Starting phenix.real_space_refine on Fri Jul 3 13:51:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7l2l_23132/07_2026/7l2l_23132.cif Found real_map, /net/cci-nas-00/data/ceres_data/7l2l_23132/07_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 { model { file = "/net/cci-nas-00/data/ceres_data/7l2l_23132/07_2026/7l2l_23132.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7l2l_23132/07_2026/7l2l_23132.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7l2l_23132/07_2026/7l2l_23132.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7l2l_23132/07_2026/7l2l_23132.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7l2l_23132/07_2026/7l2l_23132.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7l2l_23132/07_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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: 2.91, 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: 1.05 Conformation dependent library (CDL) restraints added in 473.4 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: 0.21 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: 1.84 Time building geometry restraints manager: 1.33 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: 7856 17.73 - 35.47: 578 35.47 - 53.20: 52 53.20 - 70.94: 23 70.94 - 88.67: 7 Dihedral angle restraints: 8516 sinusoidal: 3432 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 8513 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: 2.270 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: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 11.990 Find NCS groups from input model: 0.400 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:0.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 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 : 12.333 88.671 5244 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/Z covalent geometry : bond 0.01629 / 0.79 (14608) covalent geometry : angle 1.14173 / 0.58 (19800) hydrogen bonds : bond 0.15277 / 10.43 ( 904) hydrogen bonds : angle 6.08879 / 4.36 ( 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 : 0.376 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: 0.1218 time to fit residues: 110.9741 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 : 0.575 ------------------------------------------------------------------------------- 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... ** 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 687 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.174404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.131860 restraints weight = 22459.582| |-----------------------------------------------------------------------------| r_work (start): 0.3594 rms_B_bonded: 2.88 r_work: 0.3454 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.2727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 14608 Z= 0.178 Angle : 0.662 7.768 19800 Z= 0.350 Chirality : 0.041 0.212 2240 Planarity : 0.004 0.039 2400 Dihedral : 6.419 79.634 1930 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.39 % Allowed : 13.82 % Favored : 83.79 % 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: 0.34 (0.20), residues: 1692 helix: 1.12 (0.15), residues: 1136 sheet: -1.41 (0.62), residues: 68 loop : -1.62 (0.28), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 355 TYR 0.030 0.002 TYR D 351 PHE 0.022 0.002 PHE C 659 TRP 0.015 0.002 TRP A 697 HIS 0.005 0.001 HIS C 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.18 (14608) covalent geometry : angle 0.66188 / 0.35 (19800) hydrogen bonds : bond 0.05473 / 3.74 ( 904) hydrogen bonds : angle 4.59335 / 3.28 ( 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 647 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 610 time to evaluate : 0.598 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: 0.8358 (mm) cc_final: 0.8014 (mm) REVERT: A 431 LYS cc_start: 0.9009 (ttpt) cc_final: 0.8769 (ttpt) REVERT: A 475 VAL cc_start: 0.9101 (p) cc_final: 0.8716 (t) REVERT: A 478 GLU cc_start: 0.8148 (mt-10) cc_final: 0.7751 (mt-10) REVERT: A 517 PHE cc_start: 0.9114 (t80) cc_final: 0.8715 (t80) REVERT: A 521 LEU cc_start: 0.9240 (mt) cc_final: 0.9033 (mp) REVERT: A 555 TYR cc_start: 0.9137 (m-80) cc_final: 0.8363 (m-80) REVERT: A 561 GLN cc_start: 0.7976 (tt0) cc_final: 0.6813 (pm20) REVERT: A 570 GLU cc_start: 0.8721 (tt0) cc_final: 0.8410 (tt0) REVERT: A 577 LEU cc_start: 0.8935 (tp) cc_final: 0.8611 (tt) REVERT: A 579 ARG cc_start: 0.7763 (ptp-170) cc_final: 0.7011 (mtm-85) REVERT: A 681 LEU cc_start: 0.8613 (mt) cc_final: 0.8128 (mt) REVERT: A 695 ASN cc_start: 0.7756 (m-40) cc_final: 0.7290 (m-40) REVERT: A 700 GLN cc_start: 0.8446 (tp40) cc_final: 0.7594 (tm-30) REVERT: A 743 ARG cc_start: 0.7768 (mtp85) cc_final: 0.6832 (mpt180) REVERT: C 429 PHE cc_start: 0.7722 (p90) cc_final: 0.7110 (t80) REVERT: C 474 ARG cc_start: 0.7847 (ttp-110) cc_final: 0.5969 (mpt180) REVERT: C 478 GLU cc_start: 0.8430 (mt-10) cc_final: 0.8007 (mt-10) REVERT: C 480 LEU cc_start: 0.9017 (OUTLIER) cc_final: 0.8625 (mp) REVERT: C 511 TYR cc_start: 0.8972 (t80) cc_final: 0.8642 (t80) REVERT: C 551 ASN cc_start: 0.8984 (m-40) cc_final: 0.8468 (m-40) REVERT: C 555 TYR cc_start: 0.9306 (m-80) cc_final: 0.8961 (m-80) REVERT: C 570 GLU cc_start: 0.8756 (tt0) cc_final: 0.8052 (tt0) REVERT: D 397 GLU cc_start: 0.8452 (mt-10) cc_final: 0.8033 (mt-10) REVERT: D 401 TYR cc_start: 0.7315 (m-80) cc_final: 0.6886 (m-80) REVERT: D 425 LYS cc_start: 0.9024 (mtmt) cc_final: 0.8745 (mtpp) REVERT: D 426 TRP cc_start: 0.9039 (t-100) cc_final: 0.8508 (t-100) REVERT: D 429 PHE cc_start: 0.7691 (p90) cc_final: 0.6878 (t80) REVERT: D 432 ARG cc_start: 0.7810 (mmt180) cc_final: 0.7610 (mmt180) REVERT: D 478 GLU cc_start: 0.8206 (mt-10) cc_final: 0.7805 (mt-10) REVERT: D 494 GLN cc_start: 0.9079 (tt0) cc_final: 0.8729 (tm-30) REVERT: D 517 PHE cc_start: 0.9141 (t80) cc_final: 0.8938 (t80) REVERT: D 550 THR cc_start: 0.9283 (p) cc_final: 0.9046 (p) REVERT: D 551 ASN cc_start: 0.9033 (m-40) cc_final: 0.8703 (m110) REVERT: D 555 TYR cc_start: 0.9165 (m-80) cc_final: 0.8686 (m-80) REVERT: D 577 LEU cc_start: 0.8976 (tp) cc_final: 0.8722 (tt) REVERT: D 629 SER cc_start: 0.8764 (p) cc_final: 0.8539 (m) REVERT: D 651 GLU cc_start: 0.8265 (mp0) cc_final: 0.7995 (mm-30) REVERT: D 653 TYR cc_start: 0.8008 (p90) cc_final: 0.7746 (p90) REVERT: D 696 ILE cc_start: 0.8282 (tt) cc_final: 0.8071 (mt) REVERT: D 743 ARG cc_start: 0.8607 (mtm180) cc_final: 0.7753 (tmm160) REVERT: B 429 PHE cc_start: 0.7636 (p90) cc_final: 0.7157 (t80) REVERT: B 466 LYS cc_start: 0.8172 (mmtm) cc_final: 0.7426 (tptt) REVERT: B 474 ARG cc_start: 0.7753 (ttp-110) cc_final: 0.5901 (mpt180) REVERT: B 478 GLU cc_start: 0.8543 (mt-10) cc_final: 0.8093 (mt-10) REVERT: B 517 PHE cc_start: 0.9080 (t80) cc_final: 0.8858 (t80) REVERT: B 551 ASN cc_start: 0.9127 (m-40) cc_final: 0.8687 (m110) REVERT: B 555 TYR cc_start: 0.9238 (m-80) cc_final: 0.9009 (m-80) REVERT: B 568 MET cc_start: 0.8399 (OUTLIER) cc_final: 0.8068 (mtp) REVERT: B 629 SER cc_start: 0.8837 (p) cc_final: 0.8636 (m) REVERT: B 662 LEU cc_start: 0.8941 (mt) cc_final: 0.8542 (mt) REVERT: B 687 ASN cc_start: 0.6950 (OUTLIER) cc_final: 0.6388 (m-40) REVERT: B 689 ILE cc_start: 0.7683 (mm) cc_final: 0.7338 (mm) REVERT: B 695 ASN cc_start: 0.7865 (m-40) cc_final: 0.7371 (m-40) REVERT: B 700 GLN cc_start: 0.8141 (tm-30) cc_final: 0.7299 (tm-30) outliers start: 37 outliers final: 18 residues processed: 625 average time/residue: 0.1088 time to fit residues: 100.9318 Evaluate side-chains 563 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 542 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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: 5.9990 chunk 52 optimal weight: 0.3980 chunk 78 optimal weight: 0.5980 chunk 99 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 chunk 41 optimal weight: 7.9990 chunk 162 optimal weight: 0.8980 chunk 12 optimal weight: 0.8980 chunk 51 optimal weight: 6.9990 chunk 28 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 297 ASN C 320 HIS C 498 GLN C 695 ASN D 297 ASN D 498 GLN ** B 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 