Starting phenix.real_space_refine on Thu Jul 2 13:08:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8i3b_35148/07_2026/8i3b_35148.cif Found real_map, /net/cci-nas-00/data/ceres_data/8i3b_35148/07_2026/8i3b_35148.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.08 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8i3b_35148/07_2026/8i3b_35148.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8i3b_35148/07_2026/8i3b_35148.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8i3b_35148/07_2026/8i3b_35148.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8i3b_35148/07_2026/8i3b_35148.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8i3b_35148/07_2026/8i3b_35148.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8i3b_35148/07_2026/8i3b_35148.cif" } resolution = 3.08 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= 0.001 sd= 0.052 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 6 5.49 5 S 52 5.16 5 C 5624 2.51 5 N 1446 2.21 5 O 1518 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 54 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8646 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 550, 4292 Classifications: {'peptide': 550} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 19, 'TRANS': 530} Chain breaks: 5 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 4292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 550, 4292 Classifications: {'peptide': 550} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 19, 'TRANS': 530} Chain breaks: 5 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.94, per 1000 atoms: 0.22 Number of scatterers: 8646 At special positions: 0 Unit cell: (80.51, 93.79, 122.01, 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 52 16.00 P 6 15.00 O 1518 8.00 N 1446 7.00 C 5624 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: 0.70 Conformation dependent library (CDL) restraints added in 416.1 milliseconds 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2028 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 6 sheets defined 54.5% alpha, 8.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'A' and resid 106 through 115 Processing helix chain 'A' and resid 137 through 140 removed outlier: 3.653A pdb=" N LYS A 140 " --> pdb=" O GLN A 137 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 137 through 140' Processing helix chain 'A' and resid 156 through 169 Processing helix chain 'A' and resid 174 through 181 Processing helix chain 'A' and resid 185 through 190 Processing helix chain 'A' and resid 210 through 219 removed outlier: 4.183A pdb=" N SER A 216 " --> pdb=" O ARG A 212 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA A 218 " --> pdb=" O ARG A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 252 Processing helix chain 'A' and resid 297 through 301 Processing helix chain 'A' and resid 311 through 319 removed outlier: 3.890A pdb=" N PHE A 315 " --> pdb=" O ASN A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 347 removed outlier: 3.577A pdb=" N THR A 340 " --> pdb=" O ASN A 336 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N THR A 347 " --> pdb=" O THR A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 357 Processing helix chain 'A' and resid 381 through 401 removed outlier: 3.594A pdb=" N LEU A 393 " --> pdb=" O GLN A 389 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU A 397 " --> pdb=" O LEU A 393 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ARG A 401 " --> pdb=" O LEU A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 425 removed outlier: 3.637A pdb=" N TRP A 425 " --> pdb=" O CYS A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 455 removed outlier: 3.800A pdb=" N LEU A 439 " --> pdb=" O ASP A 435 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N SER A 444 " --> pdb=" O LEU A 440 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLY A 448 " --> pdb=" O SER A 444 " (cutoff:3.500A) Proline residue: A 451 - end of helix Processing helix chain 'A' and resid 456 through 458 No H-bonds generated for 'chain 'A' and resid 456 through 458' Processing helix chain 'A' and resid 459 through 461 No H-bonds generated for 'chain 'A' and resid 459 through 461' Processing helix chain 'A' and resid 462 through 473 removed outlier: 4.027A pdb=" N ARG A 468 " --> pdb=" O ALA A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 489 removed outlier: 3.756A pdb=" N ALA A 483 " --> pdb=" O SER A 479 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N HIS A 484 " --> pdb=" O TYR A 480 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N LEU A 486 " --> pdb=" O MET A 482 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU A 489 " --> pdb=" O VAL A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 506 removed outlier: 3.878A pdb=" N ALA A 497 " --> pdb=" O LEU A 493 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N PHE A 502 " --> pdb=" O SER A 498 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N TRP A 505 " --> pdb=" O THR A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 540 removed outlier: 3.627A pdb=" N PHE A 516 " --> pdb=" O GLY A 512 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLY A 532 " --> pdb=" O LEU A 528 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LEU A 533 " --> pdb=" O ALA A 529 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLY A 534 " --> pdb=" O SER A 530 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N GLY A 538 " --> pdb=" O GLY A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 561 removed outlier: 3.993A pdb=" N THR A 549 " --> pdb=" O LYS A 545 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ILE A 550 " --> pdb=" O LYS A 546 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N THR A 552 " --> pdb=" O SER A 548 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N VAL A 553 " --> pdb=" O THR A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 575 through 580 removed outlier: 4.185A pdb=" N VAL A 579 " --> pdb=" O TRP A 575 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N SER A 580 " --> pdb=" O MET A 576 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 575 through 580' Processing helix chain 'A' and resid 581 through 595 removed outlier: 3.807A pdb=" N CYS A 585 " --> pdb=" O THR A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 604 Processing helix chain 'A' and