Starting phenix.real_space_refine on Mon Jun 30 00:24:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8u3l_41866/06_2025/8u3l_41866_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u3l_41866/06_2025/8u3l_41866.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8u3l_41866/06_2025/8u3l_41866.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u3l_41866/06_2025/8u3l_41866.map" model { file = "/net/cci-nas-00/data/ceres_data/8u3l_41866/06_2025/8u3l_41866_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u3l_41866/06_2025/8u3l_41866_trim.cif" } resolution = 3.7 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= 0.003 sd= 0.068 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: 7 Type Number sf(0) Gaussians P 4 5.49 5 S 100 5.16 5 Na 1 4.78 5 C 11452 2.51 5 N 2804 2.21 5 O 3100 1.98 5 H 17492 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 34953 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 8701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 8701 Classifications: {'peptide': 533} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 518} Chain: "A" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 35 Unusual residues: {' NA': 1, '3PH': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 14 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 3 Classifications: {'water': 1} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 3 Classifications: {'water': 1} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 3 Classifications: {'water': 1} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 3 Classifications: {'water': 1} Restraints were copied for chains: B, C, D Time building chain proxies: 28.56, per 1000 atoms: 0.82 Number of scatterers: 34953 At special positions: 0 Unit cell: (124.44, 124.44, 115.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 100 16.00 P 4 15.00 Na 1 11.00 O 3100 8.00 N 2804 7.00 C 11452 6.00 H 17492 1.00 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: 10.17 Conformation dependent library (CDL) restraints added in 3.0 seconds 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4032 Finding SS restraints... Secondary structure from input PDB file: 92 helices and 4 sheets defined 64.5% alpha, 2.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.40 Creating SS restraints... Processing helix chain 'A' and resid 203 through 211 removed outlier: 3.565A pdb=" N ILE A 207 " --> pdb=" O THR A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 223 Processing helix chain 'A' and resid 233 through 237 Processing helix chain 'A' and resid 250 through 258 Processing helix chain 'A' and resid 261 through 269 Processing helix chain 'A' and resid 286 through 295 Processing helix chain 'A' and resid 298 through 320 Processing helix chain 'A' and resid 335 through 344 Processing helix chain 'A' and resid 345 through 354 removed outlier: 3.592A pdb=" N GLN A 354 " --> pdb=" O ALA A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 366 Processing helix chain 'A' and resid 394 through 402 Processing helix chain 'A' and resid 408 through 413 removed outlier: 4.329A pdb=" N LEU A 413 " --> pdb=" O ARG A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 454 removed outlier: 3.697A pdb=" N ARG A 420 " --> pdb=" O GLU A 416 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N LYS A 431 " --> pdb=" O ASP A 427 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N ARG A 432 " --> pdb=" O ARG A 428 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N TYR A 454 " --> pdb=" O ALA A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 500 Processing helix chain 'A' and resid 504 through 509 removed outlier: 4.287A pdb=" N VAL A 508 " --> pdb=" O LYS A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 531 Processing helix chain 'A' and resid 536 through 551 Processing helix chain 'A' and resid 552 through 557 removed outlier: 3.926A pdb=" N ARG A 557 " --> pdb=" O TYR A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 599 removed outlier: 3.728A pdb=" N LEU A 577 " --> pdb=" O ILE A 573 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N CYS A 578 " --> pdb=" O LEU A 574 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N ARG A 579 " --> pdb=" O ARG A 575 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N PHE A 582 " --> pdb=" O CYS A 578 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N VAL A 583 " --> pdb=" O ARG A 579 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N TYR A 584 " --> pdb=" O PHE A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 639 Processing helix chain 'A' and resid 640 through 642 No H-bonds generated for 'chain 'A' and resid 640 through 642' Processing helix chain 'A' and resid 655 through 684 removed outlier: 3.681A pdb=" N GLU A 684 " --> pdb=" O ALA A 680 " (cutoff:3.500A) Processing helix chain 'A' and resid 689 through 711 removed outlier: 3.702A pdb=" N ASN A 695 " --> pdb=" O GLN A 691 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 211 removed outlier: 3.565A pdb=" N ILE D 207 " --> pdb=" O THR D 203 " (cutoff:3.500A) Processing helix chain 'D' and resid 213 through 223 Processing helix chain 'D' and resid 233 through 237 Processing helix chain 'D' and resid 250 through 258 Processing helix chain 'D' and resid 261 through 269 Processing helix chain 'D' and resid 286 through 295 Processing helix chain 'D' and resid 298 through 320 Processing helix chain 'D' and resid 335 through 344 Processing helix chain 'D' and resid 345 through 354 removed outlier: 3.592A pdb=" N GLN D 354 " --> pdb=" O ALA D 350 " (cutoff:3.500A) Processing helix chain 'D' and resid 362 through 366 Processing helix chain 'D' and resid 394 through 402 Processing helix chain 'D' and resid 408 through 413 removed outlier: 4.329A pdb=" N LEU D 413 " --> pdb=" O ARG D 409 " (cutoff:3.500A) Processing helix chain 'D' and resid 415 through 454 removed outlier: 3.697A pdb=" N ARG D 420 " --> pdb=" O GLU D 416 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N LYS D 431 " --> pdb=" O