297 ASN B 364 HIS B 498 GLN B 560 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.175048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.132765 restraints weight = 22602.616| |-----------------------------------------------------------------------------| r_work (start): 0.3611 rms_B_bonded: 2.93 r_work: 0.3471 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.3339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14608 Z= 0.150 Angle : 0.589 7.879 19800 Z= 0.315 Chirality : 0.040 0.183 2240 Planarity : 0.003 0.029 2400 Dihedral : 5.875 67.583 1930 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 2.58 % Allowed : 17.38 % Favored : 80.04 % 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: 0.48 (0.20), residues: 1692 helix: 1.24 (0.15), residues: 1144 sheet: -1.44 (0.64), residues: 68 loop : -1.64 (0.28), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 721 TYR 0.028 0.002 TYR D 351 PHE 0.028 0.002 PHE B 438 TRP 0.019 0.001 TRP A 697 HIS 0.004 0.001 HIS C 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.15 (14608) covalent geometry : angle 0.58862 / 0.31 (19800) hydrogen bonds : bond 0.04774 / 3.25 ( 904) hydrogen bonds : angle 4.36391 / 3.10 ( 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 616 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 576 time to evaluate : 0.519 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: A 387 ILE cc_start: 0.8346 (mm) cc_final: 0.8134 (mm) REVERT: A 394 SER cc_start: 0.8135 (p) cc_final: 0.7542 (p) REVERT: A 419 ASN cc_start: 0.7514 (p0) cc_final: 0.7240 (p0) REVERT: A 475 VAL cc_start: 0.9104 (p) cc_final: 0.8714 (t) REVERT: A 478 GLU cc_start: 0.8141 (mt-10) cc_final: 0.7707 (mt-10) REVERT: A 494 GLN cc_start: 0.8937 (tt0) cc_final: 0.8390 (tm-30) REVERT: A 498 GLN cc_start: 0.8124 (mt0) cc_final: 0.7473 (mt0) REVERT: A 499 ARG cc_start: 0.8247 (mmp80) cc_final: 0.7974 (mmp80) REVERT: A 547 MET cc_start: 0.8764 (mtp) cc_final: 0.8319 (mtp) REVERT: A 551 ASN cc_start: 0.9143 (m-40) cc_final: 0.8865 (m110) REVERT: A 555 TYR cc_start: 0.9026 (m-80) cc_final: 0.8194 (m-80) REVERT: A 561 GLN cc_start: 0.8014 (tt0) cc_final: 0.6772 (pm20) REVERT: A 570 GLU cc_start: 0.8740 (tt0) cc_final: 0.8365 (tt0) REVERT: A 577 LEU cc_start: 0.8903 (tp) cc_final: 0.8662 (tt) REVERT: A 579 ARG cc_start: 0.7644 (ptp-170) cc_final: 0.6896 (mtm180) REVERT: A 647 LEU cc_start: 0.9129 (tp) cc_final: 0.8826 (tp) REVERT: A 653 TYR cc_start: 0.7903 (p90) cc_final: 0.7432 (p90) REVERT: A 681 LEU cc_start: 0.8449 (mt) cc_final: 0.7750 (mt) REVERT: A 695 ASN cc_start: 0.7811 (m-40) cc_final: 0.7189 (m-40) REVERT: A 700 GLN cc_start: 0.8481 (tp40) cc_final: 0.7625 (tm-30) REVERT: A 701 ARG cc_start: 0.8974 (mmm-85) cc_final: 0.8713 (mmm-85) REVERT: A 720 PHE cc_start: 0.5717 (m-80) cc_final: 0.5142 (p90) REVERT: C 425 LYS cc_start: 0.9053 (mtmt) cc_final: 0.8683 (mtpp) REVERT: C 429 PHE cc_start: 0.7614 (p90) cc_final: 0.7059 (t80) REVERT: C 474 ARG cc_start: 0.7894 (ttp-110) cc_final: 0.6007 (mpt180) REVERT: C 478 GLU cc_start: 0.8478 (mt-10) cc_final: 0.7996 (mt-10) REVERT: C 511 TYR cc_start: 0.8838 (t80) cc_final: 0.8591 (t80) REVERT: C 551 ASN cc_start: 0.8932 (m-40) cc_final: 0.8474 (m-40) REVERT: C 555 TYR cc_start: 0.9264 (m-80) cc_final: 0.8908 (m-80) REVERT: C 570 GLU cc_start: 0.8760 (tt0) cc_final: 0.8085 (tt0) REVERT: C 694 LYS cc_start: 0.8994 (mttt) cc_final: 0.8725 (ptmt) REVERT: C 695 ASN cc_start: 0.7501 (OUTLIER) cc_final: 0.7142 (m-40) REVERT: D 397 GLU cc_start: 0.8485 (mt-10) cc_final: 0.8075 (mt-10) REVERT: D 425 LYS cc_start: 0.9078 (mtmt) cc_final: 0.8795 (mtpp) REVERT: D 429 PHE cc_start: 0.7636 (p90) cc_final: 0.7119 (t80) REVERT: D 478 GLU cc_start: 0.8223 (mt-10) cc_final: 0.7760 (mt-10) REVERT: D 498 GLN cc_start: 0.8129 (OUTLIER) cc_final: 0.7841 (pt0) REVERT: D 512 SER cc_start: 0.8816 (OUTLIER) cc_final: 0.8534 (m) REVERT: D 550 THR cc_start: 0.9169 (p) cc_final: 0.8923 (p) REVERT: D 551 ASN cc_start: 0.9008 (m-40) cc_final: 0.8713 (m110) REVERT: D 555 TYR cc_start: 0.9146 (m-80) cc_final: 0.8755 (m-80) REVERT: D 570 GLU cc_start: 0.8698 (tt0) cc_final: 0.8480 (tt0) REVERT: D 651 GLU cc_start: 0.8280 (mp0) cc_final: 0.7995 (mm-30) REVERT: D 653 TYR cc_start: 0.7928 (p90) cc_final: 0.7617 (p90) REVERT: D 669 LEU cc_start: 0.9139 (OUTLIER) cc_final: 0.8930 (mm) REVERT: B 429 PHE cc_start: 0.7704 (p90) cc_final: 0.7217 (t80) REVERT: B 466 LYS cc_start: 0.8170 (mmtm) cc_final: 0.7389 (tptt) REVERT: B 474 ARG cc_start: 0.7759 (ttp-110) cc_final: 0.5979 (mpt180) REVERT: B 478 GLU cc_start: 0.8535 (mt-10) cc_final: 0.8058 (mt-10) REVERT: B 495 TYR cc_start: 0.9154 (t80) cc_final: 0.8921 (t80) REVERT: B 512 SER cc_start: 0.8876 (OUTLIER) cc_final: 0.8541 (m) REVERT: B 553 LEU cc_start: 0.9080 (mp) cc_final: 0.8848 (mp) REVERT: B 555 TYR cc_start: 0.9115 (m-80) cc_final: 0.8709 (m-80) REVERT: B 568 MET cc_start: 0.8348 (OUTLIER) cc_final: 0.7923 (mtp) REVERT: B 572 MET cc_start: 0.8897 (ttp) cc_final: 0.8685 (ttp) REVERT: B 653 TYR cc_start: 0.7933 (p90) cc_final: 0.7441 (p90) REVERT: B 687 ASN cc_start: 0.7129 (OUTLIER) cc_final: 0.6299 (m-40) REVERT: B 694 LYS cc_start: 0.8775 (ptmt) cc_final: 0.8309 (pptt) REVERT: B 700 GLN cc_start: 0.8038 (tm-30) cc_final: 0.7320 (tm-30) outliers start: 40 outliers final: 17 residues processed: 593 average time/residue: 0.0977 time to fit residues: 86.0308 Evaluate side-chains 549 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 525 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 564 ILE Chi-restraints excluded: chain A residue 641 THR Chi-restraints excluded: chain C residue 368 LYS Chi-restraints excluded: chain C residue 408 ASN Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain C residue 564 ILE Chi-restraints excluded: chain C residue 695 ASN 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 564 ILE Chi-restraints excluded: chain D residue 579 ARG Chi-restraints excluded: chain D residue 669 LEU Chi-restraints excluded: chain D residue 673 LEU Chi-restraints excluded: chain D residue 685 THR Chi-restraints excluded: chain D residue 698 LYS 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: 0.7980 chunk 151 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 41 optimal weight: 5.9990 chunk 129 optimal weight: 0.9980 chunk 23 optimal weight: 4.9990 chunk 137 optimal weight: 0.9990 chunk 105 optimal weight: 0.0470 chunk 71 optimal weight: 3.9990 chunk 98 optimal weight: 0.9980 overall best weight: 0.7678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4134 r_free = 0.4134 target = 0.176163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.134683 restraints weight = 22503.479| |-----------------------------------------------------------------------------| r_work (start): 0.3623 rms_B_bonded: 2.90 r_work: 0.3483 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.3665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14608 Z= 0.145 Angle : 0.594 8.669 19800 Z= 0.314 Chirality : 0.039 0.182 2240 Planarity : 0.003 0.028 2400 Dihedral : 5.604 60.243 1930 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 2.58 % Allowed : 19.12 % Favored : 78.29 % 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: 0.51 (0.20), residues: 1692 helix: 1.25 (0.15), residues: 1144 sheet: -1.40 (0.63), residues: 68 loop : -1.61 (0.28), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 355 TYR 0.029 0.002 TYR D 511 PHE 0.027 0.001 PHE C 438 TRP 0.009 0.001 TRP A 697 HIS 0.004 0.001 HIS A 358 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 (14608) covalent geometry : angle 0.59449 / 0.31 (19800) hydrogen bonds : bond 0.04395 / 2.98 ( 904) hydrogen bonds : angle 4.28206 / 3.04 ( 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 585 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 545 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 387 ILE cc_start: 0.8392 (mm) cc_final: 0.8167 (mm) REVERT: A 408 ASN cc_start: 0.7942 (m110) cc_final: 0.7164 (t0) REVERT: A 428 ARG cc_start: 0.8186 (tmt170) cc_final: 0.7969 (tmt170) REVERT: A 475 VAL cc_start: 0.9099 (p) cc_final: 0.8880 (t) REVERT: A 512 SER cc_start: 0.8757 (OUTLIER) cc_final: 0.8545 (m) REVERT: A 555 TYR cc_start: 0.8927 (m-80) cc_final: 0.8056 (m-80) REVERT: A 561 GLN cc_start: 0.8079 (tt0) cc_final: 0.6817 (pm20) REVERT: A 570 GLU cc_start: 0.8763 (tt0) cc_final: 0.8466 (tt0) REVERT: A 577 LEU cc_start: 0.8884 (tp) cc_final: 0.8644 (tt) REVERT: A 579 ARG cc_start: 0.7658 (ptp-170) cc_final: 0.7085 (mtm180) REVERT: A 637 LEU cc_start: 0.9274 (mt) cc_final: 0.9039 (mp) REVERT: A 647 LEU cc_start: 0.9161 (tp) cc_final: 0.8877 (tp) REVERT: A 653 TYR cc_start: 0.7884 (p90) cc_final: 0.7648 (p90) REVERT: A 681 LEU cc_start: 0.8515 (mt) cc_final: 0.8065 (mt) REVERT: A 695 ASN cc_start: 0.7763 (m-40) cc_final: 0.7225 (m-40) REVERT: A 700 GLN cc_start: 0.8386 (tp40) cc_final: 0.7602 (tm-30) REVERT: A 701 ARG cc_start: 0.8974 (mmm-85) cc_final: 0.8750 (mmm-85) REVERT: C 387 ILE cc_start: 0.8420 (mm) cc_final: 0.7958 (mm) REVERT: C 425 LYS cc_start: 0.9103 (mtmt) cc_final: 0.8866 (mtmt) REVERT: C 429 PHE cc_start: 0.7667 (p90) cc_final: 0.7259 (t80) REVERT: C 431 LYS cc_start: 0.9096 (ttpt) cc_final: 0.8817 (tttt) REVERT: C 474 ARG cc_start: 0.7927 (ttp-110) cc_final: 0.6049 (mpt180) REVERT: C 478 GLU cc_start: 0.8415 (mt-10) cc_final: 0.7986 (mt-10) REVERT: C 511 TYR cc_start: 0.8922 (t80) cc_final: 0.8696 (t80) REVERT: C 551 ASN cc_start: 0.8903 (m-40) cc_final: 0.8488 (m-40) REVERT: C 555 TYR cc_start: 0.9173 (m-80) cc_final: 0.8754 (m-80) REVERT: C 570 GLU cc_start: 0.8760 (tt0) cc_final: 0.8112 (tt0) REVERT: C 647 LEU cc_start: 0.9158 (tp) cc_final: 0.8798 (tp) REVERT: C 694 LYS cc_start: 0.8986 (mttt) cc_final: 0.8694 (ptmt) REVERT: C 706 LEU cc_start: 0.9285 (mp) cc_final: 0.9067 (mp) REVERT: C 709 GLU cc_start: 0.8691 (mt-10) cc_final: 0.8407 (mt-10) REVERT: D 397 GLU cc_start: 0.8482 (mt-10) cc_final: 0.8098 (mt-10) REVERT: D 420 ARG cc_start: 0.8526 (mmm160) cc_final: 0.8202 (mmm160) REVERT: D 425 LYS cc_start: 0.9034 (mtmt) cc_final: 0.8783 (mtpp) REVERT: D 429 PHE cc_start: 0.7642 (p90) cc_final: 0.7158 (t80) REVERT: D 474 ARG cc_start: 0.7947 (ttp80) cc_final: 0.5964 (mpt180) REVERT: D 478 GLU cc_start: 0.8105 (mt-10) cc_final: 0.7571 (mt-10) REVERT: D 512 SER cc_start: 0.8842 (OUTLIER) cc_final: 0.8523 (m) REVERT: D 550 THR cc_start: 0.9125 (p) cc_final: 0.8859 (p) REVERT: D 551 ASN cc_start: 0.8996 (m-40) cc_final: 0.8715 (m110) REVERT: D 555 TYR cc_start: 0.9058 (m-80) cc_final: 0.8639 (m-80) REVERT: D 570 GLU cc_start: 0.8676 (tt0) cc_final: 0.8417 (tt0) REVERT: D 647 LEU cc_start: 0.9181 (tp) cc_final: 0.8816 (tp) REVERT: D 651 GLU cc_start: 0.8275 (mp0) cc_final: 0.7960 (mm-30) REVERT: D 653 TYR cc_start: 0.7868 (p90) cc_final: 0.7561 (p90) REVERT: B 429 PHE cc_start: 0.7652 (p90) cc_final: 0.7354 (t80) REVERT: B 466 LYS cc_start: 0.8110 (mmtm) cc_final: 0.7283 (tptm) REVERT: B 474 ARG cc_start: 0.7789 (ttp-110) cc_final: 0.5971 (mpt180) REVERT: B 478 GLU cc_start: 0.8456 (mt-10) cc_final: 0.8010 (mt-10) REVERT: B 512 SER cc_start: 0.8860 (OUTLIER) cc_final: 0.8495 (m) REVERT: B 553 LEU cc_start: 0.9014 (mp) cc_final: 0.8772 (mp) REVERT: B 555 TYR cc_start: 0.9093 (m-80) cc_final: 0.8594 (m-80) REVERT: B 557 ARG cc_start: 0.8590 (mtp85) cc_final: 0.8361 (mtp180) REVERT: B 568 MET cc_start: 0.8332 (OUTLIER) cc_final: 0.7996 (mtm) REVERT: B 572 MET cc_start: 0.8859 (ttp) cc_final: 0.8577 (ttp) REVERT: B 647 LEU cc_start: 0.9147 (tp) cc_final: 0.8780 (tp) REVERT: B 653 TYR cc_start: 0.7964 (p90) cc_final: 0.7690 (p90) REVERT: B 687 ASN cc_start: 0.7161 (OUTLIER) cc_final: 0.6276 (m-40) REVERT: B 694 LYS cc_start: 0.8786 (ptmt) cc_final: 0.8430 (pptt) REVERT: B 700 GLN cc_start: 0.7988 (tm-30) cc_final: 0.7325 (tm-30) outliers start: 40 outliers final: 24 residues processed: 561 average time/residue: 0.1101 time to fit residues: 90.7459 Evaluate side-chains 546 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 517 time to evaluate : 0.536 ------------------------------------------------------------------------------- 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 512 SER Chi-restraints excluded: chain A residue 564 ILE Chi-restraints excluded: chain A residue 641 THR Chi-restraints excluded: chain A residue 699 LEU 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 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 564 ILE Chi-restraints excluded: chain D residue 579 ARG Chi-restraints excluded: chain D residue 634 CYS Chi-restraints excluded: chain D residue 673 LEU 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 1 optimal weight: 5.9990 chunk 89 optimal weight: 0.2980 chunk 36 optimal weight: 1.9990 chunk 139 optimal weight: 0.8980 chunk 161 optimal weight: 1.9990 chunk 82 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 chunk 88 optimal weight: 8.9990 chunk 109 optimal weight: 0.9990 chunk 122 optimal weight: 3.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 297 ASN C 320 HIS C 498 GLN C 695 ASN ** B 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 560 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.175305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.133828 restraints weight = 22598.900| |-----------------------------------------------------------------------------| r_work (start): 0.3616 rms_B_bonded: 2.91 r_work: 0.3476 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.3782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14608 Z= 0.157 Angle : 0.601 11.455 19800 Z= 0.317 Chirality : 0.039 0.210 2240 Planarity : 0.003 0.028 2400 Dihedral : 5.422 57.230 1930 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 3.17 % Allowed : 19.25 % Favored : 77.58 % 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: 0.68 (0.20), residues: 1692 helix: 1.38 (0.15), residues: 1124 sheet: -1.22 (0.66), residues: 68 loop : -1.41 (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 511 PHE 0.030 0.002 PHE A 438 TRP 0.017 0.001 TRP A 697 HIS 0.003 0.001 HIS D 358 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.16 (14608) covalent geometry : angle 0.60109 / 0.32 (19800) hydrogen bonds : bond 0.04239 / 2.86 ( 904) hydrogen bonds : angle 4.29934 / 3.07 ( 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 590 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 541 time to evaluate : 0.414 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: A 387 ILE cc_start: 0.8518 (mm) cc_final: 0.8167 (mm) REVERT: A 408 ASN cc_start: 0.7850 (m110) cc_final: 0.7084 (t0) REVERT: A 475 VAL cc_start: 0.9131 (p) cc_final: 0.8795 (t) REVERT: A 478 GLU cc_start: 0.8067 (mt-10) cc_final: 0.7731 (mp0) REVERT: A 551 ASN cc_start: 0.9190 (m-40) cc_final: 0.8846 (m110) REVERT: A 555 TYR cc_start: 0.8989 (m-80) cc_final: 0.8214 (m-80) REVERT: A 561 GLN cc_start: 0.7922 (tt0) cc_final: 0.7616 (tt0) REVERT: A 570 GLU cc_start: 0.8750 (tt0) cc_final: 0.8417 (tt0) REVERT: A 577 LEU cc_start: 0.8889 (tp) cc_final: 0.8603 (tt) REVERT: A 579 ARG cc_start: 0.7674 (ptp-170) cc_final: 0.7131 (mtm180) REVERT: A 580 PHE cc_start: 0.8253 (t80) cc_final: 0.8030 (t80) REVERT: A 637 LEU cc_start: 0.9302 (mt) cc_final: 0.9097 (mp) REVERT: A 647 LEU cc_start: 0.9173 (tp) cc_final: 0.8934 (mt) REVERT: A 653 TYR cc_start: 0.7871 (p90) cc_final: 0.7363 (p90) REVERT: A 695 ASN cc_start: 0.7723 (m-40) cc_final: 0.7039 (m-40) REVERT: A 697 TRP cc_start: 0.8189 (t60) cc_final: 0.7799 (t60) REVERT: A 698 LYS cc_start: 0.8550 (mtmt) cc_final: 0.8142 (mptt) REVERT: A 700 GLN cc_start: 0.8441 (tp40) cc_final: 0.7687 (tm-30) REVERT: A 701 ARG cc_start: 0.8928 (mmm-85) cc_final: 0.8649 (mmm-85) REVERT: C 387 ILE cc_start: 0.8415 (mm) cc_final: 0.8000 (mm) REVERT: C 425 LYS cc_start: 0.9123 (mtmt) cc_final: 0.8892 (mtmt) REVERT: C 429 PHE cc_start: 0.7688 (p90) cc_final: 0.7294 (t80) REVERT: C 431 LYS cc_start: 0.9083 (ttpt) cc_final: 0.8790 (tttt) REVERT: C 474 ARG cc_start: 0.7955 (ttp-110) cc_final: 0.6064 (mpt180) REVERT: C 478 GLU cc_start: 0.8422 (mt-10) cc_final: 0.7957 (mt-10) REVERT: C 512 SER cc_start: 0.8702 (OUTLIER) cc_final: 0.8474 (m) REVERT: C 551 ASN cc_start: 0.8944 (m-40) cc_final: 0.8558 (m-40) REVERT: C 555 TYR cc_start: 0.9198 (m-80) cc_final: 0.8724 (m-80) REVERT: C 557 ARG cc_start: 0.8449 (OUTLIER) cc_final: 0.8084 (mtp85) REVERT: C 570 GLU cc_start: 0.8800 (tt0) cc_final: 0.8497 (tt0) REVERT: C 647 LEU cc_start: 0.9181 (tp) cc_final: 0.8804 (tp) REVERT: C 653 TYR cc_start: 0.7835 (p90) cc_final: 0.7448 (p90) REVERT: C 694 LYS cc_start: 0.9052 (mttt) cc_final: 0.8807 (mttt) REVERT: D 397 GLU cc_start: 0.8486 (mt-10) cc_final: 0.8091 (mt-10) REVERT: D 420 ARG cc_start: 0.8532 (mmm160) cc_final: 0.8256 (mmm160) REVERT: D 425 LYS cc_start: 0.9050 (mtmt) cc_final: 0.8787 (mtpp) REVERT: D 429 PHE cc_start: 0.7465 (p90) cc_final: 0.7250 (t80) REVERT: D 509 ASP cc_start: 0.8856 (OUTLIER) cc_final: 0.8527 (m-30) REVERT: D 512 SER cc_start: 0.8920 (OUTLIER) cc_final: 0.8624 (m) REVERT: D 550 THR cc_start: 0.9153 (p) cc_final: 0.8916 (p) REVERT: D 551 ASN cc_start: 0.9053 (m-40) cc_final: 0.8736 (m110) REVERT: D 555 TYR cc_start: 0.9089 (m-80) cc_final: 0.8852 (m-80) REVERT: D 570 GLU cc_start: 0.8619 (tt0) cc_final: 0.8319 (tt0) REVERT: D 651 GLU cc_start: 0.8218 (mp0) cc_final: 0.7964 (mm-30) REVERT: D 653 TYR cc_start: 0.7844 (p90) cc_final: 0.7577 (p90) REVERT: D 669 LEU cc_start: 0.9171 (OUTLIER) cc_final: 0.8962 (mm) REVERT: D 677 MET cc_start: 0.8774 (mmm) cc_final: 0.8449 (mmm) REVERT: D 694 LYS cc_start: 0.8898 (mttt) cc_final: 0.8637 (ptmt) REVERT: D 715 CYS cc_start: 0.4717 (m) cc_final: 0.4316 (m) REVERT: B 429 PHE cc_start: 0.7693 (p90) cc_final: 0.7403 (t80) REVERT: B 466 LYS cc_start: 0.8132 (mmtm) cc_final: 0.7303 (tptm) REVERT: B 474 ARG cc_start: 0.7831 (ttp-110) cc_final: 0.6015 (mpt180) REVERT: B 478 GLU cc_start: 0.8453 (mt-10) cc_final: 0.7978 (mt-10) REVERT: B 512 SER cc_start: 0.8856 (OUTLIER) cc_final: 0.8512 (m) REVERT: B 551 ASN cc_start: 0.9114 (m-40) cc_final: 0.8675 (m110) REVERT: B 553 LEU cc_start: 0.9054 (mp) cc_final: 0.8809 (mp) REVERT: B 555 TYR cc_start: 0.9073 (m-80) cc_final: 0.8522 (m-80) REVERT: B 557 ARG cc_start: 0.8571 (mtp85) cc_final: 0.8289 (mtp180) REVERT: B 653 TYR cc_start: 0.7882 (p90) cc_final: 0.7399 (p90) REVERT: B 687 ASN cc_start: 0.7143 (OUTLIER) cc_final: 0.6287 (m-40) REVERT: B 694 LYS cc_start: 0.8799 (ptmt) cc_final: 0.8404 (pptt) REVERT: B 700 GLN cc_start: 0.8018 (tm-30) cc_final: 0.7333 (tm-30) outliers start: 49 outliers final: 30 residues processed: 562 average time/residue: 0.1145 time to fit residues: 94.7706 Evaluate side-chains 540 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 503 time to evaluate : 0.522 ------------------------------------------------------------------------------- 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 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 512 SER 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 634 CYS Chi-restraints excluded: chain C residue 641 THR Chi-restraints excluded: chain C residue 695 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 512 SER Chi-restraints excluded: chain D residue 564 ILE Chi-restraints excluded: chain D residue 579 ARG Chi-restraints excluded: chain D residue 634 CYS Chi-restraints excluded: chain D residue 641 THR Chi-restraints excluded: chain D residue 669 LEU Chi-restraints excluded: chain D residue 673 LEU Chi-restraints excluded: chain D residue 685 THR Chi-restraints excluded: chain D residue 709 GLU 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 673 LEU Chi-restraints excluded: chain B residue 687 ASN Chi-restraints excluded: chain B residue 698 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 141 optimal weight: 0.6980 chunk 131 optimal weight: 7.9990 chunk 25 optimal weight: 1.9990 chunk 97 optimal weight: 0.9990 chunk 98 optimal weight: 0.9990 chunk 75 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 76 optimal weight: 5.9990 chunk 88 optimal weight: 10.0000 chunk 155 optimal weight: 0.8980 chunk 35 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 297 ASN ** B 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 498 GLN ** 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 = 0.4158 r_free = 0.4158 target = 0.177630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.136283 restraints weight = 22571.773| |-----------------------------------------------------------------------------| r_work (start): 0.3655 rms_B_bonded: 2.94 r_work: 0.3521 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.3943 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= 0.147 Angle : 0.604 11.273 19800 Z= 0.315 Chirality : 0.040 0.326 2240 Planarity : 0.003 0.028 2400 Dihedral : 5.291 56.112 1930 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 2.97 % Allowed : 20.67 % Favored : 76.36 % 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: 0.69 (0.20), residues: 1692 helix: 1.36 (0.15), residues: 1124 sheet: -1.25 (0.64), residues: 68 loop : -1.35 (0.28), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 355 TYR 0.026 0.002 TYR D 351 PHE 0.021 0.001 PHE C 438 TRP 0.015 0.001 TRP A 697 HIS 0.003 0.001 HIS D 358 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.15 (14608) covalent geometry : angle 0.60414 / 0.32 (19800) hydrogen bonds : bond 0.04107 / 2.78 ( 904) hydrogen bonds : angle 4.31564 / 3.09 ( 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 601 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 555 time to evaluate : 0.585 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: A 304 PHE cc_start: 0.7230 (t80) cc_final: 0.7009 (t80) REVERT: A 387 ILE cc_start: 0.8377 (mm) cc_final: 0.8024 (mm) REVERT: A 408 ASN cc_start: 0.7772 (m110) cc_final: 0.7214 (t0) REVERT: A 475 VAL cc_start: 0.9141 (p) cc_final: 0.8717 (t) REVERT: A 478 GLU cc_start: 0.8058 (mt-10) cc_final: 0.7659 (mp0) REVERT: A 499 ARG cc_start: 0.8254 (mmp80) cc_final: 0.8029 (mmp80) REVERT: A 551 ASN cc_start: 0.9191 (m-40) cc_final: 0.8848 (m110) REVERT: A 555 TYR cc_start: 0.8962 (m-80) cc_final: 0.8069 (m-80) REVERT: A 561 GLN cc_start: 0.7937 (tt0) cc_final: 0.6799 (mp10) REVERT: A 570 GLU cc_start: 0.8695 (tt0) cc_final: 0.8392 (tt0) REVERT: A 571 LYS cc_start: 0.8008 (OUTLIER) cc_final: 0.7545 (tptt) REVERT: A 577 LEU cc_start: 0.8846 (tp) cc_final: 0.8566 (tt) REVERT: A 579 ARG cc_start: 0.7628 (ptp-170) cc_final: 0.7100 (mtm180) REVERT: A 637 LEU cc_start: 0.9285 (mt) cc_final: 0.9082 (mp) REVERT: A 647 LEU cc_start: 0.9155 (tp) cc_final: 0.8842 (tp) REVERT: A 653 TYR cc_start: 0.7821 (p90) cc_final: 0.7329 (p90) REVERT: A 695 ASN cc_start: 0.7676 (m-40) cc_final: 0.6681 (m-40) REVERT: A 697 TRP cc_start: 0.8179 (t60) cc_final: 0.7971 (t60) REVERT: A 700 GLN cc_start: 0.8354 (tp40) cc_final: 0.7604 (tm-30) REVERT: A 701 ARG cc_start: 0.8895 (mmm-85) cc_final: 0.8584 (mmm-85) REVERT: A 706 LEU cc_start: 0.9220 (mp) cc_final: 0.8919 (mp) REVERT: C 408 ASN cc_start: 0.7717 (OUTLIER) cc_final: 0.7185 (t0) REVERT: C 425 LYS cc_start: 0.9109 (mtmt) cc_final: 0.8899 (mtmt) REVERT: C 429 PHE cc_start: 0.7713 (p90) cc_final: 0.7305 (t80) REVERT: C 474 ARG cc_start: 0.7986 (ttp-110) cc_final: 0.6079 (mpt180) REVERT: C 478 GLU cc_start: 0.8364 (mt-10) cc_final: 0.7905 (mt-10) REVERT: C 551 ASN cc_start: 0.8955 (m-40) cc_final: 0.8585 (m-40) REVERT: C 555 TYR cc_start: 0.9168 (m-80) cc_final: 0.8627 (m-80) REVERT: C 557 ARG cc_start: 0.8460 (OUTLIER) cc_final: 0.8138 (mtp85) REVERT: C 570 GLU cc_start: 0.8724 (tt0) cc_final: 0.8488 (tt0) REVERT: C 579 ARG cc_start: 0.7713 (ptp-170) cc_final: 0.6930 (mtm180) REVERT: C 647 LEU cc_start: 0.9182 (tp) cc_final: 0.8822 (tp) REVERT: C 653 TYR cc_start: 0.7832 (p90) cc_final: 0.7458 (p90) REVERT: C 694 LYS cc_start: 0.9081 (mttt) cc_final: 0.8779 (ptmt) REVERT: C 700 GLN cc_start: 0.8087 (tm-30) cc_final: 0.7125 (tm-30) REVERT: C 706 LEU cc_start: 0.9185 (mp) cc_final: 0.8896 (mp) REVERT: D 397 GLU cc_start: 0.8451 (mt-10) cc_final: 0.8062 (mt-10) REVERT: D 420 ARG cc_start: 0.8574 (mmm160) cc_final: 0.8268 (mmm160) REVERT: D 429 PHE cc_start: 0.7476 (p90) cc_final: 0.7192 (t80) REVERT: D 478 GLU cc_start: 0.8072 (mt-10) cc_final: 0.7745 (mp0) REVERT: D 509 ASP cc_start: 0.8992 (OUTLIER) cc_final: 0.8627 (m-30) REVERT: D 512 SER cc_start: 0.8848 (OUTLIER) cc_final: 