Starting phenix.real_space_refine on Wed Mar 4 15:07:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7l2l_23132/03_2026/7l2l_23132.cif Found real_map, /net/cci-nas-00/data/ceres_data/7l2l_23132/03_2026/7l2l_23132.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.42 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7l2l_23132/03_2026/7l2l_23132.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7l2l_23132/03_2026/7l2l_23132.map" model { file = "/net/cci-nas-00/data/ceres_data/7l2l_23132/03_2026/7l2l_23132.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7l2l_23132/03_2026/7l2l_23132.cif" } resolution = 3.42 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= 0.003 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: 4 Type Number sf(0) Gaussians S 92 5.16 5 C 9420 2.51 5 N 2244 2.21 5 O 2496 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14252 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3517 Classifications: {'peptide': 429} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 418} Chain breaks: 2 Chain: "C" Number of atoms: 3517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3517 Classifications: {'peptide': 429} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 418} Chain breaks: 2 Chain: "D" Number of atoms: 3517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3517 Classifications: {'peptide': 429} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 418} Chain breaks: 2 Chain: "B" Number of atoms: 3517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3517 Classifications: {'peptide': 429} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 418} Chain breaks: 2 Chain: "A" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'6EU': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'6EU': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'6EU': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'6EU': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.86, per 1000 atoms: 0.20 Number of scatterers: 14252 At special positions: 0 Unit cell: (121.776, 122.808, 101.136, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 92 16.00 O 2496 8.00 N 2244 7.00 C 9420 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.17 Conformation dependent library (CDL) restraints added in 416.6 milliseconds 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3272 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 4 sheets defined 70.3% alpha, 2.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing helix chain 'A' and resid 286 through 294 removed outlier: 3.529A pdb=" N VAL A 292 " --> pdb=" O LEU A 288 " (cutoff:3.500A) 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 362 through 366 Processing helix chain 'A' and resid 394 through 401 Processing helix chain 'A' and resid 408 through 413 removed outlier: 4.197A pdb=" N LEU A 413 " --> pdb=" O ARG A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 429 Processing helix chain 'A' and resid 429 through 454 removed outlier: 3.549A 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 506 Processing helix chain 'A' and resid 510 through 532 Processing helix chain 'A' and resid 536 through 552 removed outlier: 4.095A pdb=" N PHE A 543 " --> pdb=" O ALA A 539 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N MET A 552 " --> pdb=" O GLY A 548 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 557 removed outlier: 3.543A pdb=" N THR A 556 " --> pdb=" O MET A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 576 removed outlier: 4.572A pdb=" N ALA A 566 " --> pdb=" O MET A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 576 through 599 removed outlier: 3.576A pdb=" N PHE A 580 " --> pdb=" O ASP A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 629 through 639 Processing helix chain 'A' and resid 655 through 670 Processing helix chain 'A' and resid 672 through 712 removed outlier: 6.062A pdb=" N GLN A 691 " --> pdb=" O ASN A 687 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N GLU A 692 " --> pdb=" O LYS A 688 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N LYS A 698 " --> pdb=" O LYS A 694 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 294 removed outlier: 3.590A pdb=" N ALA C 290 " --> pdb=" O THR C 286 " (cutoff:3.500A) 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 362 through 366 Processing helix chain 'C' and resid 394 through 401 Processing helix chain 'C' and resid 408 through 413 removed outlier: 3.977A pdb=" N LEU C 413 " --> pdb=" O ARG C 409 " (cutoff:3.500A) Processing helix chain 'C' and resid 415 through 429 Processing helix chain 'C' and resid 429 through 454 Processing helix chain 'C' and resid 468 through 500 Processing helix chain 'C' and resid 502 through 506 Processing helix chain 'C' and resid 510 through 532 Processing helix chain 'C' and resid 536 through 552 removed outlier: 3.850A pdb=" N PHE C 543 " --> pdb=" O ALA C 539 " (cutoff:3.500A) Processing helix chain 'C' and resid 552 through 557 removed outlier: 4.017A pdb=" N THR C 556 " --> pdb=" O MET C 552 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ARG C 557 " --> pdb=" O LEU C 553 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 552 through 557' Processing helix chain 'C' and resid 563 through 576 Processing helix chain 'C' and resid 576 through 599 removed outlier: 3.541A pdb=" N PHE C 580 " --> pdb=" O ASP C 576 " (cutoff:3.500A) Processing helix chain 'C' and resid 629 through 639 Processing helix chain 'C' and resid 655 through 670 Processing helix chain 'C' and resid 672 through 712 removed outlier: 3.682A pdb=" N ASN C 676 " --> pdb=" O ILE C 672 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N GLN C 691 " --> pdb=" O ASN C 687 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N GLU C 692 " --> pdb=" O LYS C 688 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ASN C 695 " --> pdb=" O GLN C 691 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N LYS C 698 " --> pdb=" O LYS C 694 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 294 removed outlier: 3.545A pdb=" N ALA D 290 " --> pdb=" O THR D 286 " (cutoff:3.500A) 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 362 through 366 Processing helix chain 'D' and resid 394 through 401 Processing helix chain 'D' and resid 408 through 413 removed outlier: 4.176A pdb=" N LEU D 413 " --> pdb=" O ARG D 409 " (cutoff:3.500A) Processing helix chain 'D' and resid 415 through 429 Processing helix chain 'D' and resid 429 through 454 Processing helix chain 'D' and resid 468 through 500 Processing helix chain 'D' and resid 502 through 506 Processing helix chain 'D' and resid 510 through 532 Processing helix chain 'D' and resid 536 through 551 removed outlier: 3.887A pdb=" N PHE D 543 " --> pdb=" O ALA D 539 " (cutoff:3.500A) Processing helix chain 'D' and resid 552 through 557 removed outlier: 3.568A pdb=" N THR D 556 " --> pdb=" O MET D 552 " (cutoff:3.500A) Processing helix chain 'D' and resid 563 through 576 Processing helix chain 'D' and resid 576 through 599 removed outlier: 3.530A pdb=" N PHE D 580 " --> pdb=" O ASP D 576 " (cutoff:3.500A) Processing helix chain 'D' and resid 629 through 639 Processing helix chain 'D' and resid 655 through 670 Processing helix chain 'D' and resid 672 through 712 removed outlier: 6.202A pdb=" N GLN D 691 " --> pdb=" O ASN D 687 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N GLU D 692 " --> pdb=" O LYS D 688 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASN D 695 " --> pdb=" O GLN D 691 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N LYS D 698 " --> pdb=" O LYS D 694 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 294 removed outlier: 3.590A pdb=" N ALA B 290 " --> pdb=" O THR B 286 " (cutoff:3.500A) 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 362 through 366 Processing helix chain 'B' and resid 394 through 401 Processing helix chain 'B' and resid 408 through 413 removed outlier: 4.132A pdb=" N LEU B 413 " --> pdb=" O ARG B 409 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 429 Processing helix chain 'B' and resid 429 through 454 Processing helix chain 'B' and resid 468 through 500 Processing helix chain 'B' and resid 502 through 506 Processing helix chain 'B' and resid 510 through 532 Processing helix chain 'B' and resid 536 through 551 removed outlier: 4.097A pdb=" N PHE B 543 " --> pdb=" O ALA B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 552 through 557 removed outlier: 3.687A pdb=" N THR B 556 " --> pdb=" O MET B 552 " (cutoff:3.500A) Processing helix chain 'B' and resid 563 through 576 Processing helix chain 'B' and resid 576 through 599 removed outlier: 3.594A pdb=" N PHE B 580 " --> pdb=" O ASP B 576 " (cutoff:3.500A) Processing helix chain 'B' and resid 629 through 639 Processing helix chain 'B' and resid 655 through 670 Processing helix chain 'B' and resid 673 through 712 removed outlier: 6.360A pdb=" N GLN B 691 " --> pdb=" O ASN B 687 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N GLU B 692 " --> pdb=" O LYS B 688 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N LYS B 698 " --> pdb=" O LYS B 694 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 368 through 370 Processing sheet with id=AA2, first strand: chain 'C' and resid 368 through 370 Processing sheet with id=AA3, first strand: chain 'D' and resid 368 through 370 Processing sheet with id=AA4, first strand: chain 'B' and resid 368 through 372 removed outlier: 6.446A pdb=" N SER B 379 " --> pdb=" O GLU B 371 " (cutoff:3.500A) 904 hydrogen bonds defined for protein. 2640 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: 2.52 Time building geometry restraints manager: 1.