt0) REVERT: A 103 ARG cc_start: 0.8501 (mmm-85) cc_final: 0.8258 (mmm-85) REVERT: A 424 MET cc_start: 0.9115 (ptp) cc_final: 0.8584 (ppp) REVERT: A 616 LYS cc_start: 0.9070 (OUTLIER) cc_final: 0.8562 (mmmm) REVERT: A 643 ASP cc_start: 0.8496 (m-30) cc_final: 0.8197 (m-30) REVERT: A 645 GLU cc_start: 0.8115 (tp30) cc_final: 0.7745 (tp30) REVERT: A 657 MET cc_start: 0.8912 (tpp) cc_final: 0.8583 (tpt) REVERT: B 118 ARG cc_start: 0.7073 (tpt170) cc_final: 0.6665 (tpm170) REVERT: B 125 ASP cc_start: 0.8503 (OUTLIER) cc_final: 0.8282 (m-30) REVERT: B 230 GLU cc_start: 0.8749 (OUTLIER) cc_final: 0.8234 (tp30) REVERT: B 664 ILE cc_start: 0.8563 (pp) cc_final: 0.8229 (pp) REVERT: C 56 LEU cc_start: 0.9290 (OUTLIER) cc_final: 0.8982 (mp) REVERT: C 230 GLU cc_start: 0.8816 (OUTLIER) cc_final: 0.8442 (tp30) REVERT: C 436 GLU cc_start: 0.8169 (OUTLIER) cc_final: 0.7447 (mp0) REVERT: C 616 LYS cc_start: 0.9160 (tppp) cc_final: 0.8840 (mmmm) REVERT: C 617 ARG cc_start: 0.9095 (OUTLIER) cc_final: 0.8686 (tpt-90) outliers start: 34 outliers final: 17 residues processed: 132 average time/residue: 0.6492 time to fit residues: 94.2688 Evaluate side-chains 125 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 101 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 416 ASN Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 616 LYS Chi-restraints excluded: chain B residue 116 TYR Chi-restraints excluded: chain B residue 125 ASP Chi-restraints excluded: chain B residue 230 GLU Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 371 SER Chi-restraints excluded: chain B residue 372 CYS Chi-restraints excluded: chain B residue 483 SER Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 646 THR Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 230 GLU Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain C residue 406 ILE Chi-restraints excluded: chain C residue 436 GLU Chi-restraints excluded: chain C residue 606 VAL Chi-restraints excluded: chain C residue 609 THR Chi-restraints excluded: chain C residue 617 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 75 optimal weight: 0.2980 chunk 145 optimal weight: 3.9990 chunk 146 optimal weight: 0.5980 chunk 97 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 117 optimal weight: 4.9990 chunk 55 optimal weight: 0.0570 chunk 140 optimal weight: 0.4980 chunk 164 optimal weight: 4.9990 chunk 96 optimal weight: 3.9990 overall best weight: 0.4898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 611 GLN A 632 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.091356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.065987 restraints weight = 22908.748| |-----------------------------------------------------------------------------| r_work (start): 0.2989 rms_B_bonded: 2.18 r_work: 0.2849 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2730 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9179 moved from start: 0.1352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14741 Z= 0.130 Angle : 0.512 9.590 19990 Z= 0.277 Chirality : 0.043 0.147 2344 Planarity : 0.004 0.047 2567 Dihedral : 7.883 167.823 2090 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 2.52 % Allowed : 15.42 % Favored : 82.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 2.34 (0.20), residues: 1865 helix: 2.56 (0.18), residues: 734 sheet: 1.78 (0.25), residues: 435 loop : 0.34 (0.25), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 617 TYR 0.019 0.001 TYR B 334 PHE 0.015 0.001 PHE C 340 TRP 0.008 0.001 TRP B 184 HIS 0.001 0.000 HIS C 426 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.13 (14741) covalent geometry : angle 0.51156 / 0.28 (19990) hydrogen bonds : bond 0.05048 / 3.38 ( 859) hydrogen bonds : angle 4.79499 / 3.44 ( 2427) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 107 time to evaluate : 0.593 