Starting phenix.real_space_refine on Sat Jun 7 14:45:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8i3b_35148/06_2025/8i3b_35148.cif Found real_map, /net/cci-nas-00/data/ceres_data/8i3b_35148/06_2025/8i3b_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8i3b_35148/06_2025/8i3b_35148.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8i3b_35148/06_2025/8i3b_35148.map" model { file = "/net/cci-nas-00/data/ceres_data/8i3b_35148/06_2025/8i3b_35148.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8i3b_35148/06_2025/8i3b_35148.cif" } resolution = 3.08 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.052 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 5.68, per 1000 atoms: 0.66 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: 2.27 Conformation dependent library (CDL) restraints added in 1.1 seconds 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 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: 0.85 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: 2.61 Time building geometry restraints manager: 2.65 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 - 18.00: 4683 18.00 - 36.00: 473 36.00 - 53.99: 48 53.99 - 71.99: 18 71.99 - 89.99: 4 Dihedral angle restraints: 5226 sinusoidal: 2074 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 5223 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: 0.09 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.890 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: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 23.860 Find NCS groups from input model: 0.170 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: 0.000 Load rotamer database and sin/cos tables:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7459 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 : 14.311 89.989 3198 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.012 0.002 TRP A 426 HIS 0.013 0.002 HIS B 52 PHE 0.020 0.002 PHE A 499 TYR 0.014 0.002 TYR A 594 ARG 0.003 0.000 ARG A 158 Details of bonding type rmsd hydrogen bonds : bond 0.15313 ( 356) hydrogen bonds : angle 6.28686 ( 1038) covalent geometry : bond 0.00807 ( 8830) covalent geometry : angle 1.18908 (11980) *********************** 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 : 0.987 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: 0.7834 (mm-30) cc_final: 0.7553 (mm-30) REVERT: B 231 ASP cc_start: 0.8421 (t0) cc_final: 0.8062 (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: 0.2392 time to fit residues: 43.9990 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 : 0.913 ------------------------------------------------------------------------------- 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 92 optimal weight: 3.9990 chunk 83 optimal weight: 10.0000 chunk 46 optimal weight: 0.7980 chunk 28 optimal weight: 6.9990 chunk 56 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 86 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 52 optimal weight: 0.4980 chunk 64 optimal weight: 0.6980 chunk 99 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 HIS A 112 ASN A 265 HIS 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.161897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.122400 restraints weight = 10381.806| |-----------------------------------------------------------------------------| r_work (start): 0.3540 rms_B_bonded: 2.84 r_work: 0.3386 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7349 moved from start: 0.1581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8830 Z= 0.121 Angle : 0.595 7.660 11980 Z= 0.313 Chirality : 0.041 0.193 1426 Planarity : 0.005 0.060 1452 Dihedral : 8.507 82.908 1264 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 0.75 % Allowed : 12.61 % Favored : 86.