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 2163 1.29 - 1.42: 4101 1.42 - 1.55: 8168 1.55 - 1.68: 24 1.68 - 1.81: 152 Bond restraints: 14608 Sorted by residual: bond pdb=" CAM 6EU B 901 " pdb=" OAC 6EU B 901 " ideal model delta sigma weight residual 1.422 1.166 0.256 2.00e-02 2.50e+03 1.63e+02 bond pdb=" CAM 6EU A 901 " pdb=" OAC 6EU A 901 " ideal model delta sigma weight residual 1.422 1.167 0.255 2.00e-02 2.50e+03 1.63e+02 bond pdb=" CAM 6EU C 901 " pdb=" OAC 6EU C 901 " ideal model delta sigma weight residual 1.422 1.167 0.255 2.00e-02 2.50e+03 1.62e+02 bond pdb=" CAM 6EU D 901 " pdb=" OAC 6EU D 901 " ideal model delta sigma weight residual 1.422 1.171 0.251 2.00e-02 2.50e+03 1.57e+02 bond pdb=" CAV 6EU D 901 " pdb=" CBB 6EU D 901 " ideal model delta sigma weight residual 1.330 1.514 -0.184 2.00e-02 2.50e+03 8.43e+01 ... (remaining 14603 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.13: 19378 3.13 - 6.25: 353 6.25 - 9.38: 34 9.38 - 12.50: 24 12.50 - 15.63: 11 Bond angle restraints: 19800 Sorted by residual: angle pdb=" CAN 6EU B 901 " pdb=" CAJ 6EU B 901 " pdb=" CAO 6EU B 901 " ideal model delta sigma weight residual 115.38 131.01 -15.63 3.00e+00 1.11e-01 2.71e+01 angle pdb=" CAN 6EU C 901 " pdb=" CAJ 6EU C 901 " pdb=" OAA 6EU C 901 " ideal model delta sigma weight residual 110.99 95.68 15.31 3.00e+00 1.11e-01 2.60e+01 angle pdb=" CAN 6EU C 901 " pdb=" CAJ 6EU C 901 " pdb=" CAO 6EU C 901 " ideal model delta sigma weight residual 115.38 130.55 -15.17 3.00e+00 1.11e-01 2.56e+01 angle pdb=" CAN 6EU B 901 " pdb=" CAJ 6EU B 901 " pdb=" OAA 6EU B 901 " ideal model delta sigma weight residual 110.99 96.09 14.90 3.00e+00 1.11e-01 2.47e+01 angle pdb=" CAN 6EU A 901 " pdb=" CAJ 6EU A 901 " pdb=" OAA 6EU A 901 " ideal model delta sigma weight residual 110.99 96.11 14.88 3.00e+00 1.11e-01 2.46e+01 ... (remaining 19795 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.73: 8111 17.73 - 35.47: 634 35.47 - 53.20: 72 53.20 - 70.94: 32 70.94 - 88.67: 11 Dihedral angle restraints: 8860 sinusoidal: 3776 harmonic: 5084 Sorted by residual: dihedral pdb=" CA LEU C 647 " pdb=" C LEU C 647 " pdb=" N GLU C 648 " pdb=" CA GLU C 648 " ideal model delta harmonic sigma weight residual 180.00 153.05 26.95 0 5.00e+00 4.00e-02 2.91e+01 dihedral pdb=" CA LEU B 647 " pdb=" C LEU B 647 " pdb=" N GLU B 648 " pdb=" CA GLU B 648 " ideal model delta harmonic sigma weight residual 180.00 153.07 26.93 0 5.00e+00 4.00e-02 2.90e+01 dihedral pdb=" CA LEU A 647 " pdb=" C LEU A 647 " pdb=" N GLU A 648 " pdb=" CA GLU A 648 " ideal model delta harmonic sigma weight residual 180.00 154.23 25.77 0 5.00e+00 4.00e-02 2.66e+01 ... (remaining 8857 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.143: 2197 0.143 - 0.285: 31 0.285 - 0.427: 1 0.427 - 0.570: 7 0.570 - 0.712: 4 Chirality restraints: 2240 Sorted by residual: chirality pdb=" CAJ 6EU B 901 " pdb=" CAK 6EU B 901 " pdb=" CAN 6EU B 901 " pdb=" CAO 6EU B 901 " both_signs ideal model delta sigma weight residual False 2.66 1.94 0.71 2.00e-01 2.50e+01 1.27e+01 chirality pdb=" CAJ 6EU C 901 " pdb=" CAK 6EU C 901 " pdb=" CAN 6EU C 901 " pdb=" CAO 6EU C 901 " both_signs ideal model delta sigma weight residual False 2.66 1.95 0.71 2.00e-01 2.50e+01 1.26e+01 chirality pdb=" CAJ 6EU A 901 " pdb=" CAK 6EU A 901 " pdb=" CAN 6EU A 901 " pdb=" CAO 6EU A 901 " both_signs ideal model delta sigma weight residual False 2.66 2.02 0.64 2.00e-01 2.50e+01 1.03e+01 ... (remaining 2237 not shown) Planarity restraints: 2400 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CAM 6EU D 901 " -0.118 2.00e-02 2.50e+03 2.07e-01 4.30e+02 pdb=" CAV 6EU D 901 " 0.359 2.00e-02 2.50e+03 pdb=" CBB 6EU D 901 " -0.123 2.00e-02 2.50e+03 pdb=" CBD 6EU D 901 " -0.119 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CAM 6EU B 901 " 0.118 2.00e-02 2.50e+03 2.07e-01 4.30e+02 pdb=" CAV 6EU B 901 " -0.359 2.00e-02 2.50e+03 pdb=" CBB 6EU B 901 " 0.123 2.00e-02 2.50e+03 pdb=" CBD 6EU B 901 " 0.118 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CAM 6EU A 901 " 0.118 2.00e-02 2.50e+03 2.07e-01 4.29e+02 pdb=" CAV 6EU A 901 " -0.359 2.00e-02 2.50e+03 pdb=" CBB 6EU A 901 " 0.124 2.00e-02 2.50e+03 pdb=" CBD 6EU A 901 " 0.117 2.00e-02 2.50e+03 ... (remaining 2397 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 129 2.55 - 3.14: 12632 3.14 - 3.72: 22564 3.72 - 4.31: 31552 4.31 - 4.90: 52649 Nonbonded interactions: 119526 Sorted by model distance: nonbonded pdb=" O LEU A 588 " pdb=" OG SER A 592 " model vdw 1.961 3.040 nonbonded pdb=" O LEU C 588 " pdb=" OG SER C 592 " model vdw 1.972 3.040 nonbonded pdb=" O LEU D 588 " pdb=" OG SER D 592 " model vdw 1.984 3.040 nonbonded pdb=" OG SER C 512 " pdb=" OAI 6EU C 901 " model vdw 2.075 3.040 nonbonded pdb=" OG SER D 512 " pdb=" OAI 6EU D 901 " model vdw 2.076 3.040 ... (remaining 119521 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.280 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: 0.000 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 13.080 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 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 : 0.016 0.256 14608 Z= 0.788 Angle : 1.142 15.627 19800 Z= 0.577 Chirality : 0.069 0.712 2240 Planarity : 0.010 0.207 2400 Dihedral : 13.071 88.671 5588 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 0.06 % Allowed : 3.68 % Favored : 96.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.19), residues: 1692 helix: 0.33 (0.14), residues: 1124 sheet: -1.23 (0.65), residues: 68 loop : -1.70 (0.27), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 455 TYR 0.019 0.003 TYR C 441 PHE 0.029 0.003 PHE A 659 TRP 0.015 0.003 TRP B 740 HIS 0.008 0.002 HIS A 358 Details of bonding type rmsd covalent geometry : bond 0.01629 (14608) covalent geometry : angle 1.14173 (19800) hydrogen bonds : bond 0.15277 ( 904) hydrogen bonds : angle 6.08879 ( 2640) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 647 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 646 time to evaluate : 0.536 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: A 475 VAL cc_start: 0.9208 (p) cc_final: 0.8719 (t) REVERT: A 478 GLU cc_start: 0.7652 (mt-10) cc_final: 0.7408 (mt-10) REVERT: A 494 GLN cc_start: 0.8210 (mt0) cc_final: 0.7990 (tt0) REVERT: A 551 ASN cc_start: 0.9081 (m-40) cc_final: 0.8740 (m-40) REVERT: A 561 GLN cc_start: 0.8079 (tt0) cc_final: 0.6896 (pm20) REVERT: A 568 MET cc_start: 0.7729 (mtp) cc_final: 0.7514 (mtp) REVERT: A 577 LEU cc_start: 0.9166 (tp) cc_final: 0.8946 (tt) REVERT: A 629 SER cc_start: 0.8544 (p) cc_final: 0.8178 (m) REVERT: A 681 LEU cc_start: 0.8403 (mt) cc_final: 0.7763 (mt) REVERT: C 345 LYS cc_start: 0.8506 (mmtm) cc_final: 0.8214 (mmmm) REVERT: C 397 GLU cc_start: 0.8056 (mt-10) cc_final: 0.7833 (mt-10) REVERT: C 425 LYS cc_start: 0.8973 (mtmt) cc_final: 0.8741 (mtmt) REVERT: C 431 LYS cc_start: 0.9026 (ttpt) cc_final: 0.8709 (ttpt) REVERT: C 474 ARG cc_start: 0.7811 (ttp-110) cc_final: 0.6127 (mpt180) REVERT: C 478 GLU cc_start: 0.7929 (mt-10) cc_final: 0.7690 (mt-10) REVERT: C 551 ASN cc_start: 0.8982 (m-40) cc_final: 0.8563 (m-40) REVERT: C 569 ILE cc_start: 0.9214 (mt) cc_final: 0.9010 (mt) REVERT: C 570 GLU cc_start: 0.8138 (tt0) cc_final: 0.7883 (tt0) REVERT: C 629 SER cc_start: 0.8550 (p) cc_final: 0.8237 (m) REVERT: C 673 LEU cc_start: 0.8348 (tp) cc_final: 0.8116 (tp) REVERT: D 401 TYR cc_start: 0.7300 (m-80) cc_final: 0.7013 (m-80) REVERT: D 432 ARG cc_start: 0.7684 (mmt180) cc_final: 0.7382 (mmt180) REVERT: D 478 GLU cc_start: 0.7668 (mt-10) cc_final: 0.7358 (mt-10) REVERT: D 551 ASN cc_start: 0.8992 (m-40) cc_final: 0.8699 (m-40) REVERT: D 577 LEU cc_start: 0.9156 (tp) cc_final: 0.8910 (tt) REVERT: D 629 SER cc_start: 0.8545 (p) cc_final: 0.8197 (m) REVERT: D 672 ILE cc_start: 0.7743 (mm) cc_final: 0.7280 (mt) REVERT: D 696 ILE cc_start: 0.8577 (tt) cc_final: 0.8365 (mt) REVERT: D 740 TRP cc_start: 0.7012 (m100) cc_final: 0.6747 (m-10) REVERT: B 304 PHE cc_start: 0.7674 (t80) cc_final: 0.7457 (t80) REVERT: B 368 LYS cc_start: 0.7176 (pptt) cc_final: 0.6963 (pttt) REVERT: B 425 LYS cc_start: 0.8732 (mtpt) cc_final: 0.7778 (mtmt) REVERT: B 429 PHE cc_start: 0.7569 (p90) cc_final: 0.6678 (t80) REVERT: B 431 LYS cc_start: 0.8904 (ttmt) cc_final: 0.8687 (ttpt) REVERT: B 466 LYS cc_start: 0.7993 (mmtm) cc_final: 0.7543 (tptt) REVERT: B 474 ARG cc_start: 0.7844 (ttp-110) cc_final: 0.6238 (mpt180) REVERT: B 478 GLU cc_start: 0.8033 (mt-10) cc_final: 0.7757 (mt-10) REVERT: B 551 ASN cc_start: 0.9180 (m-40) cc_final: 0.8734 (m110) REVERT: B 629 SER cc_start: 0.8521 (p) cc_final: 0.8224 (m) outliers start: 1 outliers final: 1 residues processed: 647 average time/residue: 0.1328 time to fit residues: 120.0418 Evaluate side-chains 476 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 475 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 687 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 4.9990 chunk 149 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 297 ASN C 297 ASN C 320 HIS C 498 GLN D 297 ASN ** D 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 533 GLN D 687 ASN ** B 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 297 ASN B 498 GLN B 687 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.174404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.131908 restraints weight = 22449.731| |-----------------------------------------------------------------------------| r_work (start): 0.3594 rms_B_bonded: 2.87 r_work: 0.3454 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.2709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 14608 Z= 0.182 Angle : 0.659 7.903 19800 Z= 0.350 Chirality : 0.041 0.196 2240 Planarity : 0.004 0.042 2400 Dihedral : 7.677 78.854 2274 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 2.58 % Allowed : 13.31 % Favored : 84.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.20), residues: 1692 helix: 1.06 (0.15), residues: 1140 sheet: -1.38 (0.62), residues: 68 loop : -1.60 (0.29), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 579 TYR 0.029 0.002 TYR D 351 PHE 0.022 0.002 PHE C 659 TRP 0.016 0.002 TRP A 697 HIS 0.005 0.001 HIS C 320 Details of bonding type rmsd covalent geometry : bond 0.00361 (14608) covalent geometry : angle 0.65949 (19800) hydrogen bonds : bond 0.05458 ( 904) hydrogen bonds : angle 4.60148 ( 2640) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 650 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 610 time to evaluate : 0.511 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: symmetry clash REVERT: A 387 ILE cc_start: 0.8359 (mm) cc_final: 0.8011 (mm) REVERT: A 431 LYS cc_start: 0.9006 (ttpt) cc_final: 0.8769 (ttpt) REVERT: A 475 VAL cc_start: 0.9100 (p) cc_final: 0.8731 (t) REVERT: A 478 GLU cc_start: 0.8144 (mt-10) cc_final: 0.7756 (mt-10) REVERT: A 517 PHE cc_start: 0.9118 (t80) cc_final: 0.8713 (t80) REVERT: A 521 LEU cc_start: 0.9237 (mt) cc_final: 0.9032 (mp) REVERT: A 547 MET cc_start: 0.8747 (mtp) cc_final: 0.8542 (mtp) REVERT: A 555 TYR cc_start: 0.9141 (m-80) cc_final: 0.8365 (m-80) REVERT: A 561 GLN cc_start: 0.7998 (tt0) cc_final: 0.6861 (pm20) REVERT: A 570 GLU cc_start: 0.8705 (tt0) cc_final: 0.8390 (tt0) REVERT: A 577 LEU cc_start: 0.8947 (tp) cc_final: 0.8587 (tt) REVERT: A 579 ARG cc_start: 0.7756 (ptp-170) cc_final: 0.7013 (mtm180) REVERT: A 681 LEU cc_start: 0.8597 (mt) cc_final: 0.8100 (mt) REVERT: A 695 ASN cc_start: 0.7754 (m-40) cc_final: 0.7296 (m-40) REVERT: A 700 GLN cc_start: 0.8497 (tp40) cc_final: 0.7616 (tm-30) REVERT: A 743 ARG cc_start: 0.7766 (mtp85) cc_final: 0.6831 (mpt180) REVERT: C 429 PHE cc_start: 0.7721 (p90) cc_final: 0.7161 (t80) REVERT: C 474 ARG cc_start: 0.7840 (ttp-110) cc_final: 0.5964 (mpt180) REVERT: C 478 GLU cc_start: 0.8425 (mt-10) cc_final: 0.8004 (mt-10) REVERT: C 480 LEU cc_start: 0.9007 (OUTLIER) cc_final: 0.8611 (mp) REVERT: C 511 TYR cc_start: 0.8965 (t80) cc_final: 0.8651 (t80) REVERT: C 551 ASN cc_start: 0.8975 (m-40) cc_final: 0.8451 (m-40) REVERT: C 555 TYR cc_start: 0.9307 (m-80) cc_final: 0.8977 (m-80) REVERT: C 570 GLU cc_start: 0.8754 (tt0) cc_final: 0.8050 (tt0) REVERT: C 695 ASN cc_start: 0.7480 (m-40) cc_final: 0.6918 (m-40) REVERT: D 397 GLU cc_start: 0.8452 (mt-10) cc_final: 0.8033 (mt-10) REVERT: D 401 TYR cc_start: 0.7336 (m-80) cc_final: 0.6899 (m-80) REVERT: D 426 TRP cc_start: 0.9037 (t-100) cc_final: 0.8513 (t-100) REVERT: D 429 PHE cc_start: 0.7672 (p90) cc_final: 0.6934 (t80) REVERT: D 432 ARG cc_start: 0.7812 (mmt180) cc_final: 0.7606 (mmt180) REVERT: D 478 GLU cc_start: 0.8203 (mt-10) cc_final: 0.7796 (mt-10) REVERT: D 494 GLN cc_start: 0.9072 (tt0) cc_final: 0.8721 (tm-30) REVERT: D 517 PHE cc_start: 0.9140 (t80) cc_final: 0.8930 (t80) REVERT: D 550 THR cc_start: 0.9294 (p) cc_final: 0.9070 (p) REVERT: D 551 ASN cc_start: 0.9025 (m-40) cc_final: 0.8694 (m110) REVERT: D 555 TYR cc_start: 0.9171 (m-80) cc_final: 0.8687 (m-80) REVERT: D 577 LEU cc_start: 0.8982 (tp) cc_final: 0.8720 (tt) REVERT: D 629 SER cc_start: 0.8759 (p) cc_final: 0.8541 (m) REVERT: D 651 GLU cc_start: 0.8260 (mp0) cc_final: 0.7990 (mm-30) REVERT: D 653 TYR cc_start: 0.8038 (p90) cc_final: 0.7780 (p90) REVERT: D 696 ILE cc_start: 0.8256 (tt) cc_final: 0.8051 (mt) REVERT: D 743 ARG cc_start: 0.8601 (mtm180) cc_final: 0.7749 (tmm160) REVERT: B 429 PHE cc_start: 0.7630 (p90) cc_final: 0.7155 (t80) REVERT: B 466 LYS cc_start: 0.8173 (mmtm) cc_final: 0.7432 (tptt) REVERT: B 474 ARG cc_start: 0.7747 (ttp-110) cc_final: 0.5901 (mpt180) REVERT: B 478 GLU cc_start: 0.8539 (mt-10) cc_final: 0.8087 (mt-10) REVERT: B 517 PHE cc_start: 0.9067 (t80) cc_final: 0.8836 (t80) REVERT: B 551 ASN cc_start: 0.9119 (m-40) cc_final: 0.8669 (m110) REVERT: B 555 TYR cc_start: 0.9240 (m-80) cc_final: 0.9012 (m-80) REVERT: B 568 MET cc_start: 0.8401 (OUTLIER) cc_final: 0.8067 (mtp) REVERT: B 687 ASN cc_start: 0.6994 (OUTLIER) cc_final: 0.6421 (m-40) REVERT: B 689 ILE cc_start: 0.7693 (mm) cc_final: 0.7361 (mm) REVERT: B 695 ASN cc_start: 0.7862 (m-40) cc_final: 0.7367 (m-40) REVERT: B 700 GLN cc_start: 0.8140 (tm-30) cc_final: 0.7292 (tm-30) outliers start: 40 outliers final: 20 residues processed: 625 average time/residue: 0.1089 time to fit residues: 100.9518 Evaluate side-chains 553 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 530 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 641 THR Chi-restraints excluded: chain C residue 300 ASP Chi-restraints excluded: chain C residue 368 LYS Chi-restraints excluded: chain C residue 480 LEU Chi-restraints excluded: chain C residue 564 ILE Chi-restraints excluded: chain C residue 641 THR Chi-restraints excluded: chain C residue 685 THR Chi-restraints excluded: chain D residue 480 LEU Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 564 ILE Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain D residue 579 ARG Chi-restraints excluded: chain D residue 641 THR Chi-restraints excluded: chain B residue 383 ASP Chi-restraints excluded: chain B residue 547 MET Chi-restraints excluded: chain B residue 564 ILE Chi-restraints excluded: chain B residue 568 MET Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 641 THR Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain B residue 687 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 44 optimal weight: 6.9990 chunk 52 optimal weight: 0.7980 chunk 78 optimal weight: 0.7980 chunk 99 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 chunk 41 optimal weight: 7.9990 chunk 162 optimal weight: 2.9990 chunk 12 optimal weight: 9.9990 chunk 51 optimal weight: 10.0000 chunk 28 optimal weight: 0.9980 chunk 17 optimal weight: 0.1980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 297 ASN C 320 HIS C 498 GLN D 297 ASN D 498 GLN ** B 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 297 ASN B 364 HIS B 560 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.175772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.133757 restraints weight = 22552.790| |-----------------------------------------------------------------------------| r_work (start): 0.3615 rms_B_bonded: 2.92 r_work: 0.3474 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.3352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14608 Z= 0.149 Angle : 0.584 7.902 19800 Z= 0.313 Chirality : 0.039 0.215 2240 Planarity : 0.003 0.029 2400 Dihedral : 7.181 64.470 2274 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 2.26 % Allowed : 17.25 % Favored : 80.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.20), residues: 1692 helix: 1.21 (0.15), residues: 1144 sheet: -1.47 (0.63), residues: 68 loop : -1.69 (0.27), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 721 TYR 0.033 0.002 TYR D 351 PHE 0.027 0.002 PHE B 438 TRP 0.018 0.001 TRP A 697 HIS 0.004 0.001 HIS C 320 Details of bonding type rmsd covalent geometry : bond 0.00305 (14608) covalent geometry : angle 0.58386 (19800) hydrogen bonds : bond 0.04729 ( 904) hydrogen bonds : angle 4.36064 ( 2640) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 615 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 580 time to evaluate : 0.501 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: A 387 ILE cc_start: 0.8313 (mm) cc_final: 0.8091 (mm) REVERT: A 394 SER cc_start: 0.8107 (p) cc_final: 0.7387 (p) REVERT: A 419 ASN cc_start: 0.7491 (p0) cc_final: 0.7217 (p0) REVERT: A 475 VAL cc_start: 0.9100 (p) cc_final: 0.8729 (t) REVERT: A 478 GLU cc_start: 0.8142 (mt-10) cc_final: 0.7718 (mt-10) REVERT: A 512 SER cc_start: 0.8749 (OUTLIER) cc_final: 0.8535 (m) REVERT: A 547 MET cc_start: 0.8701 (mtp) cc_final: 0.8267 (mtp) REVERT: A 551 ASN cc_start: 0.9134 (m-40) cc_final: 0.8893 (m110) REVERT: A 555 TYR cc_start: 0.8997 (m-80) cc_final: 0.8165 (m-80) REVERT: A 561 GLN cc_start: 0.8029 (tt0) cc_final: 0.6786 (pm20) REVERT: A 570 GLU cc_start: 0.8726 (tt0) cc_final: 0.8341 (tt0) REVERT: A 577 LEU cc_start: 0.8863 (tp) cc_final: 0.8611 (tt) REVERT: A 579 ARG cc_start: 0.7610 (ptp-170) cc_final: 0.6860 (mtm180) REVERT: A 637 LEU cc_start: 0.9075 (mp) cc_final: 0.8793 (mp) REVERT: A 647 LEU cc_start: 0.9141 (tp) cc_final: 0.8916 (mt) REVERT: A 653 TYR cc_start: 0.7893 (p90) cc_final: 0.7411 (p90) REVERT: A 681 LEU cc_start: 0.8460 (mt) cc_final: 0.7755 (mt) REVERT: A 695 ASN cc_start: 0.7823 (m-40) cc_final: 0.7200 (m-40) REVERT: A 700 GLN cc_start: 0.8474 (tp40) cc_final: 0.7616 (tm-30) REVERT: A 701 ARG cc_start: 0.8988 (mmm-85) cc_final: 0.8739 (mmm-85) REVERT: A 720 PHE cc_start: 0.5634 (m-80) cc_final: 0.5077 (p90) REVERT: C 425 LYS cc_start: 0.9062 (mtmt) cc_final: 0.8691 (mtpp) REVERT: C 429 PHE cc_start: 0.7630 (p90) cc_final: 0.7030 (t80) REVERT: C 474 ARG cc_start: 0.7879 (ttp-110) cc_final: 0.6011 (mpt180) REVERT: C 478 GLU cc_start: 0.8479 (mt-10) cc_final: 0.8005 (mt-10) REVERT: C 511 TYR cc_start: 0.8828 (t80) cc_final: 0.8580 (t80) REVERT: C 551 ASN cc_start: 0.8920 (m-40) cc_final: 0.8450 (m-40) REVERT: C 555 TYR cc_start: 0.9210 (m-80) cc_final: 0.8823 (m-80) REVERT: C 570 GLU cc_start: 0.8758 (tt0) cc_final: 0.8088 (tt0) REVERT: C 694 LYS cc_start: 0.8946 (mttt) cc_final: 0.8743 (ptmt) REVERT: D 397 GLU cc_start: 0.8487 (mt-10) cc_final: 0.8074 (mt-10) REVERT: D 425 LYS cc_start: 0.9042 (mtmt) cc_final: 0.8726 (mtpp) REVERT: D 429 PHE cc_start: 0.7611 (p90) cc_final: 0.7067 (t80) REVERT: D 478 GLU cc_start: 0.8216 (mt-10) cc_final: 0.7755 (mt-10) REVERT: D 498 GLN cc_start: 0.8111 (OUTLIER) cc_final: 0.7882 (pt0) REVERT: D 512 SER cc_start: 0.8798 (OUTLIER) cc_final: 0.8542 (m) REVERT: D 550 THR cc_start: 0.9174 (p) cc_final: 0.8943 (p) REVERT: D 551 ASN cc_start: 0.9007 (m-40) cc_final: 0.8698 (m110) REVERT: D 555 TYR cc_start: 0.9138 (m-80) cc_final: 0.8811 (m-80) REVERT: D 651 GLU cc_start: 0.8274 (mp0) cc_final: 0.7986 (mm-30) REVERT: D 653 TYR cc_start: 0.7920 (p90) cc_final: 0.7613 (p90) REVERT: B 429 PHE cc_start: 0.7715 (p90) cc_final: 0.7255 (t80) REVERT: B 466 LYS cc_start: 0.8168 (mmtm) cc_final: 0.7387 (tptt) REVERT: B 474 ARG cc_start: 0.7743 (ttp-110) cc_final: 0.5979 (mpt180) REVERT: B 478 GLU cc_start: 0.8551 (mt-10) cc_final: 0.8073 (mt-10) REVERT: B 512 SER cc_start: 0.8861 (OUTLIER) cc_final: 0.8496 (m) REVERT: B 555 TYR cc_start: 0.9126 (m-80) cc_final: 0.8663 (m-80) REVERT: B 568 MET cc_start: 0.8353 (OUTLIER) cc_final: 0.7970 (mtp) REVERT: B 687 ASN cc_start: 0.7129 (OUTLIER) cc_final: 0.6302 (m-40) REVERT: B 694 LYS cc_start: 0.8754 (ptmt) cc_final: 0.8302 (pptt) REVERT: B 700 GLN cc_start: 0.8023 (tm-30) cc_final: 0.7309 (tm-30) REVERT: B 709 GLU cc_start: 0.8590 (mt-10) cc_final: 0.8370 (mt-10) outliers start: 35 outliers final: 17 residues processed: 596 average time/residue: 0.1132 time to fit residues: 99.4192 Evaluate side-chains 543 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 520 time to evaluate : 0.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 512 SER Chi-restraints excluded: chain A residue 564 ILE Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 641 THR Chi-restraints excluded: chain C residue 368 LYS Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain C residue 564 ILE Chi-restraints excluded: chain D residue 498 GLN Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 512 SER Chi-restraints excluded: chain D residue 547 MET Chi-restraints excluded: chain D residue 564 ILE Chi-restraints excluded: chain D residue 579 ARG Chi-restraints excluded: chain D residue 673 LEU Chi-restraints excluded: chain D residue 709 GLU Chi-restraints excluded: chain B residue 383 ASP Chi-restraints excluded: chain B residue 475 VAL Chi-restraints excluded: chain B residue 512 SER Chi-restraints excluded: chain B residue 564 ILE Chi-restraints excluded: chain B residue 568 MET Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain B residue 687 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 145 optimal weight: 7.9990 chunk 151 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 13 optimal weight: 3.9990 chunk 41 optimal weight: 9.9990 chunk 129 optimal weight: 0.5980 chunk 23 optimal weight: 0.9990 chunk 137 optimal weight: 0.9990 chunk 105 optimal weight: 0.0980 chunk 71 optimal weight: 0.9980 chunk 98 optimal weight: 0.7980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 297 ASN C 320 HIS C 498 GLN D 498 GLN ** B 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 498 GLN B 560 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.176786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.135157 restraints weight = 22533.009| |-----------------------------------------------------------------------------| r_work (start): 0.3626 rms_B_bonded: 2.94 r_work: 0.3486 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.3726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14608 Z= 0.140 Angle : 0.596 9.535 19800 Z= 0.314 Chirality : 0.040 0.201 2240 Planarity : 0.003 0.028 2400 Dihedral : 7.112 64.166 2274 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 2.39 % Allowed : 18.48 % Favored : 79.