Starting phenix.real_space_refine on Sun Oct 25 05:57:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7lpc_23476/10_2026/7lpc_23476_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lpc_23476/10_2026/7lpc_23476.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7lpc_23476/10_2026/7lpc_23476.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lpc_23476/10_2026/7lpc_23476.map" model { file = "/net/cci-nas-00/data/ceres_data/7lpc_23476/10_2026/7lpc_23476_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lpc_23476/10_2026/7lpc_23476_neut.cif" } resolution = 3.06 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 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 28 5.49 5 S 84 5.16 5 C 10144 2.51 5 N 2292 2.21 5 O 2708 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15256 Number of models: 1 Model: "" Number of chains: 2 Chain: "C" Number of atoms: 3526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 454, 3526 Classifications: {'peptide': 454} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 52} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 442} Chain breaks: 1 Unresolved non-hydrogen bonds: 187 Unresolved non-hydrogen angles: 232 Unresolved non-hydrogen dihedrals: 145 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'ARG:plan': 5, 'ASP:plan': 6, 'GLU:plan': 13, 'TYR:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 105 Chain: "C" Number of atoms: 288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 288 Unusual residues: {'6OU': 6, 'LBN': 2, 'T7X': 1, 'YFP': 1} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 222 Unresolved non-hydrogen angles: 240 Unresolved non-hydrogen dihedrals: 230 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'YFP:plan-3': 1, 'T7X:plan-2': 1, 'T7X:plan-4': 1, 'T7X:plan-5': 1, 'T7X:plan-6': 1, 'LBN:plan-3': 1, '6OU:plan-1': 3, '6OU:plan-3': 2, '6OU:plan-2': 1} Unresolved non-hydrogen planarities: 39 Restraints were copied for chains: A, B, D Time building chain proxies: 3.38, per 1000 atoms: 0.22 Number of scatterers: 15256 At special positions: 0 Unit cell: (119.769, 119.769, 101.426, 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 84 16.00 P 28 15.00 O 2708 8.00 N 2292 7.00 C 10144 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS C 386 " - pdb=" SG CYS C 390 " distance=2.05 Simple disulfide: pdb=" SG CYS A 386 " - pdb=" SG CYS A 390 " distance=2.05 Simple disulfide: pdb=" SG CYS B 386 " - pdb=" SG CYS B 390 " distance=2.05 Simple disulfide: pdb=" SG CYS D 386 " - pdb=" SG CYS D 390 " distance=2.05 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.70 Conformation dependent library (CDL) restraints added in 537.6 milliseconds 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3440 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 4 sheets defined 67.6% alpha, 5.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... 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 Processing helix chain 'C' and resid 394 through 401 Processing helix chain 'C' and resid 411 through 414 Processing helix chain 'C' and resid 415 through 429 removed outlier: 3.630A pdb=" N ARG C 420 " --> pdb=" O GLU C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 454 removed outlier: 3.757A pdb=" N ILE C 433 " --> pdb=" O PHE C 429 " (cutoff:3.500A) Processing helix chain 'C' and resid 468 through 500 Processing helix chain 'C' and resid 502 through 509 Processing helix chain 'C' and resid 510 through 532 Processing helix chain 'C' and resid 536 through 552 removed outlier: 3.752A pdb=" N SER C 540 " --> pdb=" O GLU C 536 " (cutoff:3.500A) Processing helix chain 'C' and resid 553 through 558 removed outlier: 3.719A pdb=" N ARG C 557 " --> pdb=" O TYR C 554 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLY C 558 " --> pdb=" O TYR C 555 " (cutoff:3.500A) Processing helix chain 'C' and resid 559 through 599 removed outlier: 3.999A pdb=" N LEU C 577 " --> pdb=" O ILE C 573 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N CYS C 578 " --> pdb=" O LEU C 574 " (cutoff:3.500A) Processing helix chain 'C' and resid 629 through 640 removed outlier: 3.881A pdb=" N PHE C 640 " --> pdb=" O GLU C 636 " (cutoff:3.500A) Processing helix chain 'C' and resid 641 through 643 No H-bonds generated for 'chain 'C' and resid 641 through 643' Processing helix chain 'C' and resid 655 through 671 removed outlier: 3.621A pdb=" N PHE C 659 " --> pdb=" O PHE C 655 " (cutoff:3.500A) Processing helix chain 'C' and resid 673 through 689 Processing helix chain 'C' and resid 689 through 712 removed outlier: 3.906A pdb=" N LYS C 694 " --> pdb=" O ALA C 690 " (cutoff:3.500A) 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 Processing helix chain 'A' and resid 394 through 401 Processing helix chain 'A' and resid 411 through 414 Processing helix chain 'A' and resid 415 through 429 removed outlier: 3.631A pdb=" N ARG A 420 " --> pdb=" O GLU A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 454 removed outlier: 3.757A pdb=" N ILE A 433 " --> pdb=" O PHE A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 500 Processing helix chain 'A' and resid 502 through 509 Processing helix chain 'A' and resid 510 through 532 Processing helix chain 'A' and resid 536 through 552 removed outlier: 3.752A pdb=" N SER A 540 " --> pdb=" O GLU A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 553 through 558 removed outlier: 3.719A pdb=" N ARG A 557 " --> pdb=" O TYR A 554 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLY A 558 " --> pdb=" O TYR A 555 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 599 removed outlier: 3.998A pdb=" N LEU A 577 " --> pdb=" O ILE A 573 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N CYS A 578 " --> pdb=" O LEU A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 629 through 640 removed outlier: 3.880A pdb=" N PHE A 640 " --> pdb=" O GLU A 636 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 643 No H-bonds generated for 'chain 'A' and resid 641 through 643' Processing helix chain 'A' and resid 655 through 671 removed outlier: 3.621A pdb=" N PHE A 659 " --> pdb=" O PHE A 655 " (cutoff:3.500A) Processing helix chain 'A' and resid 673 through 689 Processing helix chain 'A' and resid 689 through 712 removed outlier: 3.906A pdb=" N LYS A 694 " --> pdb=" O ALA A 690 " (cutoff:3.500A) 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 Processing helix chain 'B' and resid 394 through 401 Processing helix chain 'B' and resid 411 through 414 Processing helix chain 'B' and resid 415 through 429 removed outlier: 3.630A pdb=" N ARG B 420 " --> pdb=" O GLU B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 