Starting phenix.real_space_refine on Thu Feb 13 07:46:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8i3b_35148/02_2025/8i3b_35148.cif Found real_map, /net/cci-nas-00/data/ceres_data/8i3b_35148/02_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_35148/02_2025/8i3b_35148.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8i3b_35148/02_2025/8i3b_35148.map" model { file = "/net/cci-nas-00/data/ceres_data/8i3b_35148/02_2025/8i3b_35148.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8i3b_35148/02_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-5592/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: 5.40, per 1000 atoms: 0.62 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: 2.32 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: 0.84 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: 2.30 Time building geometry restraints manager: 2.60 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 21.930 Find NCS groups from input model: 0.150 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.000 ------------------------------------------------------------------------------- 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= 0.513 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 *********************** 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 : 0.954 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: 0.2413 time to fit residues: 44.3261 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 : 0.957 ------------------------------------------------------------------------------- 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: 0.9980 chunk 99 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.4025 r_free = 0.4025 target = 0.161848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.122206 restraints weight = 10388.556| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 2.86 r_work: 0.3378 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7354 moved from start: 0.1542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8830 Z= 0.183 Angle : 0.599 7.711 11980 Z= 0.315 Chirality : 0.042 0.201 1426 Planarity : 0.005 0.060 1452 Dihedral : 8.571 82.587 1264 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 0.85 % Allowed : 12.71 % Favored : 86.43 % 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: -3.66 (0.22), residues: 1076 helix: -1.90 (0.18), residues: 606 sheet: -2.56 (0.55), residues: 60 loop : -3.08 (0.25), residues: 410 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 0.012 0.001 TYR B 152 ARG 0.005 0.000 ARG A 401 *********************** 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 117 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 109 time to evaluate : 0.770 Fit side-chains REVERT: A 152 TYR cc_start: 0.8951 (m-80) cc_final: 0.8291 (m-80) REVERT: A 231 ASP cc_start: 0.8439 (t0) cc_final: 0.8093 (t70) REVERT: A 286 CYS cc_start: 0.7935 (p) cc_final: 0.7465 (p) REVERT: A 293 ARG cc_start: 0.6560 (mmt-90) cc_final: 0.6018 (mmp80) REVERT: A 315 PHE cc_start: 0.6697 (t80) cc_final: 0.6223 (t80) REVERT: A 462 GLU cc_start: 0.7886 (mm-30) cc_final: 0.7589 (mm-30) REVERT: A 492 GLU cc_start: 0.7618 (tp30) cc_final: 0.6357 (tp30) REVERT: A 573 MET cc_start: 0.8506 (ttm) cc_final: 0.8052 (ttm) REVERT: B 152 TYR cc_start: 0.8979 (m-80) cc_final: 0.8343 (m-80) REVERT: B 183 GLU cc_start: 0.6792 (mp0) cc_final: 0.6566 (mp0) REVERT: B 231 ASP cc_start: 0.8500 (t0) cc_final: 0.8185 (t70) REVERT: B 462 GLU cc_start: 0.7846 (mm-30) cc_final: 0.7577 (mm-30) REVERT: B 492 GLU cc_start: 0.7602 (tp30) cc_final: 0.6371 (tp30) REVERT: B 508 TYR cc_start: 0.7604 (t80) cc_final: 0.7340 (t80) REVERT: B 573 MET cc_start: 0.8505 (ttm) cc_final: 0.8179 (ttm) outliers start: 8 outliers final: 6 residues processed: 117 average time/residue: 0.2576 time to fit residues: 40.3336 Evaluate side-chains 99 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 93 time to evaluate : 0.936 ------------------------------------------------------------------------------- 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 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 107 optimal weight: 0.0770 chunk 70 optimal weight: 2.9990 chunk 