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.20), residues: 1692 helix: 1.28 (0.15), residues: 1136 sheet: -1.37 (0.63), residues: 68 loop : -1.68 (0.27), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 721 TYR 0.033 0.002 TYR D 511 PHE 0.012 0.001 PHE A 582 TRP 0.008 0.001 TRP B 740 HIS 0.004 0.001 HIS A 358 Details of bonding type rmsd covalent geometry : bond 0.00293 (14608) covalent geometry : angle 0.59597 (19800) hydrogen bonds : bond 0.04364 ( 904) hydrogen bonds : angle 4.25904 ( 2640) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 591 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 554 time to evaluate : 0.544 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 387 ILE cc_start: 0.8349 (mm) cc_final: 0.8006 (mm) REVERT: A 408 ASN cc_start: 0.7928 (m110) cc_final: 0.7131 (t0) REVERT: A 428 ARG cc_start: 0.8163 (tmt170) cc_final: 0.7948 (tmt170) REVERT: A 438 PHE cc_start: 0.8941 (t80) cc_final: 0.8713 (t80) REVERT: A 475 VAL cc_start: 0.9066 (p) cc_final: 0.8851 (t) REVERT: A 494 GLN cc_start: 0.8941 (tt0) cc_final: 0.8227 (tm-30) REVERT: A 498 GLN cc_start: 0.7931 (mt0) cc_final: 0.7413 (mt0) REVERT: A 512 SER cc_start: 0.8794 (OUTLIER) cc_final: 0.8525 (m) REVERT: A 555 TYR cc_start: 0.8926 (m-80) cc_final: 0.8075 (m-80) REVERT: A 561 GLN cc_start: 0.8087 (tt0) cc_final: 0.6828 (pm20) REVERT: A 570 GLU cc_start: 0.8745 (tt0) cc_final: 0.8491 (tt0) REVERT: A 577 LEU cc_start: 0.8822 (tp) cc_final: 0.8566 (tt) REVERT: A 579 ARG cc_start: 0.7653 (ptp-170) cc_final: 0.7089 (mtm180) REVERT: A 637 LEU cc_start: 0.9125 (mp) cc_final: 0.8804 (mm) REVERT: A 647 LEU cc_start: 0.9147 (tp) cc_final: 0.8877 (tp) REVERT: A 653 TYR cc_start: 0.7889 (p90) cc_final: 0.7642 (p90) REVERT: A 681 LEU cc_start: 0.8524 (mt) cc_final: 0.8040 (mt) REVERT: A 695 ASN cc_start: 0.7795 (m-40) cc_final: 0.7263 (m-40) REVERT: A 700 GLN cc_start: 0.8382 (tp40) cc_final: 0.7590 (tm-30) REVERT: A 701 ARG cc_start: 0.8977 (mmm-85) cc_final: 0.8747 (mmm-85) REVERT: C 387 ILE cc_start: 0.8355 (mm) cc_final: 0.7891 (mm) REVERT: C 429 PHE cc_start: 0.7602 (p90) cc_final: 0.7307 (t80) REVERT: C 474 ARG cc_start: 0.7936 (ttp-110) cc_final: 0.6046 (mpt180) REVERT: C 478 GLU cc_start: 0.8423 (mt-10) cc_final: 0.8006 (mt-10) REVERT: C 511 TYR cc_start: 0.8928 (t80) cc_final: 0.8711 (t80) REVERT: C 551 ASN cc_start: 0.8924 (m-40) cc_final: 0.8525 (m-40) REVERT: C 555 TYR cc_start: 0.9194 (m-80) cc_final: 0.8660 (m-80) REVERT: C 570 GLU cc_start: 0.8780 (tt0) cc_final: 0.8145 (tt0) REVERT: C 647 LEU cc_start: 0.9162 (tp) cc_final: 0.8827 (tp) REVERT: C 706 LEU cc_start: 0.9282 (mp) cc_final: 0.9063 (mp) REVERT: C 709 GLU cc_start: 0.8706 (mt-10) cc_final: 0.8427 (mt-10) REVERT: D 397 GLU cc_start: 0.8478 (mt-10) cc_final: 0.8087 (mt-10) REVERT: D 425 LYS cc_start: 0.9031 (mtmt) cc_final: 0.8737 (mtpp) REVERT: D 429 PHE cc_start: 0.7652 (p90) cc_final: 0.7158 (t80) REVERT: D 474 ARG cc_start: 0.7919 (ttp80) cc_final: 0.5955 (mpt180) REVERT: D 478 GLU cc_start: 0.8101 (mt-10) cc_final: 0.7565 (mt-10) REVERT: D 509 ASP cc_start: 0.8774 (OUTLIER) cc_final: 0.8442 (m-30) REVERT: D 512 SER cc_start: 0.8871 (OUTLIER) cc_final: 0.8584 (m) REVERT: D 550 THR cc_start: 0.9124 (p) cc_final: 0.8896 (p) REVERT: D 551 ASN cc_start: 0.8981 (m-40) cc_final: 0.8695 (m110) REVERT: D 555 TYR cc_start: 0.9013 (m-80) cc_final: 0.8663 (m-80) REVERT: D 647 LEU cc_start: 0.9179 (tp) cc_final: 0.8840 (tp) REVERT: D 651 GLU cc_start: 0.8244 (mp0) cc_final: 0.7930 (mm-30) REVERT: D 653 TYR cc_start: 0.7845 (p90) cc_final: 0.7529 (p90) REVERT: B 429 PHE cc_start: 0.7694 (p90) cc_final: 0.7388 (t80) REVERT: B 466 LYS cc_start: 0.8123 (mmtm) cc_final: 0.7283 (tptm) REVERT: B 474 ARG cc_start: 0.7777 (ttp-110) cc_final: 0.5962 (mpt180) REVERT: B 478 GLU cc_start: 0.8497 (mt-10) cc_final: 0.8065 (mt-10) REVERT: B 512 SER cc_start: 0.8851 (OUTLIER) cc_final: 0.8435 (m) REVERT: B 555 TYR cc_start: 0.9064 (m-80) cc_final: 0.8579 (m-80) REVERT: B 557 ARG cc_start: 0.8566 (mtp85) cc_final: 0.8331 (mtp180) REVERT: B 568 MET cc_start: 0.8434 (OUTLIER) cc_final: 0.8020 (mtp) REVERT: B 572 MET cc_start: 0.8712 (OUTLIER) cc_final: 0.8448 (ttm) REVERT: B 637 LEU cc_start: 0.9147 (mp) cc_final: 0.8891 (mm) REVERT: B 647 LEU cc_start: 0.9142 (tp) cc_final: 0.8831 (tp) REVERT: B 687 ASN cc_start: 0.7180 (OUTLIER) cc_final: 0.6281 (m-40) REVERT: B 694 LYS cc_start: 0.8795 (ptmt) cc_final: 0.8413 (pptt) REVERT: B 700 GLN cc_start: 0.7934 (tm-30) cc_final: 0.7328 (tm-30) outliers start: 37 outliers final: 22 residues processed: 570 average time/residue: 0.1136 time to fit residues: 94.5153 Evaluate side-chains 544 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 515 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 512 SER Chi-restraints excluded: chain A residue 564 ILE Chi-restraints excluded: chain A residue 641 THR Chi-restraints excluded: chain A residue 708 THR Chi-restraints excluded: chain C residue 368 LYS Chi-restraints excluded: chain C residue 408 ASN Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain C residue 564 ILE Chi-restraints excluded: chain C residue 571 LYS Chi-restraints excluded: chain C residue 641 THR Chi-restraints excluded: chain C residue 677 MET Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 509 ASP Chi-restraints excluded: chain D residue 510 SER Chi-restraints excluded: chain D residue 512 SER Chi-restraints excluded: chain D residue 547 MET Chi-restraints excluded: chain D residue 564 ILE Chi-restraints excluded: chain D residue 579 ARG Chi-restraints excluded: chain B residue 383 ASP Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 475 VAL Chi-restraints excluded: chain B residue 512 SER Chi-restraints excluded: chain B residue 564 ILE Chi-restraints excluded: chain B residue 568 MET Chi-restraints excluded: chain B residue 572 MET Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain B residue 687 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 1 optimal weight: 0.9990 chunk 89 optimal weight: 5.9990 chunk 36 optimal weight: 1.9990 chunk 139 optimal weight: 0.3980 chunk 161 optimal weight: 2.9990 chunk 82 optimal weight: 0.9990 chunk 3 optimal weight: 4.9990 chunk 113 optimal weight: 0.9980 chunk 88 optimal weight: 8.9990 chunk 109 optimal weight: 0.0470 chunk 122 optimal weight: 6.9990 overall best weight: 0.6882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 297 ASN C 498 GLN ** B 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 498 GLN B 560 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.176892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.135561 restraints weight = 22546.239| |-----------------------------------------------------------------------------| r_work (start): 0.3632 rms_B_bonded: 2.92 r_work: 0.3490 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.3888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14608 Z= 0.136 Angle : 0.583 10.149 19800 Z= 0.308 Chirality : 0.039 0.272 2240 Planarity : 0.003 0.028 2400 Dihedral : 6.974 64.577 2274 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 2.78 % Allowed : 19.44 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.20), residues: 1692 helix: 1.42 (0.15), residues: 1124 sheet: -1.30 (0.64), residues: 68 loop : -1.33 (0.28), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 355 TYR 0.026 0.002 TYR D 351 PHE 0.030 0.001 PHE C 438 TRP 0.012 0.001 TRP A 697 HIS 0.002 0.001 HIS A 358 Details of bonding type rmsd covalent geometry : bond 0.00289 (14608) covalent geometry : angle 0.58277 (19800) hydrogen bonds : bond 0.04131 ( 904) hydrogen bonds : angle 4.26380 ( 2640) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 598 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 555 time to evaluate : 0.556 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 387 ILE cc_start: 0.8300 (mm) cc_final: 0.7947 (mm) REVERT: A 408 ASN cc_start: 0.7854 (m110) cc_final: 0.7144 (t0) REVERT: A 475 VAL cc_start: 0.9123 (p) cc_final: 0.8807 (t) REVERT: A 478 GLU cc_start: 0.8132 (mt-10) cc_final: 0.7737 (mp0) REVERT: A 551 ASN cc_start: 0.9162 (m-40) cc_final: 0.8878 (m110) REVERT: A 555 TYR cc_start: 0.8866 (m-80) cc_final: 0.7978 (m-80) REVERT: A 561 GLN cc_start: 0.7942 (tt0) cc_final: 0.6599 (pm20) REVERT: A 570 GLU cc_start: 0.8742 (tt0) cc_final: 0.8488 (tt0) REVERT: A 577 LEU cc_start: 0.8819 (tp) cc_final: 0.8555 (tt) REVERT: A 579 ARG cc_start: 0.7607 (ptp-170) cc_final: 0.7017 (mtm180) REVERT: A 580 PHE cc_start: 0.8185 (t80) cc_final: 0.7953 (t80) REVERT: A 637 LEU cc_start: 0.9133 (mp) cc_final: 0.8822 (mp) REVERT: A 647 LEU cc_start: 0.9168 (tp) cc_final: 0.8892 (tp) REVERT: A 653 TYR cc_start: 0.7841 (p90) cc_final: 0.7351 (p90) REVERT: A 695 ASN cc_start: 0.7735 (m-40) cc_final: 0.7057 (m-40) REVERT: A 697 TRP cc_start: 0.8174 (t60) cc_final: 0.7783 (t60) REVERT: A 698 LYS cc_start: 0.8533 (mtmt) cc_final: 0.8100 (mptt) REVERT: A 700 GLN cc_start: 0.8416 (tp40) cc_final: 0.7661 (tm-30) REVERT: A 701 ARG cc_start: 0.8912 (mmm-85) cc_final: 0.8654 (mmm-85) REVERT: C 429 PHE cc_start: 0.7614 (p90) cc_final: 0.7254 (t80) REVERT: C 474 ARG cc_start: 0.7971 (ttp-110) cc_final: 0.6074 (mpt180) REVERT: C 478 GLU cc_start: 0.8444 (mt-10) cc_final: 0.7976 (mt-10) REVERT: C 512 SER cc_start: 0.8694 (OUTLIER) cc_final: 0.8484 (m) REVERT: C 551 ASN cc_start: 0.8901 (m-40) cc_final: 0.8534 (m-40) REVERT: C 555 TYR cc_start: 0.9137 (m-80) cc_final: 0.8577 (m-80) REVERT: C 570 GLU cc_start: 0.8786 (tt0) cc_final: 0.8535 (tt0) REVERT: C 572 MET cc_start: 0.8100 (mtt) cc_final: 0.7728 (mtt) REVERT: C 647 LEU cc_start: 0.9160 (tp) cc_final: 0.8807 (tp) REVERT: C 653 TYR cc_start: 0.7694 (p90) cc_final: 0.7234 (p90) REVERT: C 674 LEU cc_start: 0.8878 (tp) cc_final: 0.8413 (tp) REVERT: C 700 GLN cc_start: 0.8089 (tm-30) cc_final: 0.7135 (tm-30) REVERT: C 706 LEU cc_start: 0.9254 (mp) cc_final: 0.8993 (mp) REVERT: D 397 GLU cc_start: 0.8484 (mt-10) cc_final: 0.8088 (mt-10) REVERT: D 425 LYS cc_start: 0.9057 (mtmt) cc_final: 0.8750 (mtpp) REVERT: D 429 PHE cc_start: 0.7476 (p90) cc_final: 