Starting phenix.real_space_refine on Wed Mar 4 02:36:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wle_32583/03_2026/7wle_32583.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wle_32583/03_2026/7wle_32583.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.62 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wle_32583/03_2026/7wle_32583.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wle_32583/03_2026/7wle_32583.map" model { file = "/net/cci-nas-00/data/ceres_data/7wle_32583/03_2026/7wle_32583.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wle_32583/03_2026/7wle_32583.cif" } resolution = 3.62 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= 0.001 sd= 0.016 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 42 5.16 5 C 6650 2.51 5 N 1690 2.21 5 O 1806 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10188 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 662, 5094 Classifications: {'peptide': 662} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 26, 'TRANS': 635} Chain breaks: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'ARG:plan': 3} Unresolved non-hydrogen planarities: 15 Chain: "B" Number of atoms: 5094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 662, 5094 Classifications: {'peptide': 662} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 26, 'TRANS': 635} Chain breaks: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'ARG:plan': 3} Unresolved non-hydrogen planarities: 15 Time building chain proxies: 2.29, per 1000 atoms: 0.22 Number of scatterers: 10188 At special positions: 0 Unit cell: (84.056, 125.552, 123.424, 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 42 16.00 O 1806 8.00 N 1690 7.00 C 6650 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: 0.66 Conformation dependent library (CDL) restraints added in 586.8 milliseconds 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2460 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 4 sheets defined 64.3% alpha, 2.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'A' and resid 29 through 34 removed outlier: 3.603A pdb=" N GLN A 34 " --> pdb=" O LEU A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 50 Processing helix chain 'A' and resid 57 through 69 removed outlier: 4.012A pdb=" N ALA A 61 " --> pdb=" O SER A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 78 removed outlier: 3.915A pdb=" N TYR A 78 " --> pdb=" O LEU A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 109 removed outlier: 3.972A pdb=" N LEU A 107 " --> pdb=" O MET A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 130 Proline residue: A 123 - end of helix removed outlier: 3.921A pdb=" N VAL A 129 " --> pdb=" O LEU A 125 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N PHE A 130 " --> pdb=" O THR A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 155 removed outlier: 3.613A pdb=" N MET A 155 " --> pdb=" O VAL A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 206 removed outlier: 3.866A pdb=" N LEU A 206 " --> pdb=" O VAL A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 215 Processing helix chain 'A' and resid 216 through 240 removed outlier: 3.924A pdb=" N ILE A 238 " --> pdb=" O SER A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 263 Processing helix chain 'A' and resid 268 through 292 Processing helix chain 'A' and resid 301 through 316 removed outlier: 3.662A pdb=" N ILE A 305 " --> pdb=" O PRO A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 344 No H-bonds generated for 'chain 'A' and resid 342 through 344' Processing helix chain 'A' and resid 345 through 351 removed outlier: 3.596A pdb=" N MET A 349 " --> pdb=" O LEU A 345 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA A 351 " --> pdb=" O SER A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 370 Processing helix chain 'A' and resid 371 through 374 Processing helix chain 'A' and resid 380 through 396 removed outlier: 3.620A pdb=" N GLU A 384 " --> pdb=" O ASP A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 416 removed outlier: 3.508A pdb=" N THR A 410 " --> pdb=" O ALA A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 437 Processing helix chain 'A' and resid 448 through 458 removed outlier: 4.312A pdb=" N VAL A 454 " --> pdb=" O LEU A 450 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N ILE A 455 " --> pdb=" O ALA A 451 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 463 Processing helix chain 'A' and resid 466 through 473 removed outlier: 4.311A pdb=" N ARG A 470 " --> pdb=" O CYS A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 515 removed outlier: 3.653A pdb=" N ALA A 479 " --> pdb=" O ASN A 475 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N LEU A 494 " --> pdb=" O ILE A 490 " (cutoff:3.500A) removed outlier: 8.821A pdb=" N ASP A 495 " --> pdb=" O ILE A 491 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N LEU A 496 " --> pdb=" O LEU A 492 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LEU A 498 " --> pdb=" O LEU A 494 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N LEU A 499 " --> pdb=" O ASP A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 570 Processing helix chain 'A' and resid 573 through 595 Processing helix chain 'A' and resid 669 through 685 Processing helix chain 'A' and resid 698 through 706 Processing helix chain 'A' and resid 714 through 718 removed outlier: 3.567A pdb=" N ARG A 717 " --> pdb=" O ARG A 714 " (cutoff:3.500A) Processing helix chain 'A' and resid 721 through 733 removed outlier: 3.819A pdb=" N VAL A 733 " --> pdb=" O LEU A 729 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.606A pdb=" N GLN B 34 " --> pdb=" O LEU B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 50 removed outlier: 3.511A pdb=" N SER B 49 " --> pdb=" O THR B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 69 removed outlier: 3.999A pdb=" N ALA B 61 " --> pdb=" O SER B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 109 removed outlier: 3.964A pdb=" N LEU B 107 " --> pdb=" O MET B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 130 Proline residue: B 123 - end of helix removed outlier: 3.960A pdb=" N VAL B 129 " --> pdb=" O LEU B 125 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N PHE B 130 " --> pdb=" O THR B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 155 removed outlier: 3.649A pdb=" N MET B 155 " --> pdb=" O VAL B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 206 removed outlier: 3.894A pdb=" N LEU B 206 " --> pdb=" O VAL B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 215 Processing helix chain 'B' and resid 216 through 240 removed outlier: 3.672A pdb=" N ALA B 226 " --> pdb=" O GLY B 222 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ILE B 238 " --> pdb=" O SER B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 263 Processing helix chain 'B' and resid 268 through 292 Processing helix chain 'B' and resid 301 through 316 removed outlier: 3.683A pdb=" N ILE B 305 " --> pdb=" O PRO B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 344 No H-bonds generated for 'chain 'B' and resid 342 through 344' Processing helix chain 'B' and resid 345 through 351 removed outlier: 3.601A pdb=" N MET B 349 " --> pdb=" O LEU B 345 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA B 351 " --> pdb=" O SER B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 352 through 370 Processing helix chain 'B' and resid 371 through 374 Processing helix chain 'B' and resid 380 through 396 removed outlier: 3.564A pdb=" N GLU B 384 " --> pdb=" O ASP B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 416 Processing helix chain 'B' and resid 421 through 437 Processing helix chain 'B' and resid 448 through 458 removed outlier: 4.297A pdb=" N VAL B 454 " --> pdb=" O LEU B 450 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ILE B 455 " --> pdb=" O ALA B 451 " (cutoff:3.500A) Processing helix chain 'B' and resid 458 through 463 Processing helix chain 'B' and resid 464 through 466 No H-bonds generated for 'chain 'B' and resid 464 through 466' Processing helix chain 'B' and resid 467 through 475 Processing helix chain 'B' and resid 475 through 515 removed outlier: 3.792A pdb=" N ALA B 479 " --> pdb=" O ASN B 475 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N LEU B 494 " --> pdb=" O ILE B 490 " (cutoff:3.500A) removed outlier: 8.898A pdb=" N ASP B 495 " --> pdb=" O ILE B 491 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N LEU B 496 " --> pdb=" O LEU B 492 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LEU B 498 " --> pdb=" O LEU B 494 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N LEU B 499 " --> pdb=" O ASP B 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 558 through 570 Processing helix chain 'B' and resid 573 through 595 Processing helix chain 'B' and resid 669 through 685 Processing helix chain 'B' and resid 698 through 706 Processing helix chain 'B' and resid 714 through 718 removed outlier: 3.547A pdb=" N ARG B 717 " --> pdb=" O ARG B 714 " (cutoff:3.500A) Processing helix chain 'B' and resid 721 through 733 removed outlier: 3.825A pdb=" N VAL B 733 " --> pdb=" O LEU B 729 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 138 through 139 Processing sheet with id=AA2, first strand: chain 'A' and resid 530 through 532 removed outlier: 3.723A pdb=" N ASN A 519 " --> pdb=" O ARG A 549 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ARG A 549 " --> pdb=" O ASN A 519 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ILE A 547 " --> pdb=" O LEU A 521 " (cutoff:3.500A) removed outlier: 8.441A pdb=" N SER A 523 " --> pdb=" O VAL A 545 " (cutoff:3.500A) removed outlier: 12.636A pdb=" N VAL A 545 " --> pdb=" O SER A 523 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N LYS A 546 " --> pdb=" O VAL A 659 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N LEU A 658 " --> pdb=" O TYR A 691 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 138 through 139 Processing sheet with id=AA4, first strand: chain 'B' and resid 530 through 532 removed outlier: 3.682A pdb=" N ASN B 519 " --> pdb=" O ARG B 549 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ARG B 549 " --> pdb=" O ASN B 519 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ILE B 547 " --> pdb=" O LEU B 521 " (cutoff:3.500A) removed outlier: 8.492A pdb=" N SER B 523 " --> pdb=" O VAL B 545 " (cutoff:3.500A) removed outlier: 12.675A pdb=" N VAL B 545 " --> pdb=" O SER B 523 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N LYS B 546 " --> pdb=" O VAL B 659 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N LEU B 658 " --> pdb=" O TYR B 691 " (cutoff:3.500A) 576 hydrogen bonds defined for protein. 