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 103 ARG cc_start: 0.8474 (mmm-85) cc_final: 0.8050 (mmm160) REVERT: A 424 MET cc_start: 0.9128 (ptp) cc_final: 0.8593 (ppp) REVERT: A 616 LYS cc_start: 0.9081 (OUTLIER) cc_final: 0.8601 (mmmm) REVERT: A 643 ASP cc_start: 0.8480 (m-30) cc_final: 0.8198 (m-30) REVERT: A 645 GLU cc_start: 0.8106 (tp30) cc_final: 0.7699 (tp30) REVERT: A 657 MET cc_start: 0.8912 (tpp) cc_final: 0.8563 (tpt) REVERT: B 125 ASP cc_start: 0.8572 (OUTLIER) cc_final: 0.8360 (m-30) REVERT: B 230 GLU cc_start: 0.8720 (OUTLIER) cc_final: 0.8204 (tp30) REVERT: B 664 ILE cc_start: 0.8568 (pp) cc_final: 0.8195 (pp) REVERT: C 56 LEU cc_start: 0.9252 (OUTLIER) cc_final: 0.8939 (mp) REVERT: C 230 GLU cc_start: 0.8735 (OUTLIER) cc_final: 0.8376 (tp30) REVERT: C 436 GLU cc_start: 0.8238 (OUTLIER) cc_final: 0.7542 (mp0) REVERT: C 616 LYS cc_start: 0.9160 (tppp) cc_final: 0.8845 (mmmm) REVERT: C 617 ARG cc_start: 0.9102 (OUTLIER) cc_final: 0.8699 (tpt-90) outliers start: 40 outliers final: 22 residues processed: 138 average time/residue: 0.6387 time to fit residues: 97.0514 Evaluate side-chains 128 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 99 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 416 ASN Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 616 LYS Chi-restraints excluded: chain B residue 116 TYR Chi-restraints excluded: chain B residue 125 ASP Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 230 GLU Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 371 SER Chi-restraints excluded: chain B residue 372 CYS Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 606 VAL Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 646 THR Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 230 GLU Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain C residue 406 ILE Chi-restraints excluded: chain C residue 436 GLU Chi-restraints excluded: chain C residue 606 VAL Chi-restraints excluded: chain C residue 609 THR Chi-restraints excluded: chain C residue 617 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 122 optimal weight: 3.9990 chunk 161 optimal weight: 0.2980 chunk 109 optimal weight: 0.0980 chunk 130 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 chunk 162 optimal weight: 0.4980 chunk 46 optimal weight: 0.7980 chunk 95 optimal weight: 4.9990 chunk 123 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 155 ASN A 611 GLN A 632 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.091921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.066899 restraints weight = 23189.229| |-----------------------------------------------------------------------------| r_work (start): 0.3016 rms_B_bonded: 2.20 r_work: 0.2877 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2760 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9175 moved from start: 0.1421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14741 Z= 0.127 Angle : 0.522 11.020 19990 Z= 0.280 Chirality : 0.043 0.148 2344 Planarity : 0.004 0.064 2567 Dihedral : 7.804 166.336 2090 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.95 % Allowed : 16.24 % Favored : 81.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 2.43 (0.20), residues: 1865 helix: 2.66 (0.18), residues: 728 sheet: 1.79 (0.25), residues: 437 loop : 0.39 (0.25), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG B 661 TYR 0.021 0.001 TYR B 334 PHE 0.015 0.001 PHE C 340 TRP 0.008 0.001 TRP B 184 HIS 0.002 0.000 HIS C 426 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.13 (14741) covalent geometry : angle 0.52199 / 0.28 (19990) hydrogen bonds : bond 0.04881 / 3.27 ( 859) hydrogen bonds : angle 4.72936 / 3.39 ( 2427) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 100 time to evaluate : 0.598 Fit side-chains revert: symmetry clash REVERT: A 94 GLN cc_start: 0.7953 (mm-40) cc_final: 0.7369 (mt0) REVERT: A 103 ARG cc_start: 0.8453 (mmm-85) cc_final: 0.8058 (mmm160) REVERT: A 424 MET cc_start: 0.9121 (ptp) cc_final: 0.8609 (ppp) REVERT: A 616 LYS cc_start: 0.9088 (OUTLIER) cc_final: 0.8611 (mmmm) REVERT: A 645 GLU cc_start: 0.8021 (tp30) cc_final: 0.7600 (tp30) REVERT: A 657 MET cc_start: 0.8903 (tpp) cc_final: 0.8544 (tpt) REVERT: B 118 ARG cc_start: 0.6991 (tpm170) cc_final: 0.6750 (tpp-160) REVERT: B 125 ASP cc_start: 0.8525 (OUTLIER) cc_final: 0.8314 (m-30) REVERT: B 230 GLU cc_start: 0.8703 (OUTLIER) cc_final: 0.8181 (tp30) REVERT: B 282 GLU cc_start: 0.8276 (pm20) cc_final: 0.7970 (pp20) REVERT: B 645 GLU cc_start: 0.8417 (mm-30) cc_final: 0.7723 (tm-30) REVERT: B 664 ILE cc_start: 0.8527 (pp) cc_final: 0.8204 (pp) REVERT: C 56 LEU cc_start: 0.9238 (OUTLIER) cc_final: 0.8926 (mp) REVERT: C 230 GLU cc_start: 0.8760 (OUTLIER) cc_final: 0.8396 (tp30) REVERT: C 436 GLU cc_start: 0.8182 (OUTLIER) cc_final: 0.7980 (mp0) REVERT: C 616 LYS cc_start: 0.9168 (tppp) cc_final: 0.8873 (mmmm) REVERT: C 617 ARG cc_start: 0.9078 (OUTLIER) cc_final: 0.8689 (tpt-90) outliers start: 31 outliers final: 20 residues processed: 123 average time/residue: 0.6568 time to fit residues: 88.8500 Evaluate side-chains 128 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 101 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 416 ASN Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 616 LYS Chi-restraints excluded: chain B residue 116 TYR Chi-restraints excluded: chain B residue 125 ASP Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 230 GLU Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 371 SER Chi-restraints excluded: chain B residue 372 CYS Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 606 VAL Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 646 THR Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 230 GLU Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain C residue 406 ILE Chi-restraints excluded: chain C residue 436 GLU Chi-restraints excluded: chain C residue 606 VAL Chi-restraints excluded: chain C residue 609 THR Chi-restraints excluded: chain C residue 617 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 129 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 chunk 183 optimal weight: 4.9990 chunk 11 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 63 optimal weight: 4.9990 chunk 110 optimal weight: 2.9990 chunk 148 optimal weight: 3.9990 chunk 56 optimal weight: 4.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 611 GLN A 632 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.088177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.062790 restraints weight = 23255.497| |-----------------------------------------------------------------------------| r_work (start): 0.2930 rms_B_bonded: 2.19 r_work: 0.2786 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2668 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9234 moved from start: 0.1028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.058 14741 Z= 0.317 Angle : 0.633 10.642 19990 Z= 0.343 Chirality : 0.049 0.164 2344 Planarity : 0.005 0.065 2567 Dihedral : 8.215 167.856 2090 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 2.20 % Allowed : 15.92 % Favored : 81.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 2.11 (0.19), residues: 1865 helix: 2.29 (0.18), residues: 734 sheet: 1.77 (0.25), residues: 436 loop : 0.22 (0.24), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 617 TYR 0.021 0.002 TYR B 334 PHE 0.018 0.002 PHE A 340 TRP 0.006 0.002 TRP C 184 HIS 0.004 0.001 HIS C 243 Details of bonding type rmsd/Z covalent geometry : bond 0.00720 / 0.32 (14741) covalent geometry : angle 0.63281 / 0.34 (19990) hydrogen bonds : bond 0.06624 / 4.43 ( 859) hydrogen bonds : angle 5.22343 / 3.78 ( 2427) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 107 time to