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.47 (0.22), residues: 1076 helix: -1.82 (0.19), residues: 592 sheet: -2.53 (0.55), residues: 60 loop : -2.83 (0.26), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 447 HIS 0.006 0.001 HIS A 52 PHE 0.017 0.001 PHE A 315 TYR 0.013 0.001 TYR B 152 ARG 0.004 0.000 ARG A 401 Details of bonding type rmsd hydrogen bonds : bond 0.03091 ( 356) hydrogen bonds : angle 4.11253 ( 1038) covalent geometry : bond 0.00274 ( 8830) covalent geometry : angle 0.59466 (11980) *********************** 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 116 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 109 time to evaluate : 0.925 Fit side-chains REVERT: A 152 TYR cc_start: 0.8940 (m-80) cc_final: 0.8289 (m-80) REVERT: A 231 ASP cc_start: 0.8432 (t0) cc_final: 0.8090 (t70) REVERT: A 286 CYS cc_start: 0.7931 (p) cc_final: 0.7464 (p) REVERT: A 293 ARG cc_start: 0.6602 (mmt-90) cc_final: 0.6050 (mmp80) REVERT: A 315 PHE cc_start: 0.6695 (t80) cc_final: 0.6192 (t80) REVERT: A 462 GLU cc_start: 0.7877 (mm-30) cc_final: 0.7574 (mm-30) REVERT: A 492 GLU cc_start: 0.7604 (tp30) cc_final: 0.6363 (tp30) REVERT: A 573 MET cc_start: 0.8512 (ttm) cc_final: 0.8207 (ttm) REVERT: B 152 TYR cc_start: 0.8969 (m-80) cc_final: 0.8328 (m-80) REVERT: B 183 GLU cc_start: 0.6788 (mp0) cc_final: 0.6553 (mp0) REVERT: B 231 ASP cc_start: 0.8494 (t0) cc_final: 0.8182 (t70) REVERT: B 462 GLU cc_start: 0.7831 (mm-30) cc_final: 0.7557 (mm-30) REVERT: B 492 GLU cc_start: 0.7614 (tp30) cc_final: 0.6371 (tp30) REVERT: B 508 TYR cc_start: 0.7590 (t80) cc_final: 0.7333 (t80) REVERT: B 573 MET cc_start: 0.8490 (ttm) cc_final: 0.8163 (ttm) outliers start: 7 outliers final: 5 residues processed: 116 average time/residue: 0.2477 time to fit residues: 38.3702 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 : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 265 HIS Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 197 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 107 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 76 optimal weight: 4.9990 chunk 27 optimal weight: 20.0000 chunk 21 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 55 optimal weight: 7.9990 chunk 25 optimal weight: 2.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3940 r_free = 0.3940 target = 0.154157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.114955 restraints weight = 10698.549| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 2.76 r_work: 0.3294 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.1962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.049 8830 Z= 0.272 Angle : 0.710 8.530 11980 Z= 0.361 Chirality : 0.047 0.173 1426 Planarity : 0.005 0.060 1452 Dihedral : 8.655 82.590 1256 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.53 % Favored : 92.47 % Rotamer: Outliers : 2.46 % Allowed : 14.64 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.31 (0.22), residues: 1076 helix: -1.59 (0.19), residues: 608 sheet: -2.37 (0.54), residues: 62 loop : -2.97 (0.25), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 447 HIS 0.006 0.001 HIS A 219 PHE 0.018 0.002 PHE A 446 TYR 0.013 0.002 TYR A 565 ARG 0.005 0.000 ARG A 180 Details of bonding type rmsd hydrogen bonds : bond 0.04009 ( 356) hydrogen bonds : angle 4.16511 ( 1038) covalent geometry : bond 0.00668 ( 8830) covalent geometry : angle 0.71045 (11980) *********************** 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 116 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 93 time to evaluate : 0.942 Fit side-chains REVERT: A 152 TYR cc_start: 0.8930 (m-80) cc_final: 0.8369 (m-80) REVERT: A 231 ASP cc_start: 0.8637 (t0) cc_final: 0.8249 (t0) REVERT: A 286 CYS cc_start: 0.7903 (p) cc_final: 0.7480 (p) REVERT: A 462 GLU cc_start: 0.8045 (mm-30) cc_final: 0.7600 (mm-30) REVERT: A 492 GLU cc_start: 0.7566 (tp30) cc_final: 0.6544 (tp30) REVERT: A 573 MET cc_start: 0.8545 (ttm) cc_final: 0.8182 (ttm) REVERT: B 231 ASP cc_start: 0.8615 (t0) cc_final: 0.8222 (t0) REVERT: B 286 CYS cc_start: 0.7967 (p) cc_final: 0.7527 (p) REVERT: B 492 GLU cc_start: 0.7563 (tp30) cc_final: 0.6528 (tp30) REVERT: B 508 TYR