1683 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: 1.55 Time building geometry restraints manager: 0.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1614 1.32 - 1.44: 2671 1.44 - 1.56: 6041 1.56 - 1.69: 0 1.69 - 1.81: 64 Bond restraints: 10390 Sorted by residual: bond pdb=" CA THR A 225 " pdb=" C THR A 225 " ideal model delta sigma weight residual 1.523 1.442 0.081 1.37e-02 5.33e+03 3.45e+01 bond pdb=" CA THR A 224 " pdb=" C THR A 224 " ideal model delta sigma weight residual 1.523 1.450 0.073 1.35e-02 5.49e+03 2.90e+01 bond pdb=" CA ALA A 228 " pdb=" C ALA A 228 " ideal model delta sigma weight residual 1.524 1.464 0.060 1.27e-02 6.20e+03 2.24e+01 bond pdb=" CA ALA A 227 " pdb=" C ALA A 227 " ideal model delta sigma weight residual 1.523 1.459 0.064 1.37e-02 5.33e+03 2.15e+01 bond pdb=" N ALA A 228 " pdb=" CA ALA A 228 " ideal model delta sigma weight residual 1.459 1.410 0.049 1.19e-02 7.06e+03 1.69e+01 ... (remaining 10385 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.92: 13969 1.92 - 3.85: 129 3.85 - 5.77: 17 5.77 - 7.69: 4 7.69 - 9.61: 1 Bond angle restraints: 14120 Sorted by residual: angle pdb=" N GLY A 222 " pdb=" CA GLY A 222 " pdb=" C GLY A 222 " ideal model delta sigma weight residual 112.83 103.22 9.61 1.22e+00 6.72e-01 6.21e+01 angle pdb=" N ALA A 228 " pdb=" CA ALA A 228 " pdb=" C ALA A 228 " ideal model delta sigma weight residual 111.07 104.91 6.16 1.07e+00 8.73e-01 3.32e+01 angle pdb=" N ALA A 227 " pdb=" CA ALA A 227 " pdb=" C ALA A 227 " ideal model delta sigma weight residual 112.23 105.18 7.05 1.26e+00 6.30e-01 3.13e+01 angle pdb=" N THR A 225 " pdb=" CA THR A 225 " pdb=" C THR A 225 " ideal model delta sigma weight residual 112.23 105.81 6.42 1.26e+00 6.30e-01 2.60e+01 angle pdb=" N ALA A 226 " pdb=" CA ALA A 226 " pdb=" C ALA A 226 " ideal model delta sigma weight residual 112.89 108.24 4.65 1.24e+00 6.50e-01 1.41e+01 ... (remaining 14115 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.20: 5882 17.20 - 34.39: 242 34.39 - 51.59: 47 51.59 - 68.78: 3 68.78 - 85.98: 4 Dihedral angle restraints: 6178 sinusoidal: 2360 harmonic: 3818 Sorted by residual: dihedral pdb=" CA LEU A 694 " pdb=" C LEU A 694 " pdb=" N LEU A 695 " pdb=" CA LEU A 695 " ideal model delta harmonic sigma weight residual 180.00 161.10 18.90 0 5.00e+00 4.00e-02 1.43e+01 dihedral pdb=" CA LEU B 694 " pdb=" C LEU B 694 " pdb=" N LEU B 695 " pdb=" CA LEU B 695 " ideal model delta harmonic sigma weight residual 180.00 161.27 18.73 0 5.00e+00 4.00e-02 1.40e+01 dihedral pdb=" CA LEU A 695 " pdb=" C LEU A 695 " pdb=" N GLN A 696 " pdb=" CA GLN A 696 " ideal model delta harmonic sigma weight residual -180.00 -161.84 -18.16 0 5.00e+00 4.00e-02 1.32e+01 ... (remaining 6175 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1464 0.055 - 0.110: 236 0.110 - 0.165: 12 0.165 - 0.220: 1 0.220 - 0.275: 1 Chirality restraints: 1714 Sorted by residual: chirality pdb=" CA PHE A 223 " pdb=" N PHE A 223 " pdb=" C PHE A 223 " pdb=" CB PHE A 223 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.28 2.00e-01 2.50e+01 1.90e+00 chirality pdb=" CA THR A 224 " pdb=" N THR A 224 " pdb=" C THR A 224 " pdb=" CB THR A 224 " both_signs ideal model delta sigma weight residual False 2.53 2.32 0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CA THR B 224 " pdb=" N THR B 224 " pdb=" C THR B 224 " pdb=" CB THR B 224 " both_signs ideal model delta sigma weight residual False 2.53 2.38 0.15 2.00e-01 2.50e+01 5.69e-01 ... (remaining 1711 not shown) Planarity restraints: 1756 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY A 221 " 0.010 2.00e-02 2.50e+03 1.96e-02 3.83e+00 pdb=" C GLY A 221 " -0.034 2.00e-02 2.50e+03 pdb=" O GLY A 221 " 0.013 2.00e-02 2.50e+03 pdb=" N GLY A 222 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU B 75 " 0.026 5.00e-02 4.00e+02 3.94e-02 2.48e+00 pdb=" N PRO B 76 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO B 76 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 76 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 653 " -0.024 5.00e-02 4.00e+02 3.69e-02 2.18e+00 pdb=" N PRO B 654 " 0.064 5.00e-02 4.00e+02 pdb=" CA PRO B 654 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 654 " -0.020 5.00e-02 4.00e+02 ... (remaining 1753 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 2032 2.77 - 3.30: 10943 3.30 - 3.84: 17076 3.84 - 4.37: 19505 4.37 - 4.90: 32536 Nonbonded interactions: 82092 Sorted by model distance: nonbonded pdb=" O HIS A 135 " pdb=" OG1 THR A 410 " model vdw 2.240 3.040 nonbonded pdb=" O HIS B 135 " pdb=" OG1 THR B 410 " model vdw 2.248 3.040 nonbonded pdb=" NE2 GLN B 101 " pdb=" OG SER B 408 " model vdw 2.249 3.120 nonbonded pdb=" NE2 GLN A 101 " pdb=" OG SER A 408 " model vdw 2.260 3.120 nonbonded pdb=" O VAL B 453 " pdb=" ND2 ASN B 457 " model vdw 2.272 3.120 ... (remaining 82087 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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.440 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: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.170 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 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 : 0.003 0.081 10390 Z= 0.207 Angle : 0.499 9.614 14120 Z= 0.305 Chirality : 0.038 0.275 1714 Planarity : 0.004 0.039 1756 Dihedral : 9.906 85.978 3718 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 5.25 % Allowed : 6.41 % Favored : 88.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.62 (0.19), residues: 1316 helix: -1.46 (0.16), residues: 808 sheet: -2.61 (0.85), residues: 20 loop : -4.00 (0.21), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 213 TYR 0.005 0.001 TYR B 20 PHE 0.008 0.001 PHE B 555 TRP 0.010 0.001 TRP B 83 HIS 0.002 0.000 HIS B 535 Details of bonding type rmsd covalent geometry : bond 0.00312 (10390) covalent geometry : angle 0.49894 (14120) hydrogen bonds : bond 0.13515 ( 576) hydrogen bonds : angle 5.32232 ( 1683) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 409 time to evaluate : 0.315 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 77 LYS cc_start: 0.7862 (ttpt) cc_final: 0.7479 (ttpt) REVERT: A 90 SER cc_start: 0.8494 (t) cc_final: 0.8044 (p) REVERT: A 94 THR cc_start: 0.8154 (t) cc_final: 0.7861 (p) REVERT: A 128 PHE cc_start: 0.8528 (t80) cc_final: 0.7859 (t80) REVERT: A 132 THR cc_start: 0.6792 (OUTLIER) cc_final: 0.6384 (t) REVERT: A 195 LEU cc_start: 0.8522 (OUTLIER) cc_final: 0.8173 (tp) REVERT: A 203 PHE cc_start: 0.7748 (OUTLIER) cc_final: 0.7158 (m-80) REVERT: A 230 GLN cc_start: 0.8129 (tp40) cc_final: 0.7651 (tm-30) REVERT: A 237 LYS cc_start: 0.8406 (pttt) cc_final: 0.8043 (pttt) REVERT: A 244 THR cc_start: 0.7634 (t) cc_final: 0.7184 (p) REVERT: A 259 GLU cc_start: 0.7598 (OUTLIER) cc_final: 0.7106 (tm-30) REVERT: A 260 ILE cc_start: 0.8452 (mt) cc_final: 0.7801 (mt) REVERT: A 263 ASN cc_start: 0.8373 (t0) cc_final: 0.8075 (t0) REVERT: A 315 TYR cc_start: 0.6669 (t80) cc_final: 0.6417 (t80) REVERT: A 345 LEU cc_start: 0.8630 (tp) cc_final: 0.7940 (tp) REVERT: A 349 MET cc_start: 0.6269 (mmm) cc_final: 0.5756 (mmm) REVERT: A 350 LEU cc_start: 0.8567 (tp) cc_final: 0.8293 (tt) REVERT: A 354 PHE cc_start: 0.7470 (OUTLIER) cc_final: 0.7132 (t80) REVERT: A 356 ILE cc_start: 0.7419 (mt) cc_final: 0.6244 (mt) REVERT: A 473 LYS cc_start: 0.8260 (mttp) cc_final: 0.7988 (mttp) REVERT: A 573 ASP cc_start: 0.7470 (t0) cc_final: 0.6927 (p0) REVERT: A 577 VAL cc_start: 0.8360 (m) cc_final: 0.8057 (p) REVERT: A 580 LYS cc_start: 0.8012 (mmmt) cc_final: 0.7769 (tttt) REVERT: A 581 ARG cc_start: 0.8372 (tpt170) cc_final: 0.8109 (tpt170) REVERT: A 583 LYS cc_start: 0.8640 (OUTLIER) cc_final: 0.8069 (tmmt) REVERT: A 713 ILE cc_start: 0.7737 (OUTLIER) cc_final: 0.7375 (tt) REVERT: A 715 LYS cc_start: 0.8648 (ptpt) cc_final: 0.8294 (ptpp) REVERT: B 79 ARG cc_start: 0.7355 (OUTLIER) cc_final: 0.7018 (ptt-90) REVERT: B 80 VAL cc_start: 0.9391 (OUTLIER) cc_final: 0.9189 (t) REVERT: B 90 SER cc_start: 0.8703 (t) cc_final: 0.8227 (p) REVERT: B 94 THR cc_start: 0.8439 (t) cc_final: 0.8184 (p) REVERT: B 129 VAL cc_start: 0.8173 (p) cc_final: 0.7941 (p) REVERT: B 130 PHE cc_start: 0.7358 (m-80) cc_final: 0.7120 (m-80) REVERT: B 132 THR cc_start: 0.6746 (OUTLIER) cc_final: 0.6261 (t) REVERT: B 150 SER cc_start: 0.8283 (t) cc_final: 0.7936 (p) REVERT: B 196 VAL cc_start: 0.7824 (t) cc_final: 0.7544 (p) REVERT: B 206 LEU cc_start: 0.8133 (pt) cc_final: 0.7925 (pp) REVERT: B 213 ARG cc_start: 0.7767 (mtp180) cc_final: 0.7283 (mtp180) REVERT: B 237 LYS cc_start: 0.8359 (pttt) cc_final: 0.7777 (ptmm) REVERT: B 242 VAL cc_start: 0.7584 (t) cc_final: 0.7340 (m) REVERT: B 244 THR cc_start: 0.7852 (t) cc_final: 0.7492 (m) REVERT: B 250 ILE cc_start: 0.8541 (pt) cc_final: 0.8100 (mm) REVERT: B 287 GLU cc_start: 0.7423 (pp20) cc_final: 0.6791 (pp20) REVERT: B 356 ILE cc_start: 0.6644 (mt) cc_final: 0.5753 (mt) REVERT: B 400 CYS cc_start: 0.7621 (m) cc_final: 0.7419 (m) REVERT: B 466 CYS cc_start: 0.7981 (t) cc_final: 0.7219 (t) REVERT: B 473 LYS cc_start: 0.8259 (mttp) cc_final: 0.8058 (ttmm) REVERT: B 486 CYS cc_start: 0.8759 (t) cc_final: 0.8461 (t) REVERT: B 488 MET cc_start: 0.7437 (tpp) cc_final: 0.7162 (tpp) REVERT: B 531 LYS cc_start: 0.8634 (mmtm) cc_final: 0.8305 (mmmm) REVERT: B 556 TYR cc_start: 0.8921 (p90) cc_final: 0.8653 (p90) REVERT: B 583 LYS cc_start: 0.8401 (OUTLIER) cc_final: 0.7871 (tmmt) REVERT: B 682 GLU cc_start: 0.7404 (tp30) cc_final: 0.6809 (tp30) REVERT: B 689 ASN cc_start: 0.8192 (m110) cc_final: 0.7830 (m110) REVERT: B 705 GLN cc_start: 0.8471 (tt0) cc_final: 0.8211 (tt0) outliers start: 59 outliers final: 17 residues processed: 450 average time/residue: 0.1220 time to fit residues: 73.1244 Evaluate side-chains 341 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 313 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 203 PHE Chi-restraints excluded: chain A residue 259 GLU Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 583 LYS Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 695 LEU Chi-restraints excluded: chain A residue 713 ILE Chi-restraints excluded: chain B residue 79 ARG Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 259 GLU Chi-restraints excluded: chain B residue 405 THR Chi-restraints excluded: chain B residue 449 VAL Chi-restraints excluded: chain B residue 583 LYS Chi-restraints excluded: chain B residue 688 VAL Chi-restraints excluded: chain B residue 690 VAL Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 699 VAL Chi-restraints excluded: chain B residue 713 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 98 optimal weight: 0.6980 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 0.0000 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 0.0670 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 0.8980 overall best weight: 0.4122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 200 GLN A 241 ASN A 262 GLN A 289 ASN A 318 ASN A 383 GLN A 446 GLN A 457 ASN A 474 GLN A 684 GLN A 723 HIS B 34 GLN B 262 GLN B 318 ASN B 446 GLN B 474 GLN B 535 HIS B 684 GLN B 723 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.134639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.117481 restraints weight = 21109.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.120833 restraints weight = 10569.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.123034 restraints weight = 6312.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.124557 restraints weight = 4245.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.125590 restraints weight = 3170.362| |-----------------------------------------------------------------------------| r_work (final): 0.3725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 moved from start: 0.2940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10390 Z= 0.151 Angle : 0.644 8.200 14120 Z= 0.332 Chirality : 0.042 0.253 1714 Planarity : 0.004 0.034 1756 Dihedral : 6.819 102.496 1465 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 4.72 % Allowed : 17.70 % Favored : 77.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.01 (0.22), residues: 1316 helix: -0.25 (0.18), residues: 810 sheet: 0.02 (1.02), residues: 20 loop : -3.32 (0.24), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 39 TYR 0.023 0.002 TYR A 530 PHE 0.029 0.001 PHE A 719 TRP 0.010 0.001 TRP B 83 HIS 0.005 0.001 HIS B 728 Details of bonding type rmsd covalent geometry : bond 0.00341 (10390) covalent geometry : angle 0.64442 (14120) hydrogen bonds : bond 0.03759 ( 576) hydrogen bonds : angle 3.95568 ( 1683) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 331 time to evaluate : 0.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 GLU cc_start: 0.8036 (OUTLIER) cc_final: 0.6801 (pm20) REVERT: A 77 LYS cc_start: 0.7957 (ttpt) cc_final: 0.7542 (ttpt) REVERT: A 90 SER cc_start: 0.8486 (t) cc_final: 0.8021 (p) REVERT: A 94 THR cc_start: 0.8353 (t) cc_final: 0.8122 (p) REVERT: A 118 TYR cc_start: 0.6956 (m-10) cc_final: 0.6687 (m-80) REVERT: A 128 PHE cc_start: 0.8534 (t80) cc_final: 0.8283 (t80) REVERT: A 195 LEU cc_start: 0.8669 (OUTLIER) cc_final: 0.8246 (tm) REVERT: A 230 GLN cc_start: 0.8059 (tp40) cc_final: 0.7858 (tm-30) REVERT: A 259 GLU cc_start: 0.7574 (OUTLIER) cc_final: 0.7139 (tm-30) REVERT: A 260 ILE cc_start: 0.8566 (mt) cc_final: 0.7942 (mt) REVERT: A 263 ASN cc_start: 0.8343 (t0) cc_final: 0.7917 (t0) REVERT: A 350 LEU cc_start: 0.8600 (tp) cc_final: 0.8250 (tt) REVERT: A 426 ILE cc_start: 0.8021 (tp) cc_final: 0.7814 (mm) REVERT: A 432 MET cc_start: 0.7300 (tmm) cc_final: 0.6951 (tmm) REVERT: A 466 CYS cc_start: 0.7700 (t) cc_final: 0.7271 (t) REVERT: A 473 LYS cc_start: 0.8356 (mttp) cc_final: 0.8107 (mttp) REVERT: A 530 TYR cc_start: 0.8231 (m-80) cc_final: 0.7898 (m-80) REVERT: A 580 LYS cc_start: 0.8140 (mmmt) cc_final: 0.7895 (tttt) REVERT: A 583 LYS cc_start: 0.8540 (OUTLIER) cc_final: 0.7989 (tmmt) REVERT: B 80 VAL cc_start: 0.9384 (OUTLIER) cc_final: 0.8858 (t) REVERT: B 90 SER cc_start: 0.8749 (t) cc_final: 0.8247 (p) REVERT: B 94 THR cc_start: 0.8638 (t) cc_final: 0.8262 (p) REVERT: B 132 THR cc_start: 0.7028 (OUTLIER) cc_final: 0.6352 (t) REVERT: B 150 SER cc_start: 0.8326 (t) cc_final: 0.8049 (p) REVERT: B 230 GLN cc_start: 0.8191 (tm-30) cc_final: 0.7906 (tm-30) REVERT: B 239 VAL cc_start: 0.8281 (OUTLIER) cc_final: 0.8078 (p) REVERT: B 244 THR cc_start: 0.8100 (t) cc_final: 0.7292 (m) REVERT: B 250 ILE cc_start: 0.8552 (pt) cc_final: 0.8268 (mm) REVERT: B 259 GLU cc_start: 0.7476 (OUTLIER) cc_final: 0.6728 (tm-30) REVERT: B 384 GLU cc_start: 0.7549 (mm-30) cc_final: 0.7174 (tp30) REVERT: B 394 PHE cc_start: 0.8248 (t80) cc_final: 0.7960 (t80) REVERT: B 400 CYS cc_start: 0.7592 (m) cc_final: 0.7385 (m) REVERT: B 432 MET cc_start: 0.7231 (tmm) cc_final: 0.7030 (tmm) REVERT: B 462 PHE cc_start: 0.8497 (m-80) cc_final: 0.8280 (m-80) REVERT: B 463 MET cc_start: 0.7408 (tmm) cc_final: 0.7101 (tmm) REVERT: B 466 CYS cc_start: 0.7957 (t) cc_final: 0.7484 (t) REVERT: B 470 ARG cc_start: 0.6666 (mtp180) cc_final: 0.6395 (mtp180) REVERT: B 473 LYS cc_start: 0.8379 (mttp) cc_final: 0.8129 (mtpp) REVERT: B 486 CYS cc_start: 0.8675 (t) cc_final: 0.8423 (t) REVERT: B 488 MET cc_start: 0.7390 (tpp) cc_final: 0.6916 (tpp) REVERT: B 513 VAL cc_start: 0.9141 (OUTLIER) cc_final: 0.8909 (p) REVERT: B 531 LYS cc_start: 0.8617 (mmtm) cc_final: 0.8257 (mmmm) REVERT: B 537 LYS cc_start: 0.8201 (mmmm) cc_final: 0.7139 (ttpp) REVERT: B 556 TYR cc_start: 0.8964 (p90) cc_final: 0.8708 (p90) REVERT: B 564 LYS cc_start: 0.8673 (OUTLIER) cc_final: 0.8466 (ttmm) REVERT: B 578 TYR cc_start: 0.7796 (t80) cc_final: 0.7242 (t80) REVERT: B 581 ARG cc_start: 0.8223 (tpp-160) cc_final: 0.7807 (tpp-160) REVERT: B 583 LYS cc_start: 0.8285 (OUTLIER) cc_final: 0.7758 (tmmt) REVERT: B 681 LYS cc_start: 0.8381 (mptt) cc_final: 0.8060 (mptt) REVERT: B 715 LYS cc_start: 0.8692 (ptpt) cc_final: 0.8413 (ptpp) outliers start: 53 outliers final: 18 residues processed: 361 average time/residue: 0.1043 time to fit residues: 51.1530 Evaluate side-chains 351 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 322 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 GLU Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 259 GLU Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 564 LYS Chi-restraints excluded: chain A residue 583 LYS Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 695 LEU Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 259 GLU Chi-restraints excluded: chain B residue 405 THR Chi-restraints excluded: chain B residue 449 VAL Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain B residue 564 LYS Chi-restraints excluded: chain B residue 583 LYS Chi-restraints excluded: chain B residue 690 VAL Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 699 VAL Chi-restraints excluded: chain B residue 713 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 63 optimal weight: 0.9990 chunk 125 optimal weight: 0.0870 chunk 122 optimal weight: 3.9990 chunk 28 optimal weight: 0.9980 chunk 34 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 chunk 69 optimal weight: 0.7980 chunk 81 optimal weight: 10.0000 chunk 32 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 128 optimal weight: 0.7980 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 457 ASN B 35 GLN B 689 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.131383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.114321 restraints weight = 21234.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.117657 restraints weight = 10553.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.119709 restraints weight = 6225.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.121186 restraints weight = 4219.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.121950 restraints weight = 3145.415| |-----------------------------------------------------------------------------| r_work (final): 0.3643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.3752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 10390 Z= 0.172 Angle : 0.644 8.106 14120 Z= 0.332 Chirality : 0.042 0.175 1714 Planarity : 0.004 0.053 1756 Dihedral : 6.550 95.489 1450 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 12.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 5.07 % Allowed : 18.24 % Favored : 76.