resid 639 through 656 removed outlier: 3.549A pdb=" N LEU A 644 " --> pdb=" O GLY A 640 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ARG A 650 " --> pdb=" O PHE A 646 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 115 Processing helix chain 'B' and resid 137 through 140 removed outlier: 3.652A pdb=" N LYS B 140 " --> pdb=" O GLN B 137 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 137 through 140' Processing helix chain 'B' and resid 156 through 169 Processing helix chain 'B' and resid 174 through 181 Processing helix chain 'B' and resid 185 through 190 Processing helix chain 'B' and resid 210 through 219 removed outlier: 4.182A pdb=" N SER B 216 " --> pdb=" O ARG B 212 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA B 218 " --> pdb=" O ARG B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 252 Processing helix chain 'B' and resid 297 through 301 Processing helix chain 'B' and resid 311 through 319 removed outlier: 3.889A pdb=" N PHE B 315 " --> pdb=" O ASN B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 347 removed outlier: 3.578A pdb=" N THR B 340 " --> pdb=" O ASN B 336 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N THR B 347 " --> pdb=" O THR B 343 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 357 Processing helix chain 'B' and resid 381 through 401 removed outlier: 3.594A pdb=" N LEU B 393 " --> pdb=" O GLN B 389 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU B 397 " --> pdb=" O LEU B 393 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ARG B 401 " --> pdb=" O LEU B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 425 removed outlier: 3.637A pdb=" N TRP B 425 " --> pdb=" O CYS B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 434 through 455 removed outlier: 3.799A pdb=" N LEU B 439 " --> pdb=" O ASP B 435 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N SER B 444 " --> pdb=" O LEU B 440 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLY B 448 " --> pdb=" O SER B 444 " (cutoff:3.500A) Proline residue: B 451 - end of helix Processing helix chain 'B' and resid 456 through 458 No H-bonds generated for 'chain 'B' and resid 456 through 458' Processing helix chain 'B' and resid 459 through 461 No H-bonds generated for 'chain 'B' and resid 459 through 461' Processing helix chain 'B' and resid 462 through 473 removed outlier: 4.026A pdb=" N ARG B 468 " --> pdb=" O ALA B 464 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 489 removed outlier: 3.756A pdb=" N ALA B 483 " --> pdb=" O SER B 479 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N HIS B 484 " --> pdb=" O TYR B 480 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N LEU B 486 " --> pdb=" O MET B 482 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU B 489 " --> pdb=" O VAL B 485 " (cutoff:3.500A) Processing helix chain 'B' and resid 493 through 506 removed outlier: 3.878A pdb=" N ALA B 497 " --> pdb=" O LEU B 493 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N PHE B 502 " --> pdb=" O SER B 498 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N TRP B 505 " --> pdb=" O THR B 501 " (cutoff:3.500A) Processing helix chain 'B' and resid 512 through 540 removed outlier: 3.627A pdb=" N PHE B 516 " --> pdb=" O GLY B 512 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLY B 532 " --> pdb=" O LEU B 528 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LEU B 533 " --> pdb=" O ALA B 529 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLY B 534 " --> pdb=" O SER B 530 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N GLY B 538 " --> pdb=" O GLY B 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 561 removed outlier: 3.994A pdb=" N THR B 549 " --> pdb=" O LYS B 545 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ILE B 550 " --> pdb=" O LYS B 546 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N THR B 552 " --> pdb=" O SER B 548 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N VAL B 553 " --> pdb=" O THR B 549 " (cutoff:3.500A) Processing helix chain 'B' and resid 575 through 580 removed outlier: 4.185A pdb=" N VAL B 579 " --> pdb=" O TRP B 575 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N SER B 580 " --> pdb=" O MET B 576 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 575 through 580' Processing helix chain 'B' and resid 581 through 595 removed outlier: 3.807A pdb=" N CYS B 585 " --> pdb=" O THR B 581 " (cutoff:3.500A) Processing helix chain 'B' and resid 598 through 604 Processing helix chain 'B' and resid 639 through 656 removed outlier: 3.548A pdb=" N LEU B 644 " --> pdb=" O GLY B 640 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ARG B 650 " --> pdb=" O PHE B 646 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 80 through 91 removed outlier: 5.624A pdb=" N ARG A 81 " --> pdb=" O LYS A 50 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N LYS A 50 " --> pdb=" O ARG A 81 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ILE A 83 " --> pdb=" O ARG A 48 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N ARG A 48 " --> pdb=" O ILE A 83 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N SER A 85 " --> pdb=" O CYS A 46 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N CYS A 46 " --> pdb=" O SER A 85 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N VAL A 87 " --> pdb=" O ASP A 44 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 97 through 100 removed outlier: 6.221A pdb=" N ALA A 98 " --> pdb=" O LEU A 279 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N LEU A 281 " --> pdb=" O ALA A 98 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N LEU A 100 " --> pdb=" O LEU A 281 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N VAL A 278 " --> pdb=" O VAL A 289 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N VAL A 289 " --> pdb=" O VAL A 278 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N LEU A 280 " --> pdb=" O LEU A 287 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 142 through 145 removed outlier: 6.242A pdb=" N GLY A 143 " --> pdb=" O VAL A 229 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N LEU A 228 " --> pdb=" O VAL A 261 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 80 through 91 removed outlier: 5.623A pdb=" N ARG B 81 " --> pdb=" O LYS B 50 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N LYS B 50 " --> pdb=" O