ASP D 427 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N ARG D 432 " --> pdb=" O ARG D 428 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N TYR D 454 " --> pdb=" O ALA D 450 " (cutoff:3.500A) Processing helix chain 'D' and resid 468 through 500 Processing helix chain 'D' and resid 504 through 509 removed outlier: 4.287A pdb=" N VAL D 508 " --> pdb=" O LYS D 504 " (cutoff:3.500A) Processing helix chain 'D' and resid 512 through 531 Processing helix chain 'D' and resid 536 through 551 Processing helix chain 'D' and resid 552 through 557 removed outlier: 3.926A pdb=" N ARG D 557 " --> pdb=" O TYR D 554 " (cutoff:3.500A) Processing helix chain 'D' and resid 559 through 599 removed outlier: 3.727A pdb=" N LEU D 577 " --> pdb=" O ILE D 573 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N CYS D 578 " --> pdb=" O LEU D 574 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N ARG D 579 " --> pdb=" O ARG D 575 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N PHE D 582 " --> pdb=" O CYS D 578 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N VAL D 583 " --> pdb=" O ARG D 579 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N TYR D 584 " --> pdb=" O PHE D 580 " (cutoff:3.500A) Processing helix chain 'D' and resid 630 through 639 Processing helix chain 'D' and resid 640 through 642 No H-bonds generated for 'chain 'D' and resid 640 through 642' Processing helix chain 'D' and resid 655 through 684 removed outlier: 3.681A pdb=" N GLU D 684 " --> pdb=" O ALA D 680 " (cutoff:3.500A) Processing helix chain 'D' and resid 689 through 711 removed outlier: 3.702A pdb=" N ASN D 695 " --> pdb=" O GLN D 691 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 211 removed outlier: 3.565A pdb=" N ILE B 207 " --> pdb=" O THR B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 223 Processing helix chain 'B' and resid 233 through 237 Processing helix chain 'B' and resid 250 through 258 Processing helix chain 'B' and resid 261 through 269 Processing helix chain 'B' and resid 286 through 295 Processing helix chain 'B' and resid 298 through 320 Processing helix chain 'B' and resid 335 through 344 Processing helix chain 'B' and resid 345 through 354 removed outlier: 3.593A pdb=" N GLN B 354 " --> pdb=" O ALA B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 366 Processing helix chain 'B' and resid 394 through 402 Processing helix chain 'B' and resid 408 through 413 removed outlier: 4.329A pdb=" N LEU B 413 " --> pdb=" O ARG B 409 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 454 removed outlier: 3.697A pdb=" N ARG B 420 " --> pdb=" O GLU B 416 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N LYS B 431 " --> pdb=" O ASP B 427 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N ARG B 432 " --> pdb=" O ARG B 428 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N TYR B 454 " --> pdb=" O ALA B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 468 through 500 Processing helix chain 'B' and resid 504 through 509 removed outlier: 4.287A pdb=" N VAL B 508 " --> pdb=" O LYS B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 512 through 531 Processing helix chain 'B' and resid 536 through 551 Processing helix chain 'B' and resid 552 through 557 removed outlier: 3.927A pdb=" N ARG B 557 " --> pdb=" O TYR B 554 " (cutoff:3.500A) Processing helix chain 'B' and resid 559 through 599 removed outlier: 3.727A pdb=" N LEU B 577 " --> pdb=" O ILE B 573 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N CYS B 578 " --> pdb=" O LEU B 574 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N ARG B 579 " --> pdb=" O ARG B 575 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N PHE B 582 " --> pdb=" O CYS B 578 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N VAL B 583 " --> pdb=" O ARG B 579 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N TYR B 584 " --> pdb=" O PHE B 580 " (cutoff:3.500A) Processing helix chain 'B' and resid 630 through 639 Processing helix chain 'B' and resid 640 through 642 No H-bonds generated for 'chain 'B' and resid 640 through 642' Processing helix chain 'B' and resid 655 through 684 removed outlier: 3.681A pdb=" N GLU B 684 " --> pdb=" O ALA B 680 " (cutoff:3.500A) Processing helix chain 'B' and resid 689 through 711 removed outlier: 3.702A pdb=" N ASN B 695 " --> pdb=" O GLN B 691 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 211 removed outlier: 3.565A pdb=" N ILE C 207 " --> pdb=" O THR C 203 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 223 Processing helix chain 'C' and resid 233 through 237 Processing helix chain 'C' and resid 250 through 258 Processing helix chain 'C' and resid 261 through 269 Processing helix chain 'C' and resid 286 through 295 Processing helix chain 'C' and resid 298 through 320 Processing helix chain 'C' and resid 335 through 344 Processing helix chain 'C' and resid 345 through 354 removed outlier: 3.592A pdb=" N GLN C 354 " --> pdb=" O ALA C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 362 through 366 Processing helix chain 'C' and resid 394 through 402 Processing helix chain 'C' and resid 408 through 413 removed outlier: 4.329A pdb=" N LEU C 413 " --> pdb=" O ARG C 409 " (cutoff:3.500A) Processing helix chain 'C' and resid 415 through 454 removed outlier: 3.697A pdb=" N ARG C 420 " --> pdb=" O GLU C 416 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N LYS C 431 " --> pdb=" O ASP C 427 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N ARG C 432 " --> pdb=" O ARG C 428 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N TYR C 454 " --> pdb=" O ALA C 450 " (cutoff:3.500A) Processing helix chain 'C' and resid 468 through 500 Processing helix chain 'C' and resid 504 through 509 removed outlier: 4.287A pdb=" N VAL C 508 " --> pdb=" O LYS C 504 " (cutoff:3.500A) Processing helix chain 'C' and resid 512 through 531 Processing helix chain 'C' and resid 536 through 551 Processing helix chain 'C' and resid 552 through 557 removed outlier: 3.926A pdb=" N