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.57 (0.23), residues: 1316 helix: -0.04 (0.18), residues: 840 sheet: 0.86 (1.04), residues: 20 loop : -3.07 (0.27), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 36 TYR 0.026 0.002 TYR B 127 PHE 0.022 0.002 PHE A 130 TRP 0.012 0.001 TRP B 83 HIS 0.006 0.001 HIS B 728 Details of bonding type rmsd covalent geometry : bond 0.00382 (10390) covalent geometry : angle 0.64380 (14120) hydrogen bonds : bond 0.03558 ( 576) hydrogen bonds : angle 3.86274 ( 1683) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 326 time to evaluate : 0.390 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 77 LYS cc_start: 0.8000 (ttpt) cc_final: 0.7599 (ttpt) REVERT: A 90 SER cc_start: 0.8487 (t) cc_final: 0.7968 (p) REVERT: A 94 THR cc_start: 0.8429 (t) cc_final: 0.8149 (p) REVERT: A 128 PHE cc_start: 0.8592 (t80) cc_final: 0.8369 (t80) REVERT: A 195 LEU cc_start: 0.8863 (OUTLIER) cc_final: 0.8490 (tp) REVERT: A 230 GLN cc_start: 0.8186 (tp40) cc_final: 0.7883 (tm-30) REVERT: A 237 LYS cc_start: 0.8640 (pttt) cc_final: 0.8298 (ptmm) REVERT: A 259 GLU cc_start: 0.7671 (OUTLIER) cc_final: 0.7105 (tm-30) REVERT: A 260 ILE cc_start: 0.8622 (mt) cc_final: 0.7926 (mt) REVERT: A 350 LEU cc_start: 0.8578 (tp) cc_final: 0.8196 (tt) REVERT: A 404 THR cc_start: 0.7353 (OUTLIER) cc_final: 0.6871 (t) REVERT: A 414 GLU cc_start: 0.7418 (tm-30) cc_final: 0.7056 (tp30) REVERT: A 432 MET cc_start: 0.7419 (tmm) cc_final: 0.7018 (tmm) REVERT: A 463 MET cc_start: 0.7537 (tmm) cc_final: 0.7234 (tmm) REVERT: A 466 CYS cc_start: 0.7836 (t) cc_final: 0.7357 (t) REVERT: A 473 LYS cc_start: 0.8433 (mttp) cc_final: 0.8047 (ttmm) REVERT: A 537 LYS cc_start: 0.8012 (ttpp) cc_final: 0.7664 (ttpp) REVERT: A 546 LYS cc_start: 0.6713 (ptmm) cc_final: 0.6383 (ptmm) REVERT: A 580 LYS cc_start: 0.8175 (mmmt) cc_final: 0.7917 (mtpt) REVERT: A 583 LYS cc_start: 0.8440 (OUTLIER) cc_final: 0.7870 (tmmt) REVERT: A 689 ASN cc_start: 0.7792 (m110) cc_final: 0.7476 (m110) REVERT: B 27 TYR cc_start: 0.6849 (m-10) cc_final: 0.6623 (m-10) REVERT: B 66 LYS cc_start: 0.8488 (tptt) cc_final: 0.8130 (tppt) REVERT: B 77 LYS cc_start: 0.8330 (ttpt) cc_final: 0.7984 (ttpt) REVERT: B 80 VAL cc_start: 0.9337 (OUTLIER) cc_final: 0.9091 (t) REVERT: B 90 SER cc_start: 0.8712 (t) cc_final: 0.8080 (p) REVERT: B 94 THR cc_start: 0.8627 (t) cc_final: 0.8193 (p) REVERT: B 125 LEU cc_start: 0.9008 (tp) cc_final: 0.8775 (tp) REVERT: B 127 TYR cc_start: 0.8534 (t80) cc_final: 0.8328 (t80) REVERT: B 132 THR cc_start: 0.7292 (OUTLIER) cc_final: 0.6522 (t) REVERT: B 150 SER cc_start: 0.8320 (t) cc_final: 0.8053 (p) REVERT: B 213 ARG cc_start: 0.8223 (mtp180) cc_final: 0.7950 (mtp180) REVERT: B 230 GLN cc_start: 0.8298 (tm-30) cc_final: 0.7908 (tm-30) REVERT: B 237 LYS cc_start: 0.8583 (pttt) cc_final: 0.8132 (ptpt) REVERT: B 238 ILE cc_start: 0.8647 (tp) cc_final: 0.8316 (pt) REVERT: B 250 ILE cc_start: 0.8574 (pt) cc_final: 0.8316 (mm) REVERT: B 259 GLU cc_start: 0.7535 (OUTLIER) cc_final: 0.6811 (tm-30) REVERT: B 260 ILE cc_start: 0.8682 (mt) cc_final: 0.8226 (mt) REVERT: B 349 MET cc_start: 0.6028 (mmm) cc_final: 0.5730 (mmm) REVERT: B 354 PHE cc_start: 0.7218 (OUTLIER) cc_final: 0.7012 (t80) REVERT: B 384 GLU cc_start: 0.7680 (mm-30) cc_final: 0.7231 (tp30) REVERT: B 394 PHE cc_start: 0.8256 (t80) cc_final: 0.7918 (t80) REVERT: B 400 CYS cc_start: 0.7495 (m) cc_final: 0.7149 (m) REVERT: B 432 MET cc_start: 0.7470 (tmm) cc_final: 0.7184 (tmm) REVERT: B 463 MET cc_start: 0.7388 (tmm) cc_final: 0.7135 (tmm) REVERT: B 466 CYS cc_start: 0.8034 (t) cc_final: 0.7643 (t) REVERT: B 470 ARG cc_start: 0.6672 (mtp180) cc_final: 0.6407 (mtp180) REVERT: B 473 LYS cc_start: 0.8419 (mttp) cc_final: 0.8151 (mtpp) REVERT: B 486 CYS cc_start: 0.8717 (t) cc_final: 0.8464 (t) REVERT: B 488 MET cc_start: 0.7425 (tpp) cc_final: 0.7055 (tpp) REVERT: B 513 VAL cc_start: 0.9117 (OUTLIER) cc_final: 0.8880 (p) REVERT: B 531 LYS cc_start: 0.8622 (mmtm) cc_final: 0.8254 (mmmm) REVERT: B 556 TYR cc_start: 0.8989 (p90) cc_final: 0.8692 (p90) REVERT: B 578 TYR cc_start: 0.7843 (t80) cc_final: 0.7179 (t80) REVERT: B 581 ARG cc_start: 0.8167 (tpp-160) cc_final: 0.7819 (tpp-160) REVERT: B 583 LYS cc_start: 0.8412 (OUTLIER) cc_final: 0.7867 (tmmt) REVERT: B 705 GLN cc_start: 0.8675 (tt0) cc_final: 0.8369 (tt0) REVERT: B 714 ARG cc_start: 0.7384 (mtm-85) cc_final: 0.7072 (mtm-85) REVERT: B 715 LYS cc_start: 0.8537 (ptpt) cc_final: 0.8242 (ptpp) outliers start: 57 outliers final: 24 residues processed: 356 average time/residue: 0.1074 time to fit residues: 51.5911 Evaluate side-chains 333 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 299 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 259 GLU Chi-restraints excluded: chain A residue 349 MET Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 564 LYS Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 583 LYS Chi-restraints excluded: chain A residue 682 GLU Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 695 LEU Chi-restraints excluded: chain A residue 715 LYS Chi-restraints excluded: chain A residue 716 ASP Chi-restraints excluded: chain B residue 73 ASP Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 259 GLU Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 354 PHE Chi-restraints excluded: chain B residue 405 THR Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain B residue 583 LYS Chi-restraints excluded: chain B residue 690 VAL Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 699 VAL Chi-restraints excluded: chain B residue 703 MET Chi-restraints excluded: chain B residue 713 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 109 optimal weight: 0.7980 chunk 130 optimal weight: 0.2980 chunk 55 optimal weight: 0.7980 chunk 5 optimal weight: 0.9990 chunk 38 optimal weight: 3.9990 chunk 115 optimal weight: 0.8980 chunk 61 optimal weight: 0.8980 chunk 70 optimal weight: 5.9990 chunk 6 optimal weight: 0.4980 chunk 85 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 268 ASN A 322 ASN A 457 ASN B 567 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.125153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.108638 restraints weight = 21342.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.111834 restraints weight = 10419.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.113929 restraints weight = 6086.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.115134 restraints weight = 4020.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 63)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.116282 restraints weight = 3056.443| |-----------------------------------------------------------------------------| r_work (final): 0.3614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.4314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 10390 Z= 0.171 Angle : 0.643 8.597 14120 Z= 0.331 Chirality : 0.043 0.161 1714 Planarity : 0.004 0.072 1756 Dihedral : 6.521 96.188 1448 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 13.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 5.34 % Allowed : 20.55 % Favored : 74.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.32 (0.23), residues: 1316 helix: 0.16 (0.18), residues: 832 sheet: 1.37 (1.02), residues: 20 loop : -2.94 (0.27), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 134 TYR 0.031 0.002 TYR A 578 PHE 0.027 0.001 PHE B 128 TRP 0.013 0.001 TRP B 83 HIS 0.006 0.001 HIS B 728 Details of bonding type rmsd covalent geometry : bond 0.00388 (10390) covalent geometry : angle 0.64275 (14120) hydrogen bonds : bond 0.03521 ( 576) hydrogen bonds : angle 3.86424 ( 1683) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 325 time to evaluate : 0.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 LYS cc_start: 0.7986 (ttpt) cc_final: 0.7601 (ttpt) REVERT: A 90 SER cc_start: 0.8442 (t) cc_final: 0.7898 (p) REVERT: A 94 THR cc_start: 0.8472 (t) cc_final: 0.8095 (p) REVERT: A 134 ARG cc_start: 0.8109 (mpp80) cc_final: 0.7130 (mtm-85) REVERT: A 195 LEU cc_start: 0.8924 (OUTLIER) cc_final: 0.8541 (tp) REVERT: A 230 GLN cc_start: 0.8201 (tp40) cc_final: 0.7879 (tm-30) REVERT: A 237 LYS cc_start: 0.8702 (pttt) cc_final: 0.8354 (ptmm) REVERT: A 238 ILE cc_start: 0.8794 (tp) cc_final: 0.8556 (tp) REVERT: A 259 GLU cc_start: 0.7692 (OUTLIER) cc_final: 0.7151 (tm-30) REVERT: A 260 ILE cc_start: 0.8642 (mt) cc_final: 0.7984 (mt) REVERT: A 350 LEU cc_start: 0.8576 (tp) cc_final: 0.8205 (tt) REVERT: A 358 VAL cc_start: 0.8853 (t) cc_final: 0.8607 (p) REVERT: A 369 LYS cc_start: 0.8691 (mmmm) cc_final: 0.8441 (mmmm) REVERT: A 385 PHE cc_start: 0.8836 (OUTLIER) cc_final: 0.8565 (t80) REVERT: A 404 THR cc_start: 0.7449 (OUTLIER) cc_final: 0.7029 (t) REVERT: A 409 ARG cc_start: 0.8192 (mtm180) cc_final: 0.7641 (mtm110) REVERT: A 414 GLU cc_start: 0.7452 (tm-30) cc_final: 0.7178 (tp30) REVERT: A 426 ILE cc_start: 0.8124 (tp) cc_final: 0.7888 (mm) REVERT: A 432 MET cc_start: 0.7512 (tmm) cc_final: 0.7181 (tmm) REVERT: A 463 MET cc_start: 0.7575 (tmm) cc_final: 0.7044 (tmm) REVERT: A 466 CYS cc_start: 0.7929 (t) cc_final: 0.7454 (t) REVERT: A 473 LYS cc_start: 0.8462 (mttp) cc_final: 0.8073 (ttmm) REVERT: A 537 LYS cc_start: 0.8027 (ttpp) cc_final: 0.7638 (ttpp) REVERT: A 546 LYS cc_start: 0.6844 (ptmm) cc_final: 0.6578 (ptmm) REVERT: A 573 ASP cc_start: 0.7802 (t0) cc_final: 0.6858 (p0) REVERT: A 580 LYS cc_start: 0.8178 (mmmt) cc_final: 0.7929 (mtpt) REVERT: A 581 ARG cc_start: 0.8187 (tpt170) cc_final: 0.7842 (tpt170) REVERT: A 583 LYS cc_start: 0.8358 (OUTLIER) cc_final: 0.7825 (tmmt) REVERT: A 689 ASN cc_start: 0.7832 (m110) cc_final: 0.7570 (m110) REVERT: B 66 LYS cc_start: 0.8419 (tptt) cc_final: 0.7986 (tppt) REVERT: B 77 LYS cc_start: 0.8334 (ttpt) cc_final: 0.7968 (ttpt) REVERT: B 90 SER cc_start: 0.8656 (t) cc_final: 0.8193 (p) REVERT: B 125 LEU cc_start: 0.8996 (tp) cc_final: 0.8770 (tp) REVERT: B 126 THR cc_start: 0.8484 (t) cc_final: 0.8212 (t) REVERT: B 127 TYR cc_start: 0.8600 (t80) cc_final: 0.8322 (t80) REVERT: B 132 THR cc_start: 0.7347 (OUTLIER) cc_final: 0.6829 (t) REVERT: B 150 SER cc_start: 0.8378 (t) cc_final: 0.8114 (p) REVERT: B 195 LEU cc_start: 0.8733 (tp) cc_final: 0.8506 (tp) REVERT: B 230 GLN cc_start: 0.8375 (tm-30) cc_final: 0.7861 (tm-30) REVERT: B 237 LYS cc_start: 0.8609 (pttt) cc_final: 0.8330 (ttpp) REVERT: B 250 ILE cc_start: 0.8671 (pt) cc_final: 0.8401 (mm) REVERT: B 255 TYR cc_start: 