ARG B 81 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ILE B 83 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N ARG B 48 " --> pdb=" O ILE B 83 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N SER B 85 " --> pdb=" O CYS B 46 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N CYS B 46 " --> pdb=" O SER B 85 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N VAL B 87 " --> pdb=" O ASP B 44 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 97 through 100 removed outlier: 6.221A pdb=" N ALA B 98 " --> pdb=" O LEU B 279 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N LEU B 281 " --> pdb=" O ALA B 98 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N LEU B 100 " --> pdb=" O LEU B 281 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N VAL B 278 " --> pdb=" O VAL B 289 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N VAL B 289 " --> pdb=" O VAL B 278 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N LEU B 280 " --> pdb=" O LEU B 287 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 142 through 145 removed outlier: 6.242A pdb=" N GLY B 143 " --> pdb=" O VAL B 229 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N LEU B 228 " --> pdb=" O VAL B 261 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 356 hydrogen bonds defined for protein. 1038 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.35 Time building geometry restraints manager: 0.94 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: 2103 1.33 - 1.45: 1737 1.45 - 1.57: 4894 1.57 - 1.69: 10 1.69 - 1.81: 86 Bond restraints: 8830 Sorted by residual: bond pdb=" C4 ATP B 701 " pdb=" C5 ATP B 701 " ideal model delta sigma weight residual 1.388 1.462 -0.074 1.00e-02 1.00e+04 5.51e+01 bond pdb=" C4 ATP A 701 " pdb=" C5 ATP A 701 " ideal model delta sigma weight residual 1.388 1.461 -0.073 1.00e-02 1.00e+04 5.33e+01 bond pdb=" C5 ATP A 701 " pdb=" C6 ATP A 701 " ideal model delta sigma weight residual 1.409 1.474 -0.065 1.00e-02 1.00e+04 4.17e+01 bond pdb=" C5 ATP B 701 " pdb=" C6 ATP B 701 " ideal model delta sigma weight residual 1.409 1.473 -0.064 1.00e-02 1.00e+04 4.13e+01 bond pdb=" C5 ATP B 701 " pdb=" N7 ATP B 701 " ideal model delta sigma weight residual 1.387 1.338 0.049 1.00e-02 1.00e+04 2.39e+01 ... (remaining 8825 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.83: 11812 3.83 - 7.66: 140 7.66 - 11.49: 24 11.49 - 15.32: 0 15.32 - 19.16: 4 Bond angle restraints: 11980 Sorted by residual: angle pdb=" PB ATP B 701 " pdb=" O3B ATP B 701 " pdb=" PG ATP B 701 " ideal model delta sigma weight residual 139.87 120.71 19.16 1.00e+00 1.00e+00 3.67e+02 angle pdb=" PB ATP A 701 " pdb=" O3B ATP A 701 " pdb=" PG ATP A 701 " ideal model delta sigma weight residual 139.87 120.72 19.15 1.00e+00 1.00e+00 3.67e+02 angle pdb=" PA ATP A 701 " pdb=" O3A ATP A 701 " pdb=" PB ATP A 701 " ideal model delta sigma weight residual 136.83 120.55 16.28 1.00e+00 1.00e+00 2.65e+02 angle pdb=" PA ATP B 701 " pdb=" O3A ATP B 701 " pdb=" PB ATP B 701 " ideal model delta sigma weight residual 136.83 120.55 16.28 1.00e+00 1.00e+00 2.65e+02 angle pdb=" C5 ATP B 701 " pdb=" C4 ATP B 701 " pdb=" N3 ATP B 701 " ideal model delta sigma weight residual 126.80 118.78 8.02 1.00e+00 1.00e+00 6.43e+01 ... (remaining 11975 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.67: 4537 15.67 - 31.34: 508 31.34 - 47.02: 99 47.02 - 62.69: 16 62.69 - 78.36: 4 Dihedral angle restraints: 5164 sinusoidal: 2012 harmonic: 3152 Sorted by residual: dihedral pdb=" CA GLY B 104 " pdb=" C GLY B 104 " pdb=" N SER B 105 " pdb=" CA SER B 105 " ideal model delta harmonic sigma weight residual -180.00 -154.46 -25.54 0 5.00e+00 4.00e-02 2.61e+01 dihedral pdb=" CA GLY A 104 " pdb=" C GLY A 104 " pdb=" N SER A 105 " pdb=" CA SER A 105 " ideal model delta harmonic sigma weight residual -180.00 -154.47 -25.53 0 5.00e+00 4.00e-02 2.61e+01 dihedral pdb=" CA GLY B 631 " pdb=" C GLY B 631 " pdb=" N ASP B 632 " pdb=" CA ASP B 632 " ideal model delta harmonic sigma weight residual 180.00 -156.31 -23.69 0 5.00e+00 4.00e-02 2.25e+01 ... (remaining 5161 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 1136 0.069 - 0.138: 247 0.138 - 0.208: 31 0.208 - 0.277: 8 0.277 - 0.346: 4 Chirality restraints: 1426 Sorted by residual: chirality pdb=" CB ILE A 129 " pdb=" CA ILE A 129 " pdb=" CG1 ILE A 129 " pdb=" CG2 ILE A 129 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.35 2.00e-01 2.50e+01 2.99e+00 chirality pdb=" CB ILE B 129 " pdb=" CA ILE B 129 " pdb=" CG1 ILE B 129 " pdb=" CG2 ILE B 129 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.35 2.00e-01 2.50e+01 2.99e+00 chirality pdb=" CB VAL B 199 " pdb=" CA VAL B 199 " pdb=" CG1 VAL B 199 " pdb=" CG2 VAL B 199 " both_signs ideal model delta sigma weight residual False -2.63 -2.30 -0.33 2.00e-01 2.50e+01 2.72e+00 ... (remaining 1423 not shown) Planarity restraints: 1452 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 51 " -0.016 2.00e-02 2.50e+03 3.17e-02 1.00e+01 pdb=" C ILE A 51 " 0.055 2.00e-02 2.50e+03 pdb=" O ILE A 51 " -0.021 2.00e-02 2.50e+03 pdb=" N HIS A 52 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 51 " -0.016 2.00e-02 2.50e+03 3.15e-02 9.95e+00 pdb=" C ILE B 51 " 0.055 2.00e-02 2.50e+03 pdb=" O ILE B 51 " -0.021 2.00e-02 2.50e+03 pdb=" N HIS B 52 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 169 " 0.043 5.00e-02 4.00e+02 6.59e-02 6.94e+00 pdb=" N PRO A 170 " -0.114 5.00e-02 4.00e+02 pdb=" CA PRO A 170 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 170 " 0.036 5.00e-02 4.00e+02 ... (remaining 1449 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1981 2.78 - 3.31: 7582 3.31 - 3.84: 13599 3.84 - 4.37: 16642 4.37 - 4.90: 28822 Nonbonded interactions: 68626 Sorted by model distance: nonbonded pdb=" OG1 THR A 156 " pdb=" OE1 GLU A 159 " model vdw 2.249 3.040 nonbonded pdb=" OG1 THR B 156 " pdb=" OE1 GLU B 159 " model vdw 2.250 3.040 nonbonded pdb=" OH TYR A 578 " pdb=" OD2 ASP A 632 " model vdw 2.295 3.040 nonbonded pdb=" OH TYR B 578 " pdb=" OD2 ASP B 632 " model vdw 2.296 3.040 nonbonded pdb=" OE1 GLU B 469 " pdb=" OH TYR B 475 " model vdw 2.330 3.040 ... (remaining 68621 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.100 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 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 0.075 8830 Z= 0.401 