0.7260 (t80) REVERT: D 509 ASP cc_start: 0.8892 (OUTLIER) cc_final: 0.8552 (m-30) REVERT: D 550 THR cc_start: 0.9071 (p) cc_final: 0.8848 (p) REVERT: D 551 ASN cc_start: 0.9000 (m-40) cc_final: 0.8693 (m110) REVERT: D 647 LEU cc_start: 0.9180 (tp) cc_final: 0.8821 (tp) REVERT: D 651 GLU cc_start: 0.8181 (mp0) cc_final: 0.7944 (mm-30) REVERT: D 653 TYR cc_start: 0.7776 (p90) cc_final: 0.7494 (p90) REVERT: D 694 LYS cc_start: 0.8907 (mttt) cc_final: 0.8649 (ptmt) REVERT: D 715 CYS cc_start: 0.4686 (m) cc_final: 0.4207 (m) REVERT: B 429 PHE cc_start: 0.7603 (p90) cc_final: 0.7303 (t80) REVERT: B 466 LYS cc_start: 0.8133 (mmtm) cc_final: 0.7194 (tmtt) REVERT: B 474 ARG cc_start: 0.7822 (ttp-110) cc_final: 0.6001 (mpt180) REVERT: B 478 GLU cc_start: 0.8491 (mt-10) cc_final: 0.8020 (mt-10) REVERT: B 512 SER cc_start: 0.8839 (OUTLIER) cc_final: 0.8522 (m) REVERT: B 547 MET cc_start: 0.8648 (mtp) cc_final: 0.8237 (mtp) REVERT: B 551 ASN cc_start: 0.9089 (m-40) cc_final: 0.8598 (m110) REVERT: B 555 TYR cc_start: 0.9040 (m-80) cc_final: 0.8409 (m-80) REVERT: B 557 ARG cc_start: 0.8632 (mtp85) cc_final: 0.8326 (mtp180) REVERT: B 568 MET cc_start: 0.8447 (OUTLIER) cc_final: 0.8191 (mtp) REVERT: B 637 LEU cc_start: 0.9147 (mp) cc_final: 0.8893 (mm) REVERT: B 647 LEU cc_start: 0.9153 (tp) cc_final: 0.8820 (tp) REVERT: B 687 ASN cc_start: 0.7172 (OUTLIER) cc_final: 0.6262 (m-40) REVERT: B 694 LYS cc_start: 0.8785 (ptmt) cc_final: 0.8401 (pptt) REVERT: B 700 GLN cc_start: 0.7937 (tm-30) cc_final: 0.7374 (tm-30) REVERT: B 715 CYS cc_start: 0.4459 (m) cc_final: 0.4218 (m) outliers start: 43 outliers final: 26 residues processed: 571 average time/residue: 0.1119 time to fit residues: 93.8556 Evaluate side-chains 557 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 526 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 564 ILE Chi-restraints excluded: chain A residue 641 THR Chi-restraints excluded: chain A residue 652 ASN Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 708 THR Chi-restraints excluded: chain C residue 368 LYS Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain C residue 512 SER Chi-restraints excluded: chain C residue 547 MET Chi-restraints excluded: chain C residue 564 ILE Chi-restraints excluded: chain C residue 634 CYS Chi-restraints excluded: chain C residue 641 THR Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 509 ASP Chi-restraints excluded: chain D residue 547 MET Chi-restraints excluded: chain D residue 564 ILE Chi-restraints excluded: chain D residue 579 ARG Chi-restraints excluded: chain D residue 709 GLU Chi-restraints excluded: chain B residue 383 ASP Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 437 ASN Chi-restraints excluded: chain B residue 475 VAL Chi-restraints excluded: chain B residue 512 SER Chi-restraints excluded: chain B residue 564 ILE Chi-restraints excluded: chain B residue 568 MET Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain B residue 687 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 141 optimal weight: 0.5980 chunk 131 optimal weight: 0.9990 chunk 25 optimal weight: 3.9990 chunk 97 optimal weight: 0.9990 chunk 98 optimal weight: 0.8980 chunk 75 optimal weight: 0.6980 chunk 30 optimal weight: 0.6980 chunk 76 optimal weight: 1.9990 chunk 88 optimal weight: 0.9990 chunk 155 optimal weight: 0.9980 chunk 35 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 297 ASN ** B 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 560 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.182631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.141854 restraints weight = 22510.761| |-----------------------------------------------------------------------------| r_work (start): 0.3734 rms_B_bonded: 2.99 r_work: 0.3602 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.4064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 14608 Z= 0.139 Angle : 0.603 11.837 19800 Z= 0.315 Chirality : 0.040 0.331 2240 Planarity : 0.003 0.027 2400 Dihedral : 6.991 67.659 2274 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 2.78 % Allowed : 20.54 % Favored : 76.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.20), residues: 1692 helix: 1.44 (0.15), residues: 1120 sheet: -1.29 (0.63), residues: 68 loop : -1.39 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 355 TYR 0.025 0.002 TYR D 351 PHE 0.028 0.001 PHE A 438 TRP 0.014 0.001 TRP A 697 HIS 0.002 0.001 HIS D 358 Details of bonding type rmsd covalent geometry : bond 0.00300 (14608) covalent geometry : angle 0.60330 (19800) hydrogen bonds : bond 0.04003 ( 904) hydrogen bonds : angle 4.28391 ( 2640) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 591 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 548 time to evaluate : 0.522 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 387 ILE cc_start: 0.8292 (mm) cc_final: 0.7948 (mm) REVERT: A 408 ASN cc_start: 0.7785 (m110) cc_final: 0.7182 (t0) REVERT: A 475 VAL cc_start: 0.9154 (p) cc_final: 0.8735 (t) REVERT: A 478 GLU cc_start: 0.8067 (mt-10) cc_final: 0.7689 (mp0) REVERT: A 494 GLN cc_start: 0.8983 (tt0) cc_final: 0.8512 (tm-30) REVERT: A 551 ASN cc_start: 0.9193 (m-40) cc_final: 0.8891 (m110) REVERT: A 555 TYR cc_start: 0.8867 (m-80) cc_final: 0.8133 (m-80) REVERT: A 561 GLN cc_start: 0.7949 (tt0) cc_final: 0.6809 (mp10) REVERT: A 570 GLU cc_start: 0.8682 (tt0) cc_final: 0.8417 (tt0) REVERT: A 577 LEU cc_start: 0.8811 (tp) cc_final: 0.8495 (tt) REVERT: A 579 ARG cc_start: 0.7546 (ptp-170) cc_final: 0.7000 (mtm180) REVERT: A 637 LEU cc_start: 0.9156 (mp) cc_final: 0.8835 (mp) REVERT: A 647 LEU cc_start: 0.9145 (tp) cc_final: 0.8885 (tp) REVERT: A 653 TYR cc_start: 0.7808 (p90) cc_final: 0.7338 (p90) REVERT: A 655 PHE cc_start: 0.8325 (m-80) cc_final: 0.8116 (m-80) REVERT: A 695 ASN cc_start: 0.7671 (m-40) cc_final: 0.6676 (m-40) REVERT: A 700 GLN cc_start: 0.8340 (tp40) cc_final: 0.7634 (tm-30) REVERT: A 701 ARG cc_start: 0.8927 (mmm-85) cc_final: 0.8692 (mmm-85) REVERT: A 706 LEU cc_start: 0.9213 (mp) cc_final: 0.8920 (mp) REVERT: C 408 ASN cc_start: 0.7542 (OUTLIER) cc_final: 0.7112 (t0) REVERT: C 474 ARG cc_start: 0.7971 (ttp-110) cc_final: 0.6011 (mpt180) REVERT: C 478 GLU cc_start: 0.8414 (mt-10) cc_final: 0.7971 (mt-10) REVERT: C 540 SER cc_start: 0.8948 (t) cc_final: 0.8740 (p) REVERT: C 551 ASN cc_start: 0.8931 (m-40) cc_final: 0.8549 (m-40) REVERT: C 555 TYR cc_start: 0.9070 (m-80) cc_final: 0.8492 (m-80) REVERT: C 557 ARG cc_start: 0.8404 (OUTLIER) cc_final: 0.8075 (mtp85) REVERT: C 570 GLU cc_start: 0.8769 (tt0) cc_final: 0.8534 (tt0) REVERT: C 600 GLU cc_start: 0.7942 (pt0) cc_final: 0.7724 (pt0) REVERT: C 647 LEU cc_start: 0.9146 (tp) cc_final: 0.8835 (tp) REVERT: C 653 TYR cc_start: 0.7745 (p90) cc_final: 0.7317 (p90) REVERT: C 700 GLN cc_start: 0.8066 (tm-30) cc_final: 0.7122 (tm-30) REVERT: C 706 LEU cc_start: 0.9224 (mp) cc_final: 0.8914 (mp) REVERT: D 397 GLU cc_start: 0.8464 (mt-10) cc_final: 0.8081 (mt-10) REVERT: D 420 ARG cc_start: 0.8448 (mmm160) cc_final: 0.8178 (mmm160) REVERT: D 425 LYS cc_start: 0.9084 (mtmt) cc_final: 0.8870 (mtpp) REVERT: D 429 PHE cc_start: 0.7471 (p90) cc_final: 0.7199 (t80) REVERT: D 478 GLU cc_start: 0.8030 (mt-10) cc_final: 0.7704 (mp0) REVERT: D 509 ASP cc_start: 0.8911 (OUTLIER) cc_final: 0.8560 (m-30) REVERT: D 550 THR cc_start: 0.9074 (p) cc_final: 0.8832 (p) REVERT: D 551 ASN cc_start: 0.9051 (m-40) cc_final: 0.8718 (m110) REVERT: D 647 LEU cc_start: 0.9144 (tp) cc_final: 0.8847 (tp) REVERT: D 651 GLU cc_start: 0.8169 (mp0) cc_final: 0.7955 (mm-30) REVERT: D 653 TYR cc_start: 0.7809 (p90) cc_final: 0.7558 (p90) REVERT: D 694 LYS cc_start: 0.8965 (mttt) cc_final: 0.8699 (ptmt) REVERT: D 715 CYS cc_start: 0.4715 (m) cc_final: 0.4235 (m) REVERT: D 740 TRP cc_start: 0.5962 (m-10) cc_final: 0.5636 (m-10) REVERT: B 363 ARG cc_start: 0.6476 (OUTLIER) cc_final: 0.5327 (ptt180) REVERT: B 408 ASN cc_start: 0.7747 (m110) cc_final: 0.6871 (t0) REVERT: B 429 PHE cc_start: 0.7645 (p90) cc_final: 0.7348 (t80) REVERT: B 466 LYS cc_start: 0.8148 (mmtm) cc_final: 0.7211 (tmtt) REVERT: B 474 ARG cc_start: 0.7846 (ttp-110) cc_final: 0.6014 (mpt180) REVERT: B 478 GLU cc_start: 0.8396 (mt-10) cc_final: 0.7918 (mt-10) REVERT: B 512 SER cc_start: 0.8846 (OUTLIER) cc_final: 0.8486 (m) REVERT: B 547 MET cc_start: 0.8628 (mtp) cc_final: 0.8288 (mtp) REVERT: B 551 ASN cc_start: 0.9112 (m-40) cc_final: 0.8628 (m110) REVERT: B 555 TYR cc_start: 0.8995 (m-80) cc_final: 0.8500 (m-80) REVERT: B 557 ARG cc_start: 0.8616 (mtp85) cc_final: 0.8281 (mtp180) REVERT: B 568 MET cc_start: 0.8566 (OUTLIER) cc_final: 0.8288 (mtp) REVERT: B 647 LEU cc_start: 0.9141 (tp) cc_final: 0.8834 (tp) REVERT: B 687 ASN cc_start: 0.7160 (OUTLIER) cc_final: 0.6163 (m-40) REVERT: B 692 GLU cc_start: 0.7878 (mt-10) cc_final: 0.7424 (mp0) REVERT: B 694 LYS cc_start: 0.8760 (ptmt) cc_final: 0.8387 (pptt) REVERT: B 700 GLN cc_start: 0.8002 (tm-30) cc_final: 0.7328 (tm-30) REVERT: B 706 LEU cc_start: 0.9216 (mp) cc_final: 0.8943 (mp) REVERT: B 715 CYS cc_start: 0.4410 (m) cc_final: 0.4121 (m) outliers start: 43 outliers final: 26 residues processed: 568 average time/residue: 0.1112 time to fit residues: 92.9056 Evaluate side-chains 556 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 523 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 564 ILE Chi-restraints excluded: chain A residue 634 CYS Chi-restraints excluded: chain A residue 641 THR Chi-restraints excluded: chain A residue 652 ASN Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain C residue 368 LYS Chi-restraints excluded: chain C residue 408 ASN Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain C residue 547 MET Chi-restraints excluded: chain C residue 557 ARG Chi-restraints excluded: chain C residue 564 ILE Chi-restraints excluded: chain D residue 421 LEU Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 509 ASP Chi-restraints excluded: chain D residue 547 MET Chi-restraints excluded: chain D residue 564 ILE Chi-restraints excluded: chain D residue 579 ARG Chi-restraints excluded: chain D residue 641 THR Chi-restraints excluded: chain D residue 709 GLU Chi-restraints excluded: chain B residue 309 TYR Chi-restraints excluded: chain B residue 363 ARG Chi-restraints excluded: chain B residue 383 ASP Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 475 VAL Chi-restraints excluded: chain B residue 512 SER Chi-restraints excluded: chain B residue 564 ILE Chi-restraints excluded: chain B residue 568 MET Chi-restraints excluded: chain B residue 641 THR Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain B residue 687 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 126 optimal weight: 10.0000 chunk 62 optimal weight: 0.9990 chunk 17 optimal weight: 0.0370 chunk 41 optimal weight: 10.0000 chunk 163 optimal weight: 2.9990 chunk 84 optimal weight: 10.0000 chunk 104 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 121 optimal weight: 5.9990 chunk 52 optimal weight: 6.9990 overall best weight: 1.5664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 297 ASN C 687 ASN ** B 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.179538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.138377 restraints weight = 22565.307| |-----------------------------------------------------------------------------| r_work (start): 0.3692 rms_B_bonded: 2.98 r_work: 0.3559 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.4073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 14608 Z= 0.190 Angle : 0.649 13.751 19800 Z= 0.337 Chirality : 0.042 0.336 2240 Planarity : 0.003 0.028 2400 Dihedral : 7.114 69.358 2274 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 3.17 % Allowed : 20.54 % Favored : 76.