0.7909 (m-10) cc_final: 0.7436 (m-10) REVERT: B 259 GLU cc_start: 0.7472 (OUTLIER) cc_final: 0.6802 (tm-30) REVERT: B 260 ILE cc_start: 0.8782 (mt) cc_final: 0.8264 (mt) REVERT: B 354 PHE cc_start: 0.7214 (OUTLIER) cc_final: 0.7000 (t80) REVERT: B 384 GLU cc_start: 0.7680 (mm-30) cc_final: 0.7147 (tp30) REVERT: B 394 PHE cc_start: 0.8255 (t80) cc_final: 0.7641 (t80) REVERT: B 400 CYS cc_start: 0.7284 (m) cc_final: 0.6973 (m) REVERT: B 409 ARG cc_start: 0.7879 (mtm180) cc_final: 0.7291 (mtm110) REVERT: B 414 GLU cc_start: 0.7544 (tm-30) cc_final: 0.7016 (tp30) REVERT: B 432 MET cc_start: 0.7427 (tmm) cc_final: 0.7120 (tmm) REVERT: B 463 MET cc_start: 0.7444 (tmm) cc_final: 0.7201 (tmm) REVERT: B 466 CYS cc_start: 0.8068 (t) cc_final: 0.7675 (t) REVERT: B 470 ARG cc_start: 0.6718 (mtp180) cc_final: 0.6446 (mtp180) REVERT: B 473 LYS cc_start: 0.8448 (mttp) cc_final: 0.8198 (mtpp) REVERT: B 486 CYS cc_start: 0.8723 (t) cc_final: 0.8470 (t) REVERT: B 488 MET cc_start: 0.7448 (tpp) cc_final: 0.7084 (tpp) REVERT: B 513 VAL cc_start: 0.9152 (OUTLIER) cc_final: 0.8920 (p) REVERT: B 531 LYS cc_start: 0.8601 (mmtm) cc_final: 0.8326 (mmmm) REVERT: B 537 LYS cc_start: 0.8243 (tmtt) cc_final: 0.7763 (tptp) REVERT: B 556 TYR cc_start: 0.8990 (p90) cc_final: 0.8652 (p90) REVERT: B 578 TYR cc_start: 0.7860 (t80) cc_final: 0.7311 (t80) REVERT: B 580 LYS cc_start: 0.7851 (mmmm) cc_final: 0.7622 (mmmm) REVERT: B 581 ARG cc_start: 0.8118 (tpp-160) cc_final: 0.7822 (tpp-160) REVERT: B 583 LYS cc_start: 0.8480 (OUTLIER) cc_final: 0.7933 (tmmt) REVERT: B 705 GLN cc_start: 0.8670 (tt0) cc_final: 0.8368 (tt0) REVERT: B 714 ARG cc_start: 0.7431 (mtm-85) cc_final: 0.7165 (mtm-85) outliers start: 60 outliers final: 33 residues processed: 360 average time/residue: 0.1168 time to fit residues: 56.3146 Evaluate side-chains 351 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 308 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ARG Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 203 PHE Chi-restraints excluded: chain A residue 259 GLU Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 564 LYS Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 583 LYS Chi-restraints excluded: chain A residue 682 GLU Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 715 LYS Chi-restraints excluded: chain A residue 716 ASP Chi-restraints excluded: chain B residue 73 ASP Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 259 GLU Chi-restraints excluded: chain B residue 283 MET Chi-restraints excluded: chain B residue 354 PHE Chi-restraints excluded: chain B residue 383 GLN Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 405 THR Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 583 LYS Chi-restraints excluded: chain B residue 690 VAL Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 699 VAL Chi-restraints excluded: chain B residue 703 MET Chi-restraints excluded: chain B residue 713 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 73 optimal weight: 1.9990 chunk 5 optimal weight: 0.2980 chunk 78 optimal weight: 0.6980 chunk 75 optimal weight: 0.8980 chunk 119 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 27 optimal weight: 5.9990 chunk 9 optimal weight: 0.9980 chunk 23 optimal weight: 0.0970 chunk 53 optimal weight: 0.1980 chunk 126 optimal weight: 1.9990 overall best weight: 0.4378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 268 ASN A 289 ASN A 322 ASN B 457 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.129467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.112502 restraints weight = 21037.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.115777 restraints weight = 10383.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.117895 restraints weight = 6107.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.119320 restraints weight = 4048.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.120209 restraints weight = 3003.543| |-----------------------------------------------------------------------------| r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.4593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10390 Z= 0.144 Angle : 0.659 9.232 14120 Z= 0.334 Chirality : 0.043 0.238 1714 Planarity : 0.004 0.042 1756 Dihedral : 6.428 95.045 1445 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 4.09 % Allowed : 22.42 % Favored : 73.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.13 (0.23), residues: 1316 helix: 0.29 (0.18), residues: 832 sheet: 1.71 (1.04), residues: 20 loop : -2.83 (0.28), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 134 TYR 0.031 0.002 TYR B 323 PHE 0.028 0.001 PHE B 128 TRP 0.012 0.001 TRP B 83 HIS 0.005 0.001 HIS B 728 Details of bonding type rmsd covalent geometry : bond 0.00334 (10390) covalent geometry : angle 0.65941 (14120) hydrogen bonds : bond 0.03426 ( 576) hydrogen bonds : angle 3.84245 ( 1683) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 317 time to evaluate : 0.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 LYS cc_start: 0.8040 (ttpt) cc_final: 0.7611 (ttpt) REVERT: A 90 SER cc_start: 0.8510 (t) cc_final: 0.7944 (p) REVERT: A 94 THR cc_start: 0.8519 (t) cc_final: 0.8205 (p) REVERT: A 153 LEU cc_start: 0.8867 (mt) cc_final: 0.8666 (mm) REVERT: A 195 LEU cc_start: 0.8911 (OUTLIER) cc_final: 0.8508 (tp) REVERT: A 230 GLN cc_start: 0.8173 (tp40) cc_final: 0.7881 (tm-30) REVERT: A 237 LYS cc_start: 0.8709 (pttt) cc_final: 0.8338 (ttpp) REVERT: A 238 ILE cc_start: 0.8818 (tp) cc_final: 0.8560 (tp) REVERT: A 255 TYR cc_start: 0.7659 (m-10) cc_final: 0.7366 (m-10) REVERT: A 259 GLU cc_start: 0.7685 (OUTLIER) cc_final: 0.7148 (tm-30) REVERT: A 260 ILE cc_start: 0.8652 (mt) cc_final: 0.8020 (mt) REVERT: A 263 ASN cc_start: 0.8318 (t0) cc_final: 0.8013 (t0) REVERT: A 322 ASN cc_start: 0.7031 (OUTLIER) cc_final: 0.6741 (t0) REVERT: A 350 LEU cc_start: 0.8500 (tp) cc_final: 0.8120 (tt) REVERT: A 358 VAL cc_start: 0.8900 (t) cc_final: 0.8656 (p) REVERT: A 369 LYS cc_start: 0.8713 (mmmm) cc_final: 0.8500 (mmmm) REVERT: A 404 THR cc_start: 0.7500 (OUTLIER) cc_final: 0.7005 (t) REVERT: A 409 ARG cc_start: 0.8174 (mtm180) cc_final: 0.7636 (mtm110) REVERT: A 414 GLU cc_start: 0.7446 (tm-30) cc_final: 0.7184 (tp30) REVERT: A 426 ILE cc_start: 0.8116 (tp) cc_final: 0.7896 (mm) REVERT: A 432 MET cc_start: 0.7519 (tmm) cc_final: 0.7178 (tmm) REVERT: A 463 MET cc_start: 0.7561 (tmm) cc_final: 0.7094 (tmm) REVERT: A 466 CYS cc_start: 0.7970 (t) cc_final: 0.7505 (t) REVERT: A 473 LYS cc_start: 0.8477 (mttp) cc_final: 0.8050 (ttmm) REVERT: A 476 LYS cc_start: 0.9143 (mtmm) cc_final: 0.8919 (mtmm) REVERT: A 546 LYS cc_start: 0.6835 (ptmm) cc_final: 0.6419 (ptmm) REVERT: A 580 LYS cc_start: 0.8167 (mmmt) cc_final: 0.7914 (tttt) REVERT: A 583 LYS cc_start: 0.8458 (OUTLIER) cc_final: 0.7885 (tmmt) REVERT: A 689 ASN cc_start: 0.7762 (m110) cc_final: 0.7504 (m110) REVERT: B 66 LYS cc_start: 0.8405 (tptt) cc_final: 0.7951 (tppt) REVERT: B 77 LYS cc_start: 0.8345 (ttpt) cc_final: 0.7967 (ttpt) REVERT: B 90 SER cc_start: 0.8646 (t) cc_final: 0.8130 (p) REVERT: B 125 LEU cc_start: 0.9006 (tp) cc_final: 0.8783 (tp) REVERT: B 126 THR cc_start: 0.8488 (t) cc_final: 0.8259 (t) REVERT: B 127 TYR cc_start: 0.8611 (t80) cc_final: 0.8296 (t80) REVERT: B 132 THR cc_start: 0.7539 (OUTLIER) cc_final: 0.6883 (t) REVERT: B 150 SER cc_start: 0.8325 (t) cc_final: 0.8064 (p) REVERT: B 230 GLN cc_start: 0.8386 (tm-30) cc_final: 0.7555 (tm-30) REVERT: B 237 LYS cc_start: 0.8553 (pttt) cc_final: 0.8266 (ttpp) REVERT: B 238 ILE cc_start: 0.8795 (tp) cc_final: 0.8372 (pt) REVERT: B 250 ILE cc_start: 0.8641 (pt) cc_final: 0.8389 (mm) REVERT: B 255 TYR cc_start: 0.7925 (m-10) cc_final: 0.7444 (m-10) REVERT: B 260 ILE cc_start: 0.8778 (mt) cc_final: 0.8456 (mt) REVERT: B 354 PHE cc_start: 0.7201 (OUTLIER) cc_final: 0.6973 (t80) REVERT: B 384 GLU cc_start: 0.7707 (mm-30) cc_final: 0.7180 (tp30) REVERT: B 394 PHE cc_start: 0.8269 (t80) cc_final: 0.7655 (t80) REVERT: B 398 PHE cc_start: 0.6858 (m-80) cc_final: 0.6517 (m-10) REVERT: B 400 CYS cc_start: 0.7287 (m) cc_final: 0.7035 (m) REVERT: B 409 ARG cc_start: 0.7883 (mtm180) cc_final: 0.7516 (ttm110) REVERT: B 414 GLU cc_start: 0.7543 (tm-30) cc_final: 0.7020 (tp30) REVERT: B 432 MET cc_start: 0.7487 (tmm) cc_final: 0.7226 (tmm) REVERT: B 463 MET cc_start: 0.7413 (tmm) cc_final: 0.7172 (tmm) REVERT: B 466 CYS cc_start: 0.8075 (t) cc_final: 0.7699 (t) REVERT: B 470 ARG cc_start: 0.6708 (mtp180) cc_final: 0.6435 (mtp180) REVERT: B 473 LYS cc_start: 0.8426 (mttp) cc_final: 0.8173 (mtpp) REVERT: B 486 CYS cc_start: 0.8732 (t) cc_final: 0.8472 (t) REVERT: B 488 MET cc_start: 0.7475 (tpp) cc_final: 0.7096 (tpp) REVERT: B 513 VAL cc_start: 0.9159 (OUTLIER) cc_final: 0.8930 (p) REVERT: B 531 LYS cc_start: 0.8612 (mmtm) cc_final: 0.8406 (mmmm) REVERT: B 537 LYS cc_start: 0.8243 (tmtt) cc_final: 0.7608 (tmtt) REVERT: B 556 TYR cc_start: 0.8987 (p90) cc_final: 0.8640 (p90) REVERT: B 578 TYR cc_start: 0.7770 (t80) cc_final: 0.7228 (t80) REVERT: B 580 LYS cc_start: 0.7881 (mmmm) cc_final: 0.7629 (mmmm) REVERT: B 581 ARG cc_start: 0.8171 (tpp-160) cc_final: 0.7850 (tpp-160) REVERT: B 583 LYS cc_start: 0.8458 (OUTLIER) cc_final: 0.7907 (tmmt) REVERT: B 681 LYS cc_start: 0.8323 (mptt) cc_final: 0.8019 (mptt) REVERT: B 705 GLN cc_start: 0.8673 (tt0) cc_final: 0.8343 (tt0) REVERT: B 714 ARG cc_start: 0.7413 (mtm-85) cc_final: 0.7139 (mtm-85) outliers start: 46 outliers final: 25 residues processed: 342 average time/residue: 0.1253 time to fit residues: 57.0425 Evaluate side-chains 349 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 315 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ARG Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 259 GLU Chi-restraints excluded: chain A residue 322 ASN Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 564 LYS Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 583 LYS Chi-restraints excluded: chain A residue 682 GLU Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 715 LYS Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 283 MET Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 354 PHE Chi-restraints excluded: chain B residue 383 GLN Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 405 THR Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 583 LYS Chi-restraints excluded: chain B residue 690 VAL Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 699 VAL Chi-restraints excluded: chain B residue 703 MET Chi-restraints excluded: chain B residue 713 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 56 optimal weight: 2.9990 chunk 92 optimal weight: 0.5980 chunk 102 optimal weight: 0.7980 chunk 22 optimal weight: 0.0030 chunk 76 optimal weight: 0.8980 chunk 80 optimal weight: 7.9990 chunk 27 optimal weight: 5.9990 chunk 3 optimal weight: 0.0040 chunk 35 optimal weight: 0.9980 chunk 34 optimal weight: 0.8980 chunk 95 optimal weight: 2.9990 overall best weight: 0.4602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 200 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.129001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.111931 restraints weight = 21233.