cc_start: 0.7648 (t80) cc_final: 0.7430 (t80) outliers start: 23 outliers final: 18 residues processed: 110 average time/residue: 0.1745 time to fit residues: 28.6396 Evaluate side-chains 106 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 88 time to evaluate : 0.927 ------------------------------------------------------------------------------- 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 265 HIS 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 51 optimal weight: 4.9990 chunk 92 optimal weight: 2.9990 chunk 67 optimal weight: 0.7980 chunk 3 optimal weight: 0.9990 chunk 48 optimal weight: 3.9990 chunk 94 optimal weight: 1.9990 chunk 86 optimal weight: 4.9990 chunk 35 optimal weight: 0.0020 chunk 99 optimal weight: 0.9980 chunk 27 optimal weight: 20.0000 chunk 21 optimal weight: 1.9990 overall best weight: 0.9592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 273 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.161823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.122543 restraints weight = 10564.288| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 2.74 r_work: 0.3409 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.2216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8830 Z= 0.130 Angle : 0.559 7.296 11980 Z= 0.290 Chirality : 0.041 0.142 1426 Planarity : 0.004 0.056 1452 Dihedral : 8.235 84.386 1256 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 1.71 % Allowed : 16.13 % Favored : 82.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.51 (0.23), residues: 1076 helix: -0.90 (0.20), residues: 612 sheet: -2.23 (0.57), residues: 60 loop : -2.68 (0.26), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 447 HIS 0.004 0.001 HIS A 219 PHE 0.027 0.001 PHE A 315 TYR 0.009 0.001 TYR B 152 ARG 0.002 0.000 ARG B 180 Details of bonding type rmsd hydrogen bonds : bond 0.02929 ( 356) hydrogen bonds : angle 3.80457 ( 1038) covalent geometry : bond 0.00304 ( 8830) covalent geometry : angle 0.55929 (11980) *********************** 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 112 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 96 time to evaluate : 0.914 Fit side-chains REVERT: A 231 ASP cc_start: 0.8529 (t0) cc_final: 0.8208 (t70) REVERT: A 286 CYS cc_start: 0.7812 (p) cc_final: 0.7400 (p) REVERT: A 492 GLU cc_start: 0.7388 (tp30) cc_final: 0.6436 (tp30) REVERT: B 152 TYR cc_start: 0.8954 (m-80) cc_final: 0.8435 (m-80) REVERT: B 231 ASP cc_start: 0.8567 (t0) cc_final: 0.8276 (t70) REVERT: B 286 CYS cc_start: 0.7904 (p) cc_final: 0.7526 (p) REVERT: B 409 LEU cc_start: 0.8110 (OUTLIER) cc_final: 0.7802 (tt) REVERT: B 462 GLU cc_start: 0.7800 (mm-30) cc_final: 0.7538 (mm-30) REVERT: B 492 GLU cc_start: 0.7410 (tp30) cc_final: 0.6428 (tp30) outliers start: 16 outliers final: 11 residues processed: 106 average time/residue: 0.1775 time to fit residues: 27.4161 Evaluate side-chains 102 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 90 time to evaluate : 0.884 ------------------------------------------------------------------------------- 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 197 THR 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 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 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 97 optimal weight: 0.6980 chunk 71 optimal weight: 5.9990 chunk 87 optimal weight: 0.6980 chunk 50 optimal weight: 4.9990 chunk 80 optimal weight: 8.9990 chunk 7 optimal weight: 0.3980 chunk 98 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 26 optimal weight: 7.9990 chunk 84 optimal weight: 1.9990 chunk 106 optimal weight: 9.