76 optimal weight: 4.9990 chunk 27 optimal weight: 20.0000 chunk 21 optimal weight: 4.9990 chunk 38 optimal weight: 0.0970 chunk 31 optimal weight: 0.5980 chunk 45 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 55 optimal weight: 6.9990 chunk 25 optimal weight: 1.9990 overall best weight: 1.1540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 427 HIS B 273 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.159741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.120291 restraints weight = 10533.277| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 2.80 r_work: 0.3356 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.1885 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= 0.226 Angle : 0.584 7.355 11980 Z= 0.302 Chirality : 0.042 0.148 1426 Planarity : 0.004 0.057 1452 Dihedral : 8.254 83.554 1256 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 1.92 % Allowed : 13.68 % Favored : 84.40 % 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: -2.88 (0.23), residues: 1076 helix: -1.17 (0.20), residues: 604 sheet: -2.30 (0.55), residues: 60 loop : -2.89 (0.26), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 447 HIS 0.007 0.001 HIS A 265 PHE 0.012 0.001 PHE A 442 TYR 0.008 0.001 TYR A 152 ARG 0.002 0.000 ARG A 180 *********************** 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 114 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 96 time to evaluate : 0.964 Fit side-chains REVERT: A 152 TYR cc_start: 0.8886 (m-80) cc_final: 0.8213 (m-80) REVERT: A 231 ASP cc_start: 0.8509 (t0) cc_final: 0.8169 (t70) REVERT: A 286 CYS cc_start: 0.7897 (p) cc_final: 0.7488 (p) REVERT: A 462 GLU cc_start: 0.7888 (mm-30) cc_final: 0.7506 (mm-30) REVERT: A 492 GLU cc_start: 0.7519 (tp30) cc_final: 0.6461 (tp30) REVERT: A 573 MET cc_start: 0.8506 (ttm) cc_final: 0.7940 (ttm) REVERT: A 576 MET cc_start: 0.8150 (mtp) cc_final: 0.7714 (mtm) REVERT: B 152 TYR cc_start: 0.8914 (m-80) cc_final: 0.8324 (m-80) REVERT: B 231 ASP cc_start: 0.8525 (t0) cc_final: 0.8221 (t70) REVERT: B 286 CYS cc_start: 0.7956 (p) cc_final: 0.7475 (p) REVERT: B 462 GLU cc_start: 0.7872 (mm-30) cc_final: 0.7538 (mm-30) REVERT: B 492 GLU cc_start: 0.7501 (tp30) cc_final: 0.6423 (tp30) REVERT: B 508 TYR cc_start: 0.7622 (t80) cc_final: 0.7387 (t80) REVERT: B 573 MET cc_start: 0.8547 (ttm) cc_final: 0.8257 (ttm) outliers start: 18 outliers final: 15 residues processed: 110 average time/residue: 0.1751 time to fit residues: 28.7206 Evaluate side-chains 105 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 90 time to evaluate : 0.962 ------------------------------------------------------------------------------- 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 265 HIS 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 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: 10.0000 chunk 92 optimal weight: 5.9990 chunk 67 optimal weight: 3.9990 chunk 3 optimal weight: 4.9990 chunk 48 optimal weight: 1.9990 chunk 94 optimal weight: 0.5980 chunk 86 optimal weight: 2.9990 chunk 35 optimal weight: 0.4980 chunk 99 optimal weight: 4.9990 chunk 27 optimal weight: 20.0000 chunk 21 optimal weight: 2.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 254 HIS B 254 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.156798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.117343 restraints weight = 10639.977| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 2.78 r_work: 0.3316 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.2166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 8830 Z= 0.315 Angle : 0.625 7.198 11980 Z= 0.320 Chirality : 0.044 0.160 1426 Planarity : 0.004 0.057 1452 Dihedral : 8.403 83.416 1256 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Rotamer: Outliers : 2.24 % Allowed : 15.92 % Favored : 81.84 % 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: -2.57 (0.23), residues: 1076 helix: -0.96 (0.20), residues: 610 sheet: -2.17 (0.57), residues: 60 loop : -2.71 (0.26), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 447 HIS 0.005 0.001 HIS A 219 PHE 0.017 0.002 PHE A 315 TYR 0.009 0.001 TYR A 565 ARG 0.002 0.000 ARG A 180 *********************** 