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.115287 restraints weight = 10459.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.117151 restraints weight = 6085.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.118724 restraints weight = 4190.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.119426 restraints weight = 3092.649| |-----------------------------------------------------------------------------| r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.4813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 10390 Z= 0.145 Angle : 0.659 9.492 14120 Z= 0.334 Chirality : 0.043 0.218 1714 Planarity : 0.004 0.043 1756 Dihedral : 5.861 88.081 1442 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 4.63 % Allowed : 23.49 % Favored : 71.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.01 (0.23), residues: 1316 helix: 0.38 (0.18), residues: 830 sheet: 2.04 (1.05), residues: 20 loop : -2.79 (0.28), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 134 TYR 0.029 0.002 TYR B 323 PHE 0.029 0.001 PHE B 128 TRP 0.014 0.002 TRP B 83 HIS 0.007 0.001 HIS B 728 Details of bonding type rmsd covalent geometry : bond 0.00334 (10390) covalent geometry : angle 0.65884 (14120) hydrogen bonds : bond 0.03456 ( 576) hydrogen bonds : angle 3.85080 ( 1683) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 315 time to evaluate : 0.402 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 29 GLU cc_start: 0.6938 (mp0) cc_final: 0.6404 (mp0) REVERT: A 77 LYS cc_start: 0.8066 (ttpt) cc_final: 0.7631 (ttpt) REVERT: A 90 SER cc_start: 0.8511 (t) cc_final: 0.7941 (p) REVERT: A 94 THR cc_start: 0.8511 (t) cc_final: 0.8198 (p) REVERT: A 134 ARG cc_start: 0.8108 (mpp80) cc_final: 0.7859 (mpp80) REVERT: A 153 LEU cc_start: 0.8882 (mt) cc_final: 0.8680 (mm) REVERT: A 195 LEU cc_start: 0.8892 (OUTLIER) cc_final: 0.8607 (tp) REVERT: A 230 GLN cc_start: 0.8147 (tp40) cc_final: 0.7868 (tm-30) REVERT: A 237 LYS cc_start: 0.8725 (pttt) cc_final: 0.8342 (ttpp) REVERT: A 238 ILE cc_start: 0.8851 (tp) cc_final: 0.8589 (tp) REVERT: A 255 TYR cc_start: 0.7672 (m-10) cc_final: 0.7427 (m-10) REVERT: A 259 GLU cc_start: 0.7701 (OUTLIER) cc_final: 0.7205 (tm-30) REVERT: A 260 ILE cc_start: 0.8669 (mt) cc_final: 0.8067 (mt) REVERT: A 287 GLU cc_start: 0.7689 (pp20) cc_final: 0.7327 (pp20) REVERT: A 358 VAL cc_start: 0.8894 (t) cc_final: 0.8633 (p) REVERT: A 404 THR cc_start: 0.7480 (OUTLIER) cc_final: 0.6994 (t) REVERT: A 409 ARG cc_start: 0.8188 (mtm180) cc_final: 0.7693 (mtm110) REVERT: A 414 GLU cc_start: 0.7505 (tm-30) cc_final: 0.6891 (tm-30) REVERT: A 426 ILE cc_start: 0.8115 (tp) cc_final: 0.7898 (mm) REVERT: A 432 MET cc_start: 0.7531 (tmm) cc_final: 0.7182 (tmm) REVERT: A 463 MET cc_start: 0.7556 (tmm) cc_final: 0.7125 (tmm) REVERT: A 466 CYS cc_start: 0.7979 (t) cc_final: 0.7524 (t) REVERT: A 473 LYS cc_start: 0.8476 (mttp) cc_final: 0.8049 (ttmm) REVERT: A 476 LYS cc_start: 0.9148 (mtmm) cc_final: 0.8919 (mtmm) REVERT: A 546 LYS cc_start: 0.6717 (ptmm) cc_final: 0.6250 (ptmm) REVERT: A 580 LYS cc_start: 0.8174 (mmmt) cc_final: 0.7913 (tttt) REVERT: A 583 LYS cc_start: 0.8455 (OUTLIER) cc_final: 0.7872 (tmmt) REVERT: A 681 LYS cc_start: 0.8281 (mptt) cc_final: 0.7929 (mptt) REVERT: B 66 LYS cc_start: 0.8443 (tptt) cc_final: 0.7921 (tppt) REVERT: B 77 LYS cc_start: 0.8374 (ttpt) cc_final: 0.8015 (ttpt) REVERT: B 90 SER cc_start: 0.8597 (t) cc_final: 0.8082 (p) REVERT: B 127 TYR cc_start: 0.8606 (t80) cc_final: 0.8347 (t80) REVERT: B 132 THR cc_start: 0.7627 (OUTLIER) cc_final: 0.6957 (t) REVERT: B 134 ARG cc_start: 0.7570 (mtm-85) cc_final: 0.7279 (mtm-85) REVERT: B 150 SER cc_start: 0.8324 (t) cc_final: 0.8056 (p) REVERT: B 181 ARG cc_start: 0.7022 (tmm-80) cc_final: 0.6815 (ppt170) REVERT: B 192 LEU cc_start: 0.8349 (tp) cc_final: 0.8125 (tp) REVERT: B 230 GLN cc_start: 0.8403 (tm-30) cc_final: 0.7598 (tm-30) REVERT: B 236 LEU cc_start: 0.8948 (tp) cc_final: 0.8695 (tp) REVERT: B 237 LYS cc_start: 0.8574 (pttt) cc_final: 0.8171 (ttmt) REVERT: B 238 ILE cc_start: 0.8806 (tp) cc_final: 0.8431 (pt) REVERT: B 250 ILE cc_start: 0.8643 (pt) cc_final: 0.8419 (mm) REVERT: B 255 TYR cc_start: 0.7939 (m-10) cc_final: 0.7495 (m-10) REVERT: B 260 ILE cc_start: 0.8779 (mt) cc_final: 0.8462 (mt) REVERT: B 354 PHE cc_start: 0.7233 (OUTLIER) cc_final: 0.6997 (t80) REVERT: B 384 GLU cc_start: 0.7729 (mm-30) cc_final: 0.7197 (tp30) REVERT: B 398 PHE cc_start: 0.6882 (m-80) cc_final: 0.6568 (m-10) REVERT: B 400 CYS cc_start: 0.7265 (m) cc_final: 0.7027 (m) REVERT: B 409 ARG cc_start: 0.7898 (mtm180) cc_final: 0.7637 (ttm110) REVERT: B 414 GLU cc_start: 0.7573 (tm-30) cc_final: 0.7246 (tp30) REVERT: B 432 MET cc_start: 0.7504 (tmm) cc_final: 0.7248 (tmm) REVERT: B 463 MET cc_start: 0.7437 (tmm) cc_final: 0.7210 (tmm) REVERT: B 466 CYS cc_start: 0.8069 (t) cc_final: 0.7729 (t) REVERT: B 470 ARG cc_start: 0.6715 (mtp180) cc_final: 0.6470 (mtp180) REVERT: B 473 LYS cc_start: 0.8414 (mttp) cc_final: 0.8174 (mtpp) REVERT: B 486 CYS cc_start: 0.8735 (t) cc_final: 0.8476 (t) REVERT: B 488 MET cc_start: 0.7469 (tpp) cc_final: 0.7092 (tpp) REVERT: B 513 VAL cc_start: 0.9176 (OUTLIER) cc_final: 0.8940 (p) REVERT: B 531 LYS cc_start: 0.8620 (mmtm) cc_final: 0.8371 (mmmm) REVERT: B 537 LYS cc_start: 0.8254 (tmtt) cc_final: 0.7799 (tmtt) REVERT: B 556 TYR cc_start: 0.9003 (p90) cc_final: 0.8651 (p90) REVERT: B 578 TYR cc_start: 0.7728 (t80) cc_final: 0.7188 (t80) REVERT: B 580 LYS cc_start: 0.7892 (mmmm) cc_final: 0.7602 (mmmm) REVERT: B 581 ARG cc_start: 0.8181 (tpp-160) cc_final: 0.7848 (tpp-160) REVERT: B 583 LYS cc_start: 0.8486 (OUTLIER) cc_final: 0.7939 (tmmt) REVERT: B 705 GLN cc_start: 0.8674 (tt0) cc_final: 0.8362 (tt0) REVERT: B 714 ARG cc_start: 0.7421 (mtm-85) cc_final: 0.7139 (mtm-85) outliers start: 52 outliers final: 28 residues processed: 348 average time/residue: 0.1184 time to fit residues: 55.1207 Evaluate side-chains 337 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 301 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ARG Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 259 GLU Chi-restraints excluded: chain A residue 397 PHE Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 461 MET Chi-restraints excluded: chain A residue 583 LYS Chi-restraints excluded: chain A residue 682 GLU Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 713 ILE Chi-restraints excluded: chain A residue 715 LYS Chi-restraints excluded: chain A residue 716 ASP Chi-restraints excluded: chain B residue 73 ASP Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 283 MET Chi-restraints excluded: chain B residue 348 ASP Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 354 PHE Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 405 THR Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain B residue 583 LYS Chi-restraints excluded: chain B residue 690 VAL Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 699 VAL Chi-restraints excluded: chain B residue 703 MET Chi-restraints excluded: chain B residue 713 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 122 optimal weight: 0.6980 chunk 63 optimal weight: 0.2980 chunk 22 optimal weight: 0.0030 chunk 83 optimal weight: 0.8980 chunk 33 optimal weight: 0.5980 chunk 61 optimal weight: 0.9990 chunk 40 optimal weight: 3.9990 chunk 52 optimal weight: 0.7980 chunk 99 optimal weight: 0.9980 chunk 127 optimal weight: 0.6980 chunk 100 optimal weight: 0.6980 overall best weight: 0.4590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 322 ASN A 324 ASN ** B 289 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 = 0.3792 r_free = 0.3792 target = 0.130185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.112837 restraints weight = 20930.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.116223 restraints weight = 10392.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.118340 restraints weight = 6110.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.119728 restraints weight = 4107.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.120375 restraints weight = 3078.796| |-----------------------------------------------------------------------------| r_work (final): 0.3589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.4996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 10390 Z= 0.146 Angle : 0.666 7.636 14120 Z= 0.341 Chirality : 0.043 0.211 1714 Planarity : 0.004 0.045 1756 Dihedral : 5.859 88.373 1442 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 4.27 % Allowed : 24.38 % Favored : 71.