0.8570 (m) REVERT: D 550 THR cc_start: 0.9122 (p) cc_final: 0.8916 (p) REVERT: D 551 ASN cc_start: 0.9073 (m-40) cc_final: 0.8745 (m110) REVERT: D 570 GLU cc_start: 0.8632 (tt0) cc_final: 0.8285 (tt0) REVERT: D 647 LEU cc_start: 0.9179 (tp) cc_final: 0.8878 (tp) REVERT: D 651 GLU cc_start: 0.8196 (mp0) cc_final: 0.7956 (mm-30) REVERT: D 653 TYR cc_start: 0.7859 (p90) cc_final: 0.7607 (p90) REVERT: D 694 LYS cc_start: 0.8941 (mttt) cc_final: 0.8679 (ptmt) REVERT: D 715 CYS cc_start: 0.4852 (m) cc_final: 0.4346 (m) REVERT: D 740 TRP cc_start: 0.5979 (m-10) cc_final: 0.5658 (m-10) REVERT: B 363 ARG cc_start: 0.6482 (OUTLIER) cc_final: 0.5344 (ptt180) REVERT: B 429 PHE cc_start: 0.7679 (p90) cc_final: 0.7380 (t80) REVERT: B 466 LYS cc_start: 0.8137 (mmtm) cc_final: 0.7311 (tptm) REVERT: B 474 ARG cc_start: 0.7835 (ttp-110) cc_final: 0.5975 (mpt180) REVERT: B 478 GLU cc_start: 0.8402 (mt-10) cc_final: 0.7936 (mt-10) REVERT: B 512 SER cc_start: 0.8860 (OUTLIER) cc_final: 0.8508 (m) REVERT: B 547 MET cc_start: 0.8685 (mtp) cc_final: 0.8292 (mtp) REVERT: B 551 ASN cc_start: 0.9112 (m-40) cc_final: 0.8657 (m110) REVERT: B 553 LEU cc_start: 0.9051 (mp) cc_final: 0.8794 (mp) REVERT: B 555 TYR cc_start: 0.9083 (m-80) cc_final: 0.8478 (m-80) REVERT: B 557 ARG cc_start: 0.8503 (mtp85) cc_final: 0.8220 (mtp180) REVERT: B 572 MET cc_start: 0.8571 (ttp) cc_final: 0.7942 (ttp) REVERT: B 647 LEU cc_start: 0.9176 (tp) cc_final: 0.8882 (tp) REVERT: B 653 TYR cc_start: 0.7852 (p90) cc_final: 0.7391 (p90) REVERT: B 687 ASN cc_start: 0.7109 (OUTLIER) cc_final: 0.6147 (m-40) REVERT: B 700 GLN cc_start: 0.8045 (tm-30) cc_final: 0.7340 (tm-30) REVERT: B 706 LEU cc_start: 0.9219 (mp) cc_final: 0.8957 (mp) REVERT: B 715 CYS cc_start: 0.4516 (m) cc_final: 0.4187 (m) outliers start: 46 outliers final: 29 residues processed: 574 average time/residue: 0.1193 time to fit residues: 100.1030 Evaluate side-chains 563 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 526 time to evaluate : 0.524 ------------------------------------------------------------------------------- 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 571 LYS Chi-restraints excluded: chain A residue 652 ASN 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 547 MET Chi-restraints excluded: chain C residue 550 THR 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 677 MET 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 512 SER Chi-restraints excluded: chain D residue 564 ILE Chi-restraints excluded: chain D residue 572 MET Chi-restraints excluded: chain D residue 579 ARG Chi-restraints excluded: chain D residue 634 CYS Chi-restraints excluded: chain D residue 641 THR Chi-restraints excluded: chain D residue 673 LEU Chi-restraints excluded: chain D residue 685 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 421 LEU Chi-restraints excluded: chain B residue 475 VAL Chi-restraints excluded: chain B residue 512 SER 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: 0.5980 chunk 17 optimal weight: 0.0670 chunk 41 optimal weight: 9.9990 chunk 163 optimal weight: 0.9990 chunk 84 optimal weight: 10.0000 chunk 104 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 121 optimal weight: 0.9980 chunk 52 optimal weight: 6.9990 overall best weight: 0.6720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 297 ASN C 695 ASN ** B 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 560 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.182530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.141826 restraints weight = 22511.571| |-----------------------------------------------------------------------------| r_work (start): 0.3734 rms_B_bonded: 2.99 r_work: 0.3599 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.4121 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= 0.139 Angle : 0.626 13.669 19800 Z= 0.323 Chirality : 0.040 0.297 2240 Planarity : 0.003 0.063 2400 Dihedral : 5.163 54.768 1930 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 2.58 % Allowed : 21.32 % Favored : 76.10 % 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: 1.20 (0.15), residues: 1148 sheet: -1.35 (0.63), residues: 68 loop : -1.52 (0.28), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 355 TYR 0.028 0.002 TYR C 511 PHE 0.030 0.001 PHE A 438 TRP 0.011 0.001 TRP A 697 HIS 0.002 0.001 HIS A 358 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 (14608) covalent geometry : angle 0.62578 / 0.32 (19800) hydrogen bonds : bond 0.04011 / 2.71 ( 904) hydrogen bonds : angle 4.30890 / 3.07 ( 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: 40 poor density : 545 time to evaluate : 0.538 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: A 387 ILE cc_start: 0.8392 (mm) cc_final: 0.8040 (mm) REVERT: A 408 ASN cc_start: 0.7702 (m110) cc_final: 0.7203 (t0) REVERT: A 475 VAL cc_start: 0.9173 (p) cc_final: 0.8751 (t) REVERT: A 478 GLU cc_start: 0.8018 (mt-10) cc_final: 0.7676 (mp0) REVERT: A 480 LEU cc_start: 0.9169 (mm) cc_final: 0.8724 (mm) REVERT: A 499 ARG cc_start: 0.8245 (mmp80) cc_final: 0.7987 (mmp80) REVERT: A 551 ASN cc_start: 0.9195 (m-40) cc_final: 0.8865 (m110) REVERT: A 555 TYR cc_start: 0.8891 (m-80) cc_final: 0.8257 (m-80) REVERT: A 561 GLN cc_start: 0.7940 (tt0) cc_final: 0.6806 (mp10) REVERT: A 570 GLU cc_start: 0.8629 (tt0) cc_final: 0.8399 (tt0) REVERT: A 571 LYS cc_start: 0.7935 (OUTLIER) cc_final: 0.7502 (tptt) REVERT: A 577 LEU cc_start: 0.8818 (tp) cc_final: 0.8516 (tt) REVERT: A 579 ARG cc_start: 0.7557 (ptp-170) cc_final: 0.7039 (mtm180) REVERT: A 637 LEU cc_start: 0.9288 (mt) cc_final: 0.9083 (mp) REVERT: A 647 LEU cc_start: 0.9128 (tp) cc_final: 0.8874 (tp) REVERT: A 653 TYR cc_start: 0.7763 (p90) cc_final: 0.7294 (p90) REVERT: A 695 ASN cc_start: 0.7616 (m-40) cc_final: 0.6554 (m-40) REVERT: A 700 GLN cc_start: 0.8361 (tp40) cc_final: 0.7580 (tm-30) REVERT: A 706 LEU cc_start: 0.9217 (mp) cc_final: 0.8908 (mp) REVERT: C 408 ASN cc_start: 0.7685 (OUTLIER) cc_final: 0.7260 (t0) REVERT: C 412 MET cc_start: 0.8640 (ttm) cc_final: 0.8308 (ttm) REVERT: C 425 LYS cc_start: 0.9095 (mtmt) cc_final: 0.8866 (mtmt) REVERT: C 429 PHE cc_start: 0.7700 (p90) cc_final: 0.7289 (t80) REVERT: C 474 ARG cc_start: 0.8011 (ttp-110) cc_final: 0.6065 (mpt180) REVERT: C 478 GLU cc_start: 0.8329 (mt-10) cc_final: 0.7855 (mt-10) REVERT: C 551 ASN cc_start: 0.8919 (m-40) cc_final: 0.8565 (m-40) REVERT: C 555 TYR cc_start: 0.9089 (m-80) cc_final: 0.8559 (m-80) REVERT: C 570 GLU cc_start: 0.8735 (tt0) cc_final: 0.8470 (tt0) REVERT: C 647 LEU cc_start: 0.9157 (tp) cc_final: 0.8858 (tp) REVERT: C 653 TYR cc_start: 0.7788 (p90) cc_final: 0.7455 (p90) REVERT: C 694 LYS cc_start: 0.9037 (mttt) cc_final: 0.8787 (ptmt) REVERT: C 700 GLN cc_start: 0.8089 (tm-30) cc_final: 0.7168 (tm-30) REVERT: D 397 GLU cc_start: 0.8460 (mt-10) cc_final: 0.8081 (mt-10) REVERT: D 478 GLU cc_start: 0.8029 (mt-10) cc_final: 0.7635 (mp0) REVERT: D 509 ASP cc_start: 0.9019 (OUTLIER) cc_final: 0.8665 (m-30) REVERT: D 536 GLU cc_start: 0.8472 (mp0) cc_final: 0.8234 (mp0) REVERT: D 550 THR cc_start: 0.9099 (p) cc_final: 0.8864 (p) REVERT: D 551 ASN cc_start: 0.9019 (m-40) cc_final: 0.8682 (m110) REVERT: D 570 GLU cc_start: 0.8702 (tt0) cc_final: 0.8240 (tt0) REVERT: D 647 LEU cc_start: 0.9132 (tp) cc_final: 0.8887 (tp) REVERT: D 651 GLU cc_start: 0.8152 (mp0) cc_final: 0.7942 (mm-30) REVERT: D 653 TYR cc_start: 0.7755 (p90) cc_final: 0.7513 (p90) REVERT: D 694 LYS cc_start: 0.8929 (mttt) cc_final: 0.8685 (ptmt) REVERT: D 715 CYS cc_start: 0.4529 (m) cc_final: 0.4105 (m) REVERT: D 740 TRP cc_start: 0.6008 (m-10) cc_final: 0.5722 (m-10) REVERT: B 363 ARG cc_start: 0.6442 (OUTLIER) cc_final: 0.5302 (ptt180) REVERT: B 429 PHE cc_start: 0.7669 (p90) cc_final: 0.7383 (t80) REVERT: B 466 LYS cc_start: 0.8138 (mmtm) cc_final: 0.7222 (tmtt) REVERT: B 474 ARG cc_start: 0.7896 (ttp-110) cc_final: 0.6005 (mpt180) REVERT: B 478 GLU cc_start: 0.8365 (mt-10) cc_final: 0.7908 (mt-10) REVERT: B 498 GLN cc_start: 0.8440 (pp30) cc_final: 0.7877 (pp30) REVERT: B 512 SER cc_start: 0.8851 (OUTLIER) cc_final: 0.8512 (m) REVERT: B 547 MET