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 114 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 93 time to evaluate : 0.907 Fit side-chains REVERT: A 231 ASP cc_start: 0.8532 (t0) cc_final: 0.8226 (t70) REVERT: A 286 CYS cc_start: 0.7858 (p) cc_final: 0.7495 (p) REVERT: A 409 LEU cc_start: 0.8138 (OUTLIER) cc_final: 0.7823 (tt) REVERT: A 492 GLU cc_start: 0.7470 (tp30) cc_final: 0.6472 (tp30) REVERT: B 231 ASP cc_start: 0.8562 (t0) cc_final: 0.8239 (t70) REVERT: B 286 CYS cc_start: 0.7899 (p) cc_final: 0.7514 (p) REVERT: B 409 LEU cc_start: 0.8083 (OUTLIER) cc_final: 0.7768 (tt) REVERT: B 492 GLU cc_start: 0.7495 (tp30) cc_final: 0.6464 (tp30) REVERT: B 573 MET cc_start: 0.8601 (ttm) cc_final: 0.8361 (ttm) outliers start: 21 outliers final: 16 residues processed: 108 average time/residue: 0.1701 time to fit residues: 27.4466 Evaluate side-chains 107 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 89 time to evaluate : 0.908 ------------------------------------------------------------------------------- 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 97 optimal weight: 0.9990 chunk 71 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 chunk 50 optimal weight: 4.9990 chunk 80 optimal weight: 6.9990 chunk 7 optimal weight: 0.0000 chunk 98 optimal weight: 0.5980 chunk 88 optimal weight: 4.9990 chunk 26 optimal weight: 4.9990 chunk 84 optimal weight: 3.9990 chunk 106 optimal weight: 7.9990 overall best weight: 1.7190 ------------------------------------------------------------------------------- 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 = 0.4007 r_free = 0.4007 target = 0.158912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.119648 restraints weight = 10641.594| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 2.73 r_work: 0.3368 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.2328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 8830 Z= 0.299 Angle : 0.605 7.181 11980 Z= 0.310 Chirality : 0.044 0.212 1426 Planarity : 0.004 0.057 1452 Dihedral : 8.324 83.711 1256 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer: Outliers : 2.78 % Allowed : 16.35 % Favored : 80.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.22 (0.24), residues: 1076 helix: -0.77 (0.20), residues: 614 sheet: -1.81 (0.59), residues: 62 loop : -2.42 (0.27), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 447 HIS 0.005 0.001 HIS B 219 PHE 0.018 0.001 PHE A 315 TYR 0.011 0.001 TYR B 152 ARG 0.002 0.000 ARG A 410 *********************** 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 118 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 92 time to evaluate : 0.923 Fit side-chains REVERT: A 152 TYR cc_start: 0.8904 (m-80) cc_final: 0.8458 (m-80) REVERT: A 183 GLU cc_start: 0.6658 (OUTLIER) cc_final: 0.6395 (mp0) REVERT: A 231 ASP cc_start: 0.8558 (t0) cc_final: 0.8234 (t70) REVERT: A 286 CYS cc_start: 0.7839 (p) cc_final: 0.7475 (p) REVERT: A 409 LEU cc_start: 0.8129 (OUTLIER) cc_final: 0.7816 (tt) REVERT: A 462 GLU cc_start: 0.7844 (mm-30) cc_final: 0.7557 (mm-30) REVERT: A 492 GLU cc_start: 0.7382 (tp30) cc_final: 0.6375 (tp30) REVERT: B 97 MET cc_start: 0.6566 (tpt) cc_final: 0.5995 (tpt) REVERT: B 137 GLN cc_start: 0.8895 (mp10) cc_final: 0.8660 (mp10) REVERT: B 152 TYR cc_start: 0.8951 (m-80) cc_final: 0.8388 (m-80) REVERT: B 231 ASP cc_start: 0.8537 (t0) cc_final: 0.8214 (t70) REVERT: B 273 GLN cc_start: 0.8643 (mm-40) cc_final: 0.8333 (mt0) REVERT: B 286 CYS cc_start: 0.7924 (p) cc_final: 0.7537 (p) REVERT: B 409 LEU cc_start: 0.8113 (OUTLIER) cc_final: 0.7800 (tt) REVERT: B 462 GLU cc_start: 0.7928 (mm-30) cc_final: 0.7397 (mm-30) REVERT: B 492 GLU cc_start: 0.7454 (tp30) cc_final: 0.6430 (tp30) outliers start: 26 outliers final: 19 residues processed: 112 average time/residue: 0.1793 time to fit residues: 29.8853 Evaluate side-chains 113 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 91 time to evaluate : 0.993 ------------------------------------------------------------------------------- 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 183 GLU Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 265 HIS Chi-restraints excluded: chain A