454 removed outlier: 3.757A pdb=" N ILE B 433 " --> pdb=" O PHE B 429 " (cutoff:3.500A) Processing helix chain 'B' and resid 468 through 500 Processing helix chain 'B' and resid 502 through 509 Processing helix chain 'B' and resid 510 through 532 Processing helix chain 'B' and resid 536 through 552 removed outlier: 3.753A pdb=" N SER B 540 " --> pdb=" O GLU B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 553 through 558 removed outlier: 3.718A pdb=" N ARG B 557 " --> pdb=" O TYR B 554 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLY B 558 " --> pdb=" O TYR B 555 " (cutoff:3.500A) Processing helix chain 'B' and resid 559 through 599 removed outlier: 3.998A pdb=" N LEU B 577 " --> pdb=" O ILE B 573 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N CYS B 578 " --> pdb=" O LEU B 574 " (cutoff:3.500A) Processing helix chain 'B' and resid 629 through 640 removed outlier: 3.882A pdb=" N PHE B 640 " --> pdb=" O GLU B 636 " (cutoff:3.500A) Processing helix chain 'B' and resid 641 through 643 No H-bonds generated for 'chain 'B' and resid 641 through 643' Processing helix chain 'B' and resid 655 through 671 removed outlier: 3.621A pdb=" N PHE B 659 " --> pdb=" O PHE B 655 " (cutoff:3.500A) Processing helix chain 'B' and resid 673 through 689 Processing helix chain 'B' and resid 689 through 712 removed outlier: 3.906A pdb=" N LYS B 694 " --> pdb=" O ALA B 690 " (cutoff:3.500A) 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 Processing helix chain 'D' and resid 394 through 401 Processing helix chain 'D' and resid 411 through 414 Processing helix chain 'D' and resid 415 through 429 removed outlier: 3.630A pdb=" N ARG D 420 " --> pdb=" O GLU D 416 " (cutoff:3.500A) Processing helix chain 'D' and resid 429 through 454 removed outlier: 3.757A pdb=" N ILE D 433 " --> pdb=" O PHE D 429 " (cutoff:3.500A) Processing helix chain 'D' and resid 468 through 500 Processing helix chain 'D' and resid 502 through 509 Processing helix chain 'D' and resid 510 through 532 Processing helix chain 'D' and resid 536 through 552 removed outlier: 3.752A pdb=" N SER D 540 " --> pdb=" O GLU D 536 " (cutoff:3.500A) Processing helix chain 'D' and resid 553 through 558 removed outlier: 3.718A pdb=" N ARG D 557 " --> pdb=" O TYR D 554 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLY D 558 " --> pdb=" O TYR D 555 " (cutoff:3.500A) Processing helix chain 'D' and resid 559 through 599 removed outlier: 3.998A pdb=" N LEU D 577 " --> pdb=" O ILE D 573 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N CYS D 578 " --> pdb=" O LEU D 574 " (cutoff:3.500A) Processing helix chain 'D' and resid 629 through 640 removed outlier: 3.881A pdb=" N PHE D 640 " --> pdb=" O GLU D 636 " (cutoff:3.500A) Processing helix chain 'D' and resid 641 through 643 No H-bonds generated for 'chain 'D' and resid 641 through 643' Processing helix chain 'D' and resid 655 through 671 removed outlier: 3.621A pdb=" N PHE D 659 " --> pdb=" O PHE D 655 " (cutoff:3.500A) Processing helix chain 'D' and resid 673 through 689 Processing helix chain 'D' and resid 689 through 712 removed outlier: 3.905A pdb=" N LYS D 694 " --> pdb=" O ALA D 690 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 368 through 373 removed outlier: 5.681A pdb=" N THR C 370 " --> pdb=" O LEU C 381 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N LEU C 381 " --> pdb=" O THR C 370 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TRP C 372 " --> pdb=" O SER C 379 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N ASP C 737 " --> pdb=" O VAL C 728 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 368 through 373 removed outlier: 5.680A pdb=" N THR A 370 " --> pdb=" O LEU A 381 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N LEU A 381 " --> pdb=" O THR A 370 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TRP A 372 " --> pdb=" O SER A 379 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N ASP A 737 " --> pdb=" O VAL A 728 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 368 through 373 removed outlier: 5.680A pdb=" N THR B 370 " --> pdb=" O LEU B 381 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N LEU B 381 " --> pdb=" O THR B 370 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TRP B 372 " --> pdb=" O SER B 379 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N ASP B 737 " --> pdb=" O VAL B 728 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 368 through 373 removed outlier: 5.681A pdb=" N THR D 370 " --> pdb=" O LEU D 381 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N LEU D 381 " --> pdb=" O THR D 370 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TRP D 372 " --> pdb=" O SER D 379 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N ASP D 737 " --> pdb=" O VAL D 728 " (cutoff:3.500A) 944 hydrogen bonds defined for protein. 2796 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.61 Time building geometry restraints manager: 2.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2196 1.31 - 1.44: 4487 1.44 - 1.57: 8643 1.57 - 1.70: 70 1.70 - 1.83: 180 Bond restraints: 15576 Sorted by residual: bond pdb=" O22 6OU D 910 " pdb=" P23 6OU D 910 " ideal model delta sigma weight residual 1.643 1.779 -0.136 2.00e-02 2.50e+03 4.64e+01 bond pdb=" O22 6OU A 910 " pdb=" P23 6OU A 910 " ideal model delta sigma weight residual 1.643 1.779 -0.136 2.00e-02 2.50e+03 4.61e+01 bond pdb=" O22 6OU C 910 " pdb=" P23 6OU C 910 " ideal model delta sigma weight residual 1.643 1.779 -0.136 2.00e-02 2.50e+03 4.61e+01 bond pdb=" O22 6OU B 910 " pdb=" P23 6OU B 910 " ideal model delta sigma weight residual 1.643 1.779 -0.136 2.00e-02 2.50e+03 4.60e+01 bond pdb=" O2 LBN B 905 " pdb=" P1 LBN B 905 " ideal model delta sigma weight residual 1.650 1.784 -0.134 2.00e-02 2.50e+03 4.46e+01 ... (remaining 15571 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.98: 20159 2.98 - 5.97: 701 5.97 - 8.95: 44 8.95 - 11.93: 29 11.93 - 14.91: 23 Bond angle restraints: 20956 Sorted by residual: angle pdb=" O1 T7X D 904 " pdb=" P1 T7X D 904 " pdb=" O13 T7X D 904 " ideal model delta sigma weight residual 94.60 109.51 -14.91 3.00e+00 1.11e-01 2.47e+01 angle pdb=" O1 T7X A 904 " pdb=" P1 T7X A 904 " pdb=" O13 T7X A 904 " ideal model delta sigma weight residual 94.60 109.51 -14.91 3.00e+00 1.11e-01 2.47e+01 angle pdb=" O1 T7X B 904 " pdb=" P1 T7X B 904 " pdb=" O13 T7X B 904 " ideal model delta sigma weight residual 94.60 109.51 -14.91 3.00e+00 1.11e-01 2.47e+01 angle pdb=" O1 T7X C 904 " pdb=" P1 T7X C 904 " pdb=" O13 T7X C 904 " ideal model delta sigma weight residual 94.60 109.50 -14.90 3.00e+00 1.11e-01 2.47e+01 angle pdb=" O1 LBN C 905 " pdb=" P1 LBN C 905 " pdb=" O2 LBN C 905 " ideal model delta sigma weight residual 93.45 107.71 -14.26 3.00e+00 1.11e-01 2.26e+01 ... (remaining 20951 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.08: 8683 34.08 - 68.16: 469 68.16 - 102.24: 64 102.24 - 136.31: 32 136.31 - 170.39: 36 Dihedral angle restraints: 9284 sinusoidal: 3932 harmonic: 5352 Sorted by residual: dihedral pdb=" CB CYS D 386 " pdb=" SG CYS D 386 " pdb=" SG CYS D 390 " pdb=" CB CYS D 390 " ideal model delta sinusoidal sigma weight residual 93.00 40.92 52.08 1 1.00e+01 1.00e-02 3.70e+01 dihedral pdb=" CB CYS C 386 " pdb=" SG CYS C 386 " pdb=" SG CYS C 390 " pdb=" CB CYS C 390 " ideal model delta sinusoidal sigma weight residual 93.00 40.94 52.06 1 1.00e+01 1.00e-02 3.70e+01 dihedral pdb=" CB CYS A 386 " pdb=" SG CYS A 386 " pdb=" SG CYS A 390 " pdb=" CB CYS A 390 " ideal model delta sinusoidal sigma weight residual 93.00 40.95 52.05 1 1.00e+01 1.00e-02 3.70e+01 ... (remaining 9281 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.965: 2304 0.965 - 1.930: 0 1.930 - 2.895: 0 2.895 - 3.860: 0 3.860 - 4.825: 4 Chirality restraints: 2308 Sorted by residual: chirality pdb=" C1 T7X A 904 " pdb=" C2 T7X A 904 " pdb=" C6 T7X A 904 " pdb=" O1 T7X A 904 " both_signs ideal model delta sigma weight residual False -2.42 2.41 -4.83 2.00e-01 2.50e+01 5.82e+02 chirality pdb=" C1 T7X C 904 " pdb=" C2 T7X C 904 " pdb=" C6 T7X C 904 " pdb=" O1 T7X C 904 " both_signs ideal model delta sigma weight residual False -2.42 2.40 -4.82 2.00e-01 2.50e+01 5.82e+02 chirality pdb=" C1 T7X B 904 " pdb=" C2 T7X B 904 " pdb=" C6 T7X B 904 " pdb=" O1 T7X B 904 " both_signs ideal model delta sigma weight residual False -2.42 2.40 -4.82 2.00e-01 2.50e+01 5.81e+02 ... (remaining 2305 not shown) Planarity restraints: 2512 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 369 " -0.026 2.00e-02 2.50e+03 3.52e-02 2.17e+01 pdb=" CG PHE B 369 " 0.078 2.00e-02 2.50e+03 pdb=" CD1 PHE B 369 " -0.036 2.00e-02 2.50e+03 pdb=" CD2 PHE B 369 " -0.018 2.00e-02 2.50e+03 pdb=" CE1 PHE B 369 " 0.012 2.00e-02 2.50e+03 pdb=" CE2 PHE B 369 " -0.005 2.00e-02 2.50e+03 pdb=" CZ PHE B 369 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 369 " -0.025 2.00e-02 2.50e+03 3.52e-02 2.17e+01 pdb=" CG PHE D 369 " 0.078 2.00e-02 2.50e+03 pdb=" CD1 PHE D 369 " -0.037 2.00e-02 2.50e+03 pdb=" CD2 PHE D 369 " -0.018 2.00e-02 2.50e+03 pdb=" CE1 PHE D 369 " 0.012 2.00e-02 2.50e+03 pdb=" CE2 PHE D 369 " -0.005 2.00e-02 2.50e+03 pdb=" CZ PHE D 369 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 369 " -0.026 2.00e-02 2.50e+03 3.52e-02 2.16e+01 pdb=" CG PHE C 369 " 0.078 2.00e-02 2.50e+03 pdb=" CD1 PHE C 369 " -0.036 2.00e-02 2.50e+03 pdb=" CD2 PHE C 369 " -0.018 2.00e-02 2.50e+03 pdb=" CE1 PHE C 369 " 0.012 2.00e-02 2.50e+03 pdb=" CE2 PHE C 369 " -0.006 2.00e-02 2.50e+03 pdb=" CZ PHE C 369 " -0.005 2.00e-02 2.50e+03 ... (remaining 2509 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 1064 2.73 - 3.27: 14988 3.27 - 3.82: 23844 3.82 - 4.36: 29039 4.36 - 4.90: 51897 Nonbonded interactions: 120832 Sorted by model distance: nonbonded pdb=" N GLU D 536 " pdb=" OE1 GLU D 536 " model vdw 2.188 3.120 nonbonded pdb=" N GLU A 536 " pdb=" OE1 GLU A 536 " model vdw 2.189 3.120 nonbonded pdb=" N GLU C 536 " pdb=" OE1 GLU C 536 " model vdw 2.189 3.120 nonbonded pdb=" N GLU B 536 " pdb=" OE1 GLU B 536 " model vdw 2.189 3.120 nonbonded pdb=" O PHE B 517 " pdb=" OG SER B 520 " model vdw 2.364 3.040 ... (remaining 120827 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: 0.05 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'A' selection = chain 'B' 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 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: 1.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.080 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 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 : 0.014 0.136 15580 Z= 0.624 Angle : 1.226 14.915 20964 Z= 0.515 Chirality : 0.214 4.825 2308 Planarity : 0.004 0.036 2512 Dihedral : 24.464 170.393 5832 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.19), residues: 1800 helix: 1.60 (0.15), residues: 1140 sheet: -1.57 (0.50), residues: 84 loop : -1.26 (0.24), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 420 TYR 0.043 0.002 TYR B 401 PHE 0.078 0.003 PHE B 369 TRP 0.011 0.002 TRP B 697 HIS 0.006 0.002 HIS C 410 Details of bonding type rmsd/Z covalent geometry : bond 0.01359 / 0.62 (15576) covalent geometry : angle 1.22526 / 0.52 (20956) SS BOND : bond 0.01628 / 0.77 ( 4) SS BOND : angle 1.96963 / 1.04 ( 8) hydrogen bonds : bond 0.12679 / 8.82 ( 944) hydrogen bonds : angle 5.48281 / 4.00 ( 2796) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 181 time to evaluate : 0.524 Fit side-chains REVERT: C 677 MET cc_start: 0.8268 (ttt) cc_final: 0.8029 (ttp) REVERT: C 743 ARG cc_start: 0.7621 (ttm-80) cc_final: 0.7335 (ttm110) REVERT: A 478 GLU cc_start: 0.6902 (mt-10) cc_final: 0.6624 (mt-10) REVERT: A 504 LYS cc_start: 0.7028 (mmtt) cc_final: 0.6309 (mmtt) REVERT: D 536 GLU cc_start: 0.8217 (mp0) cc_final: 0.7942 (mp0) REVERT: D 677 MET cc_start: 0.8354 (ttt) cc_final: 0.8035 (ttp) outliers start: 0 outliers final: 0 residues processed: 181 average time/residue: 0.1258 time to fit residues: 33.9275 Evaluate side-chains 158 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 158 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: [98, 107, 10, 66, 130, 124, 103, 77, 122, 91, 149] chunk 98 optimal weight: 20.0000 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 10.0000 chunk 149 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 700 GLN A 354 GLN A 700 GLN B 354 GLN B 498 GLN B 700 GLN D 354 GLN D 700 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.189883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.138592 restraints weight = 14791.570| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 2.60 r_work: 0.3039 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2887 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.1975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15580 Z= 0.120 Angle : 0.490 6.238 20964 Z= 0.253 Chirality : 0.038 0.193 2308 Planarity : 0.003 0.030 2512 Dihedral : 24.186 176.879 2888 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 0.85 % Allowed : 3.59 % Favored : 95.