ARG C 557 " --> pdb=" O TYR C 554 " (cutoff:3.500A) Processing helix chain 'C' and resid 559 through 599 removed outlier: 3.727A pdb=" N LEU C 577 " --> pdb=" O ILE C 573 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N CYS C 578 " --> pdb=" O LEU C 574 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N ARG C 579 " --> pdb=" O ARG C 575 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N PHE C 582 " --> pdb=" O CYS C 578 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N VAL C 583 " --> pdb=" O ARG C 579 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N TYR C 584 " --> pdb=" O PHE C 580 " (cutoff:3.500A) Processing helix chain 'C' and resid 630 through 639 Processing helix chain 'C' and resid 640 through 642 No H-bonds generated for 'chain 'C' and resid 640 through 642' Processing helix chain 'C' and resid 655 through 684 removed outlier: 3.681A pdb=" N GLU C 684 " --> pdb=" O ALA C 680 " (cutoff:3.500A) Processing helix chain 'C' and resid 689 through 711 removed outlier: 3.702A pdb=" N ASN C 695 " --> pdb=" O GLN C 691 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 369 through 374 removed outlier: 5.959A pdb=" N THR A 370 " --> pdb=" O LEU A 381 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N LEU A 381 " --> pdb=" O THR A 370 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N TRP A 372 " --> pdb=" O SER A 379 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 369 through 374 removed outlier: 5.959A pdb=" N THR D 370 " --> pdb=" O LEU D 381 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N LEU D 381 " --> pdb=" O THR D 370 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N TRP D 372 " --> pdb=" O SER D 379 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 369 through 374 removed outlier: 5.959A pdb=" N THR B 370 " --> pdb=" O LEU B 381 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N LEU B 381 " --> pdb=" O THR B 370 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N TRP B 372 " --> pdb=" O SER B 379 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 369 through 374 removed outlier: 5.959A pdb=" N THR C 370 " --> pdb=" O LEU C 381 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N LEU C 381 " --> pdb=" O THR C 370 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N TRP C 372 " --> pdb=" O SER C 379 " (cutoff:3.500A) 984 hydrogen bonds defined for protein. 2856 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: 11.98 Time building geometry restraints manager: 12.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 17248 1.03 - 1.23: 252 1.23 - 1.42: 7632 1.42 - 1.61: 10060 1.61 - 1.81: 172 Bond restraints: 35364 Sorted by residual: bond pdb=" N ARG D 212 " pdb=" H ARG D 212 " ideal model delta sigma weight residual 0.860 1.037 -0.177 2.00e-02 2.50e+03 7.82e+01 bond pdb=" N SER D 278 " pdb=" H SER D 278 " ideal model delta sigma weight residual 0.860 1.037 -0.177 2.00e-02 2.50e+03 7.81e+01 bond pdb=" N SER C 278 " pdb=" H SER C 278 " ideal model delta sigma weight residual 0.860 1.037 -0.177 2.00e-02 2.50e+03 7.81e+01 bond pdb=" N ARG C 212 " pdb=" H ARG C 212 " ideal model delta sigma weight residual 0.860 1.037 -0.177 2.00e-02 2.50e+03 7.81e+01 bond pdb=" N SER C 253 " pdb=" H SER C 253 " ideal model delta sigma weight residual 0.860 1.037 -0.177 2.00e-02 2.50e+03 7.80e+01 ... (remaining 35359 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.81: 63472 2.81 - 5.61: 196 5.61 - 8.42: 12 8.42 - 11.22: 12 11.22 - 14.03: 4 Bond angle restraints: 63696 Sorted by residual: angle pdb=" O13 3PH C 901 " pdb=" P 3PH C 901 " pdb=" O14 3PH C 901 " ideal model delta sigma weight residual 115.01 100.98 14.03 3.00e+00 1.11e-01 2.19e+01 angle pdb=" O13 3PH A 901 " pdb=" P 3PH A 901 " pdb=" O14 3PH A 901 " ideal model delta sigma weight residual 115.01 101.02 13.99 3.00e+00 1.11e-01 2.17e+01 angle pdb=" O13 3PH B 901 " pdb=" P 3PH B 901 " pdb=" O14 3PH B 901 " ideal model delta sigma weight residual 115.01 101.02 13.99 3.00e+00 1.11e-01 2.17e+01 angle pdb=" O13 3PH D 901 " pdb=" P 3PH D 901 " pdb=" O14 3PH D 901 " ideal model delta sigma weight residual 115.01 101.06 13.95 3.00e+00 1.11e-01 2.16e+01 angle pdb=" N GLU A 536 " pdb=" CA GLU A 536 " pdb=" C GLU A 536 " ideal model delta sigma weight residual 113.28 108.63 4.65 1.22e+00 6.72e-01 1.45e+01 ... (remaining 63691 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.90: 15939 29.90 - 59.80: 685 59.80 - 89.70: 48 89.70 - 119.60: 8 119.60 - 149.50: 4 Dihedral angle restraints: 16684 sinusoidal: 8868 harmonic: 7816 Sorted by residual: dihedral pdb=" C21 3PH C 901 " pdb=" C2 3PH C 901 " pdb=" O21 3PH C 901 " pdb=" C3 3PH C 901 " ideal model delta sinusoidal sigma weight residual 147.58 -62.92 -149.50 1 3.00e+01 1.11e-03 1.99e+01 dihedral pdb=" C21 3PH D 901 " pdb=" C2 3PH D 901 " pdb=" O21 3PH D 901 " pdb=" C3 3PH D 901 " ideal model delta sinusoidal sigma weight residual 147.58 -62.98 -149.44 1 3.00e+01 1.11e-03 1.99e+01 dihedral pdb=" C21 3PH B 901 " pdb=" C2 3PH B 901 " pdb=" O21 3PH B 901 " pdb=" C3 3PH B 901 " ideal model delta sinusoidal sigma weight residual 147.58 -62.98 -149.44 1 3.00e+01 1.11e-03 1.99e+01 ... (remaining 16681 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 1603 0.026 - 0.051: 636 0.051 - 0.077: 337 0.077 - 0.103: 94 0.103 - 0.128: 34 Chirality restraints: 2704 Sorted by residual: chirality pdb=" CB THR D 258 " pdb=" CA THR D 258 " pdb=" OG1 THR D 258 " pdb=" CG2 THR D 258 " both_signs ideal model delta sigma weight residual False 2.55 2.42 0.13 2.00e-01 2.50e+01 4.13e-01 chirality pdb=" CB THR A 258 " pdb=" CA THR A 258 " pdb=" OG1 THR A 258 " pdb=" CG2 THR A 258 " both_signs ideal model delta sigma weight residual False 2.55 2.43 0.13 2.00e-01 2.50e+01 4.00e-01 chirality pdb=" CB THR C 258 " pdb=" CA THR C 258 " pdb=" OG1 THR C 258 " pdb=" CG2 THR C 258 " both_signs ideal model delta sigma weight residual False 2.55 2.43 0.13 2.00e-01 2.50e+01 3.94e-01 ... (remaining 2701 not shown) Planarity restraints: 5056 