residue 398 LEU 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 32 optimal weight: 0.6980 chunk 2 optimal weight: 1.9990 chunk 68 optimal weight: 0.0470 chunk 36 optimal weight: 0.9990 chunk 107 optimal weight: 0.8980 chunk 89 optimal weight: 2.9990 chunk 37 optimal weight: 5.9990 chunk 4 optimal weight: 0.7980 chunk 8 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 chunk 25 optimal weight: 5.9990 overall best weight: 0.6880 ------------------------------------------------------------------------------- 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 = 0.4048 r_free = 0.4048 target = 0.162937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.123844 restraints weight = 10395.100| |-----------------------------------------------------------------------------| r_work (start): 0.3572 rms_B_bonded: 2.72 r_work: 0.3423 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.2496 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= 0.164 Angle : 0.534 7.180 11980 Z= 0.275 Chirality : 0.041 0.219 1426 Planarity : 0.004 0.054 1452 Dihedral : 7.982 84.962 1256 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 2.67 % Allowed : 17.09 % Favored : 80.24 % 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: -1.60 (0.25), residues: 1076 helix: -0.25 (0.21), residues: 598 sheet: -1.71 (0.64), residues: 60 loop : -2.10 (0.28), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 447 HIS 0.003 0.000 HIS A 219 PHE 0.029 0.001 PHE A 315 TYR 0.008 0.001 TYR B 152 ARG 0.001 0.000 ARG A 158 *********************** 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 123 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 98 time to evaluate : 0.931 Fit side-chains REVERT: A 97 MET cc_start: 0.6565 (tpt) cc_final: 0.5980 (tpt) REVERT: A 152 TYR cc_start: 0.8880 (m-80) cc_final: 0.8140 (m-80) REVERT: A 231 ASP cc_start: 0.8574 (t0) cc_final: 0.8280 (t70) REVERT: A 286 CYS cc_start: 0.7804 (p) cc_final: 0.7480 (p) REVERT: A 409 LEU cc_start: 0.8145 (OUTLIER) cc_final: 0.7846 (tt) REVERT: A 462 GLU cc_start: 0.7796 (mm-30) cc_final: 0.7252 (mm-30) REVERT: A 492 GLU cc_start: 0.7321 (tp30) cc_final: 0.6393 (tp30) REVERT: B 97 MET cc_start: 0.6515 (tpt) cc_final: 0.5954 (tpt) REVERT: B 137 GLN cc_start: 0.8899 (mp10) cc_final: 0.8669 (mp10) REVERT: B 152 TYR cc_start: 0.8872 (m-80) cc_final: 0.8277 (m-80) REVERT: B 231 ASP cc_start: 0.8565 (t0) cc_final: 0.8272 (t70) REVERT: B 273 GLN cc_start: 0.8669 (mm-40) cc_final: 0.8330 (mt0) REVERT: B 286 CYS cc_start: 0.7858 (p) cc_final: 0.7584 (p) REVERT: B 288 PHE cc_start: 0.7396 (t80) cc_final: 0.7157 (t80) REVERT: B 409 LEU cc_start: 0.8104 (OUTLIER) cc_final: 0.7807 (tt) REVERT: B 462 GLU cc_start: 0.7852 (mm-30) cc_final: 0.7358 (mm-30) REVERT: B 492 GLU cc_start: 0.7338 (tp30) cc_final: 0.6388 (tp30) outliers start: 25 outliers final: 19 residues processed: 116 average time/residue: 0.1870 time to fit residues: 31.7949 Evaluate side-chains 113 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 92 time to evaluate : 1.022 ------------------------------------------------------------------------------- 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 398 LEU 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 156 THR 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 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: 0.8980 chunk 103 optimal weight: 3.9990 chunk 15 optimal weight: 4.9990 chunk 81 optimal weight: 5.9990 chunk 29 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 70 optimal weight: 0.7980 chunk 39 optimal weight: 0.8980 chunk 74 optimal weight: 5.9990 chunk 8 optimal weight: 5.9990 chunk 26 optimal weight: 3.