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.31 (0.20), residues: 1800 helix: 2.81 (0.15), residues: 1144 sheet: -1.38 (0.46), residues: 84 loop : -0.74 (0.25), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 721 TYR 0.009 0.001 TYR B 511 PHE 0.019 0.001 PHE B 369 TRP 0.018 0.002 TRP B 740 HIS 0.002 0.000 HIS C 410 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.12 (15576) covalent geometry : angle 0.48969 / 0.25 (20956) SS BOND : bond 0.00727 / 0.34 ( 4) SS BOND : angle 0.55814 / 0.30 ( 8) hydrogen bonds : bond 0.04754 / 3.30 ( 944) hydrogen bonds : angle 3.89666 / 2.85 ( 2796) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 195 time to evaluate : 0.575 Fit side-chains REVERT: C 504 LYS cc_start: 0.6531 (mmtt) cc_final: 0.5658 (mmtt) REVERT: C 568 MET cc_start: 0.8665 (mtt) cc_final: 0.8263 (mtp) REVERT: C 743 ARG cc_start: 0.7985 (ttm-80) cc_final: 0.7686 (tpp-160) REVERT: B 504 LYS cc_start: 0.7241 (mmtt) cc_final: 0.5851 (mmtt) REVERT: B 568 MET cc_start: 0.8677 (mtt) cc_final: 0.8475 (mtt) REVERT: B 654 ASP cc_start: 0.8567 (m-30) cc_final: 0.8191 (m-30) REVERT: B 677 MET cc_start: 0.8890 (ttt) cc_final: 0.8679 (ttp) REVERT: D 504 LYS cc_start: 0.7243 (mmtt) cc_final: 0.5728 (mmtt) REVERT: D 568 MET cc_start: 0.8638 (mtt) cc_final: 0.8408 (mtp) REVERT: D 677 MET cc_start: 0.8794 (ttt) cc_final: 0.8465 (ttm) REVERT: D 688 LYS cc_start: 0.8202 (mttt) cc_final: 0.7781 (mptt) outliers start: 12 outliers final: 7 residues processed: 204 average time/residue: 0.1242 time to fit residues: 37.5595 Evaluate side-chains 184 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 177 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 660 ILE Chi-restraints excluded: chain D residue 286 THR Chi-restraints excluded: chain D residue 406 THR Chi-restraints excluded: chain D residue 660 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: [150, 65, 63, 93, 148, 130, 131, 142, 174, 45, 133] chunk 150 optimal weight: 5.9990 chunk 65 optimal weight: 1.9990 chunk 63 optimal weight: 0.7980 chunk 93 optimal weight: 0.9990 chunk 148 optimal weight: 4.9990 chunk 130 optimal weight: 0.7980 chunk 131 optimal weight: 0.9990 chunk 142 optimal weight: 0.9990 chunk 174 optimal weight: 0.3980 chunk 45 optimal weight: 30.0000 chunk 133 optimal weight: 30.0000 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 498 GLN A 354 GLN A 498 GLN B 354 GLN B 498 GLN D 423 GLN D 498 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.188422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.135828 restraints weight = 14989.300| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 3.02 r_work: 0.2993 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2838 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.2545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 15580 Z= 0.109 Angle : 0.447 6.418 20964 Z= 0.232 Chirality : 0.037 0.263 2308 Planarity : 0.003 0.035 2512 Dihedral : 21.458 163.889 2888 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.06 % Allowed : 4.93 % Favored : 94.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.75 (0.20), residues: 1800 helix: 3.16 (0.15), residues: 1140 sheet: -1.01 (0.47), residues: 84 loop : -0.60 (0.25), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 743 TYR 0.007 0.001 TYR A 530 PHE 0.013 0.001 PHE A 369 TRP 0.009 0.001 TRP A 740 HIS 0.001 0.000 HIS C 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.11 (15576) covalent geometry : angle 0.44700 / 0.23 (20956) SS BOND : bond 0.00344 / 0.16 ( 4) SS BOND : angle 0.60477 / 0.35 ( 8) hydrogen bonds : bond 0.04566 / 3.17 ( 944) hydrogen bonds : angle 3.75521 / 2.74 ( 2796) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 193 time to evaluate : 0.526 Fit side-chains REVERT: C 401 TYR cc_start: 0.8543 (m-10) cc_final: 0.8183 (m-10) REVERT: C 504 LYS cc_start: 0.6725 (mmtt) cc_final: 0.5757 (mmtt) REVERT: C 509 ASP cc_start: 0.7684 (m-30) cc_final: 0.7472 (m-30) REVERT: A 397 GLU cc_start: 0.7495 (mt-10) cc_final: 0.7180 (mt-10) REVERT: A 504 LYS cc_start: 0.6966 (mmtt) cc_final: 0.5884 (mmtt) REVERT: A 677 MET cc_start: 0.8806 (ttt) cc_final: 0.8559 (ttm) REVERT: B 387 ILE cc_start: 0.8788 (OUTLIER) cc_final: 0.8475 (mm) REVERT: B 445 MET cc_start: 0.9171 (mmm) cc_final: 0.8519 (mmm) REVERT: B 504 LYS cc_start: 0.7371 (mmtt) cc_final: 0.5964 (mmtt) REVERT: B 568 MET cc_start: 0.8704 (mtt) cc_final: 0.8503 (mtt) REVERT: B 677 MET cc_start: 0.8798 (ttt) cc_final: 0.8553 (ttm) REVERT: B 743 ARG cc_start: 0.8000 (ttm-80) cc_final: 0.7747 (tpp-160) REVERT: D 504 LYS cc_start: 0.7335 (mmtt) cc_final: 0.5862 (mmtt) REVERT: D 509 ASP cc_start: 0.7850 (m-30) cc_final: 0.7615 (m-30) REVERT: D 654 ASP cc_start: 0.8609 (m-30) cc_final: 0.8357 (m-30) REVERT: D 688 LYS cc_start: 0.7992 (mttt) cc_final: 0.7570 (mptt) outliers start: 15 outliers final: 4 residues processed: 200 average time/residue: 0.1208 time to fit residues: 36.0735 Evaluate side-chains 183 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 178 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 708 THR Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain B residue 387 ILE Chi-restraints excluded: chain B residue 660 ILE Chi-restraints excluded: chain D residue 601 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: [56, 59, 150, 30, 118, 155, 1, 62, 125, 176, 124] chunk 56 optimal weight: 9.9990 chunk 59 optimal weight: 2.9990 chunk 150 optimal weight: 5.9990 chunk 30 optimal weight: 0.6980 chunk 118 optimal weight: 4.9990 chunk 155 optimal weight: 0.7980 chunk 1 optimal weight: 5.9990 chunk 62 optimal weight: 2.9990 chunk 125 optimal weight: 0.9980 chunk 176 optimal weight: 7.9990 chunk 124 optimal weight: 0.6980 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 498 GLN A 354 GLN B 354 GLN D 354 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.185000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.132145 restraints weight = 14890.639| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 2.52 r_work: 0.2971 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2818 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.2960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15580 Z= 0.128 Angle : 0.478 6.782 20964 Z= 0.246 Chirality : 0.038 0.262 2308 Planarity : 0.003 0.037 2512 Dihedral : 21.017 164.652 2888 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 0.77 % Allowed : 6.13 % Favored : 93.