evaluate : 0.724 Fit side-chains revert: symmetry clash REVERT: A 424 MET cc_start: 0.9131 (ptp) cc_final: 0.8634 (ppp) REVERT: A 616 LYS cc_start: 0.9105 (OUTLIER) cc_final: 0.8610 (mmmm) REVERT: A 645 GLU cc_start: 0.8094 (tp30) cc_final: 0.7746 (tp30) REVERT: A 657 MET cc_start: 0.8938 (tpp) cc_final: 0.8581 (tpt) REVERT: B 125 ASP cc_start: 0.8552 (OUTLIER) cc_final: 0.8340 (m-30) REVERT: B 230 GLU cc_start: 0.8872 (OUTLIER) cc_final: 0.8339 (tp30) REVERT: B 645 GLU cc_start: 0.8427 (mm-30) cc_final: 0.7682 (tm-30) REVERT: B 664 ILE cc_start: 0.8567 (pp) cc_final: 0.8232 (pp) REVERT: C 56 LEU cc_start: 0.9312 (OUTLIER) cc_final: 0.8982 (mp) REVERT: C 230 GLU cc_start: 0.8915 (OUTLIER) cc_final: 0.8525 (tp30) REVERT: C 436 GLU cc_start: 0.8231 (OUTLIER) cc_final: 0.7522 (mp0) REVERT: C 616 LYS cc_start: 0.9166 (tppp) cc_final: 0.8872 (mmmm) REVERT: C 617 ARG cc_start: 0.9137 (OUTLIER) cc_final: 0.8675 (tpt-90) outliers start: 35 outliers final: 19 residues processed: 135 average time/residue: 0.6185 time to fit residues: 92.4957 Evaluate side-chains 128 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 102 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 416 ASN Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 616 LYS Chi-restraints excluded: chain B residue 116 TYR Chi-restraints excluded: chain B residue 125 ASP Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 230 GLU Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 371 SER Chi-restraints excluded: chain B residue 372 CYS Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 483 SER Chi-restraints excluded: chain B residue 606 VAL Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 646 THR Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 230 GLU Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain C residue 406 ILE Chi-restraints excluded: chain C residue 436 GLU Chi-restraints excluded: chain C residue 606 VAL Chi-restraints excluded: chain C residue 609 THR Chi-restraints excluded: chain C residue 617 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 29 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 83 optimal weight: 0.9980 chunk 131 optimal weight: 3.9990 chunk 146 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 118 optimal weight: 4.9990 chunk 106 optimal weight: 0.7980 chunk 70 optimal weight: 1.9990 chunk 93 optimal weight: 0.7980 chunk 4 optimal weight: 2.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 611 GLN A 632 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.089754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.064441 restraints weight = 23050.432| |-----------------------------------------------------------------------------| r_work (start): 0.2964 rms_B_bonded: 2.19 r_work: 0.2821 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2703 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9211 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 : 0.004 0.047 14741 Z= 0.183 Angle : 0.565 10.955 19990 Z= 0.306 Chirality : 0.045 0.152 2344 Planarity : 0.004 0.049 2567 Dihedral : 8.068 167.564 2090 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.76 % Allowed : 16.49 % Favored : 81.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 2.22 (0.20), residues: 1865 helix: 2.38 (0.18), residues: 739 sheet: 1.75 (0.25), residues: 436 loop : 0.32 (0.25), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 617 TYR 0.022 0.002 TYR B 334 PHE 0.017 0.001 PHE C 340 TRP 0.004 0.001 TRP C 184 HIS 0.002 0.000 HIS C 243 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.18 (14741) covalent geometry : angle 0.56458 / 0.31 (19990) hydrogen bonds : bond 0.05800 / 3.88 ( 859) hydrogen bonds : angle 5.01745 / 3.62 ( 2427) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7354.62 seconds wall clock time: 125 minutes 54.08 seconds (7554.08 seconds total)