Angle : 1.189 19.156 11980 Z= 0.754 Chirality : 0.062 0.346 1426 Planarity : 0.007 0.066 1452 Dihedral : 13.770 78.359 3136 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.83 % Favored : 91.17 % Rotamer: Outliers : 1.50 % Allowed : 6.94 % Favored : 91.56 % 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: -5.42 (0.18), residues: 1076 helix: -3.50 (0.13), residues: 614 sheet: -2.64 (0.44), residues: 80 loop : -3.65 (0.24), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 158 TYR 0.014 0.002 TYR A 594 PHE 0.020 0.002 PHE A 499 TRP 0.012 0.002 TRP A 426 HIS 0.013 0.002 HIS B 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00807 / 0.40 ( 8830) covalent geometry : angle 1.18908 / 0.75 (11980) hydrogen bonds : bond 0.15313 / 10.34 ( 356) hydrogen bonds : angle 6.28686 / 4.31 ( 1038) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 124 time to evaluate : 0.339 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 231 ASP cc_start: 0.8413 (t0) cc_final: 0.8055 (t70) REVERT: A 462 GLU cc_start: 0.7835 (mm-30) cc_final: 0.7553 (mm-30) REVERT: B 231 ASP cc_start: 0.8421 (t0) cc_final: 0.8061 (t70) REVERT: B 462 GLU cc_start: 0.7766 (mm-30) cc_final: 0.7430 (mm-30) REVERT: B 546 LYS cc_start: 0.7629 (mttt) cc_final: 0.7397 (mttm) outliers start: 14 outliers final: 7 residues processed: 137 average time/residue: 0.1084 time to fit residues: 20.0917 Evaluate side-chains 94 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 87 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain B residue 39 THR Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 342 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 108 optimal weight: 2.9990 chunk 49 optimal weight: 0.6980 chunk 97 optimal weight: 0.7980 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 10.0000 chunk 100 optimal weight: 0.9980 chunk 106 optimal weight: 10.0000 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 52 HIS A 112 ASN A 395 HIS B 52 HIS ** B 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 395 HIS B 427 HIS B 434 HIS B 567 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.161508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.121810 restraints weight = 10447.426| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 2.87 r_work: 0.3378 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.1532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8830 Z= 0.123 Angle : 0.596 7.675 11980 Z= 0.312 Chirality : 0.042 0.193 1426 Planarity : 0.005 0.060 1452 Dihedral : 6.756 82.462 1202 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 0.75 % Allowed : 13.14 % Favored : 86.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -3.67 (0.22), residues: 1076 helix: -1.91 (0.18), residues: 606 sheet: -2.59 (0.54), residues: 60 loop : -3.08 (0.25), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 401 TYR 0.013 0.001 TYR B 152 PHE 0.017 0.001 PHE A 315 TRP 0.010 0.001 TRP B 447 HIS 0.006 0.001 HIS A 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.12 ( 8830) covalent geometry : angle 0.59611 / 0.31 (11980) hydrogen bonds : bond 0.03203 / 2.09 ( 356) hydrogen bonds : angle 4.14447 / 2.86 ( 1038) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 108 time to evaluate : 0.320 Fit side-chains REVERT: A 152 TYR cc_start: 0.8948 (m-80) cc_final: 0.8277 (m-80) REVERT: A 231 ASP cc_start: 0.8439 (t0) cc_final: 0.8093 (t70) REVERT: A 286 CYS cc_start: 0.7943 (p) cc_final: 0.7482 (p) REVERT: A 293 ARG cc_start: 0.6509 (mmt-90) cc_final: 0.5984 (mmp80) REVERT: A 315 PHE cc_start: 0.6700 (t80) cc_final: 0.6202 (t80) REVERT: A 462 GLU cc_start: 0.7843 (mm-30) cc_final: 0.7569 (mm-30) REVERT: A 492 GLU cc_start: 0.7619 (tp30) cc_final: 0.6410 (tp30) REVERT: B 152 TYR cc_start: 0.8984 (m-80) cc_final: 0.8345 (m-80) REVERT: B 183 GLU cc_start: 0.6808 (mp0) cc_final: 0.6574 (mp0) REVERT: B 231 ASP cc_start: 0.8496 (t0) cc_final: 0.8184 (t70) REVERT: B 462 GLU cc_start: 0.7840 (mm-30) cc_final: 0.7571 (mm-30) REVERT: B 492 GLU cc_start: 0.7598 (tp30) cc_final: 0.6364 (tp30) REVERT: B 508 TYR cc_start: 0.7606 (t80) cc_final: 0.7344 (t80) REVERT: B 573 MET cc_start: 0.8442 (ttm) cc_final: 0.8082 (ttm) outliers start: 7 outliers final: 5 residues processed: 115 average time/residue: 0.1120 time to fit residues: 17.3566 Evaluate side-chains 98 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 93 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 280 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 79 optimal weight: 1.9990 chunk 95 optimal weight: 3.9990 chunk 73 optimal weight: 5.9990 chunk 53 optimal weight: 2.9990 chunk 27 optimal weight: 20.0000 chunk 26 optimal weight: 7.9990 chunk 86 optimal weight: 0.9980 chunk 106 optimal weight: 8.9990 chunk 0 optimal weight: 7.9990 chunk 90 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 254 HIS A 427 HIS B 254 HIS B 273 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.155556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.116311 restraints weight = 10611.984| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 2.78 r_work: 0.3307 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.1954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 8830 Z= 0.222 Angle : 0.652 7.432 11980 Z= 0.335 Chirality : 0.045 0.167 1426 Planarity : 0.005 0.059 1452 Dihedral : 6.469 82.954 1194 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.34 % Favored : 92.66 % Rotamer: Outliers : 2.14 % Allowed : 14.96 % Favored : 82.