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 652 " -0.018 2.00e-02 2.50e+03 1.76e-02 4.65e+00 pdb=" CG ASN C 652 " 0.001 2.00e-02 2.50e+03 pdb=" OD1 ASN C 652 " 0.018 2.00e-02 2.50e+03 pdb=" ND2 ASN C 652 " -0.002 2.00e-02 2.50e+03 pdb="HD21 ASN C 652 " 0.025 2.00e-02 2.50e+03 pdb="HD22 ASN C 652 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 652 " 0.018 2.00e-02 2.50e+03 1.76e-02 4.63e+00 pdb=" CG ASN A 652 " -0.000 2.00e-02 2.50e+03 pdb=" OD1 ASN A 652 " -0.018 2.00e-02 2.50e+03 pdb=" ND2 ASN A 652 " 0.002 2.00e-02 2.50e+03 pdb="HD21 ASN A 652 " -0.025 2.00e-02 2.50e+03 pdb="HD22 ASN A 652 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN D 652 " 0.018 2.00e-02 2.50e+03 1.74e-02 4.53e+00 pdb=" CG ASN D 652 " -0.000 2.00e-02 2.50e+03 pdb=" OD1 ASN D 652 " -0.018 2.00e-02 2.50e+03 pdb=" ND2 ASN D 652 " 0.001 2.00e-02 2.50e+03 pdb="HD21 ASN D 652 " -0.025 2.00e-02 2.50e+03 pdb="HD22 ASN D 652 " 0.024 2.00e-02 2.50e+03 ... (remaining 5053 not shown) Histogram of nonbonded interaction distances: 1.68 - 2.26: 4696 2.26 - 2.85: 77231 2.85 - 3.43: 84736 3.43 - 4.02: 111651 4.02 - 4.60: 172352 Nonbonded interactions: 450666 Sorted by model distance: nonbonded pdb=" OE1 GLU C 371 " pdb="HH22 ARG C 743 " model vdw 1.677 2.450 nonbonded pdb=" OE1 GLU B 371 " pdb="HH22 ARG B 743 " model vdw 1.677 2.450 nonbonded pdb=" OE1 GLU A 371 " pdb="HH22 ARG A 743 " model vdw 1.677 2.450 nonbonded pdb=" OE1 GLU D 371 " pdb="HH22 ARG D 743 " model vdw 1.677 2.450 nonbonded pdb=" O SER D 366 " pdb="HH22 ARG D 739 " model vdw 1.691 2.450 ... (remaining 450661 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 197 through 752 or resid 901)) selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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 group one per residue 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: 7.160 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: 0.630 Extract box with map and model: 1.440 Check model and map are aligned: 0.250 Set scattering table: 0.310 Process input model: 85.020 Find NCS groups from input model: 1.240 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 99.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 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 : 0.005 0.122 17872 Z= 0.236 Angle : 0.646 14.026 24172 Z= 0.337 Chirality : 0.037 0.128 2704 Planarity : 0.003 0.028 2984 Dihedral : 15.862 149.498 6528 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 1.34 (0.19), residues: 2124 helix: 2.45 (0.15), residues: 1280 sheet: None (None), residues: 0 loop : -1.73 (0.21), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 272 HIS 0.001 0.000 HIS D 364 PHE 0.017 0.001 PHE C 490 TYR 0.013 0.001 TYR D 565 ARG 0.004 0.000 ARG A 331 Details of bonding type rmsd hydrogen bonds : bond 0.14029 ( 984) hydrogen bonds : angle 5.02626 ( 2856) covalent geometry : bond 0.00461 (17872) covalent geometry : angle 0.64590 (24172) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 222 time to evaluate : 2.566 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 222 average time/residue: 0.6326 time to fit residues: 215.3199 Evaluate side-chains 198 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 198 time to evaluate : 2.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 179 optimal weight: 0.5980 chunk 160 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 108 optimal weight: 20.0000 chunk 85 optimal weight: 1.9990 chunk 166 optimal weight: 6.9990 chunk 64 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 123 optimal weight: 7.9990 chunk 192 optimal weight: 0.9980 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 GLN D 202 GLN B 202 GLN C 202 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.153944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.106042 restraints weight = 77003.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.109425 restraints weight = 43601.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.110143 restraints weight = 31864.912| |-----------------------------------------------------------------------------| r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.0864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.021 17872 Z= 0.159 Angle : 0.499 4.535 24172 Z= 0.278 Chirality : 0.036 0.128 2704 Planarity : 0.003 0.028 2984 Dihedral : 8.483 140.047 2472 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 0.42 % Allowed : 5.94 % Favored : 93.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 1.14 (0.19), residues: 2124 helix: 2.26 (0.15), residues: 1296 sheet: -0.59 (0.66), residues: 72 loop : -1.94 (0.22), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 372 HIS 0.003 0.001 HIS A 378 PHE 0.011 0.001 PHE A 649 TYR 0.009 0.001 TYR B 453 ARG 0.002 0.000 ARG B 363 Details of bonding type rmsd hydrogen bonds : bond 0.06199 ( 984) hydrogen bonds : angle 4.25732 ( 2856) covalent geometry : bond 0.00358 (17872) covalent geometry : angle 0.49901 (24172) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 202 time to evaluate : 2.664 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 357 ILE cc_start: 0.7628 (mm) cc_final: 0.7368 (tt) REVERT: D 357 ILE cc_start: 0.7626 (mm) cc_final: 0.7369 (tt) REVERT: B 357 ILE cc_start: 0.7625 (mm) cc_final: 0.7366 (tt) REVERT: C 357 ILE cc_start: 0.7625 (mm) cc_final: 0.7366 (tt) outliers start: 8 outliers final: 8 residues processed: 202 average time/residue: 0.6632 time to fit residues: 202.6825 Evaluate side-chains 204 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 196 time to evaluate : 2.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 552 MET Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 552 MET Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 552 MET Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 552 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 176 optimal weight: 8.9990 chunk 55 optimal weight: 7.9990 chunk 198 optimal weight: 1.9990 chunk 186 optimal weight: 0.8980 chunk 43 optimal weight: 1.9990 chunk 109 optimal weight: 20.0000 chunk 7 optimal weight: 9.9990 chunk 106 optimal weight: 10.0000 chunk 66 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- 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 = 0.3894 r_free = 0.3894 target = 0.152927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.103037 restraints weight = 77473.