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- 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 = 0.4024 r_free = 0.4024 target = 0.160343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.121079 restraints weight = 10607.461| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 2.72 r_work: 0.3374 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.2549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8830 Z= 0.271 Angle : 0.596 8.104 11980 Z= 0.300 Chirality : 0.043 0.216 1426 Planarity : 0.004 0.055 1452 Dihedral : 7.983 84.276 1256 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 2.99 % Allowed : 16.88 % Favored : 80.13 % 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: -1.77 (0.25), residues: 1076 helix: -0.37 (0.21), residues: 616 sheet: -1.69 (0.65), residues: 60 loop : -2.30 (0.28), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 447 HIS 0.005 0.001 HIS A 219 PHE 0.027 0.001 PHE A 315 TYR 0.009 0.001 TYR A 584 ARG 0.001 0.000 ARG A 470 *********************** 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 : 0.925 Fit side-chains REVERT: A 97 MET cc_start: 0.6724 (tpt) cc_final: 0.6095 (tpt) REVERT: A 137 GLN cc_start: 0.8900 (mp10) cc_final: 0.8656 (mp10) REVERT: A 231 ASP cc_start: 0.8567 (t0) cc_final: 0.8244 (t70) REVERT: A 286 CYS cc_start: 0.7827 (p) cc_final: 0.7605 (p) REVERT: A 409 LEU cc_start: 0.8172 (OUTLIER) cc_final: 0.7868 (tt) REVERT: A 492 GLU cc_start: 0.7371 (tp30) cc_final: 0.6376 (tp30) REVERT: A 576 MET cc_start: 0.8357 (mtm) cc_final: 0.8093 (mtt) REVERT: B 97 MET cc_start: 0.6672 (tpt) cc_final: 0.6118 (tpt) REVERT: B 137 GLN cc_start: 0.8905 (mp10) cc_final: 0.8674 (mp10) REVERT: B 152 TYR cc_start: 0.8904 (m-80) cc_final: 0.8692 (m-80) REVERT: B 231 ASP cc_start: 0.8567 (t0) cc_final: 0.8250 (t70) REVERT: B 273 GLN cc_start: 0.8628 (mm-40) cc_final: 0.8299 (mt0) REVERT: B 409 LEU cc_start: 0.8155 (OUTLIER) cc_final: 0.7850 (tt) REVERT: B 462 GLU cc_start: 0.7867 (mm-30) cc_final: 0.7554 (mm-30) REVERT: B 492 GLU cc_start: 0.7383 (tp30) cc_final: 0.6374 (tp30) REVERT: B 576 MET cc_start: 0.8338 (mtm) cc_final: 0.8094 (mtt) outliers start: 28 outliers final: 20 residues processed: 118 average time/residue: 0.1705 time to fit residues: 29.8330 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 : 0.894 ------------------------------------------------------------------------------- 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 265 HIS Chi-restraints excluded: chain A residue 398 LEU 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 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: 3.9990 chunk 81 optimal weight: 1.9990 chunk 36 optimal weight: 0.0980 chunk 62 optimal weight: 8.9990 chunk 25 optimal weight: 0.9980 chunk 21 optimal weight: 0.6980 chunk 29 optimal weight: 3.9990 chunk 24 optimal weight: 9.9990 chunk 41 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 71 optimal weight: 0.8980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 311 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.162611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.123390 restraints weight = 10691.914| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 2.75 r_work: 0.3404 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 moved from start: 0.2669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8830 Z= 0.191 Angle : 0.553 7.985 11980 Z= 0.280 Chirality : 0.041 0.204 1426 Planarity : 0.004 0.054 1452 Dihedral : 7.771 84.835 1256 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 2.78 % Allowed : 17.63 % 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: -1.53 (0.25), residues: 1076 helix: -0.16 (0.21), residues: 616 sheet: -1.58 (0.67), residues: 60 loop : -2.21 (0.29), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 447 HIS 0.004 0.000 HIS A 219 PHE 0.024 0.001 PHE A 315 TYR 0.008 0.001 TYR A 152 ARG 0.001 0.000 ARG B 158 *********************** 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: 26 poor density : 97 time to evaluate : 0.926 Fit side-chains revert: symmetry clash REVERT: A 97 MET cc_start: 0.6614 (tpt) cc_final: 0.6023 (tpt) REVERT: A 137 GLN cc_start: 0.8901 (mp10) cc_final: 0.8652 (mp10) REVERT: A 152 TYR cc_start: 0.8874 (m-80) cc_final: 0.8597 (m-80) REVERT: A 231 ASP cc_start: 0.8547 (t0) cc_final: 0.8224 (t70) REVERT: A 286 CYS cc_start: 0.7800 (p) cc_final: 0.7465 (p) REVERT: A 409 LEU cc_start: 0.8088 (OUTLIER) cc_final: 0.7787 (tt) REVERT: A 492 GLU cc_start: 0.7311 (tp30) cc_final: 0.6293 (tp30) REVERT: A 576 MET cc_start: 0.8324 (mtm) cc_final: 0.8042 (mtm) REVERT: B 97 MET cc_start: 0.6596 (tpt) cc_final: 0.6041 (tpt) REVERT: B 137 GLN cc_start: 0.8895 (mp10) cc_final: 0.8576 (pt0) REVERT: B 152 TYR cc_start: 0.8877 (m-80) cc_final: 0.8674 (m-80) REVERT: B 159 GLU cc_start: 0.7275 (OUTLIER) cc_final: 0.6437 (mp0) REVERT: B 231 ASP cc_start: 0.8543 (t0) cc_final: 0.8225 (t70) REVERT: B 273 GLN cc_start: 0.8640 (mm-40) cc_final: 0.8313 (mt0) REVERT: B 409 LEU cc_start: 0.8074 (OUTLIER) cc_final: 0.7776 (tt) REVERT: B 492 GLU cc_start: 0.7349 (tp30) cc_final: 0.6304 (tp30) REVERT: B 576 MET cc_start: 0.8288 (mtm) cc_final: 0.8025 (mtt) outliers start: 26 outliers final: 19 residues processed: 118 average time/residue: 0.1794 time to fit residues: 30.9537 Evaluate side-chains 113 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 91 time to evaluate : 0.914 ------------------------------------------------------------------------------- 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 265 HIS Chi-restraints excluded: chain A residue 398 LEU 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 173 LEU 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 50 optimal weight: 4.9990 chunk 59 optimal weight: 4.9990 chunk 36 optimal weight: 0.3980 chunk 82 optimal weight: 20.0000 chunk 2 optimal weight: 3.9990 chunk 91 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 31 optimal weight: 5.9990 chunk 71 optimal weight: 3.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- 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 = 0.3990 r_free = 0.3990 target = 0.157414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.118156 restraints weight = 10682.497| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 2.70 r_work: 0.3340 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.2675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 8830 Z= 0.381 Angle : 0.658 8.816 11980 Z= 0.329 Chirality : 0.046 0.210 1426 Planarity : 0.005 0.055 1452 Dihedral : 8.034 82.826 1256 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.53 % Favored : 92.47 % Rotamer: Outliers : 2.88 % Allowed : 18.06 % 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: -1.75 (0.25), residues: 1076 helix: -0.42 (0.21), residues: 616 sheet: -1.55 (0.65), residues: 62 loop : -2.18 (0.29), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 447 HIS 0.006 0.001 HIS A 219 PHE 0.023 0.002 PHE A 315 TYR 0.011 0.002 TYR B 565 ARG 0.002 0.000 ARG B 470 *********************** 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 120 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 93 time to evaluate : 0.969 Fit side-chains REVERT: A 97 MET cc_start: 0.6824 (tpt) cc_final: 0.6336 (tpt) REVERT: A 152 TYR cc_start: 0.8905 (m-80) cc_final: 0.8660 (m-80) REVERT: A 231 ASP cc_start: 0.8553 (t0) cc_final: 0.8119 (t0) REVERT: A 286 CYS cc_start: 0.7869 (p) cc_final: 0.7662 (p) REVERT: A 409 LEU cc_start: 0.8224 (OUTLIER) cc_final: 0.7911 (tt) REVERT: A 492 GLU cc_start: 0.7329 (tp30) cc_final: 0.6342 (tp30) REVERT: B 97 MET cc_start: 0.6846 (tpt) cc_final: 0.6338 (tpt) REVERT: B 152 TYR cc_start: 0.8933 (m-80) cc_final: 0.8633 (m-80) REVERT: B 231 ASP cc_start: 0.8557 (t0) cc_final: 0.8132 (t0) REVERT: B 273 GLN cc_start: 0.8657 (mm-40) cc_final: 0.8329 (mt0) REVERT: B 286 CYS cc_start: 0.7856 (p) cc_final: 0.7538 (p) REVERT: B 409 LEU cc_start: 0.8171 (OUTLIER) cc_final: 0.7857 (tt) REVERT: B 492 GLU cc_start: 0.7353 (tp30) cc_final: 0.6351 (tp30) REVERT: B 576 MET cc_start: 0.8398 (mtm) cc_final: 0.8110 (mtt) outliers start: 27 outliers final: 20 residues processed: 113 average time/residue: 0.1761 time to fit residues: 29.5644 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 : 1.087 ------------------------------------------------------------------------------- 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 157 VAL Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 265 HIS Chi-restraints excluded: chain A residue 398 LEU 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 65 optimal weight: 0.9980 chunk 98 optimal weight: 0.9980 chunk 71 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 74 optimal weight: 4.9990 chunk 96 optimal weight: 0.9980 chunk 43 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 28 optimal weight: 7.