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.161239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.122010 restraints weight = 10564.654| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 2.74 r_work: 0.3396 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 moved from start: 0.2373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8830 Z= 0.143 Angle : 0.571 7.343 11980 Z= 0.291 Chirality : 0.042 0.147 1426 Planarity : 0.004 0.056 1452 Dihedral : 8.043 84.584 1256 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 1.71 % Allowed : 18.70 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.04 (0.24), residues: 1076 helix: -0.56 (0.21), residues: 608 sheet: -1.98 (0.61), residues: 60 loop : -2.39 (0.27), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 447 HIS 0.004 0.001 HIS A 219 PHE 0.018 0.001 PHE A 315 TYR 0.010 0.001 TYR A 152 ARG 0.001 0.000 ARG A 158 Details of bonding type rmsd hydrogen bonds : bond 0.03057 ( 356) hydrogen bonds : angle 3.72028 ( 1038) covalent geometry : bond 0.00342 ( 8830) covalent geometry : angle 0.57065 (11980) *********************** 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 108 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 92 time to evaluate : 1.186 Fit side-chains revert: symmetry clash REVERT: A 152 TYR cc_start: 0.8934 (m-80) cc_final: 0.8690 (m-80) REVERT: A 231 ASP cc_start: 0.8493 (t0) cc_final: 0.8170 (t70) REVERT: A 286 CYS cc_start: 0.7813 (p) cc_final: 0.7491 (p) REVERT: A 315 PHE cc_start: 0.6680 (t80) cc_final: 0.6480 (t80) REVERT: A 409 LEU cc_start: 0.8111 (OUTLIER) cc_final: 0.7787 (tt) REVERT: A 492 GLU cc_start: 0.7365 (tp30) cc_final: 0.6396 (tp30) REVERT: B 231 ASP cc_start: 0.8548 (t0) cc_final: 0.8244 (t70) REVERT: B 286 CYS cc_start: 0.7858 (p) cc_final: 0.7463 (p) REVERT: B 409 LEU cc_start: 0.8064 (OUTLIER) cc_final: 0.7765 (tt) REVERT: B 492 GLU cc_start: 0.7372 (tp30) cc_final: 0.6385 (tp30) outliers start: 16 outliers final: 12 residues processed: 104 average time/residue: 0.2200 time to fit residues: 34.2444 Evaluate side-chains 105 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 91 time to evaluate : 1.048 ------------------------------------------------------------------------------- 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 173 LEU Chi-restraints excluded: chain A residue 197 THR 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 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 173 LEU Chi-restraints excluded: chain B residue 197 THR 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 32 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 107 optimal weight: 0.9980 chunk 89 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 8 optimal weight: 6.9990 chunk 92 optimal weight: 5.9990 chunk 25 optimal weight: 0.9980 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 273 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.158392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.119186 restraints weight = 10492.639| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 2.70 r_work: 0.3362 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.2450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 8830 Z= 0.216 Angle : 0.631 7.212 11980 Z= 0.320 Chirality : 0.044 0.159 1426 Planarity : 0.004 0.056 1452 Dihedral : 8.264 83.474 1256 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.34 % Favored : 92.66 % Rotamer: Outliers : 2.88 % Allowed : 17.41 % Favored : 79.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.12 (0.24), residues: 1076 helix: -0.67 (0.20), residues: 616 sheet: -1.78 (0.61), residues: 62 loop : -2.42 (0.28), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 447 HIS 0.006 0.001 HIS A 219 PHE 0.018 0.002 PHE A 315 TYR 0.010 0.001 TYR A 584 ARG 0.002 0.000 ARG A 270 Details of bonding type rmsd hydrogen bonds : bond 0.03483 ( 356) hydrogen bonds : angle 3.90192 ( 1038) covalent geometry : bond 0.00525 ( 8830) covalent geometry : angle 0.63052 (11980) *********************** 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 121 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 94 time to evaluate : 0.907 Fit side-chains REVERT: A 97 MET cc_start: 0.6736 (tpt) cc_final: 0.6147 (tpt) REVERT: A 137 GLN cc_start: 0.8880 (mp10) cc_final: 0.8635 (mp10) REVERT: A 