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.108710 restraints weight = 38884.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.111065 restraints weight = 26034.785| |-----------------------------------------------------------------------------| r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.1103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 17872 Z= 0.170 Angle : 0.497 6.555 24172 Z= 0.277 Chirality : 0.036 0.122 2704 Planarity : 0.003 0.032 2984 Dihedral : 8.508 139.040 2472 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 0.90 % Allowed : 7.80 % Favored : 91.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.98 (0.19), residues: 2124 helix: 2.18 (0.15), residues: 1296 sheet: -1.82 (0.58), residues: 92 loop : -1.96 (0.22), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 372 HIS 0.001 0.000 HIS B 364 PHE 0.012 0.001 PHE B 649 TYR 0.010 0.001 TYR B 453 ARG 0.002 0.000 ARG A 721 Details of bonding type rmsd hydrogen bonds : bond 0.06410 ( 984) hydrogen bonds : angle 4.19473 ( 2856) covalent geometry : bond 0.00388 (17872) covalent geometry : angle 0.49681 (24172) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 200 time to evaluate : 2.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 268 LEU cc_start: 0.8042 (OUTLIER) cc_final: 0.7827 (mp) REVERT: D 268 LEU cc_start: 0.8047 (OUTLIER) cc_final: 0.7831 (mp) REVERT: B 268 LEU cc_start: 0.8049 (OUTLIER) cc_final: 0.7834 (mp) REVERT: C 268 LEU cc_start: 0.8044 (OUTLIER) cc_final: 0.7828 (mp) outliers start: 17 outliers final: 12 residues processed: 201 average time/residue: 0.6763 time to fit residues: 210.3371 Evaluate side-chains 212 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 196 time to evaluate : 2.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 552 MET Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 552 MET Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 552 MET Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 552 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 182 optimal weight: 1.9990 chunk 210 optimal weight: 10.0000 chunk 106 optimal weight: 20.0000 chunk 71 optimal weight: 4.9990 chunk 68 optimal weight: 0.6980 chunk 191 optimal weight: 2.9990 chunk 126 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 209 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 181 optimal weight: 1.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- 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 = 0.3897 r_free = 0.3897 target = 0.153198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.103267 restraints weight = 77475.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.109037 restraints weight = 38824.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.111677 restraints weight = 25960.193| |-----------------------------------------------------------------------------| r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.1260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.020 17872 Z= 0.156 Angle : 0.480 5.782 24172 Z= 0.268 Chirality : 0.035 0.118 2704 Planarity : 0.003 0.031 2984 Dihedral : 8.534 136.133 2472 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 1.49 % Allowed : 9.50 % Favored : 89.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 1.21 (0.19), residues: 2124 helix: 2.51 (0.15), residues: 1244 sheet: -1.75 (0.60), residues: 92 loop : -1.83 (0.21), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 272 HIS 0.001 0.000 HIS B 364 PHE 0.012 0.001 PHE C 649 TYR 0.008 0.001 TYR B 453 ARG 0.002 0.000 ARG A 721 Details of bonding type rmsd hydrogen bonds : bond 0.06137 ( 984) hydrogen bonds : angle 4.07423 ( 2856) covalent geometry : bond 0.00352 (17872) covalent geometry : angle 0.48049 (24172) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 200 time to evaluate : 2.908 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 682 MET cc_start: 0.7903 (tmm) cc_final: 0.7684 (tmm) REVERT: D 682 MET cc_start: 0.7953 (tmm) cc_final: 0.7659 (tmm) REVERT: C 682 MET cc_start: 0.7988 (tmm) cc_final: 0.7743 (tmm) outliers start: 28 outliers final: 21 residues processed: 212 average time/residue: 0.6355 time to fit residues: 207.4984 Evaluate side-chains 221 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 200 time to evaluate : 2.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 388 ASP Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 509 ASP Chi-restraints excluded: chain A residue 552 MET Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 357 ILE Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 509 ASP Chi-restraints excluded: chain D residue 552 MET Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 509 ASP Chi-restraints excluded: chain B residue 552 MET Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 357 ILE Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 509 ASP Chi-restraints excluded: chain C residue 552 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 167 optimal weight: 9.9990 chunk 193 optimal weight: 1.9990 chunk 100 optimal weight: 0.0970 chunk 180 optimal weight: 0.8980 chunk 18 optimal weight: 4.9990 chunk 158 optimal weight: 9.9990 chunk 63 optimal weight: 5.9990 chunk 124 optimal weight: 0.9980 chunk 174 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 overall best weight: 1.3982 ------------------------------------------------------------------------------- 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 = 0.3913 r_free = 0.3913 target = 0.154618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.105686 restraints weight = 77565.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.110444 restraints weight = 41451.