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.59 (0.20), residues: 1800 helix: 3.02 (0.15), residues: 1140 sheet: -0.96 (0.50), residues: 84 loop : -0.64 (0.25), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 721 TYR 0.008 0.001 TYR B 530 PHE 0.013 0.001 PHE B 649 TRP 0.013 0.002 TRP A 740 HIS 0.001 0.000 HIS C 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 (15576) covalent geometry : angle 0.47810 / 0.25 (20956) SS BOND : bond 0.00760 / 0.39 ( 4) SS BOND : angle 0.98081 / 0.55 ( 8) hydrogen bonds : bond 0.05146 / 3.57 ( 944) hydrogen bonds : angle 3.79134 / 2.77 ( 2796) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 203 time to evaluate : 0.531 Fit side-chains REVERT: C 445 MET cc_start: 0.9192 (mmm) cc_final: 0.8984 (mmp) REVERT: C 491 ARG cc_start: 0.8129 (mtp180) cc_final: 0.7902 (mmm-85) REVERT: C 504 LYS cc_start: 0.6927 (mmtt) cc_final: 0.5914 (mmtt) REVERT: C 601 ASP cc_start: 0.7557 (t0) cc_final: 0.7299 (m-30) REVERT: A 491 ARG cc_start: 0.8215 (mtp180) cc_final: 0.7980 (mmm-85) REVERT: A 688 LYS cc_start: 0.7999 (mttt) cc_final: 0.7581 (mptt) REVERT: A 692 GLU cc_start: 0.7752 (tt0) cc_final: 0.7529 (tt0) REVERT: A 743 ARG cc_start: 0.8035 (tpp-160) cc_final: 0.7814 (tpp80) REVERT: B 445 MET cc_start: 0.9193 (mmm) cc_final: 0.8984 (mmp) REVERT: B 491 ARG cc_start: 0.8185 (mtp180) cc_final: 0.7963 (mmm-85) REVERT: B 504 LYS cc_start: 0.7502 (mmtt) cc_final: 0.6142 (mmtt) REVERT: B 568 MET cc_start: 0.8718 (mtt) cc_final: 0.8442 (mtt) REVERT: B 654 ASP cc_start: 0.8788 (m-30) cc_final: 0.8477 (m-30) REVERT: B 688 LYS cc_start: 0.8020 (mttt) cc_final: 0.7602 (mptt) REVERT: B 692 GLU cc_start: 0.7748 (tt0) cc_final: 0.7532 (tt0) REVERT: B 710 LYS cc_start: 0.7632 (mttm) cc_final: 0.7252 (mtpt) REVERT: D 445 MET cc_start: 0.9215 (mmm) cc_final: 0.8919 (mmp) REVERT: D 491 ARG cc_start: 0.8164 (mtp180) cc_final: 0.7946 (mmm-85) REVERT: D 504 LYS cc_start: 0.7499 (mmtt) cc_final: 0.6078 (mmtt) REVERT: D 509 ASP cc_start: 0.7967 (m-30) cc_final: 0.7754 (m-30) REVERT: D 654 ASP cc_start: 0.8807 (m-30) cc_final: 0.8533 (m-30) REVERT: D 688 LYS cc_start: 0.8010 (mttt) cc_final: 0.7592 (mptt) REVERT: D 692 GLU cc_start: 0.7738 (tt0) cc_final: 0.7498 (tt0) outliers start: 11 outliers final: 5 residues processed: 210 average time/residue: 0.1250 time to fit residues: 38.5685 Evaluate side-chains 206 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 201 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 708 THR Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain B residue 601 ASP Chi-restraints excluded: chain D residue 601 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: [107, 17, 102, 84, 5, 18, 21, 76, 132, 0, 106] chunk 107 optimal weight: 4.9990 chunk 17 optimal weight: 2.9990 chunk 102 optimal weight: 9.9990 chunk 84 optimal weight: 1.9990 chunk 5 optimal weight: 10.0000 chunk 18 optimal weight: 3.9990 chunk 21 optimal weight: 6.9990 chunk 76 optimal weight: 0.6980 chunk 132 optimal weight: 5.9990 chunk 0 optimal weight: 30.0000 chunk 106 optimal weight: 0.7980 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 354 GLN A 354 GLN B 354 GLN D 354 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.183723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.134190 restraints weight = 14910.138| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 2.32 r_work: 0.2857 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.3311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 15580 Z= 0.176 Angle : 0.547 8.266 20964 Z= 0.276 Chirality : 0.041 0.322 2308 Planarity : 0.003 0.040 2512 Dihedral : 21.638 172.212 2888 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 0.77 % Allowed : 7.04 % Favored : 92.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.16 (0.19), residues: 1800 helix: 2.68 (0.15), residues: 1144 sheet: -0.97 (0.51), residues: 84 loop : -0.87 (0.24), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 739 TYR 0.010 0.002 TYR B 530 PHE 0.018 0.002 PHE C 649 TRP 0.015 0.002 TRP B 740 HIS 0.002 0.001 HIS D 358 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.18 (15576) covalent geometry : angle 0.54674 / 0.28 (20956) SS BOND : bond 0.00435 / 0.21 ( 4) SS BOND : angle 1.20214 / 0.66 ( 8) hydrogen bonds : bond 0.05968 / 4.14 ( 944) hydrogen bonds : angle 3.90729 / 2.85 ( 2796) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 203 time to evaluate : 0.452 Fit side-chains REVERT: C 445 MET cc_start: 0.9176 (mmm) cc_final: 0.8789 (mmp) REVERT: C 504 LYS cc_start: 0.7328 (mmtt) cc_final: 0.6130 (mptt) REVERT: C 509 ASP cc_start: 0.8057 (m-30) cc_final: 0.7754 (m-30) REVERT: C 601 ASP cc_start: 0.7515 (t0) cc_final: 0.7252 (m-30) REVERT: C 688 LYS cc_start: 0.7891 (mttt) cc_final: 0.7565 (mptt) REVERT: C 692 GLU cc_start: 0.7705 (tt0) cc_final: 0.7488 (tt0) REVERT: C 740 TRP cc_start: 0.6720 (m100) cc_final: 0.6498 (m100) REVERT: A 536 GLU cc_start: 0.9010 (mp0) cc_final: 0.8738 (mp0) REVERT: A 688 LYS cc_start: 0.7975 (mttt) cc_final: 0.7598 (mptt) REVERT: A 692 GLU cc_start: 0.7691 (tt0) cc_final: 0.7468 (tt0) REVERT: B 504 LYS cc_start: 0.7472 (mmtt) cc_final: 0.6014 (mmtt) REVERT: B 568 MET cc_start: 0.8545 (mtt) cc_final: 0.8251 (mtt) REVERT: B 654 ASP cc_start: 0.8763 (m-30) cc_final: 0.8446 (m-30) REVERT: B 688 LYS cc_start: 0.7951 (mttt) cc_final: 0.7584 (mptt) REVERT: B 692 GLU cc_start: 0.7717 (tt0) cc_final: 0.7490 (tt0) REVERT: D 445 MET cc_start: 0.9200 (mmm) cc_final: 0.8821 (mmp) REVERT: D 504 LYS cc_start: 0.7325 (mmtt) cc_final: 0.5831 (mmtt) REVERT: D 509 ASP cc_start: 0.7918 (m-30) cc_final: 0.7641 (m-30) REVERT: D 536 GLU cc_start: 0.9021 (mp0) cc_final: 0.8763 (mp0) REVERT: D 654 ASP cc_start: 0.8786 (m-30) cc_final: 0.8505 (m-30) REVERT: D 688 LYS cc_start: 0.7848 (mttt) cc_final: 0.7542 (mptt) REVERT: D 692 GLU cc_start: 0.7686 (tt0) cc_final: 0.7450 (tt0) outliers start: 11 outliers final: 8 residues processed: 210 average time/residue: 0.1147 time to fit residues: 36.2233 Evaluate side-chains 206 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 198 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 708 THR Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 601 ASP Chi-restraints excluded: chain B residue 601 ASP Chi-restraints excluded: chain B residue 660 ILE Chi-restraints excluded: chain D residue 601 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: [46, 119, 122, 159, 8, 94, 55, 112, 127, 179, 130] chunk 46 optimal weight: 9.9990 chunk 119 optimal weight: 0.8980 chunk 122 optimal weight: 0.4980 chunk 159 optimal weight: 0.5980 chunk 8 optimal weight: 7.9990 chunk 94 optimal weight: 0.8980 chunk 55 optimal weight: 8.9990 chunk 112 optimal weight: 4.9990 chunk 127 optimal weight: 0.9990 chunk 179 optimal weight: 9.9990 chunk 130 optimal weight: 2.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 354 GLN A 354 GLN B 354 GLN D 354 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.187489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.135903 restraints weight = 14913.501| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 2.31 r_work: 0.3010 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.3475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 15580 Z= 0.104 Angle : 0.434 6.397 20964 Z= 0.227 Chirality : 0.036 0.222 2308 Planarity : 0.003 0.040 2512 Dihedral : 20.067 179.019 2888 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 0.70 % Allowed : 7.68 % Favored : 91.