231 ASP cc_start: 0.8557 (t0) cc_final: 0.8144 (t0) REVERT: A 286 CYS cc_start: 0.7844 (p) cc_final: 0.7628 (p) REVERT: A 409 LEU cc_start: 0.8152 (OUTLIER) cc_final: 0.7827 (tt) REVERT: A 492 GLU cc_start: 0.7427 (tp30) cc_final: 0.6452 (tp30) REVERT: B 97 MET cc_start: 0.6636 (tpt) cc_final: 0.6173 (tpt) REVERT: B 137 GLN cc_start: 0.8886 (mp10) cc_final: 0.8646 (mp10) REVERT: B 152 TYR cc_start: 0.8906 (m-80) cc_final: 0.8656 (m-80) REVERT: B 231 ASP cc_start: 0.8564 (t0) cc_final: 0.8167 (t0) REVERT: B 286 CYS cc_start: 0.7903 (p) cc_final: 0.7658 (p) REVERT: B 409 LEU cc_start: 0.8155 (OUTLIER) cc_final: 0.7845 (tt) REVERT: B 492 GLU cc_start: 0.7405 (tp30) cc_final: 0.6413 (tp30) REVERT: B 576 MET cc_start: 0.8380 (mtm) cc_final: 0.8156 (mtt) outliers start: 27 outliers final: 20 residues processed: 115 average time/residue: 0.1648 time to fit residues: 28.1862 Evaluate side-chains 112 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 90 time to evaluate : 1.004 ------------------------------------------------------------------------------- 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 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 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 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 2 optimal weight: 7.9990 chunk 103 optimal weight: 0.7980 chunk 15 optimal weight: 0.0170 chunk 81 optimal weight: 9.9990 chunk 29 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 70 optimal weight: 0.6980 chunk 39 optimal weight: 2.9990 chunk 74 optimal weight: 5.9990 chunk 8 optimal weight: 4.9990 chunk 26 optimal weight: 20.0000 overall best weight: 1.3022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 273 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.160391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.121099 restraints weight = 10569.211| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 2.74 r_work: 0.3381 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.2547 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= 0.153 Angle : 0.575 7.198 11980 Z= 0.293 Chirality : 0.042 0.150 1426 Planarity : 0.004 0.054 1452 Dihedral : 8.108 84.248 1256 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 2.78 % Allowed : 18.16 % Favored : 79.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.82 (0.25), residues: 1076 helix: -0.42 (0.21), residues: 616 sheet: -1.64 (0.64), residues: 62 loop : -2.31 (0.28), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 447 HIS 0.005 0.001 HIS A 219 PHE 0.025 0.001 PHE A 315 TYR 0.013 0.001 TYR A 152 ARG 0.002 0.000 ARG B 158 Details of bonding type rmsd hydrogen bonds : bond 0.03083 ( 356) hydrogen bonds : angle 3.77434 ( 1038) covalent geometry : bond 0.00371 ( 8830) covalent geometry : angle 0.57538 (11980) *********************** 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 119 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 93 time to evaluate : 1.269 Fit side-chains REVERT: A 97 MET cc_start: 0.6635 (tpt) cc_final: 0.6007 (tpt) REVERT: A 137 GLN cc_start: 0.8885 (mp10) cc_final: 0.8640 (mp10) REVERT: A 152 TYR cc_start: 0.8921 (m-80) cc_final: 0.8345 (m-80) REVERT: A 231 ASP cc_start: 0.8546 (t0) cc_final: 0.8214 (t70) REVERT: A 286 CYS cc_start: 0.7803 (p) cc_final: 0.7594 (p) REVERT: A 409 LEU cc_start: 0.8115 (OUTLIER) cc_final: 0.7795 (tt) REVERT: A 462 GLU cc_start: 0.7776 (mm-30) cc_final: 0.7537 (mm-30) REVERT: A 492 GLU cc_start: 0.7382 (tp30) cc_final: 0.6374 (tp30) REVERT: A 576 MET cc_start: 0.8347 (mtm) cc_final: 0.8120 (mtt) REVERT: B 97 MET cc_start: 0.6581 (tpt) cc_final: 0.6014 (tpt) REVERT: B 137 GLN cc_start: 0.8897 (mp10) cc_final: 0.8661 (mp10) REVERT: B 152 TYR cc_start: 0.8881 (m-80) cc_final: 0.8658 (m-80) REVERT: B 231 ASP cc_start: 0.8557 (t0) cc_final: 0.8243 (t70) REVERT: B 286 CYS cc_start: 0.7888 (p) cc_final: 0.7677 (p) REVERT: B 409 LEU cc_start: 0.8106 (OUTLIER) cc_final: 0.7802 (tt) REVERT: B 492 GLU cc_start: 