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.113619 restraints weight = 28982.950| |-----------------------------------------------------------------------------| r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.1339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 17872 Z= 0.126 Angle : 0.457 5.063 24172 Z= 0.253 Chirality : 0.035 0.119 2704 Planarity : 0.003 0.030 2984 Dihedral : 8.301 133.077 2472 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 1.27 % Allowed : 11.46 % Favored : 87.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 1.35 (0.19), residues: 2124 helix: 2.64 (0.15), residues: 1244 sheet: -1.64 (0.61), residues: 92 loop : -1.82 (0.21), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 272 HIS 0.001 0.000 HIS D 364 PHE 0.011 0.001 PHE C 580 TYR 0.006 0.001 TYR D 653 ARG 0.002 0.000 ARG D 579 Details of bonding type rmsd hydrogen bonds : bond 0.05535 ( 984) hydrogen bonds : angle 3.90723 ( 2856) covalent geometry : bond 0.00276 (17872) covalent geometry : angle 0.45676 (24172) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 200 time to evaluate : 2.874 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 20 residues processed: 212 average time/residue: 0.6355 time to fit residues: 207.2376 Evaluate side-chains 220 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 200 time to evaluate : 2.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 388 ASP Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 357 ILE Chi-restraints excluded: chain D residue 388 ASP Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 593 THR Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 388 ASP Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 593 THR Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 357 ILE Chi-restraints excluded: chain C residue 388 ASP Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 593 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 88 optimal weight: 2.9990 chunk 84 optimal weight: 0.9980 chunk 60 optimal weight: 7.9990 chunk 205 optimal weight: 0.9980 chunk 117 optimal weight: 1.9990 chunk 66 optimal weight: 7.9990 chunk 70 optimal weight: 10.0000 chunk 183 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 126 optimal weight: 3.9990 chunk 152 optimal weight: 3.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- 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 = 0.3904 r_free = 0.3904 target = 0.153795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.114731 restraints weight = 77333.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.119437 restraints weight = 74483.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.120046 restraints weight = 55411.946| |-----------------------------------------------------------------------------| r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.1466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 17872 Z= 0.138 Angle : 0.474 7.411 24172 Z= 0.261 Chirality : 0.035 0.119 2704 Planarity : 0.003 0.030 2984 Dihedral : 8.213 132.019 2472 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 1.59 % Allowed : 11.36 % Favored : 87.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 1.31 (0.19), residues: 2124 helix: 2.61 (0.15), residues: 1244 sheet: -1.67 (0.62), residues: 92 loop : -1.83 (0.21), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 272 HIS 0.002 0.000 HIS B 364 PHE 0.010 0.001 PHE C 649 TYR 0.007 0.001 TYR B 453 ARG 0.002 0.000 ARG A 721 Details of bonding type rmsd hydrogen bonds : bond 0.05709 ( 984) hydrogen bonds : angle 3.91222 ( 2856) covalent geometry : bond 0.00308 (17872) covalent geometry : angle 0.47423 (24172) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 200 time to evaluate : 3.020 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 26 residues processed: 220 average time/residue: 0.6819 time to fit residues: 232.7685 Evaluate side-chains 222 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 196 time to evaluate : 4.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 388 ASP Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 509 ASP Chi-restraints excluded: chain A residue 572 MET Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 357 ILE Chi-restraints excluded: chain D residue 388 ASP Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 509 ASP Chi-restraints excluded: chain D residue 572 MET Chi-restraints excluded: chain D residue 593 THR Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 388 ASP Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 509 ASP Chi-restraints excluded: chain B residue 593 THR Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 357 ILE Chi-restraints excluded: chain C residue 388 ASP Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 509 ASP Chi-restraints excluded: chain C residue 593 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 206 optimal weight: 0.9980 chunk 51 optimal weight: 9.9990 chunk 40 optimal weight: 0.0670 chunk 97 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 152 optimal weight: 5.9990 chunk 143 optimal weight: 3.9990 chunk 105 optimal weight: 7.9990 chunk 47 optimal weight: 3.9990 chunk 108 optimal weight: 4.9990 chunk 162 optimal weight: 20.0000 overall best weight: 1.5722 ------------------------------------------------------------------------------- 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 = 0.3910 r_free = 0.3910 target = 0.154262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.114676 restraints weight = 77491.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.113386 restraints weight = 69617.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.115293 restraints weight = 67326.524| |-----------------------------------------------------------------------------| r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.1522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 17872 Z= 0.136 Angle : 0.473 6.848 24172 Z= 0.260 Chirality : 0.035 0.119 2704 Planarity : 0.003 0.031 2984 Dihedral : 8.110 130.068 2472 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 1.49 % Allowed : 11.73 % Favored : 86.