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.20), residues: 1692 helix: 1.16 (0.15), residues: 1148 sheet: -1.26 (0.64), residues: 68 loop : -1.53 (0.28), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 355 TYR 0.026 0.002 TYR C 351 PHE 0.031 0.002 PHE C 438 TRP 0.027 0.001 TRP A 697 HIS 0.003 0.001 HIS D 358 Details of bonding type rmsd covalent geometry : bond 0.00428 (14608) covalent geometry : angle 0.64926 (19800) hydrogen bonds : bond 0.04175 ( 904) hydrogen bonds : angle 4.35995 ( 2640) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 585 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 536 time to evaluate : 0.476 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 304 PHE cc_start: 0.7415 (t80) cc_final: 0.7205 (t80) REVERT: A 387 ILE cc_start: 0.8387 (mm) cc_final: 0.8055 (mm) REVERT: A 408 ASN cc_start: 0.7791 (m110) cc_final: 0.7245 (t0) REVERT: A 475 VAL cc_start: 0.9184 (p) cc_final: 0.8971 (t) REVERT: A 478 GLU cc_start: 0.8054 (mt-10) cc_final: 0.7746 (mp0) REVERT: A 511 TYR cc_start: 0.8678 (t80) cc_final: 0.8356 (t80) REVERT: A 551 ASN cc_start: 0.9197 (m-40) cc_final: 0.8888 (m110) REVERT: A 555 TYR cc_start: 0.9014 (m-80) cc_final: 0.8341 (m-80) REVERT: A 561 GLN cc_start: 0.8040 (tt0) cc_final: 0.6939 (mp10) REVERT: A 571 LYS cc_start: 0.7985 (OUTLIER) cc_final: 0.7400 (tptt) REVERT: A 577 LEU cc_start: 0.8895 (tp) cc_final: 0.8619 (tt) REVERT: A 647 LEU cc_start: 0.9161 (tp) cc_final: 0.8914 (tp) REVERT: A 653 TYR cc_start: 0.7913 (p90) cc_final: 0.7525 (p90) REVERT: A 700 GLN cc_start: 0.8388 (tp40) cc_final: 0.7645 (tm-30) REVERT: A 701 ARG cc_start: 0.8972 (mmm-85) cc_final: 0.8669 (mmm-85) REVERT: A 706 LEU cc_start: 0.9217 (mp) cc_final: 0.8912 (mp) REVERT: C 387 ILE cc_start: 0.8464 (mm) cc_final: 0.7932 (mm) REVERT: C 397 GLU cc_start: 0.8477 (mt-10) cc_final: 0.8206 (pt0) REVERT: C 408 ASN cc_start: 0.7598 (OUTLIER) cc_final: 0.7219 (t0) REVERT: C 425 LYS cc_start: 0.8735 (mtmt) cc_final: 0.8168 (tptt) REVERT: C 474 ARG cc_start: 0.8001 (ttp-110) cc_final: 0.5993 (mpt180) REVERT: C 478 GLU cc_start: 0.8326 (mt-10) cc_final: 0.7847 (mt-10) REVERT: C 540 SER cc_start: 0.8987 (t) cc_final: 0.8780 (p) REVERT: C 551 ASN cc_start: 0.9002 (m-40) cc_final: 0.8634 (m-40) REVERT: C 555 TYR cc_start: 0.9099 (m-80) cc_final: 0.8654 (m-80) REVERT: C 557 ARG cc_start: 0.8434 (OUTLIER) cc_final: 0.8084 (mtp85) REVERT: C 653 TYR cc_start: 0.7903 (p90) cc_final: 0.7486 (p90) REVERT: C 662 LEU cc_start: 0.9070 (mt) cc_final: 0.8831 (mt) REVERT: C 706 LEU cc_start: 0.9212 (mp) cc_final: 0.8911 (mp) REVERT: C 709 GLU cc_start: 0.8730 (mt-10) cc_final: 0.8349 (mt-10) REVERT: D 397 GLU cc_start: 0.8471 (mt-10) cc_final: 0.8098 (mt-10) REVERT: D 420 ARG cc_start: 0.8507 (mmm160) cc_final: 0.8235 (mmm160) REVERT: D 429 PHE cc_start: 0.7453 (p90) cc_final: 0.7248 (t80) REVERT: D 478 GLU cc_start: 0.8029 (mt-10) cc_final: 0.7601 (mp0) REVERT: D 509 ASP cc_start: 0.8897 (OUTLIER) cc_final: 0.8554 (m-30) REVERT: D 536 GLU cc_start: 0.8492 (mp0) cc_final: 0.8259 (mp0) REVERT: D 550 THR cc_start: 0.9182 (p) cc_final: 0.8971 (p) REVERT: D 551 ASN cc_start: 0.9178 (m-40) cc_final: 0.8812 (m110) REVERT: D 651 GLU cc_start: 0.8199 (mp0) cc_final: 0.7984 (mm-30) REVERT: D 653 TYR cc_start: 0.7913 (p90) cc_final: 0.7667 (p90) REVERT: D 694 LYS cc_start: 0.9000 (mttt) cc_final: 0.8708 (ptmt) REVERT: D 715 CYS cc_start: 0.4687 (m) cc_final: 0.4258 (m) REVERT: D 740 TRP cc_start: 0.6049 (m-10) cc_final: 0.5787 (m-10) REVERT: B 363 ARG cc_start: 0.6474 (OUTLIER) cc_final: 0.5295 (ptt180) REVERT: B 408 ASN cc_start: 0.7774 (m110) cc_final: 0.6925 (t0) REVERT: B 420 ARG cc_start: 0.8428 (mmm160) cc_final: 0.7961 (mmm160) REVERT: B 466 LYS cc_start: 0.8178 (mmtm) cc_final: 0.7329 (tptm) REVERT: B 474 ARG cc_start: 0.7919 (ttp-110) cc_final: 0.6009 (mpt180) REVERT: B 478 GLU cc_start: 0.8314 (mt-10) cc_final: 0.7814 (mt-10) REVERT: B 498 GLN cc_start: 0.8514 (pp30) cc_final: 0.8222 (pp30) REVERT: B 512 SER cc_start: 0.8940 (OUTLIER) cc_final: 0.8616 (m) REVERT: B 547 MET cc_start: 0.8679 (mtp) cc_final: 0.8452 (mtp) REVERT: B 551 ASN cc_start: 0.9171 (m-40) cc_final: 0.8729 (m110) REVERT: B 555 TYR cc_start: 0.9120 (m-80) cc_final: 0.8652 (m-80) REVERT: B 568 MET cc_start: 0.8518 (OUTLIER) cc_final: 0.8163 (mtp) REVERT: B 647 LEU cc_start: 0.9190 (tp) cc_final: 0.8851 (tp) REVERT: B 700 GLN cc_start: 0.8116 (tm-30) cc_final: 0.7385 (tm-30) REVERT: B 706 LEU cc_start: 0.9210 (mp) cc_final: 0.8918 (mp) REVERT: B 715 CYS cc_start: 0.4467 (m) cc_final: 0.4168 (m) outliers start: 49 outliers final: 37 residues processed: 552 average time/residue: 0.1148 time to fit residues: 93.0835 Evaluate side-chains 558 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 514 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 TYR Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 498 GLN Chi-restraints excluded: chain A residue 564 ILE Chi-restraints excluded: chain A residue 571 LYS Chi-restraints excluded: chain A residue 634 CYS Chi-restraints excluded: chain A residue 641 THR Chi-restraints excluded: chain A residue 652 ASN Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain C residue 368 LYS Chi-restraints excluded: chain C residue 408 ASN Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain C residue 547 MET Chi-restraints excluded: chain C residue 557 ARG Chi-restraints excluded: chain C residue 564 ILE Chi-restraints excluded: chain C residue 641 THR Chi-restraints excluded: chain C residue 652 ASN Chi-restraints excluded: chain D residue 421 LEU Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 509 ASP Chi-restraints excluded: chain D residue 547 MET Chi-restraints excluded: chain D residue 564 ILE Chi-restraints excluded: chain D residue 579 ARG Chi-restraints excluded: chain D residue 641 THR Chi-restraints excluded: chain D residue 652 ASN Chi-restraints excluded: chain D residue 673 LEU Chi-restraints excluded: chain D residue 709 GLU Chi-restraints excluded: chain B residue 309 TYR Chi-restraints excluded: chain B residue 363 ARG Chi-restraints excluded: chain B residue 383 ASP Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 475 VAL Chi-restraints excluded: chain B residue 512 SER Chi-restraints excluded: chain B residue 564 ILE Chi-restraints excluded: chain B residue 568 MET Chi-restraints excluded: chain B residue 641 THR Chi-restraints excluded: chain B residue 652 ASN Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain B residue 687 ASN Chi-restraints excluded: chain B residue 698 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 137 optimal weight: 0.9980 chunk 156 optimal weight: 0.4980 chunk 32 optimal weight: 3.9990 chunk 58 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 92 optimal weight: 7.9990 chunk 71 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 chunk 60 optimal weight: 6.9990 chunk 96 optimal weight: 9.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 297 ASN ** B 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.180645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.139839 restraints weight = 22566.103| |-----------------------------------------------------------------------------| r_work (start): 0.3712 rms_B_bonded: 2.98 r_work: 0.3580 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.4245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 14608 Z= 0.159 Angle : 0.643 12.747 19800 Z= 0.334 Chirality : 0.041 0.327 2240 Planarity : 0.003 0.028 2400 Dihedral : 6.984 67.337 2274 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 13.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 2.91 % Allowed : 21.71 % Favored : 75.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.20), residues: 1692 helix: 1.13 (0.15), residues: 1144 sheet: -1.24 (0.65), residues: 68 loop : -1.54 (0.28), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 499 TYR 0.025 0.002 TYR C 351 PHE 0.014 0.001 PHE A 582 TRP 0.018 0.001 TRP A 697 HIS 0.002 0.001 HIS A 358 Details of bonding type rmsd covalent geometry : bond 0.00357 (14608) covalent geometry : angle 0.64277 (19800) hydrogen bonds : bond 0.04103 ( 904) hydrogen bonds : angle 4.40724 ( 2640) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 580 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 535 time to evaluate : 0.539 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 387 ILE cc_start: 0.8225 (mm) cc_final: 0.7896 (mm) REVERT: A 408 ASN cc_start: 0.7721 (m110) cc_final: 0.7327 (t0) REVERT: A 478 GLU cc_start: 0.8058 (mt-10) cc_final: 0.7790 (mp0) REVERT: A 551 ASN cc_start: 0.9177 (m-40) cc_final: 0.8849 (m110) REVERT: A 555 TYR cc_start: 0.8998 (m-80) cc_final: 0.8342 (m-80) REVERT: A 561 GLN cc_start: 0.8041 (tt0) cc_final: 0.6927 (mp10) REVERT: A 571 LYS cc_start: 0.7827 (OUTLIER) cc_final: 0.7402 (tptt) REVERT: A 577 LEU cc_start: 0.8826 (tp) cc_final: 0.8512 (tt) REVERT: A 653 TYR cc_start: 0.7897 (p90) cc_final: 0.7531 (p90) REVERT: A 655 PHE cc_start: 0.8331 (m-80) cc_final: 0.8124 (m-80) REVERT: A 695 ASN cc_start: 0.7686 (m110) cc_final: 0.7449 (m-40) REVERT: A 697 TRP cc_start: 0.8263 (t60) cc_final: 0.7859 (t60) REVERT: A 700 GLN cc_start: 0.8386 (tp40) cc_final: 0.7609 (tm-30) REVERT: A 706 LEU cc_start: 0.9220 (mp) cc_final: 0.8923 (mp) REVERT: C 387 ILE cc_start: 0.8468 (mm) cc_final: 0.7963 (mm) REVERT: C 397 GLU cc_start: 0.8468 (mt-10) cc_final: 0.8235 (pt0) REVERT: C 408 ASN cc_start: 0.7596 (OUTLIER) cc_final: 0.7221 (t0) REVERT: C 425 LYS cc_start: 0.8727 (mtmt) cc_final: 0.8173 (tptp) REVERT: C 478 GLU cc_start: 0.8272 (mt-10) cc_final: 0.7880 (mt-10) REVERT: C 540 SER