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -2.95 (0.23), residues: 1076 helix: -1.33 (0.20), residues: 594 sheet: -2.43 (0.55), residues: 60 loop : -2.71 (0.26), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 180 TYR 0.011 0.002 TYR B 565 PHE 0.015 0.002 PHE A 446 TRP 0.011 0.001 TRP B 447 HIS 0.005 0.001 HIS A 219 Details of bonding type rmsd/Z covalent geometry : bond 0.00538 / 0.22 ( 8830) covalent geometry : angle 0.65236 / 0.33 (11980) hydrogen bonds : bond 0.03735 / 2.43 ( 356) hydrogen bonds : angle 4.05032 / 2.83 ( 1038) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 93 time to evaluate : 0.402 Fit side-chains REVERT: A 152 TYR cc_start: 0.8913 (m-80) cc_final: 0.8339 (m-80) REVERT: A 231 ASP cc_start: 0.8524 (t0) cc_final: 0.8211 (t70) REVERT: A 286 CYS cc_start: 0.7885 (p) cc_final: 0.7462 (p) REVERT: A 462 GLU cc_start: 0.7969 (mm-30) cc_final: 0.7538 (mm-30) REVERT: A 492 GLU cc_start: 0.7641 (tp30) cc_final: 0.6541 (tp30) REVERT: A 573 MET cc_start: 0.8628 (ttm) cc_final: 0.8346 (ttm) REVERT: B 231 ASP cc_start: 0.8557 (t0) cc_final: 0.8179 (t0) REVERT: B 273 GLN cc_start: 0.8383 (mt0) cc_final: 0.8116 (mm-40) REVERT: B 286 CYS cc_start: 0.7920 (p) cc_final: 0.7485 (p) REVERT: B 492 GLU cc_start: 0.7560 (tp30) cc_final: 0.6498 (tp30) REVERT: B 508 TYR cc_start: 0.7639 (t80) cc_final: 0.7422 (t80) REVERT: B 573 MET cc_start: 0.8507 (ttm) cc_final: 0.8261 (ttm) outliers start: 20 outliers final: 16 residues processed: 108 average time/residue: 0.0771 time to fit residues: 12.5916 Evaluate side-chains 103 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 87 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain B residue 36 PHE Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 514 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 37 optimal weight: 4.9990 chunk 29 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 24 optimal weight: 8.9990 chunk 0 optimal weight: 7.9990 chunk 54 optimal weight: 0.6980 chunk 13 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.156490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.117194 restraints weight = 10824.793| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 2.73 r_work: 0.3335 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.2254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 8830 Z= 0.248 Angle : 0.665 7.321 11980 Z= 0.339 Chirality : 0.046 0.170 1426 Planarity : 0.005 0.058 1452 Dihedral : 6.434 82.919 1194 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.34 % Favored : 92.66 % Rotamer: Outliers : 2.56 % Allowed : 16.67 % Favored : 80.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -2.59 (0.23), residues: 1076 helix: -1.13 (0.20), residues: 596 sheet: -2.11 (0.57), residues: 62 loop : -2.41 (0.27), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 410 TYR 0.013 0.002 TYR B 152 PHE 0.017 0.002 PHE A 315 TRP 0.012 0.002 TRP B 447 HIS 0.006 0.001 HIS B 219 Details of bonding type rmsd/Z covalent geometry : bond 0.00606 / 0.25 ( 8830) covalent geometry : angle 0.66462 / 0.34 (11980) hydrogen bonds : bond 0.03763 / 2.44 ( 356) hydrogen bonds : angle 4.09442 / 2.86 ( 1038) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 92 time to evaluate : 0.337 Fit side-chains REVERT: A 97 MET cc_start: 0.6769 (tpt) cc_final: 0.6185 (tpt) REVERT: A 152 TYR cc_start: 0.8912 (m-80) cc_final: 0.8616 (m-80) REVERT: A 231 ASP cc_start: 0.8642 (t0) cc_final: 0.8238 (t0) REVERT: A 286 CYS cc_start: 0.7834 (p) cc_final: 0.7436 (p) REVERT: A 492 GLU cc_start: 0.7512 (tp30) cc_final: 0.6463 (tp30) REVERT: A 573 MET cc_start: 0.8667 (ttm) cc_final: 0.8156 (ttm) REVERT: A 576 MET cc_start: 0.8512 (mtm) cc_final: 0.8237 (mtm) REVERT: B 97 MET cc_start: 0.6702 (tpt) cc_final: 0.6181 (tpt) REVERT: B 231 ASP cc_start: 0.8640 (t0) cc_final: 0.8246 (t0) REVERT: B 273 GLN cc_start: 0.8399 (mt0) cc_final: 0.8196 (mm-40) REVERT: B 286 CYS cc_start: 0.7934 (p) cc_final: 0.7656 (p) REVERT: B 492 GLU cc_start: 0.7446 (tp30) cc_final: 0.6439 (tp30) REVERT: B 573 MET cc_start: 0.8585 (ttm) cc_final: 0.8360 (ttm) outliers start: 24 outliers final: 19 residues processed: 110 average time/residue: 0.0772 time to fit residues: 12.8235 Evaluate side-chains 108 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 89 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 265 HIS Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 208 SER Chi-restraints excluded: chain B residue 265 HIS Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 514 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 53 optimal weight: 1.9990 chunk 100 optimal weight: 0.6980 chunk 17 optimal weight: 0.7980 chunk 107 optimal weight: 0.7980 chunk 94 optimal weight: 0.7980 chunk 41 optimal weight: 0.5980 chunk 57 optimal weight: 3.9990 chunk 60 optimal weight: 0.9990 chunk 32 optimal weight: 0.8980 chunk 76 optimal weight: 3.9990 chunk 24 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.162336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.123254 restraints weight = 10560.124| |-----------------------------------------------------------------------------| r_work (start): 0.3564 rms_B_bonded: 2.74 r_work: 0.3416 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.2414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8830 Z= 0.109 Angle : 0.535 7.196 11980 Z= 0.276 Chirality : 0.040 0.140 1426 Planarity : 0.004 0.055 1452 Dihedral : 6.046 84.899 1194 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 1.82 % Allowed : 17.74 % Favored : 80.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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 (0.24), residues: 1076 helix: -0.61 (0.21), residues: 610 sheet: -1.92 (0.61), residues: 60 loop : -2.36 (0.27), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 463 TYR 0.009 0.001 TYR B 152 PHE 0.025 0.001 PHE A 315 TRP 0.012 0.001 TRP A 447 HIS 0.004 0.000 HIS A 219 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 ( 8830) covalent geometry : angle 0.53490 / 0.28 (11980) hydrogen bonds : bond 0.02821 / 1.85 ( 356) hydrogen bonds : angle 3.72507 / 2.61 ( 1038) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 97 time to evaluate : 0.342 Fit side-chains REVERT: A 97 MET cc_start: 0.6540 (tpt) cc_final: 0.5938 (tpt) REVERT: A 152 TYR cc_start: 0.8829 (m-80) cc_final: 0.8617 (m-80) REVERT: A 231 ASP cc_start: 0.8519 (t0) cc_final: 0.8199 (t70) REVERT: A 286 CYS cc_start: 0.7837 (p) cc_final: 0.7532 (p) REVERT: A 409 LEU cc_start: 0.8092 (OUTLIER) cc_final: 0.7761 (tt) REVERT: A 492 GLU cc_start: 0.7415 (tp30) cc_final: 0.6393 (tp30) REVERT: A 635 MET cc_start: 0.8186 (ttt) cc_final: 0.7942 (ttm) REVERT: B 137 GLN cc_start: 0.8896 (mp10) cc_final: 0.8659 (mp10) REVERT: B 152 TYR cc_start: 0.8950 (m-80) cc_final: 0.8469 (m-80) REVERT: B 231 ASP cc_start: 0.8581 (t0) cc_final: 0.8274 (t70) REVERT: B 286 CYS cc_start: 0.7873 (p) cc_final: 0.7496 (p) REVERT: B 409 LEU cc_start: 0.8087 (OUTLIER) cc_final: 0.7780 (tt) REVERT: B 462 GLU cc_start: 0.7741 (mm-30) cc_final: 0.7519 (mm-30) REVERT: B 492 GLU cc_start: 0.7330 (tp30) cc_final: 0.6364 (tp30) outliers start: 17 outliers final: 12 residues processed: 111 average time/residue: 0.0762 time to fit