cc_start: 0.8648 (mtp) cc_final: 0.8332 (mtp) REVERT: B 551 ASN cc_start: 0.9101 (m-40) cc_final: 0.8641 (m110) REVERT: B 553 LEU cc_start: 0.9076 (mp) cc_final: 0.8803 (mp) REVERT: B 555 TYR cc_start: 0.8992 (m-80) cc_final: 0.8546 (m-80) REVERT: B 557 ARG cc_start: 0.8558 (mtp85) cc_final: 0.8305 (mtp180) REVERT: B 647 LEU cc_start: 0.9135 (tp) cc_final: 0.8906 (tp) REVERT: B 653 TYR cc_start: 0.7805 (p90) cc_final: 0.7367 (p90) REVERT: B 692 GLU cc_start: 0.7916 (mt-10) cc_final: 0.7419 (mp0) REVERT: B 694 LYS cc_start: 0.8854 (ptmt) cc_final: 0.8541 (pttm) REVERT: B 700 GLN cc_start: 0.8010 (tm-30) cc_final: 0.7323 (tm-30) REVERT: B 706 LEU cc_start: 0.9203 (mp) cc_final: 0.8920 (mp) REVERT: B 715 CYS cc_start: 0.4433 (m) cc_final: 0.4165 (m) outliers start: 40 outliers final: 26 residues processed: 561 average time/residue: 0.1136 time to fit residues: 93.3276 Evaluate side-chains 561 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 530 time to evaluate : 0.410 ------------------------------------------------------------------------------- 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 652 ASN 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 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 421 LEU Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 509 ASP Chi-restraints excluded: chain D residue 564 ILE Chi-restraints excluded: chain D residue 579 ARG Chi-restraints excluded: chain D residue 634 CYS 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 421 LEU Chi-restraints excluded: chain B residue 475 VAL Chi-restraints excluded: chain B residue 512 SER Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain B residue 687 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 137 optimal weight: 0.8980 chunk 156 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 60 optimal weight: 5.9990 chunk 96 optimal weight: 8.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4192 r_free = 0.4192 target = 0.180111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.139279 restraints weight = 22670.363| |-----------------------------------------------------------------------------| r_work (start): 0.3705 rms_B_bonded: 2.98 r_work: 0.3569 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.4189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 14608 Z= 0.177 Angle : 0.653 16.783 19800 Z= 0.337 Chirality : 0.042 0.257 2240 Planarity : 0.003 0.029 2400 Dihedral : 5.140 56.077 1930 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 2.84 % Allowed : 21.25 % Favored : 75.90 % 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: 0.42 (0.20), residues: 1692 helix: 1.12 (0.15), residues: 1148 sheet: -1.18 (0.65), residues: 68 loop : -1.51 (0.28), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 499 TYR 0.026 0.002 TYR C 351 PHE 0.032 0.002 PHE C 438 TRP 0.028 0.001 TRP A 697 HIS 0.004 0.001 HIS A 410 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.18 (14608) covalent geometry : angle 0.65280 / 0.34 (19800) hydrogen bonds : bond 0.04096 / 2.74 ( 904) hydrogen bonds : angle 4.34486 / 3.10 ( 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 578 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 534 time to evaluate : 0.442 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: 0.8414 (mm) cc_final: 0.8081 (mm) REVERT: A 408 ASN cc_start: 0.7631 (m110) cc_final: 0.7182 (t0) REVERT: A 474 ARG cc_start: 0.7923 (ttp80) cc_final: 0.6004 (mpt180) REVERT: A 478 GLU cc_start: 0.8100 (mt-10) cc_final: 0.7683 (mp0) REVERT: A 480 LEU cc_start: 0.9161 (mm) cc_final: 0.8705 (mm) REVERT: A 511 TYR cc_start: 0.8669 (t80) cc_final: 0.8456 (t80) REVERT: A 551 ASN cc_start: 0.9196 (m-40) cc_final: 0.8841 (m110) REVERT: A 555 TYR cc_start: 0.9015 (m-80) cc_final: 0.8334 (m-80) REVERT: A 561 GLN cc_start: 0.8026 (tt0) cc_final: 0.6935 (mp10) REVERT: A 571 LYS cc_start: 0.8056 (OUTLIER) cc_final: 0.7454 (tptt) REVERT: A 577 LEU cc_start: 0.8831 (tp) cc_final: 0.8521 (tt) REVERT: A 637 LEU cc_start: 0.9339 (mt) cc_final: 0.9126 (mp) REVERT: A 647 LEU cc_start: 0.9161 (tp) cc_final: 0.8884 (tp) REVERT: A 653 TYR cc_start: 0.7865 (p90) cc_final: 0.7486 (p90) REVERT: A 677 MET cc_start: 0.7600 (mmt) cc_final: 0.6737 (mmt) REVERT: A 700 GLN cc_start: 0.8390 (tp40) cc_final: 0.7621 (tm-30) REVERT: A 701 ARG cc_start: 0.8994 (mmm-85) cc_final: 0.8716 (mmm-85) REVERT: A 706 LEU cc_start: 0.9192 (mp) cc_final: 0.8833 (mp) REVERT: C 387 ILE cc_start: 0.8459 (mm) cc_final: 0.7929 (mm) REVERT: C 408 ASN cc_start: 0.7690 (OUTLIER) cc_final: 0.7249 (t0) REVERT: C 425 LYS cc_start: 0.9090 (mtmt) cc_final: 0.8851 (mtmt) REVERT: C 429 PHE cc_start: 0.7693 (p90) cc_final: 0.7380 (t80) REVERT: C 478 GLU cc_start: 0.8305 (mt-10) cc_final: 0.7903 (mt-10) REVERT: C 551 ASN cc_start: 0.8984 (m-40) cc_final: 0.8621 (m-40) REVERT: C 555 TYR cc_start: 0.9089 (m-80) cc_final: 0.8704 (m-80) REVERT: C 570 GLU cc_start: 0.8612 (tt0) cc_final: 0.8382 (tt0) REVERT: C 647 LEU cc_start: 0.9190 (tp) cc_final: 0.8793 (tp) REVERT: C 653 TYR cc_start: 0.7906 (p90) cc_final: 0.7568 (p90) REVERT: C 662 LEU cc_start: 0.9080 (mt) cc_final: 0.8825 (mt) REVERT: C 692 GLU cc_start: 0.7639 (mp0) cc_final: 0.7196 (mp0) REVERT: C 694 LYS cc_start: 0.9082 (mttt) cc_final: 0.8817 (ptmt) REVERT: D 397 GLU cc_start: 0.8476 (mt-10) cc_final: 0.8096 (mt-10) REVERT: D 420 ARG cc_start: 0.8481 (mmm160) cc_final: 0.8212 (mmm160) REVERT: D 478 GLU cc_start: 0.8040 (mt-10) cc_final: 0.7624 (mp0) REVERT: D 498 GLN cc_start: 0.7895 (pt0) cc_final: 0.7543 (pt0) REVERT: D 509 ASP cc_start: 0.8983 (OUTLIER) cc_final: 0.8647 (m-30) REVERT: D 536 GLU cc_start: 0.8485 (mp0) cc_final: 0.8243 (mp0) REVERT: D 550 THR cc_start: 0.9199 (p) cc_final: 0.8996 (p) REVERT: D 551 ASN cc_start: 0.9110 (m-40) cc_final: 0.8760 (m110) REVERT: D 570 GLU cc_start: 0.8762 (tt0) cc_final: 0.8359 (tt0) REVERT: D 647 LEU cc_start: 0.9171 (tp) cc_final: 0.8858 (tp) REVERT: D 651 GLU cc_start: 0.8184 (mp0) cc_final: 0.7962 (mm-30) REVERT: D 653 TYR cc_start: 0.7861 (p90) cc_final: 0.7610 (p90) REVERT: D 694 LYS cc_start: 0.8997 (mttt) cc_final: 0.8711 (ptmt) REVERT: D 715 CYS cc_start: 0.4650 (m) cc_final: 0.4293 (m) REVERT: D 740 TRP cc_start: 0.6207 (m-10) cc_final: 0.5981 (m-10) REVERT: B 363 ARG cc_start: 0.6469 (OUTLIER) cc_final: 0.5377 (ptt180) REVERT: B 466 LYS cc_start: 0.8137 (mmtm) cc_final: 0.7317 (tptm) REVERT: B 474 ARG cc_start: 0.7900 (ttp-110) cc_final: 0.5994 (mpt180) REVERT: B 478 GLU cc_start: 0.8311 (mt-10) cc_final: 0.7838 (mt-10) REVERT: B 511 TYR cc_start: 0.8916 (t80) cc_final: 0.8691 (t80) REVERT: B 512 SER cc_start: 0.8871 (OUTLIER) cc_final: 0.8524 (m) REVERT: B 547 MET cc_start: 0.8654 (mtp) cc_final: 0.8361 (mtp) REVERT: B 551 ASN cc_start: 0.9148 (m-40) cc_final: 0.8687 (m110) REVERT: B 553 LEU cc_start: 0.9129 (mp) cc_final: 0.8885 (mp) REVERT: B 555 TYR cc_start: 0.9008 (m-80) cc_final: 0.8580 (m-80) REVERT: B 647 LEU cc_start: 0.9181 (tp) cc_final: 0.8861 (tp) REVERT: B 653 TYR cc_start: 0.7886 (p90) cc_final: 0.7508 (p90) REVERT: B 692 GLU cc_start: 0.7982 (mt-10) cc_final: 0.7419 (mp0) REVERT: B 694 LYS cc_start: 0.8857 (ptmt) cc_final: 0.8545 (pttm) REVERT: B 700 GLN cc_start: 0.8108 (tm-30) cc_final: 0.7365 (tm-30) REVERT: B 706 LEU cc_start: 0.9212 (mp) cc_final: 0.8894 (mp) REVERT: B 715 CYS cc_start: 0.4286 (m) cc_final: 0.4063 (m) outliers start: 44 outliers final: 32 residues processed: 552 average time/residue: 0.1113 time to fit residues: 90.0598 Evaluate side-chains 558 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 521 time to evaluate : 0.522 ------------------------------------------------------------------------------- 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 652 ASN 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 634 CYS 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 634 CYS 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 685 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 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 652 ASN Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain B residue 687 