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 1.33 (0.19), residues: 2124 helix: 2.62 (0.15), residues: 1244 sheet: -1.67 (0.62), residues: 92 loop : -1.83 (0.21), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 272 HIS 0.002 0.000 HIS B 364 PHE 0.011 0.001 PHE B 580 TYR 0.007 0.001 TYR B 453 ARG 0.001 0.000 ARG A 363 Details of bonding type rmsd hydrogen bonds : bond 0.05667 ( 984) hydrogen bonds : angle 3.89472 ( 2856) covalent geometry : bond 0.00303 (17872) covalent geometry : angle 0.47318 (24172) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 196 time to evaluate : 2.845 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 28 residues processed: 216 average time/residue: 0.6385 time to fit residues: 213.1750 Evaluate side-chains 224 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 196 time to evaluate : 2.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 388 ASP Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 509 ASP Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain D residue 286 THR Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 357 ILE Chi-restraints excluded: chain D residue 388 ASP Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 509 ASP Chi-restraints excluded: chain D residue 593 THR Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 388 ASP Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 509 ASP Chi-restraints excluded: chain B residue 593 THR Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 357 ILE Chi-restraints excluded: chain C residue 388 ASP Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 509 ASP Chi-restraints excluded: chain C residue 593 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 50 optimal weight: 0.8980 chunk 163 optimal weight: 9.9990 chunk 99 optimal weight: 6.9990 chunk 6 optimal weight: 10.0000 chunk 68 optimal weight: 3.9990 chunk 160 optimal weight: 2.9990 chunk 144 optimal weight: 2.9990 chunk 111 optimal weight: 6.9990 chunk 205 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 40 optimal weight: 0.0970 overall best weight: 1.7984 ------------------------------------------------------------------------------- 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 = 0.3904 r_free = 0.3904 target = 0.153723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.114441 restraints weight = 77249.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.118201 restraints weight = 74117.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.118679 restraints weight = 63362.528| |-----------------------------------------------------------------------------| r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.1600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 17872 Z= 0.148 Angle : 0.477 6.053 24172 Z= 0.264 Chirality : 0.035 0.119 2704 Planarity : 0.003 0.031 2984 Dihedral : 7.970 128.426 2472 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 1.59 % Allowed : 11.62 % Favored : 86.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 1.28 (0.19), residues: 2124 helix: 2.58 (0.15), residues: 1244 sheet: -1.70 (0.62), residues: 92 loop : -1.84 (0.21), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 272 HIS 0.001 0.000 HIS B 364 PHE 0.011 0.001 PHE B 649 TYR 0.008 0.001 TYR D 453 ARG 0.002 0.000 ARG A 721 Details of bonding type rmsd hydrogen bonds : bond 0.05880 ( 984) hydrogen bonds : angle 3.92875 ( 2856) covalent geometry : bond 0.00336 (17872) covalent geometry : angle 0.47681 (24172) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 196 time to evaluate : 4.192 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 682 MET cc_start: 0.7994 (tmm) cc_final: 0.7728 (tmm) REVERT: B 682 MET cc_start: 0.8077 (tmm) cc_final: 0.7820 (tmm) outliers start: 30 outliers final: 28 residues processed: 216 average time/residue: 0.6451 time to fit residues: 216.3089 Evaluate side-chains 224 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 196 time to evaluate : 2.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 388 ASP Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 509 ASP Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain D residue 286 THR Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 357 ILE Chi-restraints excluded: chain D residue 388 ASP Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 509 ASP Chi-restraints excluded: chain D residue 593 THR Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 388 ASP Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 509 ASP Chi-restraints excluded: chain B residue 593 THR Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 357 ILE Chi-restraints excluded: chain C residue 388 ASP Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 509 ASP Chi-restraints excluded: chain C residue 593 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 12 optimal weight: 0.8980 chunk 140 optimal weight: 0.6980 chunk 64 optimal weight: 0.7980 chunk 145 optimal weight: 1.9990 chunk 157 optimal weight: 5.9990 chunk 39 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 158 optimal weight: 6.9990 chunk 90 optimal weight: 3.9990 chunk 177 optimal weight: 3.9990 chunk 169 optimal weight: 0.8980 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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 = 0.3917 r_free = 0.3917 target = 0.154870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.116291 restraints weight = 75913.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.115201 restraints weight = 69053.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.117777 restraints weight = 62395.586| |-----------------------------------------------------------------------------| r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.1617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 17872 Z= 0.113 Angle : 0.460 6.845 24172 Z= 0.251 Chirality : 0.034 0.119 2704 Planarity : 0.003 0.031 2984 Dihedral : 7.613 123.704 2472 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 1.06 % Allowed : 12.37 % Favored : 86.