residues: 12.7937 Evaluate side-chains 102 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 88 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 183 GLU Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain B residue 36 PHE Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 265 HIS Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 514 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 42 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 6 optimal weight: 7.9990 chunk 68 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 86 optimal weight: 0.7980 chunk 41 optimal weight: 2.9990 chunk 28 optimal weight: 0.0470 chunk 104 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 87 optimal weight: 0.9980 overall best weight: 1.3682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.160212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.120963 restraints weight = 10637.021| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 2.73 r_work: 0.3379 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.2497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8830 Z= 0.160 Angle : 0.583 7.944 11980 Z= 0.294 Chirality : 0.042 0.148 1426 Planarity : 0.004 0.056 1452 Dihedral : 6.042 84.460 1194 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 2.67 % Allowed : 17.74 % Favored : 79.59 % 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: -1.85 (0.25), residues: 1076 helix: -0.46 (0.21), residues: 610 sheet: -1.72 (0.65), residues: 60 loop : -2.26 (0.28), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 158 TYR 0.012 0.001 TYR B 152 PHE 0.028 0.001 PHE A 315 TRP 0.011 0.001 TRP B 447 HIS 0.005 0.001 HIS A 219 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.16 ( 8830) covalent geometry : angle 0.58255 / 0.29 (11980) hydrogen bonds : bond 0.03153 / 2.06 ( 356) hydrogen bonds : angle 3.75651 / 2.63 ( 1038) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 100 time to evaluate : 0.328 Fit side-chains REVERT: A 97 MET cc_start: 0.6720 (tpt) cc_final: 0.6085 (tpt) REVERT: A 137 GLN cc_start: 0.8883 (mp10) cc_final: 0.8642 (mp10) REVERT: A 152 TYR cc_start: 0.8831 (m-80) cc_final: 0.8583 (m-80) REVERT: A 231 ASP cc_start: 0.8579 (t0) cc_final: 0.8270 (t70) REVERT: A 286 CYS cc_start: 0.7829 (p) cc_final: 0.7505 (p) REVERT: A 409 LEU cc_start: 0.8117 (OUTLIER) cc_final: 0.7780 (tt) REVERT: A 492 GLU cc_start: 0.7433 (tp30) cc_final: 0.6387 (tp30) REVERT: B 97 MET cc_start: 0.6705 (tpt) cc_final: 0.6107 (tpt) REVERT: B 137 GLN cc_start: 0.8907 (mp10) cc_final: 0.8671 (mp10) REVERT: B 152 TYR cc_start: 0.8943 (m-80) cc_final: 0.8189 (m-80) REVERT: B 231 ASP cc_start: 0.8589 (t0) cc_final: 0.8259 (t70) REVERT: B 273 GLN cc_start: 0.8526 (mm-40) cc_final: 0.8216 (mt0) REVERT: B 286 CYS cc_start: 0.7878 (p) cc_final: 0.7663 (p) REVERT: B 409 LEU cc_start: 0.8132 (OUTLIER) cc_final: 0.7825 (tt) REVERT: B 462 GLU cc_start: 0.7808 (mm-30) cc_final: 0.7347 (mm-30) REVERT: B 492 GLU cc_start: 0.7384 (tp30) cc_final: 0.6372 (tp30) REVERT: B 576 MET cc_start: 0.8423 (mtm) cc_final: 0.8119 (mtm) outliers start: 25 outliers final: 20 residues processed: 121 average time/residue: 0.0871 time to fit residues: 15.4218 Evaluate side-chains 115 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 93 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 183 GLU Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 265 HIS Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 633 VAL Chi-restraints excluded: chain B residue 36 PHE Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 265 HIS Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 633 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 18 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 45 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 14 optimal weight: 0.0170 chunk 37 optimal weight: 2.9990 chunk 24 optimal weight: 0.6980 chunk 8 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 47 optimal weight: 0.0000 overall best weight: 1.1426 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.161185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.122022 restraints weight = 10666.058| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 2.72 r_work: 0.3392 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.2616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8830 Z= 0.140 Angle : 0.563 8.307 11980 Z= 0.284 Chirality : 0.042 0.144 1426 Planarity : 0.004 0.054 1452 Dihedral : 5.981 84.734 1194 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 2.99 % Allowed : 18.06 % Favored : 78.95 % 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: -1.70 (0.25), residues: 1076 helix: -0.32 (0.21), residues: 616 sheet: -1.59 (0.68), residues: 60 loop : -2.26 (0.28), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 158 TYR 0.009 0.001 TYR B 152 PHE 0.025 0.001 PHE A 315 TRP 0.011 0.001 TRP B 447 HIS 0.004 0.001 HIS A 219 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.14 ( 8830) covalent geometry : angle 0.56274 / 0.28 (11980) hydrogen bonds : bond 0.02963 / 1.94 ( 356) hydrogen bonds : angle 3.70493 / 2.59 ( 1038) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 95 time to evaluate : 0.355 Fit side-chains REVERT: A 97 MET cc_start: 0.6695 (tpt) cc_final: 0.6067 (tpt) REVERT: A 137 GLN cc_start: 0.8889 (mp10) cc_final: 0.8647 (mp10) REVERT: A 152 TYR cc_start: 0.8823 (m-80) cc_final: 0.8565 (m-80) REVERT: A 159 GLU cc_start: 0.7340 (OUTLIER) cc_final: 0.6502 (mp0) REVERT: A 231 ASP cc_start: 0.8573 (t0) cc_final: 0.8257 (t70) REVERT: A 286 CYS cc_start: 0.7798 (p) cc_final: 0.7473 (p) REVERT: A 409 LEU cc_start: 0.8118 (OUTLIER) cc_final: 0.7786 (tt) REVERT: A 492 GLU cc_start: 0.7427 (tp30) cc_final: 0.6379 (tp30) REVERT: A 635 MET cc_start: 0.8173 (ttt) cc_final: 0.7930 (ttm) REVERT: B 97 MET cc_start: 0.6690 (tpt) cc_final: 0.6043 (tpt) REVERT: B 137 GLN cc_start: 0.8904 (mp10) cc_final: 0.8672 (mp10) REVERT: B 231 ASP cc_start: 0.8576 (t0) cc_final: 0.8244 (t70) REVERT: B 273 GLN cc_start: 0.8590 (mm-40) cc_final: 0.8206 (mt0) REVERT: B 288 PHE cc_start: 0.7420 (t80) cc_final: 0.7147 (t80) REVERT: B 409 LEU cc_start: 0.8106 (OUTLIER) cc_final: 0.7808 (tt) REVERT: B 492 GLU cc_start: 0.7389 (tp30) cc_final: 0.6377 (tp30) REVERT: B 576 MET cc_start: 0.8358 (mtm) cc_final: 0.8093 (mtm) outliers start: 28 outliers