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.64 (0.20), residues: 1800 helix: 3.11 (0.15), residues: 1140 sheet: -0.68 (0.52), residues: 84 loop : -0.79 (0.24), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 721 TYR 0.007 0.001 TYR C 530 PHE 0.012 0.001 PHE A 659 TRP 0.015 0.001 TRP B 740 HIS 0.002 0.000 HIS C 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00218 / 0.10 (15576) covalent geometry : angle 0.43317 / 0.23 (20956) SS BOND : bond 0.00557 / 0.27 ( 4) SS BOND : angle 1.44970 / 0.68 ( 8) hydrogen bonds : bond 0.04423 / 3.06 ( 944) hydrogen bonds : angle 3.68766 / 2.69 ( 2796) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 205 time to evaluate : 0.534 Fit side-chains REVERT: C 445 MET cc_start: 0.9185 (mmm) cc_final: 0.8901 (mmp) REVERT: C 504 LYS cc_start: 0.7385 (mmtt) cc_final: 0.6135 (mptt) REVERT: C 509 ASP cc_start: 0.8097 (m-30) cc_final: 0.7867 (m-30) REVERT: C 688 LYS cc_start: 0.7850 (mttt) cc_final: 0.7532 (mptt) REVERT: C 692 GLU cc_start: 0.7649 (tt0) cc_final: 0.7398 (tt0) REVERT: A 536 GLU cc_start: 0.9051 (mp0) cc_final: 0.8687 (mp0) REVERT: A 688 LYS cc_start: 0.7998 (mttt) cc_final: 0.7620 (mptt) REVERT: A 692 GLU cc_start: 0.7589 (tt0) cc_final: 0.7338 (tt0) REVERT: B 504 LYS cc_start: 0.7470 (mmtt) cc_final: 0.5941 (mmtt) REVERT: B 568 MET cc_start: 0.8520 (mtt) cc_final: 0.8249 (mtt) REVERT: B 601 ASP cc_start: 0.7380 (OUTLIER) cc_final: 0.7162 (m-30) REVERT: B 654 ASP cc_start: 0.8756 (m-30) cc_final: 0.8456 (m-30) REVERT: B 677 MET cc_start: 0.8697 (ttt) cc_final: 0.8485 (ttm) REVERT: B 688 LYS cc_start: 0.7973 (mttt) cc_final: 0.7638 (mptt) REVERT: B 692 GLU cc_start: 0.7581 (tt0) cc_final: 0.7335 (tt0) REVERT: B 710 LYS cc_start: 0.7542 (mttm) cc_final: 0.7099 (mtpt) REVERT: D 445 MET cc_start: 0.9187 (mmm) cc_final: 0.8867 (mmp) REVERT: D 504 LYS cc_start: 0.7354 (mmtt) cc_final: 0.5859 (mmtt) REVERT: D 509 ASP cc_start: 0.7978 (m-30) cc_final: 0.7772 (m-30) REVERT: D 536 GLU cc_start: 0.8929 (mp0) cc_final: 0.8607 (mp0) REVERT: D 654 ASP cc_start: 0.8780 (m-30) cc_final: 0.8517 (m-30) REVERT: D 677 MET cc_start: 0.8737 (ttt) cc_final: 0.8499 (ttm) REVERT: D 688 LYS cc_start: 0.7917 (mttt) cc_final: 0.7520 (mptt) REVERT: D 692 GLU cc_start: 0.7588 (tt0) cc_final: 0.7282 (tt0) outliers start: 10 outliers final: 6 residues processed: 212 average time/residue: 0.1296 time to fit residues: 39.9855 Evaluate side-chains 204 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 197 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 708 THR Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 601 ASP Chi-restraints excluded: chain B residue 601 ASP Chi-restraints excluded: chain D residue 601 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: [39, 139, 15, 128, 69, 41, 75, 88, 59, 54, 109] chunk 39 optimal weight: 0.9990 chunk 139 optimal weight: 8.9990 chunk 15 optimal weight: 0.8980 chunk 128 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 41 optimal weight: 5.9990 chunk 75 optimal weight: 2.9990 chunk 88 optimal weight: 0.0170 chunk 59 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 109 optimal weight: 0.8980 overall best weight: 0.9622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 354 GLN A 354 GLN B 354 GLN D 354 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.190426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.140122 restraints weight = 14774.343| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 2.41 r_work: 0.3093 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.3535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 15580 Z= 0.112 Angle : 0.449 6.551 20964 Z= 0.232 Chirality : 0.037 0.242 2308 Planarity : 0.003 0.040 2512 Dihedral : 19.830 178.555 2888 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 0.77 % Allowed : 7.96 % Favored : 91.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.68 (0.20), residues: 1800 helix: 3.13 (0.14), residues: 1140 sheet: -0.48 (0.54), residues: 84 loop : -0.79 (0.24), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 721 TYR 0.008 0.001 TYR D 530 PHE 0.011 0.001 PHE A 659 TRP 0.018 0.002 TRP C 740 HIS 0.002 0.000 HIS B 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 (15576) covalent geometry : angle 0.44806 / 0.23 (20956) SS BOND : bond 0.00474 / 0.20 ( 4) SS BOND : angle 1.23958 / 0.64 ( 8) hydrogen bonds : bond 0.04731 / 3.28 ( 944) hydrogen bonds : angle 3.71075 / 2.70 ( 2796) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 201 time to evaluate : 0.536 Fit side-chains REVERT: C 445 MET cc_start: 0.9187 (mmm) cc_final: 0.8874 (mmp) REVERT: C 504 LYS cc_start: 0.7442 (mmtt) cc_final: 0.6227 (mptt) REVERT: C 509 ASP cc_start: 0.7880 (m-30) cc_final: 0.7653 (m-30) REVERT: C 536 GLU cc_start: 0.8997 (mp0) cc_final: 0.8763 (mp0) REVERT: C 688 LYS cc_start: 0.7965 (mttt) cc_final: 0.7634 (mptt) REVERT: C 692 GLU cc_start: 0.7624 (tt0) cc_final: 0.7389 (tt0) REVERT: C 741 CYS cc_start: 0.8150 (m) cc_final: 0.7724 (m) REVERT: A 536 GLU cc_start: 0.9049 (mp0) cc_final: 0.8667 (mp0) REVERT: A 688 LYS cc_start: 0.7975 (mttt) cc_final: 0.7643 (mptt) REVERT: A 692 GLU cc_start: 0.7580 (tt0) cc_final: 0.7354 (tt0) REVERT: B 445 MET cc_start: 0.9169 (mmm) cc_final: 0.8894 (mmp) REVERT: B 504 LYS cc_start: 0.7478 (mmtt) cc_final: 0.6047 (mmtt) REVERT: B 536 GLU cc_start: 0.8993 (mp0) cc_final: 0.8757 (mp0) REVERT: B 568 MET cc_start: 0.8500 (mtt) cc_final: 0.8211 (mtt) REVERT: B 654 ASP cc_start: 0.8755 (m-30) cc_final: 0.8450 (m-30) REVERT: B 688 LYS cc_start: 0.7976 (mttt) cc_final: 0.7657 (mptt) REVERT: B 692 GLU cc_start: 0.7595 (tt0) cc_final: 0.7362 (tt0) REVERT: B 710 LYS cc_start: 0.7583 (mttm) cc_final: 0.7172 (mtpt) REVERT: D 445 MET cc_start: 0.9189 (mmm) cc_final: 0.8860 (mmp) REVERT: D 504 LYS cc_start: 0.7377 (mmtt) cc_final: 0.5898 (mmtt) REVERT: D 509 ASP cc_start: 0.8008 (m-30) cc_final: 0.7789 (m-30) REVERT: D 536 GLU cc_start: 0.8981 (mp0) cc_final: 0.8638 (mp0) REVERT: D 654 ASP cc_start: 0.8744 (m-30) cc_final: 0.8471 (m-30) REVERT: D 688 LYS cc_start: 0.7950 (mttt) cc_final: 0.7629 (mptt) REVERT: D 692 GLU cc_start: 0.7650 (tt0) cc_final: 0.7419 (tt0) outliers start: 11 outliers final: 7 residues processed: 207 average time/residue: 0.1247 time to fit residues: 38.0802 Evaluate side-chains 204 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 197 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 601 ASP Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 601 ASP Chi-restraints excluded: chain D residue 465 LEU Chi-restraints excluded: chain D residue 601 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: [141, 60, 21, 36, 154, 37, 146, 30, 100, 44, 86] chunk 141 optimal weight: 0.9990 chunk 60 optimal weight: 0.7980 chunk 21 optimal weight: 5.9990 chunk 36 optimal weight: 0.7980 chunk 154 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 146 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 100 optimal weight: 8.9990 chunk 44 optimal weight: 9.9990 chunk 86 optimal weight: 8.