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.95 (0.23), residues: 1316 helix: 0.41 (0.18), residues: 830 sheet: 2.28 (1.06), residues: 20 loop : -2.74 (0.28), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 134 TYR 0.026 0.002 TYR B 323 PHE 0.030 0.001 PHE B 128 TRP 0.015 0.002 TRP A 83 HIS 0.007 0.001 HIS B 728 Details of bonding type rmsd covalent geometry : bond 0.00336 (10390) covalent geometry : angle 0.66613 (14120) hydrogen bonds : bond 0.03485 ( 576) hydrogen bonds : angle 3.85598 ( 1683) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 295 time to evaluate : 0.316 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 GLU cc_start: 0.6966 (mp0) cc_final: 0.6452 (mp0) REVERT: A 66 LYS cc_start: 0.8340 (tptt) cc_final: 0.8052 (tppt) REVERT: A 77 LYS cc_start: 0.8093 (ttpt) cc_final: 0.7664 (ttpt) REVERT: A 90 SER cc_start: 0.8476 (t) cc_final: 0.7906 (p) REVERT: A 94 THR cc_start: 0.8514 (t) cc_final: 0.8179 (p) REVERT: A 195 LEU cc_start: 0.8898 (OUTLIER) cc_final: 0.8646 (tp) REVERT: A 230 GLN cc_start: 0.8155 (tp40) cc_final: 0.7885 (tm-30) REVERT: A 237 LYS cc_start: 0.8726 (pttt) cc_final: 0.8466 (ttpp) REVERT: A 238 ILE cc_start: 0.8878 (tp) cc_final: 0.8623 (tp) REVERT: A 259 GLU cc_start: 0.7755 (OUTLIER) cc_final: 0.7207 (tm-30) REVERT: A 260 ILE cc_start: 0.8680 (mt) cc_final: 0.8092 (mt) REVERT: A 322 ASN cc_start: 0.7077 (OUTLIER) cc_final: 0.6131 (t0) REVERT: A 358 VAL cc_start: 0.8851 (t) cc_final: 0.8592 (p) REVERT: A 404 THR cc_start: 0.7507 (OUTLIER) cc_final: 0.6928 (p) REVERT: A 409 ARG cc_start: 0.8136 (mtm180) cc_final: 0.7919 (mtm110) REVERT: A 414 GLU cc_start: 0.7491 (tm-30) cc_final: 0.6883 (tm-30) REVERT: A 426 ILE cc_start: 0.8110 (tp) cc_final: 0.7889 (mm) REVERT: A 432 MET cc_start: 0.7572 (tmm) cc_final: 0.7112 (tmm) REVERT: A 463 MET cc_start: 0.7503 (tmm) cc_final: 0.7010 (tmm) REVERT: A 473 LYS cc_start: 0.8481 (mttp) cc_final: 0.8062 (mtpp) REVERT: A 546 LYS cc_start: 0.6775 (ptmm) cc_final: 0.6328 (ptmm) REVERT: A 564 LYS cc_start: 0.8419 (mttm) cc_final: 0.8187 (ttmm) REVERT: A 580 LYS cc_start: 0.8159 (mmmt) cc_final: 0.7906 (tttt) REVERT: A 583 LYS cc_start: 0.8437 (OUTLIER) cc_final: 0.7864 (tmmt) REVERT: A 714 ARG cc_start: 0.7339 (mpt180) cc_final: 0.7131 (mtm-85) REVERT: B 66 LYS cc_start: 0.8426 (tptt) cc_final: 0.7889 (tppt) REVERT: B 77 LYS cc_start: 0.8419 (ttpt) cc_final: 0.8057 (ttpt) REVERT: B 90 SER cc_start: 0.8589 (t) cc_final: 0.8080 (p) REVERT: B 125 LEU cc_start: 0.8910 (tp) cc_final: 0.8587 (tp) REVERT: B 127 TYR cc_start: 0.8598 (t80) cc_final: 0.8285 (t80) REVERT: B 132 THR cc_start: 0.7705 (OUTLIER) cc_final: 0.7110 (t) REVERT: B 134 ARG cc_start: 0.7528 (mtm-85) cc_final: 0.7284 (mtm-85) REVERT: B 150 SER cc_start: 0.8322 (t) cc_final: 0.8073 (p) REVERT: B 181 ARG cc_start: 0.7069 (tmm-80) cc_final: 0.6803 (ppt170) REVERT: B 230 GLN cc_start: 0.8424 (tm-30) cc_final: 0.8051 (tm-30) REVERT: B 236 LEU cc_start: 0.8952 (tp) cc_final: 0.8702 (tp) REVERT: B 237 LYS cc_start: 0.8571 (pttt) cc_final: 0.8169 (ttmt) REVERT: B 238 ILE cc_start: 0.8856 (tp) cc_final: 0.8460 (pt) REVERT: B 245 LYS cc_start: 0.8052 (mmtm) cc_final: 0.7828 (mmtm) REVERT: B 255 TYR cc_start: 0.7954 (m-10) cc_final: 0.7653 (m-10) REVERT: B 354 PHE cc_start: 0.7143 (OUTLIER) cc_final: 0.6822 (t80) REVERT: B 384 GLU cc_start: 0.7760 (mm-30) cc_final: 0.7146 (tp30) REVERT: B 394 PHE cc_start: 0.8252 (t80) cc_final: 0.8024 (t80) REVERT: B 398 PHE cc_start: 0.6902 (m-80) cc_final: 0.6504 (m-10) REVERT: B 400 CYS cc_start: 0.7261 (m) cc_final: 0.7001 (m) REVERT: B 404 THR cc_start: 0.7596 (OUTLIER) cc_final: 0.7121 (p) REVERT: B 409 ARG cc_start: 0.7918 (mtm180) cc_final: 0.7666 (ttm110) REVERT: B 414 GLU cc_start: 0.7552 (tm-30) cc_final: 0.6977 (tp30) REVERT: B 426 ILE cc_start: 0.8109 (tt) cc_final: 0.7665 (pt) REVERT: B 432 MET cc_start: 0.7536 (tmm) cc_final: 0.7290 (tmm) REVERT: B 463 MET cc_start: 0.7442 (tmm) cc_final: 0.7194 (tmm) REVERT: B 466 CYS cc_start: 0.8085 (t) cc_final: 0.7739 (t) REVERT: B 470 ARG cc_start: 0.6710 (mtp180) cc_final: 0.6467 (mtp180) REVERT: B 473 LYS cc_start: 0.8453 (mttp) cc_final: 0.8154 (mtpp) REVERT: B 486 CYS cc_start: 0.8726 (t) cc_final: 0.8471 (t) REVERT: B 488 MET cc_start: 0.7481 (tpp) cc_final: 0.7118 (tpp) REVERT: B 513 VAL cc_start: 0.9186 (OUTLIER) cc_final: 0.8949 (p) REVERT: B 531 LYS cc_start: 0.8583 (mmtm) cc_final: 0.8382 (mmmm) REVERT: B 537 LYS cc_start: 0.8334 (tmtt) cc_final: 0.7834 (tmtt) REVERT: B 556 TYR cc_start: 0.9004 (p90) cc_final: 0.8737 (p90) REVERT: B 578 TYR cc_start: 0.7689 (t80) cc_final: 0.7181 (t80) REVERT: B 580 LYS cc_start: 0.7916 (mmmm) cc_final: 0.7628 (mmmm) REVERT: B 581 ARG cc_start: 0.8155 (tpp-160) cc_final: 0.7815 (tpp-160) REVERT: B 583 LYS cc_start: 0.8489 (OUTLIER) cc_final: 0.7954 (tmmt) REVERT: B 681 LYS cc_start: 0.8374 (mptt) cc_final: 0.8063 (mptt) REVERT: B 705 GLN cc_start: 0.8616 (tt0) cc_final: 0.8282 (tt0) REVERT: B 714 ARG cc_start: 0.7429 (mtm-85) cc_final: 0.7142 (mtm-85) REVERT: B 724 ASP cc_start: 0.7734 (OUTLIER) cc_final: 0.7487 (t70) outliers start: 48 outliers final: 27 residues processed: 321 average time/residue: 0.1216 time to fit residues: 52.0465 Evaluate side-chains 330 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 292 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 GLU Chi-restraints excluded: chain A residue 43 ARG Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 259 GLU Chi-restraints excluded: chain A residue 322 ASN Chi-restraints excluded: chain A residue 397 PHE Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 583 LYS Chi-restraints excluded: chain A residue 682 GLU Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 713 ILE Chi-restraints excluded: chain A residue 715 LYS Chi-restraints excluded: chain A residue 716 ASP Chi-restraints excluded: chain B residue 73 ASP Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 283 MET Chi-restraints excluded: chain B residue 348 ASP Chi-restraints excluded: chain B residue 354 PHE Chi-restraints excluded: chain B residue 383 GLN Chi-restraints excluded: chain B residue 404 THR Chi-restraints excluded: chain B residue 405 THR Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain B residue 583 LYS Chi-restraints excluded: chain B residue 690 VAL Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 699 VAL Chi-restraints excluded: chain B residue 703 MET Chi-restraints excluded: chain B residue 713 ILE Chi-restraints excluded: chain B residue 724 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 106 optimal weight: 0.7980 chunk 26 optimal weight: 0.6980 chunk 29 optimal weight: 0.9980 chunk 115 optimal weight: 0.8980 chunk 69 optimal weight: 0.9990 chunk 36 optimal weight: 0.0470 chunk 127 optimal weight: 1.9990 chunk 48 optimal weight: 0.5980 chunk 86 optimal weight: 0.9980 chunk 32 optimal weight: 0.2980 chunk 77 optimal weight: 0.8980 overall best weight: 0.4878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 322 ASN A 535 HIS B 268 ASN B 514 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.118273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.101057 restraints weight = 21270.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.104193 restraints weight = 10511.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.106343 restraints weight = 6228.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.107764 restraints weight = 4182.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.108449 restraints weight = 3125.638| |-----------------------------------------------------------------------------| r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.5173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10390 Z= 0.150 Angle : 0.683 10.814 14120 Z= 0.346 Chirality : 0.044 0.208 1714 Planarity : 0.004 0.044 1756 Dihedral : 5.863 88.568 1441 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 13.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 4.18 % Allowed : 24.56 % Favored : 71.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.88 (0.23), residues: 1316 helix: 0.46 (0.18), residues: 828 sheet: 2.51 (1.09), residues: 20 loop : -2.68 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 134 TYR 0.026 0.002 TYR B 323 PHE 0.029 0.001 PHE B 128 TRP 0.011 0.002 TRP A 83 HIS 0.008 0.001 HIS B 728 Details of bonding type rmsd covalent geometry : bond 0.00344 (10390) covalent geometry : angle 0.68328 (14120) hydrogen bonds : bond 0.03520 ( 576) hydrogen bonds : angle 3.86947 ( 1683) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 300 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: A 77 LYS cc_start: 0.8020 (ttpt) cc_final: 0.7610 (ttpt) REVERT: A 90 SER cc_start: 0.8443 (t) cc_final: 0.7874 (p) REVERT: A 94 THR cc_start: 0.8540 (t) cc_final: 0.8180 (p) REVERT: A 134 ARG cc_start: 0.8116 (mpp80) cc_final: 0.7882 (mpp80) REVERT: A 195 LEU cc_start: 0.8925 (OUTLIER) cc_final: 0.8701 (tp) REVERT: A 230 GLN cc_start: 0.8126 (tp40) cc_final: 0.7897 (tm-30) REVERT: A 235 GLN cc_start: 0.8153 (mm-40) cc_final: 0.7851 (mm-40) REVERT: A 237 LYS cc_start: 0.8729 (pttt) cc_final: 0.8385 (ttpp) REVERT: A 238 ILE cc_start: 0.8907 (tp) cc_final: 0.8650 (tp) REVERT: A 259 GLU cc_start: 0.7696 (OUTLIER) cc_final: 0.7185 (tm-30) REVERT: A 260 ILE cc_start: 0.8699 (mt) cc_final: 0.8128 (mt) REVERT: A 358 VAL cc_start: 0.8885 (t) cc_final: 0.8632 (p) REVERT: A 404 THR cc_start: 0.7540 (OUTLIER) cc_final: 0.6972 (p) REVERT: A 409 ARG cc_start: 0.8144 (mtm180) cc_final: 0.7943 (mtm110) REVERT: A 414 GLU cc_start: 0.7528 (tm-30) cc_final: 0.6896 (tm-30) REVERT: A 426 ILE cc_start: 0.8138 (tp) cc_final: 0.7903 (mm) REVERT: A 432 MET cc_start: 0.7548 (tmm) cc_final: 0.7210 (tmm) REVERT: A 433 VAL cc_start: 0.7981 (m) cc_final: 0.7432 (p) REVERT: A 463 MET cc_start: 0.7469 (tmm) cc_final: 0.7005 (tmm) REVERT: A 466 CYS cc_start: 0.7938 (t) cc_final: 