cc_start: 0.8953 (t) cc_final: 0.8752 (p) REVERT: C 551 ASN cc_start: 0.8979 (m-40) cc_final: 0.8605 (m-40) REVERT: C 555 TYR cc_start: 0.9059 (m-80) cc_final: 0.8607 (m-80) REVERT: C 570 GLU cc_start: 0.8594 (tt0) cc_final: 0.8352 (tt0) REVERT: C 653 TYR cc_start: 0.7875 (p90) cc_final: 0.7446 (p90) REVERT: C 709 GLU cc_start: 0.8691 (mt-10) cc_final: 0.8313 (mt-10) REVERT: D 397 GLU cc_start: 0.8488 (mt-10) cc_final: 0.8148 (mt-10) REVERT: D 478 GLU cc_start: 0.8041 (mt-10) cc_final: 0.7626 (mp0) REVERT: D 498 GLN cc_start: 0.7904 (pt0) cc_final: 0.7590 (pt0) REVERT: D 509 ASP cc_start: 0.8948 (OUTLIER) cc_final: 0.8616 (m-30) REVERT: D 536 GLU cc_start: 0.8475 (mp0) cc_final: 0.8231 (mp0) REVERT: D 550 THR cc_start: 0.9157 (p) cc_final: 0.8945 (p) REVERT: D 551 ASN cc_start: 0.9124 (m-40) cc_final: 0.8773 (m110) REVERT: D 570 GLU cc_start: 0.8502 (tt0) cc_final: 0.8260 (tt0) REVERT: D 651 GLU cc_start: 0.8201 (mp0) cc_final: 0.7968 (mm-30) REVERT: D 653 TYR cc_start: 0.7800 (p90) cc_final: 0.7552 (p90) REVERT: D 694 LYS cc_start: 0.9024 (mttt) cc_final: 0.8753 (ptmt) REVERT: D 740 TRP cc_start: 0.6234 (m-10) cc_final: 0.6019 (m-10) REVERT: B 363 ARG cc_start: 0.6468 (OUTLIER) cc_final: 0.5288 (ptt180) REVERT: B 408 ASN cc_start: 0.7759 (m110) cc_final: 0.6966 (t0) REVERT: B 412 MET cc_start: 0.8372 (ttm) cc_final: 0.7823 (ttm) REVERT: B 420 ARG cc_start: 0.8485 (mmm160) cc_final: 0.8022 (mmm160) REVERT: B 466 LYS cc_start: 0.8219 (mmtm) cc_final: 0.7249 (tmtt) REVERT: B 474 ARG cc_start: 0.7880 (ttp-110) cc_final: 0.5979 (mpt180) REVERT: B 478 GLU cc_start: 0.8317 (mt-10) cc_final: 0.7840 (mt-10) REVERT: B 498 GLN cc_start: 0.8470 (pp30) cc_final: 0.8178 (pp30) REVERT: B 512 SER cc_start: 0.8933 (OUTLIER) cc_final: 0.8550 (m) REVERT: B 551 ASN cc_start: 0.9135 (m-40) cc_final: 0.8674 (m110) REVERT: B 555 TYR cc_start: 0.9033 (m-80) cc_final: 0.8700 (m-80) REVERT: B 557 ARG cc_start: 0.8455 (mtp85) cc_final: 0.8014 (mtp180) REVERT: B 568 MET cc_start: 0.8481 (OUTLIER) cc_final: 0.8154 (mtp) REVERT: B 647 LEU cc_start: 0.9176 (tp) cc_final: 0.8804 (tp) REVERT: B 694 LYS cc_start: 0.8892 (ptmt) cc_final: 0.8598 (pttm) REVERT: B 700 GLN cc_start: 0.8055 (tm-30) cc_final: 0.7333 (tm-30) REVERT: B 706 LEU cc_start: 0.9195 (mp) cc_final: 0.8911 (mp) REVERT: B 715 CYS cc_start: 0.4328 (m) cc_final: 0.4047 (m) outliers start: 45 outliers final: 32 residues processed: 554 average time/residue: 0.1128 time to fit residues: 91.3422 Evaluate side-chains 551 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 513 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 TYR Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 564 ILE Chi-restraints excluded: chain A residue 571 LYS Chi-restraints excluded: chain A residue 641 THR Chi-restraints excluded: chain A residue 652 ASN Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain C residue 368 LYS Chi-restraints excluded: chain C residue 408 ASN Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain C residue 547 MET Chi-restraints excluded: chain C residue 564 ILE Chi-restraints excluded: chain D residue 421 LEU Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 509 ASP Chi-restraints excluded: chain D residue 547 MET Chi-restraints excluded: chain D residue 564 ILE Chi-restraints excluded: chain D residue 579 ARG Chi-restraints excluded: chain D residue 652 ASN Chi-restraints excluded: chain D residue 673 LEU Chi-restraints excluded: chain D residue 709 GLU Chi-restraints excluded: chain B residue 309 TYR Chi-restraints excluded: chain B residue 363 ARG Chi-restraints excluded: chain B residue 383 ASP Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 475 VAL Chi-restraints excluded: chain B residue 512 SER Chi-restraints excluded: chain B residue 564 ILE Chi-restraints excluded: chain B residue 568 MET Chi-restraints excluded: chain B residue 641 THR Chi-restraints excluded: chain B residue 652 ASN Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain B residue 687 ASN Chi-restraints excluded: chain B residue 698 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 54 optimal weight: 2.9990 chunk 151 optimal weight: 0.9990 chunk 165 optimal weight: 0.9990 chunk 97 optimal weight: 4.9990 chunk 59 optimal weight: 0.2980 chunk 29 optimal weight: 0.9990 chunk 156 optimal weight: 0.5980 chunk 128 optimal weight: 4.9990 chunk 64 optimal weight: 0.7980 chunk 35 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 297 ASN ** B 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.182212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.140940 restraints weight = 22589.116| |-----------------------------------------------------------------------------| r_work (start): 0.3724 rms_B_bonded: 3.03 r_work: 0.3587 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.4415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 14608 Z= 0.147 Angle : 0.653 17.186 19800 Z= 0.339 Chirality : 0.041 0.373 2240 Planarity : 0.003 0.028 2400 Dihedral : 6.909 66.536 2274 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 13.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 2.84 % Allowed : 22.03 % Favored : 75.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.20), residues: 1692 helix: 1.16 (0.15), residues: 1140 sheet: -1.28 (0.65), residues: 68 loop : -1.60 (0.27), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 355 TYR 0.026 0.002 TYR C 351 PHE 0.032 0.001 PHE C 438 TRP 0.016 0.001 TRP A 697 HIS 0.005 0.001 HIS A 410 Details of bonding type rmsd covalent geometry : bond 0.00327 (14608) covalent geometry : angle 0.65348 (19800) hydrogen bonds : bond 0.04034 ( 904) hydrogen bonds : angle 4.43595 ( 2640) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 578 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 534 time to evaluate : 0.532 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 387 ILE cc_start: 0.8158 (mm) cc_final: 0.7835 (mm) REVERT: A 408 ASN cc_start: 0.7717 (m110) cc_final: 0.7375 (t0) REVERT: A 474 ARG cc_start: 0.7879 (ttp80) cc_final: 0.5992 (mpt180) REVERT: A 478 GLU cc_start: 0.8075 (mt-10) cc_final: 0.7705 (mp0) REVERT: A 480 LEU cc_start: 0.9114 (mm) cc_final: 0.8722 (mm) REVERT: A 499 ARG cc_start: 0.8177 (mmp80) cc_final: 0.7929 (mmp80) REVERT: A 551 ASN cc_start: 0.9147 (m-40) cc_final: 0.8837 (m110) REVERT: A 555 TYR cc_start: 0.9017 (m-80) cc_final: 0.8454 (m-80) REVERT: A 557 ARG cc_start: 0.8542 (mtp180) cc_final: 0.8044 (mtp85) REVERT: A 561 GLN cc_start: 0.7983 (tt0) cc_final: 0.6897 (mp10) REVERT: A 570 GLU cc_start: 0.8441 (tm-30) cc_final: 0.8186 (tt0) REVERT: A 571 LYS cc_start: 0.7807 (OUTLIER) cc_final: 0.7350 (tptt) REVERT: A 637 LEU cc_start: 0.9181 (mp) cc_final: 0.8858 (mp) REVERT: A 653 TYR cc_start: 0.7850 (p90) cc_final: 0.7491 (p90) REVERT: A 677 MET cc_start: 0.8138 (mmt) cc_final: 0.6751 (mmt) REVERT: A 695 ASN cc_start: 0.7629 (m110) cc_final: 0.7331 (m-40) REVERT: A 700 GLN cc_start: 0.8344 (tp40) cc_final: 0.7547 (tm-30) REVERT: A 701 ARG cc_start: 0.9006 (mmm-85) cc_final: 0.8742 (mmm-85) REVERT: A 706 LEU cc_start: 0.9205 (mp) cc_final: 0.8908 (mp) REVERT: C 387 ILE cc_start: 0.8392 (mm) cc_final: 0.7894 (mm) REVERT: C 397 GLU cc_start: 0.8469 (mt-10) cc_final: 0.7858 (pt0) REVERT: C 408 ASN cc_start: 0.7543 (OUTLIER) cc_final: 0.7212 (t0) REVERT: C 425 LYS cc_start: 0.8701 (mtmt) cc_final: 0.8123 (tptp) REVERT: C 478 GLU cc_start: 0.8279 (mt-10) cc_final: 0.7870 (mt-10) REVERT: C 540 SER cc_start: 0.8967 (t) cc_final: 0.8760 (p) REVERT: C 551 ASN cc_start: 0.8967 (m-40) cc_final: 0.8611 (m-40) REVERT: C 555 TYR cc_start: 0.9023 (m-80) cc_final: 0.8601 (m-80) REVERT: C 570 GLU cc_start: 0.8520 (tt0) cc_final: 0.8249 (tt0) REVERT: C 647 LEU cc_start: 0.9155 (tp) cc_final: 0.8924 (tp) REVERT: C 653 TYR cc_start: 0.7860 (p90) cc_final: 0.7451 (p90) REVERT: C 706 LEU cc_start: 0.9168 (mp) cc_final: 0.8817 (mp) REVERT: C 709 GLU cc_start: 0.8706 (mt-10) cc_final: 0.8335 (mt-10) REVERT: D 397 GLU cc_start: 0.8481 (mt-10) cc_final: 0.8124 (mt-10) REVERT: D 478 GLU cc_start: 0.8016 (mt-10) cc_final: 0.7591 (mp0) REVERT: D 498 GLN cc_start: 0.7912 (pt0) cc_final: 0.7639 (pt0) REVERT: D 509 ASP cc_start: 0.8935 (OUTLIER) cc_final: 0.8606 (m-30) REVERT: D 536 GLU cc_start: 0.8525 (mp0) cc_final: 0.8259 (mp0) REVERT: D 550 THR cc_start: 0.9119 (p) cc_final: 0.8903 (p) REVERT: D 551 ASN cc_start: 0.9078 (m-40) cc_final: 0.8722 (m110) REVERT: D 557 ARG cc_start: 0.8352 (mtp85) cc_final: 0.7625 (mtp180) REVERT: D 570 GLU cc_start: 0.8507 (tt0) cc_final: 0.8208 (tt0) REVERT: D 647 LEU cc_start: 0.9158 (tp) cc_final: 0.8929 (tp) REVERT: D 651 GLU cc_start: 0.8171 (mp0) cc_final: 0.7952 (mm-30) REVERT: D 653 TYR cc_start: 0.7795 (p90) cc_final: 0.7560 (p90) REVERT: D 694 LYS cc_start: 0.9034 (mttt) cc_final: 0.8752 (ptmt) REVERT: D 740 TRP cc_start: 0.6015 (m-10) cc_final: 0.5805 (m-10) REVERT: B 363 ARG cc_start: 0.6462 (OUTLIER) cc_final: 0.5302 (ptt180) REVERT: B 408 ASN cc_start: 0.7760 (m110) cc_final: 0.6976 (t0) REVERT: B 420 ARG cc_start: 0.8474 (mmm160) cc_final: 0.8013 (mmm160) REVERT: B 466 LYS cc_start: 0.8201 (mmtm) cc_final: 0.7232 (tmtt) REVERT: B 474 ARG cc_start: 0.7869 (ttp-110) cc_final: 0.5977 (mpt180) REVERT: B 478 GLU cc_start: 0.8289 (mt-10) cc_final: 0.7787 (mt-10) REVERT: B 512 SER cc_start: 0.8975 (OUTLIER) cc_final: 0.8618 (m) REVERT: B 551 ASN cc_start: 0.9097 (m-40) cc_final: 0.8599 (m110) REVERT: B 555 TYR cc_start: 0.8958 (m-80) cc_final: 0.8673 (m-80) REVERT: B 557 ARG cc_start: 0.8375 (mtp85) cc_final: 0.8012 (mtp180) REVERT: B 568 MET cc_start: 0.8490 (OUTLIER) cc_final: 0.8041 (mtp) REVERT: B 572 MET cc_start: 0.8231 (ttm) cc_final: 0.7741 (mtm) REVERT: B 647 LEU cc_start: 0.9165 (tp) cc_final: 0.8824 (tp) REVERT: B 692 GLU cc_start: 0.7929 (mt-10) cc_final: 0.7335 (mp0) REVERT: B 694 LYS cc_start: 0.8866 (ptmt) cc_final: 0.8565 (pttm) REVERT: B 700 GLN cc_start: 0.7991 (tm-30) cc_final: 0.7338 (tm-30) REVERT: B 706 LEU cc_start: 0.9167 (mp) cc_final: 0.8862 (mp) outliers start: 44 outliers final: 35 residues processed: 551 average time/residue: 0.1154 time to fit residues: 93.4408 Evaluate side-chains 556 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 515 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 TYR Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 564 ILE Chi-restraints excluded: chain A residue 571 LYS Chi-restraints excluded: chain A residue 641 THR Chi-restraints excluded: chain A residue 652 ASN Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain C residue 368 LYS Chi-restraints excluded: chain C residue 408 ASN Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain C residue 547 MET