0.7355 (tp30) cc_final: 0.6355 (tp30) REVERT: B 576 MET cc_start: 0.8363 (mtm) cc_final: 0.8104 (mtt) outliers start: 26 outliers final: 19 residues processed: 114 average time/residue: 0.1860 time to fit residues: 31.5141 Evaluate side-chains 110 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 89 time to evaluate : 0.952 ------------------------------------------------------------------------------- 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 197 THR 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 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 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 20 optimal weight: 0.6980 chunk 81 optimal weight: 0.7980 chunk 36 optimal weight: 0.0980 chunk 62 optimal weight: 8.9990 chunk 25 optimal weight: 0.8980 chunk 21 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 48 optimal weight: 0.5980 chunk 71 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.163730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.124517 restraints weight = 10643.810| |-----------------------------------------------------------------------------| r_work (start): 0.3582 rms_B_bonded: 2.75 r_work: 0.3432 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 moved from start: 0.2732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8830 Z= 0.104 Angle : 0.529 7.745 11980 Z= 0.270 Chirality : 0.040 0.135 1426 Planarity : 0.004 0.053 1452 Dihedral : 7.705 85.611 1256 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 2.46 % Allowed : 18.38 % Favored : 79.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.25), residues: 1076 helix: -0.10 (0.21), residues: 616 sheet: -1.61 (0.67), residues: 60 loop : -2.19 (0.29), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 447 HIS 0.003 0.000 HIS A 219 PHE 0.025 0.001 PHE A 315 TYR 0.008 0.001 TYR A 152 ARG 0.001 0.000 ARG A 158 Details of bonding type rmsd hydrogen bonds : bond 0.02638 ( 356) hydrogen bonds : angle 3.57614 ( 1038) covalent geometry : bond 0.00240 ( 8830) covalent geometry : angle 0.52915 (11980) *********************** 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 127 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 104 time to evaluate : 1.548 Fit side-chains REVERT: A 97 MET cc_start: 0.6524 (tpt) cc_final: 0.5913 (tpt) REVERT: A 137 GLN cc_start: 0.8884 (mp10) cc_final: 0.8644 (mp10) REVERT: A 152 TYR cc_start: 0.8845 (m-80) cc_final: 0.8234 (m-80) REVERT: A 231 ASP cc_start: 0.8531 (t0) cc_final: 0.8200 (t70) REVERT: A 286 CYS cc_start: 0.7772 (p) cc_final: 0.7443 (p) REVERT: A 409 LEU cc_start: 0.8087 (OUTLIER) cc_final: 0.7776 (tt) REVERT: A 462 GLU cc_start: 0.7711 (mm-30) cc_final: 0.7461 (mm-30) REVERT: A 492 GLU cc_start: 0.7310 (tp30) cc_final: 0.6279 (tp30) REVERT: A 576 MET cc_start: 0.8309 (mtm) cc_final: 0.8081 (mtt) REVERT: B 97 MET cc_start: 0.6485 (tpt) cc_final: 0.5917 (tpt) REVERT: B 137 GLN cc_start: 0.8895 (mp10) cc_final: 0.8577 (pt0) REVERT: B 152 TYR cc_start: 0.8854 (m-80) cc_final: 0.8642 (m-80) REVERT: B 159 GLU cc_start: 0.7259 (OUTLIER) cc_final: 0.6437 (mp0) REVERT: B 231 ASP cc_start: 0.8487 (t0) cc_final: 0.8173 (t70) REVERT: B 288 PHE cc_start: 0.7283 (t80) cc_final: 0.7052 (t80) REVERT: B 409 LEU cc_start: 0.8081 (OUTLIER) cc_final: 0.7783 (tt) REVERT: B 492 GLU cc_start: 0.7335 (tp30) cc_final: 0.6302 (tp30) REVERT: B 576 MET cc_start: 0.8308 (mtm) cc_final: 0.8056 (mtt) outliers start: 23 outliers final: 15 residues processed: 123 average time/residue: 0.2127 time to fit residues: 38.7583 Evaluate side-chains 112 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 94 time to evaluate : 0.952 ------------------------------------------------------------------------------- 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 162 VAL Chi-restraints excluded: chain A residue 183 GLU 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 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 50 optimal weight: 5.9990 chunk 59 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 82 optimal weight: 20.0000 chunk 2 optimal weight: 1.9990 chunk 91 optimal weight: 0.4980 chunk 49 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 chunk 71 optimal weight: 5.9990 overall best weight: 1.