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 1.47 (0.19), residues: 2124 helix: 2.74 (0.15), residues: 1244 sheet: -1.64 (0.62), residues: 92 loop : -1.77 (0.22), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 272 HIS 0.001 0.000 HIS B 364 PHE 0.007 0.001 PHE A 591 TYR 0.006 0.001 TYR A 653 ARG 0.001 0.000 ARG A 721 Details of bonding type rmsd hydrogen bonds : bond 0.05124 ( 984) hydrogen bonds : angle 3.75992 ( 2856) covalent geometry : bond 0.00243 (17872) covalent geometry : angle 0.46039 (24172) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 202 time to evaluate : 2.815 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 682 MET cc_start: 0.8189 (tmm) cc_final: 0.7979 (tmm) REVERT: C 682 MET cc_start: 0.8270 (tmm) cc_final: 0.8048 (tmm) outliers start: 20 outliers final: 19 residues processed: 213 average time/residue: 0.7536 time to fit residues: 244.7489 Evaluate side-chains 214 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 195 time to evaluate : 3.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain D residue 286 THR Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 357 ILE Chi-restraints excluded: chain D residue 388 ASP Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 388 ASP Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 357 ILE Chi-restraints excluded: chain C residue 388 ASP Chi-restraints excluded: chain C residue 503 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 153 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 chunk 131 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 66 optimal weight: 0.9980 chunk 51 optimal weight: 9.9990 chunk 90 optimal weight: 0.9990 chunk 100 optimal weight: 2.9990 chunk 199 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 139 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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 = 0.3901 r_free = 0.3901 target = 0.153770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.113048 restraints weight = 76740.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.111700 restraints weight = 71692.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.114137 restraints weight = 62422.474| |-----------------------------------------------------------------------------| r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.1677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 17872 Z= 0.126 Angle : 0.477 8.863 24172 Z= 0.259 Chirality : 0.035 0.118 2704 Planarity : 0.003 0.032 2984 Dihedral : 7.508 121.925 2472 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 1.11 % Allowed : 12.31 % Favored : 86.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 1.45 (0.19), residues: 2124 helix: 2.70 (0.15), residues: 1248 sheet: -1.62 (0.62), residues: 92 loop : -1.74 (0.22), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 272 HIS 0.002 0.000 HIS B 364 PHE 0.009 0.001 PHE C 649 TYR 0.006 0.001 TYR D 453 ARG 0.004 0.000 ARG D 499 Details of bonding type rmsd hydrogen bonds : bond 0.05329 ( 984) hydrogen bonds : angle 3.77708 ( 2856) covalent geometry : bond 0.00280 (17872) covalent geometry : angle 0.47725 (24172) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 194 time to evaluate : 2.689 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 20 residues processed: 206 average time/residue: 0.6285 time to fit residues: 198.4459 Evaluate side-chains 218 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 198 time to evaluate : 2.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 388 ASP Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain D residue 286 THR Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 357 ILE Chi-restraints excluded: chain D residue 388 ASP Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 388 ASP Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 357 ILE Chi-restraints excluded: chain C residue 388 ASP Chi-restraints excluded: chain C residue 503 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 108 optimal weight: 10.0000 chunk 195 optimal weight: 2.9990 chunk 162 optimal weight: 20.0000 chunk 83 optimal weight: 3.9990 chunk 53 optimal weight: 20.0000 chunk 51 optimal weight: 10.0000 chunk 61 optimal weight: 2.9990 chunk 59 optimal weight: 10.0000 chunk 121 optimal weight: 2.9990 chunk 137 optimal weight: 2.9990 chunk 200 optimal weight: 1.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- 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 = 0.3865 r_free = 0.3865 target = 0.150456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.111012 restraints weight = 76367.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.109287 restraints weight = 70891.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.111473 restraints weight = 62484.158| |-----------------------------------------------------------------------------| r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.1704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.028 17872 Z= 0.208 Angle : 0.533 8.251 24172 Z= 0.296 Chirality : 0.037 0.118 2704 Planarity : 0.004 0.042 2984 Dihedral : 7.741 122.944 2472 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.64 % Favored : 93.36 % Rotamer: Outliers : 1.06 % Allowed : 12.37 % Favored : 86.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 1.09 (0.19), residues: 2124 helix: 2.42 (0.15), residues: 1244 sheet: -1.73 (0.62), residues: 92 loop : -1.91 (0.21), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 272 HIS 0.002 0.001 HIS C 358 PHE 0.015 0.001 PHE C 649 TYR 0.012 0.001 TYR B 453 ARG 0.003 0.000 ARG D 499 Details of bonding type rmsd hydrogen bonds : bond 0.06700 ( 984) hydrogen bonds : angle 4.10747 ( 2856) covalent geometry : bond 0.00485 (17872) covalent geometry : angle 0.53257 (24172) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9003.11 seconds wall clock time: 156 minutes 22.29 seconds (9382.29 seconds total)