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 354 GLN A 354 GLN B 354 GLN D 354 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.187623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.136098 restraints weight = 14907.775| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 2.34 r_work: 0.2987 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work: 0.2835 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.3631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15580 Z= 0.128 Angle : 0.471 6.978 20964 Z= 0.242 Chirality : 0.038 0.263 2308 Planarity : 0.003 0.040 2512 Dihedral : 19.831 171.686 2888 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 0.92 % Allowed : 7.96 % Favored : 91.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.53 (0.20), residues: 1800 helix: 3.01 (0.15), residues: 1140 sheet: -1.04 (0.43), residues: 124 loop : -0.70 (0.26), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 409 TYR 0.008 0.001 TYR A 530 PHE 0.013 0.001 PHE C 649 TRP 0.018 0.002 TRP C 740 HIS 0.002 0.001 HIS B 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 (15576) covalent geometry : angle 0.47034 / 0.24 (20956) SS BOND : bond 0.00255 / 0.12 ( 4) SS BOND : angle 1.11500 / 0.62 ( 8) hydrogen bonds : bond 0.05104 / 3.54 ( 944) hydrogen bonds : angle 3.75997 / 2.74 ( 2796) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 193 time to evaluate : 0.461 Fit side-chains REVERT: C 445 MET cc_start: 0.9217 (mmm) cc_final: 0.8926 (mmp) REVERT: C 504 LYS cc_start: 0.7351 (mmtt) cc_final: 0.6091 (mptt) REVERT: C 688 LYS cc_start: 0.8039 (mttt) cc_final: 0.7607 (mptt) REVERT: C 692 GLU cc_start: 0.7827 (tt0) cc_final: 0.7610 (tt0) REVERT: C 710 LYS cc_start: 0.7702 (mttm) cc_final: 0.7398 (mtpt) REVERT: C 741 CYS cc_start: 0.8154 (m) cc_final: 0.7740 (m) REVERT: A 536 GLU cc_start: 0.9192 (mp0) cc_final: 0.8777 (mp0) REVERT: A 688 LYS cc_start: 0.8083 (mttt) cc_final: 0.7621 (mptt) REVERT: A 692 GLU cc_start: 0.7864 (tt0) cc_final: 0.7657 (tt0) REVERT: B 504 LYS cc_start: 0.7400 (mmtt) cc_final: 0.5921 (mmtt) REVERT: B 568 MET cc_start: 0.8737 (mtt) cc_final: 0.8443 (mtt) REVERT: B 688 LYS cc_start: 0.8073 (mttt) cc_final: 0.7630 (mptt) REVERT: B 692 GLU cc_start: 0.7801 (tt0) cc_final: 0.7582 (tt0) REVERT: B 710 LYS cc_start: 0.7604 (mttm) cc_final: 0.7206 (mtpt) REVERT: D 445 MET cc_start: 0.9238 (mmm) cc_final: 0.8917 (mmp) REVERT: D 504 LYS cc_start: 0.7300 (mmtt) cc_final: 0.5801 (mmtt) REVERT: D 654 ASP cc_start: 0.8805 (m-30) cc_final: 0.8530 (m-30) REVERT: D 688 LYS cc_start: 0.8059 (mttt) cc_final: 0.7603 (mptt) REVERT: D 692 GLU cc_start: 0.7802 (tt0) cc_final: 0.7574 (tt0) outliers start: 13 outliers final: 9 residues processed: 202 average time/residue: 0.1148 time to fit residues: 34.4725 Evaluate side-chains 205 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 196 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 601 ASP Chi-restraints excluded: chain C residue 708 THR Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 601 ASP Chi-restraints excluded: chain B residue 601 ASP Chi-restraints excluded: chain D residue 465 LEU Chi-restraints excluded: chain D residue 601 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: [108, 46, 36, 153, 6, 161, 166, 18, 151, 9, 87] chunk 108 optimal weight: 4.9990 chunk 46 optimal weight: 5.9990 chunk 36 optimal weight: 0.7980 chunk 153 optimal weight: 4.9990 chunk 6 optimal weight: 5.9990 chunk 161 optimal weight: 0.7980 chunk 166 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 151 optimal weight: 0.7980 chunk 9 optimal weight: 10.0000 chunk 87 optimal weight: 10.0000 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 354 GLN A 354 GLN B 354 GLN D 354 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.185575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.133742 restraints weight = 14869.507| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 2.70 r_work: 0.2933 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2775 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.3755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15580 Z= 0.136 Angle : 0.481 7.066 20964 Z= 0.247 Chirality : 0.038 0.269 2308 Planarity : 0.003 0.039 2512 Dihedral : 19.775 162.386 2888 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.06 % Allowed : 7.89 % Favored : 91.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.48 (0.20), residues: 1800 helix: 2.95 (0.15), residues: 1144 sheet: -1.12 (0.44), residues: 124 loop : -0.69 (0.26), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 409 TYR 0.009 0.001 TYR D 530 PHE 0.014 0.001 PHE D 649 TRP 0.018 0.002 TRP C 740 HIS 0.002 0.001 HIS B 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 (15576) covalent geometry : angle 0.48082 / 0.25 (20956) SS BOND : bond 0.00344 / 0.16 ( 4) SS BOND : angle 1.02662 / 0.56 ( 8) hydrogen bonds : bond 0.05241 / 3.63 ( 944) hydrogen bonds : angle 3.79319 / 2.76 ( 2796) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 196 time to evaluate : 0.540 Fit side-chains REVERT: C 445 MET cc_start: 0.9206 (mmm) cc_final: 0.8905 (mmp) REVERT: C 504 LYS cc_start: 0.7177 (mmtt) cc_final: 0.5946 (mptt) REVERT: C 688 LYS cc_start: 0.7980 (mttt) cc_final: 0.7574 (mptt) REVERT: C 692 GLU cc_start: 0.7866 (tt0) cc_final: 0.7658 (tt0) REVERT: C 710 LYS cc_start: 0.7683 (mttm) cc_final: 0.7396 (mtpt) REVERT: C 741 CYS cc_start: 0.8346 (m) cc_final: 0.7827 (m) REVERT: A 536 GLU cc_start: 0.9182 (mp0) cc_final: 0.8759 (mp0) REVERT: A 688 LYS cc_start: 0.8043 (mttt) cc_final: 0.7584 (mptt) REVERT: A 692 GLU cc_start: 0.7782 (tt0) cc_final: 0.7566 (tt0) REVERT: B 504 LYS cc_start: 0.7333 (mmtt) cc_final: 0.5889 (mmtt) REVERT: B 568 MET cc_start: 0.8739 (mtt) cc_final: 0.8440 (mtt) REVERT: B 688 LYS cc_start: 0.8050 (mttt) cc_final: 0.7600 (mptt) REVERT: B 692 GLU cc_start: 0.7801 (tt0) cc_final: 0.7585 (tt0) REVERT: B 710 LYS cc_start: 0.7599 (mttm) cc_final: 0.7193 (mtpt) REVERT: D 445 MET cc_start: 0.9232 (mmm) cc_final: 0.8913 (mmp) REVERT: D 504 LYS cc_start: 0.7226 (mmtt) cc_final: 0.5748 (mmtt) REVERT: D 536 GLU cc_start: 0.9207 (mp0) cc_final: 0.8806 (mp0) REVERT: D 654 ASP cc_start: 0.8789 (m-30) cc_final: 0.8514 (m-30) REVERT: D 688 LYS cc_start: 0.8035 (mttt) cc_final: 0.7585 (mptt) REVERT: D 692 GLU cc_start: 0.7831 (tt0) cc_final: 0.7610 (tt0) outliers start: 15 outliers final: 9 residues processed: 206 average time/residue: 0.1234 time to fit residues: 37.5038 Evaluate side-chains 201 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 192 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 601 ASP Chi-restraints excluded: chain C residue 708 THR Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 601 ASP Chi-restraints excluded: chain B residue 601 ASP Chi-restraints excluded: chain B residue 660 ILE Chi-restraints excluded: chain D residue 465 LEU Chi-restraints excluded: chain D residue 601 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: [57, 15, 45, 122, 131, 17, 81, 37, 8, 111, 166] chunk 57 optimal weight: 7.9990 chunk 15 optimal weight: 0.9980 chunk 45 optimal weight: 30.0000 chunk 122 optimal weight: 0.0470 chunk 131 optimal weight: 5.9990 chunk 17 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 8 optimal weight: 9.9990 chunk 111 optimal weight: 5.9990 chunk 166 optimal weight: 2.9990 overall best weight: 1.6084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 354 GLN A 354 GLN B 354 GLN D 354 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.186231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.134767 restraints weight = 14955.530| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 2.40 r_work: 0.2908 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.3832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15580 Z= 0.144 Angle : 0.493 7.405 20964 Z= 0.252 Chirality : 0.039 0.282 2308 Planarity : 0.003 0.039 2512 Dihedral : 19.766 158.872 2888 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 0.85 % Allowed : 8.10 % Favored : 91.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.39 (0.20), residues: 1800 helix: 2.90 (0.15), residues: 1144 sheet: -1.15 (0.44), residues: 124 loop : -0.77 (0.26), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 432 TYR 0.009 0.001 TYR A 530 PHE 0.015 0.002 PHE A 649 TRP 0.015 0.002 TRP A 740 HIS 0.002 0.001 HIS B 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.14 (15576) covalent geometry : angle 0.49229 / 0.25 (20956) SS BOND : bond 0.00375 / 0.18 ( 4) SS BOND : angle 1.03547 / 0.58 ( 8) hydrogen bonds : bond 0.05383 / 3.73 ( 944) hydrogen bonds : angle 3.80983 / 2.78 ( 2796) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 187 time to evaluate : 0.514 Fit side-chains REVERT: C 445 MET cc_start: 0.9174 (mmm) cc_final: 0.8838 (mmp) REVERT: C 504 LYS cc_start: 0.7368 (mmtt) cc_final: 0.6071 (mptt) REVERT: C 688 LYS cc_start: 0.7929 (mttt) cc_final: 0.7540 (mptt) REVERT: C 692 GLU cc_start: 0.7715 (tt0) cc_final: 0.7480 (tt0) REVERT: C 710 LYS cc_start: 0.7695 (mttm) cc_final: 0.7410 (mtpt) REVERT: C 741 CYS cc_start: 0.8375 (m) cc_final: 0.7855 (m) REVERT: A 688 LYS cc_start: 0.8011 (mttt) cc_final: 0.7627 (mptt) REVERT: A 692 GLU cc_start: 0.7665 (tt0) cc_final: 0.7443 (tt0) REVERT: B 504 LYS cc_start: 0.7474 (mmtt) cc_final: 0.6036 (mmtt) REVERT: B 568 MET cc_start: 0.8540 (mtt) cc_final: 0.8239 (mtt) REVERT: B 688 LYS cc_start: 0.8016 (mttt) cc_final: 0.7640 (mptt) REVERT: B 692 GLU cc_start: 0.7667 (tt0) cc_final: 0.7443 (tt0) REVERT: B 710 LYS cc_start: 0.7621 (mttm) cc_final: 0.7220 (mtpt) REVERT: D 445 MET cc_start: 0.9191 (mmm) cc_final: 0.8826 (mmp) REVERT: D 504 LYS cc_start: 0.7373 (mmtt) cc_final: 0.5880 (mmtt) REVERT: D 536 GLU cc_start: 0.9010 (mp0) cc_final: 0.8713 (mp0) REVERT: D 654 ASP cc_start: 0.8750 (m-30) cc_final: 0.8475 (m-30) REVERT: D 688 LYS cc_start: 0.8010 (mttt) cc_final: 0.7621 (mptt) REVERT: D 692 GLU cc_start: 0.7694 (tt0) cc_final: 0.7463 (tt0) outliers start: 12 outliers final: 12 residues processed: 195 average time/residue: 0.1230 time to fit residues: 35.4914 Evaluate side-chains 203 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 191 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 494 GLN Chi-restraints excluded: chain C residue 601 ASP Chi-restraints excluded: chain C residue 712 PHE Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 601 ASP Chi-restraints excluded: chain B residue 494 GLN Chi-restraints excluded: chain B residue 601 ASP Chi-restraints excluded: chain B residue 660 ILE Chi-restraints excluded: chain D residue 465 LEU Chi-restraints excluded: chain D residue 494 GLN Chi-restraints excluded: chain D residue 601 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: [15, 49, 30, 19, 59, 78, 66, 87, 123, 156, 125] chunk 15 optimal weight: 0.6980 chunk 49 optimal weight: 0.0980 chunk 30 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 59 optimal weight: 0.3980 chunk 78 optimal weight: 0.5980 chunk 66 optimal weight: 5.9990 chunk 87 optimal weight: 0.7980 chunk 123 optimal weight: 1.9990 chunk 156 optimal weight: 5.9990 chunk 125 optimal weight: 1.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 354 GLN A 354 GLN B 354 GLN D 354 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.192576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.143614 restraints weight = 14804.057| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 1.70 r_work: 0.3057 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work: 0.2922 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.3944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 15580 Z= 0.095 Angle : 0.420 6.050 20964 Z= 0.221 Chirality : 0.035 0.216 2308 Planarity : 0.003 0.039 2512 Dihedral : 18.611 153.598 2888 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 0.56 % Allowed : 8.52 % Favored : 90.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.72 (0.20), residues: 1800 helix: 3.21 (0.15), residues: 1136 sheet: -1.05 (0.44), residues: 124 loop : -0.69 (0.26), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 432 TYR 0.008 0.001 TYR D 530 PHE 0.012 0.001 PHE A 659 TRP 0.014 0.001 TRP C 740 HIS 0.002 0.000 HIS B 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00193 / 0.10 (15576) covalent geometry : angle 0.41983 / 0.22 (20956) SS BOND : bond 0.00195 / 0.09 ( 4) SS BOND : angle 0.89467 / 0.49 ( 8) hydrogen bonds : bond 0.04117 / 2.85 ( 944) hydrogen bonds : angle 3.64160 / 2.65 ( 2796) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3755.80 seconds wall clock time: 64 minutes 54.17 seconds (3894.17 seconds total)