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.159510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.120314 restraints weight = 10621.868| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 2.71 r_work: 0.3371 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.2723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 8830 Z= 0.189 Angle : 0.607 9.113 11980 Z= 0.305 Chirality : 0.043 0.151 1426 Planarity : 0.004 0.055 1452 Dihedral : 7.782 84.045 1256 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer: Outliers : 2.88 % Allowed : 18.38 % Favored : 78.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.25), residues: 1076 helix: -0.19 (0.21), residues: 616 sheet: -1.49 (0.65), residues: 62 loop : -2.16 (0.29), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 447 HIS 0.005 0.001 HIS A 219 PHE 0.024 0.001 PHE A 315 TYR 0.009 0.001 TYR A 584 ARG 0.002 0.000 ARG B 470 Details of bonding type rmsd hydrogen bonds : bond 0.03250 ( 356) hydrogen bonds : angle 3.77561 ( 1038) covalent geometry : bond 0.00462 ( 8830) covalent geometry : angle 0.60694 (11980) *********************** 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 119 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 92 time to evaluate : 0.972 Fit side-chains revert: symmetry clash REVERT: A 97 MET cc_start: 0.6764 (tpt) cc_final: 0.6264 (tpt) REVERT: A 152 TYR cc_start: 0.8912 (m-80) cc_final: 0.8657 (m-80) REVERT: A 159 GLU cc_start: 0.7329 (OUTLIER) cc_final: 0.6475 (mp0) REVERT: A 231 ASP cc_start: 0.8541 (t0) cc_final: 0.8221 (t70) REVERT: A 286 CYS cc_start: 0.7814 (p) cc_final: 0.7603 (p) REVERT: A 409 LEU cc_start: 0.8142 (OUTLIER) cc_final: 0.7820 (tt) REVERT: A 492 GLU cc_start: 0.7319 (tp30) cc_final: 0.6295 (tp30) REVERT: A 576 MET cc_start: 0.8352 (mtm) cc_final: 0.8082 (mtm) REVERT: B 97 MET cc_start: 0.6705 (tpt) cc_final: 0.6224 (tpt) REVERT: B 137 GLN cc_start: 0.8876 (mp10) cc_final: 0.8594 (pt0) REVERT: B 159 GLU cc_start: 0.7298 (OUTLIER) cc_final: 0.6424 (mp0) REVERT: B 231 ASP cc_start: 0.8508 (t0) cc_final: 0.8201 (t70) REVERT: B 286 CYS cc_start: 0.7798 (p) cc_final: 0.7470 (p) REVERT: B 409 LEU cc_start: 0.8173 (OUTLIER) cc_final: 0.7866 (tt) REVERT: B 492 GLU cc_start: 0.7292 (tp30) cc_final: 0.6262 (tp30) outliers start: 27 outliers final: 18 residues processed: 113 average time/residue: 0.1859 time to fit residues: 31.1234 Evaluate side-chains 111 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 89 time to evaluate : 1.350 ------------------------------------------------------------------------------- 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 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 157 VAL Chi-restraints excluded: chain B residue 159 GLU Chi-restraints excluded: chain B residue 162 VAL 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 65 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 71 optimal weight: 0.5980 chunk 29 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 74 optimal weight: 0.0020 chunk 96 optimal weight: 0.7980 chunk 43 optimal weight: 0.6980 chunk 20 optimal weight: 0.7980 chunk 30 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 overall best weight: 0.