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 54 optimal weight: 0.9990 chunk 151 optimal weight: 1.9990 chunk 165 optimal weight: 3.9990 chunk 97 optimal weight: 3.9990 chunk 59 optimal weight: 0.0270 chunk 29 optimal weight: 0.6980 chunk 156 optimal weight: 0.5980 chunk 128 optimal weight: 6.9990 chunk 64 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 48 optimal weight: 3.9990 overall best weight: 0.6240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 297 ASN ** B 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 498 GLN ** 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 = 0.4225 r_free = 0.4225 target = 0.183190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.143143 restraints weight = 22565.573| |-----------------------------------------------------------------------------| r_work (start): 0.3748 rms_B_bonded: 2.98 r_work: 0.3609 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.4397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 14608 Z= 0.141 Angle : 0.660 15.511 19800 Z= 0.340 Chirality : 0.042 0.459 2240 Planarity : 0.003 0.027 2400 Dihedral : 5.015 55.050 1930 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 2.71 % Allowed : 21.71 % Favored : 75.58 % 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: 0.40 (0.20), residues: 1692 helix: 1.11 (0.15), residues: 1148 sheet: -1.19 (0.65), residues: 68 loop : -1.54 (0.27), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 355 TYR 0.026 0.001 TYR C 351 PHE 0.028 0.001 PHE D 438 TRP 0.018 0.001 TRP A 697 HIS 0.004 0.001 HIS A 410 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 (14608) covalent geometry : angle 0.66013 / 0.34 (19800) hydrogen bonds : bond 0.04002 / 2.70 ( 904) hydrogen bonds : angle 4.40505 / 3.15 ( 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 582 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 540 time to evaluate : 0.493 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 387 ILE cc_start: 0.8297 (mm) cc_final: 0.7958 (mm) REVERT: A 408 ASN cc_start: 0.7732 (m110) cc_final: 0.7242 (t0) REVERT: A 474 ARG cc_start: 0.7891 (ttp80) cc_final: 0.5997 (mpt180) REVERT: A 478 GLU cc_start: 0.8067 (mt-10) cc_final: 0.7687 (mp0) REVERT: A 551 ASN cc_start: 0.9159 (m-40) cc_final: 0.8791 (m110) REVERT: A 555 TYR cc_start: 0.8898 (m-80) cc_final: 0.8266 (m-80) REVERT: A 561 GLN cc_start: 0.7996 (tt0) cc_final: 0.6890 (mp10) REVERT: A 571 LYS cc_start: 0.7820 (OUTLIER) cc_final: 0.7467 (tptt) REVERT: A 637 LEU cc_start: 0.9296 (mt) cc_final: 0.9083 (mp) REVERT: A 653 TYR cc_start: 0.7837 (p90) cc_final: 0.7412 (p90) REVERT: A 695 ASN cc_start: 0.7700 (m110) cc_final: 0.7333 (m-40) REVERT: A 700 GLN cc_start: 0.8378 (tp40) cc_final: 0.7639 (tm-30) REVERT: A 701 ARG cc_start: 0.8950 (mmm-85) cc_final: 0.8672 (mmm-85) REVERT: A 706 LEU cc_start: 0.9191 (mp) cc_final: 0.8864 (mp) REVERT: C 387 ILE cc_start: 0.8432 (mm) cc_final: 0.7914 (mm) REVERT: C 408 ASN cc_start: 0.7721 (OUTLIER) cc_final: 0.7407 (t0) REVERT: C 412 MET cc_start: 0.8643 (ttm) cc_final: 0.8365 (ttm) REVERT: C 425 LYS cc_start: 0.9050 (mtmt) cc_final: 0.8841 (mtmt) REVERT: C 429 PHE cc_start: 0.7628 (p90) cc_final: 0.7309 (t80) REVERT: C 478 GLU cc_start: 0.8274 (mt-10) cc_final: 0.7886 (mt-10) REVERT: C 551 ASN cc_start: 0.8925 (m-40) cc_final: 0.8570 (m-40) REVERT: C 555 TYR cc_start: 0.9009 (m-80) cc_final: 0.8573 (m-80) REVERT: C 570 GLU cc_start: 0.8585 (tt0) cc_final: 0.8375 (tt0) REVERT: C 647 LEU cc_start: 0.9135 (tp) cc_final: 0.8798 (tp) REVERT: C 653 TYR cc_start: 0.7847 (p90) cc_final: 0.7528 (p90) REVERT: C 662 LEU cc_start: 0.9050 (mt) cc_final: 0.8783 (mt) REVERT: C 692 GLU cc_start: 0.7573 (mp0) cc_final: 0.7155 (mp0) REVERT: C 694 LYS cc_start: 0.9113 (mttt) cc_final: 0.8869 (ptmt) REVERT: D 397 GLU cc_start: 0.8487 (mt-10) cc_final: 0.8141 (mt-10) REVERT: D 478 GLU cc_start: 0.8051 (mt-10) cc_final: 0.7654 (mp0) REVERT: D 498 GLN cc_start: 0.7914 (pt0) cc_final: 0.7616 (pt0) REVERT: D 509 ASP cc_start: 0.8957 (OUTLIER) cc_final: 0.8625 (m-30) REVERT: D 536 GLU cc_start: 0.8521 (mp0) cc_final: 0.8235 (mp0) REVERT: D 550 THR cc_start: 0.9119 (p) cc_final: 0.8909 (p) REVERT: D 551 ASN cc_start: 0.9031 (m-40) cc_final: 0.8681 (m110) REVERT: D 557 ARG cc_start: 0.8362 (mtp85) cc_final: 0.7656 (mtp180) REVERT: D 570 GLU cc_start: 0.8727 (tt0) cc_final: 0.8289 (tt0) REVERT: D 647 LEU cc_start: 0.9112 (tp) cc_final: 0.8849 (tp) REVERT: D 651 GLU cc_start: 0.8124 (mp0) cc_final: 0.7921 (mm-30) REVERT: D 653 TYR cc_start: 0.7760 (p90) cc_final: 0.7516 (p90) REVERT: D 694 LYS cc_start: 0.8997 (mttt) cc_final: 0.8748 (ptmt) REVERT: D 740 TRP cc_start: 0.6108 (m-10) cc_final: 0.5901 (m-10) REVERT: B 363 ARG cc_start: 0.6451 (OUTLIER) cc_final: 0.5370 (ptt180) REVERT: B 420 ARG cc_start: 0.8502 (mmm160) cc_final: 0.8050 (mmm160) REVERT: B 466 LYS cc_start: 0.8167 (mmtm) cc_final: 0.7216 (tmtt) REVERT: B 471 ASP cc_start: 0.8658 (m-30) cc_final: 0.8415 (m-30) REVERT: B 474 ARG cc_start: 0.7890 (ttp-110) cc_final: 0.5999 (mpt180) REVERT: B 478 GLU cc_start: 0.8285 (mt-10) cc_final: 0.7816 (mt-10) REVERT: B 498 GLN cc_start: 0.8554 (pp30) cc_final: 0.8352 (pp30) REVERT: B 512 SER cc_start: 0.8843 (OUTLIER) cc_final: 0.8493 (m) REVERT: B 547 MET cc_start: 0.8608 (mtp) cc_final: 0.8332 (mtp) REVERT: B 551 ASN cc_start: 0.9087 (m-40) cc_final: 0.8554 (m110) REVERT: B 553 LEU cc_start: 0.9058 (mp) cc_final: 0.8765 (mp) REVERT: B 555 TYR cc_start: 0.8963 (m-80) cc_final: 0.8372 (m-80) REVERT: B 557 ARG cc_start: 0.8552 (mtp85) cc_final: 0.8293 (mtp180) REVERT: B 560 GLN cc_start: 0.8385 (tt0) cc_final: 0.7357 (tt0) REVERT: B 572 MET cc_start: 0.8334 (ttp) cc_final: 0.8042 (ttp) REVERT: B 647 LEU cc_start: 0.9133 (tp) cc_final: 0.8878 (tp) REVERT: B 653 TYR cc_start: 0.7769 (p90) cc_final: 0.7351 (p90) REVERT: B 694 LYS cc_start: 0.8856 (ptmt) cc_final: 0.8483 (pptt) REVERT: B 697 TRP cc_start: 0.8537 (t60) cc_final: 0.8029 (t60) REVERT: B 700 GLN cc_start: 0.7978 (tm-30) cc_final: 0.7327 (tm-30) REVERT: B 706 LEU cc_start: 0.9171 (mp) cc_final: 0.8880 (mp) outliers start: 42 outliers final: 28 residues processed: 556 average time/residue: 0.1117 time to fit residues: 90.9489 Evaluate side-chains 547 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 514 time to evaluate : 0.439 ------------------------------------------------------------------------------- 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 572 MET Chi-restraints excluded: chain A residue 652 ASN 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 634 CYS Chi-restraints excluded: chain C residue 652 ASN Chi-restraints excluded: chain C residue 673 LEU 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 673 LEU 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 421 LEU Chi-restraints excluded: chain B residue 475 VAL Chi-restraints excluded: chain B residue 512 SER Chi-restraints excluded: chain B residue 579 ARG Chi-restraints excluded: chain B residue 652 ASN Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain B residue 687 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 92 optimal weight: 4.9990 chunk 32 optimal weight: 0.6980 chunk 3 optimal weight: 0.9980 chunk 154 optimal weight: 0.9990 chunk 63 optimal weight: 0.9990 chunk 76 optimal weight: 0.9980 chunk 56 optimal weight: 0.7980 chunk 143 optimal weight: 0.8980 chunk 125 optimal weight: 0.1980 chunk 149 optimal weight: 0.8980 chunk 47 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 676 ASN C 297 ASN D 320 HIS ** B 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 378 HIS ** B 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.179684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.138409 restraints weight = 22315.050| |-----------------------------------------------------------------------------| r_work (start): 0.3687 rms_B_bonded: 2.96 r_work: 0.3551 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.4604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 14608 Z= 0.146 Angle : 0.681 12.608 19800 Z= 0.355 Chirality : 0.041 0.304 2240 Planarity : 0.003 0.028 2400 Dihedral : 4.966 54.417 1930 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 13.