Chi-restraints excluded: chain C residue 564 ILE Chi-restraints excluded: chain C residue 652 ASN Chi-restraints excluded: chain D residue 421 LEU Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 509 ASP Chi-restraints excluded: chain D residue 547 MET Chi-restraints excluded: chain D residue 560 GLN Chi-restraints excluded: chain D residue 564 ILE Chi-restraints excluded: chain D residue 579 ARG Chi-restraints excluded: chain D residue 652 ASN Chi-restraints excluded: chain D residue 673 LEU Chi-restraints excluded: chain D residue 709 GLU Chi-restraints excluded: chain B residue 309 TYR Chi-restraints excluded: chain B residue 363 ARG Chi-restraints excluded: chain B residue 383 ASP Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 475 VAL Chi-restraints excluded: chain B residue 512 SER Chi-restraints excluded: chain B residue 564 ILE Chi-restraints excluded: chain B residue 568 MET Chi-restraints excluded: chain B residue 579 ARG Chi-restraints excluded: chain B residue 634 CYS Chi-restraints excluded: chain B residue 641 THR Chi-restraints excluded: chain B residue 652 ASN Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain B residue 687 ASN Chi-restraints excluded: chain B residue 698 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 92 optimal weight: 9.9990 chunk 32 optimal weight: 0.9980 chunk 3 optimal weight: 3.9990 chunk 154 optimal weight: 0.9980 chunk 63 optimal weight: 0.0970 chunk 76 optimal weight: 0.7980 chunk 56 optimal weight: 0.9980 chunk 143 optimal weight: 0.0670 chunk 125 optimal weight: 0.0770 chunk 149 optimal weight: 1.9990 chunk 47 optimal weight: 0.0040 overall best weight: 0.2086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 297 ASN D 320 HIS ** B 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.181901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.140951 restraints weight = 22400.899| |-----------------------------------------------------------------------------| r_work (start): 0.3717 rms_B_bonded: 3.00 r_work: 0.3583 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.4691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 14608 Z= 0.135 Angle : 0.665 16.626 19800 Z= 0.342 Chirality : 0.041 0.335 2240 Planarity : 0.003 0.027 2400 Dihedral : 6.709 64.815 2274 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 13.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 2.39 % Allowed : 22.93 % Favored : 74.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.21), residues: 1692 helix: 1.18 (0.15), residues: 1144 sheet: -1.22 (0.65), residues: 68 loop : -1.58 (0.28), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 499 TYR 0.026 0.001 TYR C 351 PHE 0.022 0.001 PHE A 304 TRP 0.032 0.001 TRP A 697 HIS 0.005 0.001 HIS A 410 Details of bonding type rmsd covalent geometry : bond 0.00290 (14608) covalent geometry : angle 0.66496 (19800) hydrogen bonds : bond 0.03966 ( 904) hydrogen bonds : angle 4.43586 ( 2640) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 575 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 538 time to evaluate : 0.503 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 387 ILE cc_start: 0.8187 (mm) cc_final: 0.7848 (mm) REVERT: A 408 ASN cc_start: 0.7656 (m110) cc_final: 0.7138 (t0) REVERT: A 412 MET cc_start: 0.8633 (ttm) cc_final: 0.8245 (ttm) REVERT: A 474 ARG cc_start: 0.7859 (ttp80) cc_final: 0.5999 (mpt180) REVERT: A 478 GLU cc_start: 0.8078 (mt-10) cc_final: 0.7780 (mp0) REVERT: A 499 ARG cc_start: 0.8186 (mmp80) cc_final: 0.7923 (mmp80) REVERT: A 551 ASN cc_start: 0.9074 (m-40) cc_final: 0.8745 (m110) REVERT: A 555 TYR cc_start: 0.8857 (m-80) cc_final: 0.8383 (m-80) REVERT: A 557 ARG cc_start: 0.8550 (mtp180) cc_final: 0.7712 (mtp85) REVERT: A 561 GLN cc_start: 0.7749 (tt0) cc_final: 0.6708 (mp10) REVERT: A 570 GLU cc_start: 0.8336 (tm-30) cc_final: 0.8031 (tt0) REVERT: A 571 LYS cc_start: 0.7617 (OUTLIER) cc_final: 0.7112 (tptt) REVERT: A 637 LEU cc_start: 0.9164 (mp) cc_final: 0.8909 (mm) REVERT: A 653 TYR cc_start: 0.7640 (p90) cc_final: 0.7225 (p90) REVERT: A 677 MET cc_start: 0.7956 (mmt) cc_final: 0.6533 (mmt) REVERT: A 695 ASN cc_start: 0.7736 (m110) cc_final: 0.7316 (m-40) REVERT: A 700 GLN cc_start: 0.8405 (tp40) cc_final: 0.7624 (tm-30) REVERT: A 701 ARG cc_start: 0.9033 (mmm-85) cc_final: 0.8809 (mmm-85) REVERT: A 706 LEU cc_start: 0.9198 (mp) cc_final: 0.8838 (mp) REVERT: C 364 HIS cc_start: 0.6714 (p-80) cc_final: 0.5592 (m-70) REVERT: C 387 ILE cc_start: 0.8406 (mm) cc_final: 0.7860 (mm) REVERT: C 397 GLU cc_start: 0.8479 (mt-10) cc_final: 0.7832 (pt0) REVERT: C 406 THR cc_start: 0.7244 (m) cc_final: 0.6883 (p) REVERT: C 408 ASN cc_start: 0.7644 (OUTLIER) cc_final: 0.7314 (t0) REVERT: C 425 LYS cc_start: 0.8654 (mtmt) cc_final: 0.8104 (tptp) REVERT: C 474 ARG cc_start: 0.7949 (ttp-110) cc_final: 0.5912 (mpt180) REVERT: C 478 GLU cc_start: 0.8247 (mt-10) cc_final: 0.7998 (mt-10) REVERT: C 494 GLN cc_start: 0.9009 (tt0) cc_final: 0.8699 (tm-30) REVERT: C 540 SER cc_start: 0.8913 (t) cc_final: 0.8696 (p) REVERT: C 551 ASN cc_start: 0.8908 (m-40) cc_final: 0.8585 (m-40) REVERT: C 555 TYR cc_start: 0.8877 (m-80) cc_final: 0.8339 (m-80) REVERT: C 564 ILE cc_start: 0.7269 (OUTLIER) cc_final: 0.7043 (pt) REVERT: C 570 GLU cc_start: 0.8439 (tt0) cc_final: 0.8149 (tt0) REVERT: C 647 LEU cc_start: 0.9087 (tp) cc_final: 0.8886 (tp) REVERT: C 653 TYR cc_start: 0.7690 (p90) cc_final: 0.7307 (p90) REVERT: C 709 GLU cc_start: 0.8729 (mt-10) cc_final: 0.8382 (mt-10) REVERT: D 397 GLU cc_start: 0.8501 (mt-10) cc_final: 0.8148 (mt-10) REVERT: D 435 TYR cc_start: 0.8569 (m-80) cc_final: 0.8099 (m-80) REVERT: D 478 GLU cc_start: 0.8076 (mt-10) cc_final: 0.7712 (mp0) REVERT: D 498 GLN cc_start: 0.8004 (pt0) cc_final: 0.7737 (pt0) REVERT: D 509 ASP cc_start: 0.8907 (OUTLIER) cc_final: 0.8642 (m-30) REVERT: D 550 THR cc_start: 0.8952 (p) cc_final: 0.8706 (p) REVERT: D 551 ASN cc_start: 0.9018 (m-40) cc_final: 0.8752 (m110) REVERT: D 647 LEU cc_start: 0.9110 (tp) cc_final: 0.8835 (tp) REVERT: D 653 TYR cc_start: 0.7632 (p90) cc_final: 0.7279 (p90) REVERT: D 694 LYS cc_start: 0.9104 (mttt) cc_final: 0.8818 (ptmt) REVERT: B 363 ARG cc_start: 0.6483 (OUTLIER) cc_final: 0.5255 (ptt180) REVERT: B 408 ASN cc_start: 0.7688 (m110) cc_final: 0.6954 (t0) REVERT: B 474 ARG cc_start: 0.7879 (ttp-110) cc_final: 0.6010 (mpt180) REVERT: B 478 GLU cc_start: 0.8333 (mt-10) cc_final: 0.7887 (mt-10) REVERT: B 512 SER cc_start: 0.8895 (OUTLIER) cc_final: 0.8565 (m) REVERT: B 555 TYR cc_start: 0.8909 (m-80) cc_final: 0.8648 (m-80) REVERT: B 557 ARG cc_start: 0.8351 (mtp85) cc_final: 0.8080 (mtp180) REVERT: B 568 MET cc_start: 0.8465 (OUTLIER) cc_final: 0.7992 (mtp) REVERT: B 572 MET cc_start: 0.8116 (ttm) cc_final: 0.7793 (mtm) REVERT: B 647 LEU cc_start: 0.9128 (tp) cc_final: 0.8808 (tp) REVERT: B 651 GLU cc_start: 0.7998 (mm-30) cc_final: 0.7791 (mm-30) REVERT: B 653 TYR cc_start: 0.7622 (p90) cc_final: 0.7334 (p90) REVERT: B 662 LEU cc_start: 0.8909 (mt) cc_final: 0.8685 (mt) REVERT: B 694 LYS cc_start: 0.8895 (ptmt) cc_final: 0.8624 (pttm) REVERT: B 700 GLN cc_start: 0.7865 (tm-30) cc_final: 0.7364 (tm-30) REVERT: B 706 LEU cc_start: 0.9086 (mp) cc_final: 0.8784 (mp) outliers start: 37 outliers final: 27 residues processed: 555 average time/residue: 0.1113 time to fit residues: 90.8793 Evaluate side-chains 544 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 510 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 TYR Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 564 ILE Chi-restraints excluded: chain A residue 571 LYS Chi-restraints excluded: chain A residue 652 ASN Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain C residue 368 LYS Chi-restraints excluded: chain C residue 408 ASN Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain C residue 547 MET Chi-restraints excluded: chain C residue 564 ILE Chi-restraints excluded: chain C residue 652 ASN Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 509 ASP Chi-restraints excluded: chain D residue 547 MET Chi-restraints excluded: chain D residue 560 GLN Chi-restraints excluded: chain D residue 564 ILE Chi-restraints excluded: chain D residue 579 ARG Chi-restraints excluded: chain D residue 652 ASN Chi-restraints excluded: chain D residue 709 GLU Chi-restraints excluded: chain B residue 309 TYR Chi-restraints excluded: chain B residue 363 ARG Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 475 VAL Chi-restraints excluded: chain B residue 512 SER Chi-restraints excluded: chain B residue 564 ILE Chi-restraints excluded: chain B residue 568 MET Chi-restraints excluded: chain B residue 579 ARG Chi-restraints excluded: chain B residue 634 CYS Chi-restraints excluded: chain B residue 652 ASN Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain B residue 687 ASN Chi-restraints excluded: chain B residue 698 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 145 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 106 optimal weight: 0.9990 chunk 89 optimal weight: 3.9990 chunk 96 optimal weight: 0.9980 chunk 70 optimal weight: 2.9990 chunk 124 optimal weight: 0.0040 chunk 9 optimal weight: 20.0000 chunk 53 optimal weight: 10.0000 chunk 121 optimal weight: 0.9990 chunk 92 optimal weight: 9.9990 overall best weight: 0.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 320 HIS ** B 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.179902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.138660 restraints weight = 22449.479| |-----------------------------------------------------------------------------| r_work (start): 0.3674 rms_B_bonded: 2.94 r_work: 0.3542 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.4719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 14608 Z= 0.152 Angle : 0.682 16.617 19800 Z= 0.352 Chirality : 0.042 0.338 2240 Planarity : 0.003 0.028 2400 Dihedral : 6.843 68.717 2274 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 13.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 2.65 % Allowed : 23.51 % Favored : 73.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.21), residues: 1692 helix: 1.15 (0.15), residues: 1148 sheet: -1.06 (0.66), residues: 68 loop : -1.54 (0.28), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 557 TYR 0.025 0.002 TYR B 351 PHE 0.023 0.001 PHE C 438 TRP 0.036 0.001 TRP A 697 HIS 0.004 0.001 HIS A 410 Details of bonding type rmsd covalent geometry : bond 0.00345 (14608) covalent geometry : angle 0.68169 (19800) hydrogen bonds : bond 0.03951 ( 904) hydrogen bonds : angle 4.45276 ( 2640) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3453.33 seconds wall clock time: 59 minutes 55.34 seconds (3595.34 seconds total)