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.164080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.125030 restraints weight = 10498.989| |-----------------------------------------------------------------------------| r_work (start): 0.3581 rms_B_bonded: 2.75 r_work: 0.3429 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 moved from start: 0.2874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8830 Z= 0.104 Angle : 0.550 8.305 11980 Z= 0.277 Chirality : 0.040 0.136 1426 Planarity : 0.004 0.052 1452 Dihedral : 7.659 85.313 1256 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 2.24 % Allowed : 19.12 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.26), residues: 1076 helix: 0.11 (0.21), residues: 616 sheet: -1.46 (0.68), residues: 60 loop : -2.08 (0.29), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 447 HIS 0.003 0.000 HIS A 219 PHE 0.023 0.001 PHE A 315 TYR 0.010 0.001 TYR B 152 ARG 0.001 0.000 ARG B 158 Details of bonding type rmsd hydrogen bonds : bond 0.02640 ( 356) hydrogen bonds : angle 3.58041 ( 1038) covalent geometry : bond 0.00239 ( 8830) covalent geometry : angle 0.54981 (11980) ********************** 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 115 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 94 time to evaluate : 0.930 Fit side-chains REVERT: A 97 MET cc_start: 0.6518 (tpt) cc_final: 0.5933 (tpt) REVERT: A 152 TYR cc_start: 0.8860 (m-80) cc_final: 0.8573 (m-80) REVERT: A 159 GLU cc_start: 0.7239 (OUTLIER) cc_final: 0.6440 (mp0) REVERT: A 231 ASP cc_start: 0.8401 (t0) cc_final: 0.8074 (t70) REVERT: A 286 CYS cc_start: 0.7787 (p) cc_final: 0.7519 (p) REVERT: A 409 LEU cc_start: 0.8097 (OUTLIER) cc_final: 0.7786 (tt) REVERT: A 492 GLU cc_start: 0.7270 (tp30) cc_final: 0.6266 (tp30) REVERT: B 97 MET cc_start: 0.6443 (tpt) cc_final: 0.5901 (tpt) REVERT: B 137 GLN cc_start: 0.8853 (mp10) cc_final: 0.8588 (pt0) REVERT: B 159 GLU cc_start: 0.7254 (OUTLIER) cc_final: 0.6442 (mp0) REVERT: B 231 ASP cc_start: 0.8400 (t0) cc_final: 0.8075 (t70) REVERT: B 286 CYS cc_start: 0.7741 (p) cc_final: 0.7410 (p) REVERT: B 288 PHE cc_start: 0.7143 (t80) cc_final: 0.6895 (t80) REVERT: B 409 LEU cc_start: 0.8058 (OUTLIER) cc_final: 0.7761 (tt) REVERT: B 492 GLU cc_start: 0.7258 (tp30) cc_final: 0.6238 (tp30) outliers start: 21 outliers final: 17 residues processed: 109 average time/residue: 0.1797 time to fit residues: 28.8389 Evaluate side-chains 112 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 91 time to evaluate : 1.020 ------------------------------------------------------------------------------- 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 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 157 VAL Chi-restraints excluded: chain B residue 159 GLU Chi-restraints excluded: chain B residue 183 GLU 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 47 optimal weight: 0.0870 chunk 12 optimal weight: 0.7980 chunk 108 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 97 optimal weight: 0.9980 chunk 85 optimal weight: 3.9990 chunk 6 optimal weight: 8.9990 chunk 39 optimal weight: 2.9990 chunk 28 optimal weight: 6.9990 chunk 103 optimal weight: 0.0060 chunk 50 optimal weight: 6.9990 overall best weight: 0.9776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.158234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.117638 restraints weight = 10671.150| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 2.96 r_work: 0.3315 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7379 moved from start: 0.2892 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= 0.130 Angle : 0.562 9.037 11980 Z= 0.283 Chirality : 0.041 0.140 1426 Planarity : 0.004 0.053 1452 Dihedral : 7.575 84.901 1256 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 2.67 % Allowed : 18.59 % Favored : 78.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.26), residues: 1076 helix: 0.19 (0.21), residues: 616 sheet: -1.34 (0.69), residues: 60 loop : -2.00 (0.30), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 447 HIS 0.004 0.000 HIS A 219 PHE 0.023 0.001 PHE A 315 TYR 0.013 0.001 TYR B 152 ARG 0.001 0.000 ARG B 270 Details of bonding type rmsd hydrogen bonds : bond 0.02852 ( 356) hydrogen bonds : angle 3.60552 ( 1038) covalent geometry : bond 0.00309 ( 8830) covalent geometry : angle 0.56235 (11980) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4143.08 seconds wall clock time: 72 minutes 44.31 seconds (4364.31 seconds total)