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 2.33 % Allowed : 22.87 % Favored : 74.81 % 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: 0.42 (0.20), residues: 1692 helix: 1.12 (0.15), residues: 1148 sheet: -1.11 (0.66), residues: 68 loop : -1.51 (0.28), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 355 TYR 0.027 0.001 TYR C 351 PHE 0.014 0.001 PHE A 582 TRP 0.033 0.001 TRP B 697 HIS 0.004 0.001 HIS A 410 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.15 (14608) covalent geometry : angle 0.68121 / 0.36 (19800) hydrogen bonds : bond 0.03934 / 2.66 ( 904) hydrogen bonds : angle 4.44342 / 3.18 ( 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 562 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 526 time to evaluate : 0.472 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: A 387 ILE cc_start: 0.8271 (mm) cc_final: 0.7932 (mm) REVERT: A 408 ASN cc_start: 0.7652 (m110) cc_final: 0.7197 (t0) REVERT: A 474 ARG cc_start: 0.7846 (ttp80) cc_final: 0.5998 (mpt180) REVERT: A 478 GLU cc_start: 0.8066 (mt-10) cc_final: 0.7701 (mp0) REVERT: A 551 ASN cc_start: 0.9144 (m-40) cc_final: 0.8808 (m-40) REVERT: A 555 TYR cc_start: 0.8913 (m-80) cc_final: 0.8364 (m-80) REVERT: A 561 GLN cc_start: 0.8008 (tt0) cc_final: 0.6895 (mp10) REVERT: A 562 MET cc_start: 0.7916 (mtm) cc_final: 0.7703 (mtm) REVERT: A 571 LYS cc_start: 0.7722 (OUTLIER) cc_final: 0.7306 (tptt) REVERT: A 579 ARG cc_start: 0.7480 (ptp-170) cc_final: 0.6691 (mtm180) REVERT: A 637 LEU cc_start: 0.9284 (mt) cc_final: 0.9078 (mp) REVERT: A 653 TYR cc_start: 0.7779 (p90) cc_final: 0.7414 (p90) REVERT: A 695 ASN cc_start: 0.7703 (m110) cc_final: 0.7297 (m-40) REVERT: A 700 GLN cc_start: 0.8380 (tp40) cc_final: 0.7631 (tm-30) REVERT: A 701 ARG cc_start: 0.8974 (mmm-85) cc_final: 0.8703 (mmm-85) REVERT: A 706 LEU cc_start: 0.9170 (mp) cc_final: 0.8800 (mp) REVERT: C 387 ILE cc_start: 0.8432 (mm) cc_final: 0.7899 (mm) REVERT: C 397 GLU cc_start: 0.8336 (OUTLIER) cc_final: 0.8057 (pt0) REVERT: C 408 ASN cc_start: 0.7692 (OUTLIER) cc_final: 0.7446 (t0) REVERT: C 412 MET cc_start: 0.8655 (ttm) cc_final: 0.8377 (ttm) REVERT: C 425 LYS cc_start: 0.9025 (mtmt) cc_final: 0.8790 (mtmt) REVERT: C 429 PHE cc_start: 0.7633 (p90) cc_final: 0.7367 (t80) REVERT: C 478 GLU cc_start: 0.8240 (mt-10) cc_final: 0.8004 (mt-10) REVERT: C 551 ASN cc_start: 0.8956 (m-40) cc_final: 0.8619 (m-40) REVERT: C 555 TYR cc_start: 0.8884 (m-80) cc_final: 0.8391 (m-80) REVERT: C 570 GLU cc_start: 0.8515 (tt0) cc_final: 0.8315 (tt0) REVERT: C 647 LEU cc_start: 0.9144 (tp) cc_final: 0.8790 (tp) REVERT: C 653 TYR cc_start: 0.7760 (p90) cc_final: 0.7470 (p90) REVERT: C 655 PHE cc_start: 0.8456 (m-80) cc_final: 0.8233 (m-80) REVERT: C 662 LEU cc_start: 0.9005 (mt) cc_final: 0.8734 (mt) REVERT: C 692 GLU cc_start: 0.7480 (mp0) cc_final: 0.7072 (mp0) REVERT: C 694 LYS cc_start: 0.9168 (mttt) cc_final: 0.8875 (ptmt) REVERT: D 397 GLU cc_start: 0.8532 (mt-10) cc_final: 0.8158 (mt-10) REVERT: D 478 GLU cc_start: 0.8160 (mt-10) cc_final: 0.7711 (mp0) REVERT: D 498 GLN cc_start: 0.7982 (pt0) cc_final: 0.7692 (pt0) REVERT: D 509 ASP cc_start: 0.8962 (OUTLIER) cc_final: 0.8603 (m-30) REVERT: D 536 GLU cc_start: 0.8502 (mp0) cc_final: 0.8199 (mp0) REVERT: D 551 ASN cc_start: 0.9046 (m-40) cc_final: 0.8703 (m110) REVERT: D 570 GLU cc_start: 0.8684 (tt0) cc_final: 0.8359 (tt0) REVERT: D 647 LEU cc_start: 0.9131 (tp) cc_final: 0.8845 (tp) REVERT: D 653 TYR cc_start: 0.7755 (p90) cc_final: 0.7502 (p90) REVERT: D 694 LYS cc_start: 0.9066 (mttt) cc_final: 0.8790 (ptmt) REVERT: B 363 ARG cc_start: 0.6525 (OUTLIER) cc_final: 0.5370 (ptt180) REVERT: B 420 ARG cc_start: 0.8493 (mmm160) cc_final: 0.8037 (mmm160) REVERT: B 466 LYS cc_start: 0.8151 (mmtm) cc_final: 0.7218 (tmtt) REVERT: B 474 ARG cc_start: 0.7899 (ttp-110) cc_final: 0.5984 (mpt180) REVERT: B 478 GLU cc_start: 0.8290 (mt-10) cc_final: 0.7827 (mt-10) REVERT: B 512 SER cc_start: 0.8844 (OUTLIER) cc_final: 0.8484 (m) REVERT: B 547 MET cc_start: 0.8519 (mtp) cc_final: 0.8239 (mtp) REVERT: B 551 ASN cc_start: 0.9096 (m-40) cc_final: 0.8618 (m110) REVERT: B 553 LEU cc_start: 0.9078 (mp) cc_final: 0.8766 (mp) REVERT: B 555 TYR cc_start: 0.8967 (m-80) cc_final: 0.8547 (m-80) REVERT: B 557 ARG cc_start: 0.8422 (mtp85) cc_final: 0.8190 (mtp180) REVERT: B 572 MET cc_start: 0.8390 (ttp) cc_final: 0.8038 (ttp) REVERT: B 647 LEU cc_start: 0.9137 (tp) cc_final: 0.8856 (tp) REVERT: B 653 TYR cc_start: 0.7732 (p90) cc_final: 0.7384 (p90) REVERT: B 694 LYS cc_start: 0.8946 (ptmt) cc_final: 0.8601 (pttm) REVERT: B 695 ASN cc_start: 0.7764 (m-40) cc_final: 0.7122 (m-40) REVERT: B 697 TRP cc_start: 0.8096 (t60) cc_final: 0.7143 (t60) REVERT: B 698 LYS cc_start: 0.8447 (mmmt) cc_final: 0.8189 (mmmt) REVERT: B 700 GLN cc_start: 0.7860 (tm-30) cc_final: 0.7307 (tm-30) REVERT: B 706 LEU cc_start: 0.9141 (mp) cc_final: 0.8808 (mp) outliers start: 36 outliers final: 29 residues processed: 539 average time/residue: 0.1186 time to fit residues: 93.3471 Evaluate side-chains 545 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 510 time to evaluate : 0.541 ------------------------------------------------------------------------------- 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 652 ASN Chi-restraints excluded: chain A residue 676 ASN Chi-restraints excluded: chain C residue 368 LYS Chi-restraints excluded: chain C residue 397 GLU 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 552 MET Chi-restraints excluded: chain C residue 557 ARG Chi-restraints excluded: chain C residue 634 CYS Chi-restraints excluded: chain C residue 652 ASN Chi-restraints excluded: chain C residue 673 LEU 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 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 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 421 LEU Chi-restraints excluded: chain B residue 475 VAL Chi-restraints excluded: chain B residue 512 SER Chi-restraints excluded: chain B residue 579 ARG Chi-restraints excluded: chain B residue 652 ASN Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain B residue 687 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 145 optimal weight: 2.9990 chunk 30 optimal weight: 0.5980 chunk 106 optimal weight: 3.9990 chunk 89 optimal weight: 0.5980 chunk 96 optimal weight: 0.5980 chunk 70 optimal weight: 0.6980 chunk 124 optimal weight: 5.9990 chunk 9 optimal weight: 7.9990 chunk 53 optimal weight: 6.9990 chunk 121 optimal weight: 0.9990 chunk 92 optimal weight: 1.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 297 ASN D 320 HIS ** B 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 695 ASN ** 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 = 0.4181 r_free = 0.4181 target = 0.179523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.138433 restraints weight = 22313.327| |-----------------------------------------------------------------------------| r_work (start): 0.3680 rms_B_bonded: 2.96 r_work: 0.3547 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.4569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.193 14608 Z= 0.235 Angle : 0.873 59.165 19800 Z= 0.497 Chirality : 0.040 0.255 2240 Planarity : 0.003 0.037 2400 Dihedral : 4.985 54.424 1930 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 16.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 2.45 % Allowed : 22.80 % Favored : 74.74 % Cbeta Deviations : 0.06 % 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: 1.11 (0.15), residues: 1148 sheet: -1.11 (0.66), residues: 68 loop : -1.52 (0.28), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG D 557 TYR 0.023 0.001 TYR C 351 PHE 0.013 0.001 PHE A 582 TRP 0.087 0.002 TRP B 697 HIS 0.004 0.001 HIS A 410 Details of bonding type rmsd/Z covalent geometry : bond 0.00468 / 0.24 (14608) covalent geometry : angle 0.87266 / 0.50 (19800) hydrogen bonds : bond 0.03948 / 2.68 ( 904) hydrogen bonds : angle 4.44423 / 3.18 ( 2640) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3433.01 seconds wall clock time: 59 minutes 50.62 seconds (3590.62 seconds total)