final: 21 residues processed: 118 average time/residue: 0.0842 time to fit residues: 14.9022 Evaluate side-chains 116 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 92 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 159 GLU Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 183 GLU Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 265 HIS Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 633 VAL Chi-restraints excluded: chain B residue 36 PHE Chi-restraints excluded: chain B residue 44 ASP Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 265 HIS Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 633 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 5.9990 chunk 19 optimal weight: 4.9990 chunk 101 optimal weight: 0.7980 chunk 58 optimal weight: 3.9990 chunk 106 optimal weight: 10.0000 chunk 23 optimal weight: 9.9990 chunk 24 optimal weight: 9.9990 chunk 55 optimal weight: 5.9990 chunk 2 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 chunk 15 optimal weight: 0.0010 overall best weight: 1.5390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.159342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.120092 restraints weight = 10588.626| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 2.72 r_work: 0.3367 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.2668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8830 Z= 0.175 Angle : 0.607 11.389 11980 Z= 0.302 Chirality : 0.043 0.151 1426 Planarity : 0.004 0.055 1452 Dihedral : 6.031 83.926 1194 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 3.31 % Allowed : 17.74 % Favored : 78.95 % 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: -1.66 (0.25), residues: 1076 helix: -0.33 (0.21), residues: 616 sheet: -1.46 (0.67), residues: 62 loop : -2.19 (0.29), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 410 TYR 0.009 0.001 TYR B 152 PHE 0.024 0.001 PHE A 315 TRP 0.011 0.001 TRP B 447 HIS 0.005 0.001 HIS A 219 Details of bonding type rmsd/Z covalent geometry : bond 0.00427 / 0.17 ( 8830) covalent geometry : angle 0.60731 / 0.30 (11980) hydrogen bonds : bond 0.03256 / 2.13 ( 356) hydrogen bonds : angle 3.80047 / 2.65 ( 1038) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 92 time to evaluate : 0.337 Fit side-chains revert: symmetry clash REVERT: A 97 MET cc_start: 0.6776 (tpt) cc_final: 0.6289 (tpt) REVERT: A 137 GLN cc_start: 0.8880 (mp10) cc_final: 0.8641 (mp10) REVERT: A 152 TYR cc_start: 0.8851 (m-80) cc_final: 0.8574 (m-80) REVERT: A 159 GLU cc_start: 0.7332 (OUTLIER) cc_final: 0.6466 (mp0) REVERT: A 231 ASP cc_start: 0.8559 (t0) cc_final: 0.8156 (t0) REVERT: A 286 CYS cc_start: 0.7816 (p) cc_final: 0.7613 (p) REVERT: A 288 PHE cc_start: 0.7340 (t80) cc_final: 0.7134 (t80) REVERT: A 409 LEU cc_start: 0.8116 (OUTLIER) cc_final: 0.7783 (tt) REVERT: A 492 GLU cc_start: 0.7397 (tp30) cc_final: 0.6309 (tp30) REVERT: A 576 MET cc_start: 0.8375 (mtm) cc_final: 0.8156 (mtt) REVERT: B 97 MET cc_start: 0.6699 (tpt) cc_final: 0.6199 (tpt) REVERT: B 152 TYR cc_start: 0.8862 (m-80) cc_final: 0.8625 (m-80) REVERT: B 159 GLU cc_start: 0.7298 (OUTLIER) cc_final: 0.6424 (mp0) REVERT: B 231 ASP cc_start: 0.8559 (t0) cc_final: 0.8233 (t70) REVERT: B 409 LEU cc_start: 0.8134 (OUTLIER) cc_final: 0.7827 (tt) REVERT: B 492 GLU cc_start: 0.7363 (tp30) cc_final: 0.6315 (tp30) REVERT: B 576 MET cc_start: 0.8398 (mtm) cc_final: 0.8190 (mtm) outliers start: 31 outliers final: 22 residues processed: 118 average time/residue: 0.0742 time to fit residues: 13.2420 Evaluate side-chains 118 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 92 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 159 GLU Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 183 GLU Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 265 HIS Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 633 VAL Chi-restraints excluded: chain B residue 36 PHE Chi-restraints excluded: chain B residue 44 ASP Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 159 GLU Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 265 HIS Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 633 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 61 optimal weight: 0.5980 chunk 13 optimal weight: 0.9980 chunk 90 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 105 optimal weight: 4.9990 chunk 14 optimal weight: 0.8980 chunk 66 optimal weight: 4.9990 chunk 6 optimal weight: 0.9990 chunk 62 optimal weight: 0.8980 chunk 42 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.162110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.123009 restraints weight = 10527.300| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 2.73 r_work: 0.3402 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.2773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8830 Z= 0.119 Angle : 0.567 12.427 11980 Z= 0.280 Chirality : 0.041 0.140 1426 Planarity : 0.004 0.053 1452 Dihedral : 5.890 84.912 1194 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 3.10 % Allowed : 18.27 % Favored : 78.63 % 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: -1.38 (0.25), residues: 1076 helix: -0.08 (0.21), residues: 616 sheet: -1.37 (0.68), residues: 62 loop : -2.11 (0.29), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 158 TYR 0.007 0.001 TYR B 152 PHE 0.023 0.001 PHE A 315 TRP 0.010 0.001 TRP A 447 HIS 0.004 0.000 HIS A 219 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.12 ( 8830) covalent geometry : angle 0.56678 / 0.28 (11980) hydrogen bonds : bond 0.02811 / 1.84 ( 356) hydrogen bonds : angle 3.66767 / 2.56 ( 1038) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 89 time to evaluate : 0.204 Fit side-chains REVERT: A 97 MET cc_start: 0.6680 (tpt) cc_final: 0.6106 (tpt) REVERT: A 152 TYR cc_start: 0.8809 (m-80) cc_final: 0.8544 (m-80) REVERT: A 159 GLU cc_start: 0.7317 (OUTLIER) cc_final: 0.6500 (mp0) REVERT: A 231 ASP cc_start: 0.8556 (t0) cc_final: 0.8244 (t70) REVERT: A 409 LEU cc_start: 0.8092 (OUTLIER) cc_final: 0.7765 (tt) REVERT: A 492 GLU cc_start: 0.7378 (tp30) cc_final: 0.6335 (tp30) REVERT: A 576 MET cc_start: 0.8336 (mtm) cc_final: 0.8129 (mtt) REVERT: B 97 MET cc_start: 0.6630 (tpt) cc_final: 0.6087 (tpt) REVERT: B 152 TYR cc_start: 0.8858 (m-80) cc_final: 0.8580 (m-80) REVERT: B 159 GLU cc_start: 0.7314 (OUTLIER) cc_final: 0.6486 (mp0) REVERT: B 231 ASP