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 = 0.3955 r_free = 0.3955 target = 0.156640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.116194 restraints weight = 10654.739| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 2.96 r_work: 0.3296 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 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 0.032 8830 Z= 0.204 Angle : 0.568 8.380 11980 Z= 0.287 Chirality : 0.042 0.197 1426 Planarity : 0.004 0.055 1452 Dihedral : 7.829 84.229 1256 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 2.24 % Allowed : 18.80 % 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 (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: -1.40 (0.25), residues: 1076 helix: -0.10 (0.21), residues: 616 sheet: -1.43 (0.66), residues: 62 loop : -2.10 (0.30), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 447 HIS 0.004 0.001 HIS A 219 PHE 0.025 0.001 PHE A 315 TYR 0.007 0.001 TYR A 152 ARG 0.002 0.000 ARG B 158 ********************** 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 112 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 91 time to evaluate : 1.019 Fit side-chains REVERT: A 97 MET cc_start: 0.6604 (tpt) cc_final: 0.6010 (tpt) REVERT: A 152 TYR cc_start: 0.8873 (m-80) cc_final: 0.8606 (m-80) REVERT: A 159 GLU cc_start: 0.7193 (OUTLIER) cc_final: 0.6389 (mp0) REVERT: A 231 ASP cc_start: 0.8546 (t0) cc_final: 0.8209 (t70) REVERT: A 409 LEU cc_start: 0.8041 (OUTLIER) cc_final: 0.7747 (tt) REVERT: A 492 GLU cc_start: 0.7300 (tp30) cc_final: 0.6232 (tp30) REVERT: A 576 MET cc_start: 0.8225 (mtm) cc_final: 0.8020 (mtt) REVERT: B 97 MET cc_start: 0.6574 (tpt) cc_final: 0.6015 (tpt) REVERT: B 152 TYR cc_start: 0.8897 (m-80) cc_final: 0.8630 (m-80) REVERT: B 231 ASP cc_start: 0.8556 (t0) cc_final: 0.8228 (t70) REVERT: B 273 GLN cc_start: 0.8689 (mm-40) cc_final: 0.8307 (mt0) REVERT: B 286 CYS cc_start: 0.7821 (p) cc_final: 0.7500 (p) REVERT: B 288 PHE cc_start: 0.7155 (t80) cc_final: 0.6870 (t80) REVERT: B 409 LEU cc_start: 0.8013 (OUTLIER) cc_final: 0.7722 (tt) REVERT: B 492 GLU cc_start: 0.7310 (tp30) cc_final: 0.6241 (tp30) REVERT: B 576 MET cc_start: 0.8218 (mtm) cc_final: 0.7930 (mtt) outliers start: 21 outliers final: 18 residues processed: 106 average time/residue: 0.1792 time to fit residues: 28.3697 Evaluate side-chains 109 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 88 time to evaluate : 1.053 ------------------------------------------------------------------------------- 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 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 157 VAL Chi-restraints excluded: chain B residue 162 VAL 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 47 optimal weight: 0.1980 chunk 12 optimal weight: 3.9990 chunk 108 optimal weight: 2.9990 chunk 48 optimal weight: 0.6980 chunk 97 optimal weight: 0.6980 chunk 85 optimal weight: 3.9990 chunk 6 optimal weight: 8.9990 chunk 39 optimal weight: 4.9990 chunk 28 optimal weight: 8.9990 chunk 103 optimal weight: 0.9980 chunk 50 optimal weight: 5.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- 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 = 0.3954 r_free = 0.3954 target = 0.156526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.116024 restraints weight = 10713.289| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 2.96 r_work: 0.3291 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7399 moved from start: 0.2819 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= 0.218 Angle : 0.570 8.208 11980 Z= 0.288 Chirality : 0.042 0.186 1426 Planarity : 0.004 0.053 1452 Dihedral : 7.746 84.190 1256 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 2.46 % Allowed : 18.59 % 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 (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: -1.24 (0.26), residues: 1076 helix: 0.00 (0.21), residues: 616 sheet: -1.31 (0.67), residues: 62 loop : -1.99 (0.30), residues: 398 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 0.024 0.001 PHE A 315 TYR 0.007 0.001 TYR B 584 ARG 0.001 0.000 ARG B 158 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3818.62 seconds wall clock time: 68 minutes 37.77 seconds (4117.77 seconds total)