cc_start: 0.8556 (t0) cc_final: 0.8225 (t70) REVERT: B 286 CYS cc_start: 0.7769 (p) cc_final: 0.7446 (p) REVERT: B 288 PHE cc_start: 0.7250 (t80) cc_final: 0.6943 (t80) REVERT: B 409 LEU cc_start: 0.8112 (OUTLIER) cc_final: 0.7811 (tt) REVERT: B 492 GLU cc_start: 0.7320 (tp30) cc_final: 0.6309 (tp30) REVERT: B 576 MET cc_start: 0.8384 (mtm) cc_final: 0.8180 (mtm) outliers start: 29 outliers final: 22 residues processed: 112 average time/residue: 0.0561 time to fit residues: 9.5888 Evaluate side-chains 115 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 89 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 PHE Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 159 GLU Chi-restraints excluded: chain A residue 183 GLU Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 265 HIS Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 633 VAL Chi-restraints excluded: chain B residue 36 PHE Chi-restraints excluded: chain B residue 44 ASP Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 159 GLU Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 183 GLU Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 265 HIS Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 633 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 109 optimal weight: 0.9980 chunk 73 optimal weight: 0.9980 chunk 30 optimal weight: 3.9990 chunk 89 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 18 optimal weight: 0.1980 chunk 84 optimal weight: 3.9990 chunk 26 optimal weight: 20.0000 chunk 9 optimal weight: 2.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.156047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.115401 restraints weight = 10748.097| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 2.97 r_work: 0.3282 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.2793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8830 Z= 0.148 Angle : 0.587 11.967 11980 Z= 0.290 Chirality : 0.042 0.145 1426 Planarity : 0.004 0.054 1452 Dihedral : 5.903 84.414 1194 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 3.10 % Allowed : 17.95 % Favored : 78.95 % 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: -1.34 (0.25), residues: 1076 helix: -0.06 (0.21), residues: 616 sheet: -1.38 (0.67), residues: 62 loop : -2.06 (0.29), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 401 TYR 0.009 0.001 TYR B 584 PHE 0.025 0.001 PHE A 315 TRP 0.011 0.001 TRP B 447 HIS 0.005 0.001 HIS A 219 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.15 ( 8830) covalent geometry : angle 0.58732 / 0.29 (11980) hydrogen bonds : bond 0.03032 / 1.98 ( 356) hydrogen bonds : angle 3.71902 / 2.59 ( 1038) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 88 time to evaluate : 0.296 Fit side-chains revert: symmetry clash REVERT: A 97 MET cc_start: 0.6639 (tpt) cc_final: 0.6117 (tpt) REVERT: A 152 TYR cc_start: 0.8845 (m-80) cc_final: 0.8562 (m-80) REVERT: A 159 GLU cc_start: 0.7221 (OUTLIER) cc_final: 0.6394 (mp0) REVERT: A 231 ASP cc_start: 0.8557 (t0) cc_final: 0.8225 (t70) REVERT: A 286 CYS cc_start: 0.7770 (p) cc_final: 0.7450 (p) REVERT: A 409 LEU cc_start: 0.7998 (OUTLIER) cc_final: 0.7673 (tt) REVERT: A 492 GLU cc_start: 0.7402 (tp30) cc_final: 0.6309 (tp30) REVERT: A 576 MET cc_start: 0.8203 (mtm) cc_final: 0.7935 (mtt) REVERT: B 97 MET cc_start: 0.6662 (tpt) cc_final: 0.6080 (tpt) REVERT: B 152 TYR cc_start: 0.8867 (m-80) cc_final: 0.8641 (m-80) REVERT: B 159 GLU cc_start: 0.7236 (OUTLIER) cc_final: 0.6388 (mp0) REVERT: B 231 ASP cc_start: 0.8553 (t0) cc_final: 0.8230 (t70) REVERT: B 286 CYS cc_start: 0.7817 (p) cc_final: 0.7514 (p) REVERT: B 288 PHE cc_start: 0.7141 (t80) cc_final: 0.6814 (t80) REVERT: B 409 LEU cc_start: 0.8040 (OUTLIER) cc_final: 0.7742 (tt) REVERT: B 492 GLU cc_start: 0.7377 (tp30) cc_final: 0.6323 (tp30) REVERT: B 576 MET cc_start: 0.8241 (mtm) cc_final: 0.7990 (mtm) outliers start: 29 outliers final: 24 residues processed: 110 average time/residue: 0.0670 time to fit residues: 11.1888 Evaluate side-chains 115 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 87 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 PHE Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 159 GLU Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 183 GLU Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 265 HIS Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 633 VAL Chi-restraints excluded: chain B residue 36 PHE Chi-restraints excluded: chain B residue 44 ASP Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 159 GLU Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 183 GLU Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 265 HIS Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 424 MET Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 633 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 34 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 94 optimal weight: 0.2980 chunk 107 optimal weight: 0.7980 chunk 101 optimal weight: 0.7980 chunk 103 optimal weight: 2.9990 chunk 55 optimal weight: 7.9990 chunk 1 optimal weight: 0.9990 chunk 5 optimal weight: 0.7980 chunk 64 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.158406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.117865 restraints weight = 10596.789| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 2.97 r_work: 0.3321 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.2912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8830 Z= 0.109 Angle : 0.557 11.687 11980 Z= 0.274 Chirality : 0.040 0.136 1426 Planarity : 0.004 0.054 1452 Dihedral : 5.775 85.279 1194 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 2.78 % Allowed : 18.70 % Favored : 78.53 % 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: -1.14 (0.26), residues: 1076 helix: 0.13 (0.21), residues: 616 sheet: -1.40 (0.69), residues: 60 loop : -2.02 (0.29), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 168 TYR 0.006 0.001 TYR B 152 PHE 0.024 0.001 PHE A 315 TRP 0.009 0.001 TRP A 447 HIS 0.004 0.000 HIS A 219 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.11 ( 8830) covalent geometry : angle 0.55746 / 0.27 (11980) hydrogen bonds : bond 0.02674 / 1.74 ( 356) hydrogen bonds : angle 3.59390 / 2.50 ( 1038) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1843.53 seconds wall clock time: 32 minutes 29.41 seconds (1949.41 seconds total)