0.7624 (t) REVERT: A 473 LYS cc_start: 0.8488 (mttp) cc_final: 0.8049 (ttmm) REVERT: A 476 LYS cc_start: 0.9141 (mtmm) cc_final: 0.8862 (mtmm) REVERT: A 546 LYS cc_start: 0.6804 (ptmm) cc_final: 0.6407 (ptmm) REVERT: A 580 LYS cc_start: 0.8131 (mmmt) cc_final: 0.7794 (mmmt) REVERT: A 583 LYS cc_start: 0.8418 (OUTLIER) cc_final: 0.7713 (tmmt) REVERT: A 681 LYS cc_start: 0.8292 (mptt) cc_final: 0.8026 (mptt) REVERT: A 714 ARG cc_start: 0.7340 (mpt180) cc_final: 0.7109 (mtm-85) REVERT: B 66 LYS cc_start: 0.8417 (tptt) cc_final: 0.7912 (tppt) REVERT: B 77 LYS cc_start: 0.8344 (ttpt) cc_final: 0.7995 (ttpt) REVERT: B 90 SER cc_start: 0.8543 (t) cc_final: 0.8051 (p) REVERT: B 125 LEU cc_start: 0.8865 (tp) cc_final: 0.8558 (tp) REVERT: B 127 TYR cc_start: 0.8549 (t80) cc_final: 0.8262 (t80) REVERT: B 132 THR cc_start: 0.7739 (OUTLIER) cc_final: 0.7165 (t) REVERT: B 134 ARG cc_start: 0.7521 (mtm-85) cc_final: 0.7264 (mtm-85) REVERT: B 150 SER cc_start: 0.8336 (t) cc_final: 0.8054 (p) REVERT: B 181 ARG cc_start: 0.7050 (tmm-80) cc_final: 0.6822 (ppt170) REVERT: B 230 GLN cc_start: 0.8429 (tm-30) cc_final: 0.8067 (tm-30) REVERT: B 236 LEU cc_start: 0.8965 (tp) cc_final: 0.8712 (tp) REVERT: B 237 LYS cc_start: 0.8575 (pttt) cc_final: 0.8225 (ttpt) REVERT: B 238 ILE cc_start: 0.8882 (tp) cc_final: 0.8500 (pt) REVERT: B 245 LYS cc_start: 0.8024 (mmtm) cc_final: 0.7783 (mmtm) REVERT: B 255 TYR cc_start: 0.7952 (m-10) cc_final: 0.7639 (m-10) REVERT: B 384 GLU cc_start: 0.7699 (mm-30) cc_final: 0.7155 (tp30) REVERT: B 394 PHE cc_start: 0.8209 (t80) cc_final: 0.7960 (t80) REVERT: B 398 PHE cc_start: 0.6885 (m-80) cc_final: 0.6474 (m-10) REVERT: B 404 THR cc_start: 0.7559 (OUTLIER) cc_final: 0.7123 (p) REVERT: B 405 THR cc_start: 0.8800 (OUTLIER) cc_final: 0.8344 (p) REVERT: B 409 ARG cc_start: 0.7922 (mtm180) cc_final: 0.7617 (ttm110) REVERT: B 414 GLU cc_start: 0.7537 (tm-30) cc_final: 0.7230 (tp30) REVERT: B 426 ILE cc_start: 0.8171 (tt) cc_final: 0.7739 (pt) REVERT: B 432 MET cc_start: 0.7514 (tmm) cc_final: 0.7286 (tmm) REVERT: B 463 MET cc_start: 0.7447 (OUTLIER) cc_final: 0.7204 (tmm) REVERT: B 466 CYS cc_start: 0.8055 (t) cc_final: 0.7741 (t) REVERT: B 470 ARG cc_start: 0.6687 (mtp180) cc_final: 0.6455 (mtp180) REVERT: B 473 LYS cc_start: 0.8400 (mttp) cc_final: 0.8120 (mtpp) REVERT: B 486 CYS cc_start: 0.8680 (t) cc_final: 0.8444 (t) REVERT: B 488 MET cc_start: 0.7392 (tpp) cc_final: 0.7062 (tpp) REVERT: B 513 VAL cc_start: 0.9205 (OUTLIER) cc_final: 0.8981 (p) REVERT: B 537 LYS cc_start: 0.8353 (tmtt) cc_final: 0.7847 (tmtt) REVERT: B 549 ARG cc_start: 0.7507 (ttm-80) cc_final: 0.7138 (ttt-90) REVERT: B 556 TYR cc_start: 0.8993 (p90) cc_final: 0.8734 (p90) REVERT: B 578 TYR cc_start: 0.7742 (t80) cc_final: 0.7245 (t80) REVERT: B 580 LYS cc_start: 0.7917 (mmmm) cc_final: 0.7643 (mmmm) REVERT: B 581 ARG cc_start: 0.8116 (tpp-160) cc_final: 0.7783 (tpp-160) REVERT: B 583 LYS cc_start: 0.8471 (OUTLIER) cc_final: 0.7932 (tmmt) REVERT: B 681 LYS cc_start: 0.8366 (mptt) cc_final: 0.7998 (mptt) REVERT: B 705 GLN cc_start: 0.8614 (tt0) cc_final: 0.8279 (tt0) REVERT: B 714 ARG cc_start: 0.7404 (mtm-85) cc_final: 0.7131 (mtm-85) outliers start: 47 outliers final: 29 residues processed: 325 average time/residue: 0.1147 time to fit residues: 49.5432 Evaluate side-chains 337 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 298 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ARG Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 259 GLU Chi-restraints excluded: chain A residue 397 PHE Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 564 LYS Chi-restraints excluded: chain A residue 583 LYS Chi-restraints excluded: chain A residue 682 GLU Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 715 LYS Chi-restraints excluded: chain A residue 716 ASP Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain B residue 73 ASP Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 283 MET Chi-restraints excluded: chain B residue 383 GLN Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 404 THR Chi-restraints excluded: chain B residue 405 THR Chi-restraints excluded: chain B residue 463 MET Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain B residue 583 LYS Chi-restraints excluded: chain B residue 690 VAL Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 699 VAL Chi-restraints excluded: chain B residue 703 MET Chi-restraints excluded: chain B residue 713 ILE Chi-restraints excluded: chain B residue 716 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 12 optimal weight: 0.3980 chunk 83 optimal weight: 0.5980 chunk 2 optimal weight: 2.9990 chunk 43 optimal weight: 0.6980 chunk 91 optimal weight: 3.9990 chunk 36 optimal weight: 0.4980 chunk 55 optimal weight: 0.8980 chunk 18 optimal weight: 0.5980 chunk 39 optimal weight: 0.9990 chunk 101 optimal weight: 1.9990 chunk 112 optimal weight: 0.8980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 289 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.117558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.100251 restraints weight = 21364.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.103415 restraints weight = 10579.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.105524 restraints weight = 6245.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.106994 restraints weight = 4191.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.107665 restraints weight = 3143.508| |-----------------------------------------------------------------------------| r_work (final): 0.3567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.5373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 10390 Z= 0.161 Angle : 0.704 10.771 14120 Z= 0.357 Chirality : 0.044 0.229 1714 Planarity : 0.004 0.044 1756 Dihedral : 5.904 88.892 1441 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 14.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 3.38 % Allowed : 25.71 % Favored : 70.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.87 (0.23), residues: 1316 helix: 0.45 (0.18), residues: 832 sheet: 2.51 (1.11), residues: 20 loop : -2.66 (0.28), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 134 TYR 0.026 0.002 TYR B 323 PHE 0.030 0.001 PHE B 128 TRP 0.012 0.002 TRP B 83 HIS 0.009 0.001 HIS B 728 Details of bonding type rmsd covalent geometry : bond 0.00366 (10390) covalent geometry : angle 0.70404 (14120) hydrogen bonds : bond 0.03567 ( 576) hydrogen bonds : angle 3.93808 ( 1683) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 303 time to evaluate : 0.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 SER cc_start: 0.8424 (t) cc_final: 0.7891 (p) REVERT: A 94 THR cc_start: 0.8560 (t) cc_final: 0.8188 (p) REVERT: A 195 LEU cc_start: 0.8961 (OUTLIER) cc_final: 0.8745 (tp) REVERT: A 210 PHE cc_start: 0.6687 (p90) cc_final: 0.6483 (p90) REVERT: A 230 GLN cc_start: 0.8137 (tp40) cc_final: 0.7915 (tm-30) REVERT: A 237 LYS cc_start: 0.8739 (pttt) cc_final: 0.8403 (ttpp) REVERT: A 238 ILE cc_start: 0.8935 (tp) cc_final: 0.8689 (tp) REVERT: A 259 GLU cc_start: 0.7694 (OUTLIER) cc_final: 0.7099 (tm-30) REVERT: A 260 ILE cc_start: 0.8714 (mt) cc_final: 0.8136 (mt) REVERT: A 358 VAL cc_start: 0.8906 (t) cc_final: 0.8664 (p) REVERT: A 404 THR cc_start: 0.7492 (OUTLIER) cc_final: 0.6918 (p) REVERT: A 414 GLU cc_start: 0.7503 (tm-30) cc_final: 0.6896 (tm-30) REVERT: A 426 ILE cc_start: 0.8156 (tp) cc_final: 0.7925 (mm) REVERT: A 432 MET cc_start: 0.7547 (tmm) cc_final: 0.7120 (tmm) REVERT: A 463 MET cc_start: 0.7480 (tmm) cc_final: 0.7030 (tmm) REVERT: A 466 CYS cc_start: 0.7992 (t) cc_final: 0.7560 (t) REVERT: A 473 LYS cc_start: 0.8534 (mttp) cc_final: 0.8099 (ttmm) REVERT: A 546 LYS cc_start: 0.6961 (ptmm) cc_final: 0.6514 (ptmm) REVERT: A 580 LYS cc_start: 0.8141 (mmmt) cc_final: 0.7807 (mmmt) REVERT: A 583 LYS cc_start: 0.8415 (OUTLIER) cc_final: 0.7703 (tmmt) REVERT: B 66 LYS cc_start: 0.8423 (tptt) cc_final: 0.7913 (tppt) REVERT: B 77 LYS cc_start: 0.8382 (ttpt) cc_final: 0.8028 (ttpt) REVERT: B 90 SER cc_start: 0.8549 (t) cc_final: 0.8060 (p) REVERT: B 125 LEU cc_start: 0.8832 (tp) cc_final: 0.8528 (tp) REVERT: B 127 TYR cc_start: 0.8540 (t80) cc_final: 0.8285 (t80) REVERT: B 147 MET cc_start: 0.7968 (tmm) cc_final: 0.7719 (tmm) REVERT: B 150 SER cc_start: 0.8356 (t) cc_final: 0.8062 (p) REVERT: B 202 VAL cc_start: 0.8565 (p) cc_final: 0.8345 (p) REVERT: B 230 GLN cc_start: 0.8446 (tm-30) cc_final: 0.8078 (tm-30) REVERT: B 236 LEU cc_start: 0.8972 (tp) cc_final: 0.8700 (tp) REVERT: B 237 LYS cc_start: 0.8607 (pttt) cc_final: 0.8217 (ttmt) REVERT: B 238 ILE cc_start: 0.8949 (tp) cc_final: 0.8541 (pt) REVERT: B 255 TYR cc_start: 0.7987 (m-10) cc_final: 0.7728 (m-10) REVERT: B 384 GLU cc_start: 0.7692 (mm-30) cc_final: 0.7079 (tp30) REVERT: B 394 PHE cc_start: 0.8205 (t80) cc_final: 0.7924 (t80) REVERT: B 398 PHE cc_start: 0.6881 (m-80) cc_final: 0.6569 (m-10) REVERT: B 404 THR cc_start: 0.7614 (OUTLIER) cc_final: 0.7207 (p) REVERT: B 409 ARG cc_start: 0.7964 (mtm180) cc_final: 0.7708 (ttm110) REVERT: B 414 GLU cc_start: 0.7530 (tm-30) cc_final: 0.7216 (tp30) REVERT: B 426 ILE cc_start: 0.8184 (tt) cc_final: 0.7756 (pt) REVERT: B 432 MET cc_start: 0.7541 (tmm) cc_final: 0.7332 (tmm) REVERT: B 442 LEU cc_start: 0.7738 (mt) cc_final: 0.7537 (mm) REVERT: B 463 MET cc_start: 0.7425 (OUTLIER) cc_final: 0.7172 (tmm) REVERT: B 466 CYS cc_start: 0.8052 (t) cc_final: 0.7764 (t) REVERT: B 470 ARG cc_start: 0.6689 (mtp180) cc_final: 0.6458 (mtp180) REVERT: B 473 LYS cc_start: 0.8399 (mttp) cc_final: 0.8133 (mtpp) REVERT: B 486 CYS cc_start: 0.8678 (t) cc_final: 0.8440 (t) REVERT: B 488 MET cc_start: 0.7402 (tpp) cc_final: 0.7077 (tpp) REVERT: B 513 VAL cc_start: 0.9226 (OUTLIER) cc_final: 0.9002 (p) REVERT: B 537 LYS cc_start: 0.8377 (tmtt) cc_final: 0.7862 (tmtt) REVERT: B 549 ARG cc_start: 0.7524 (ttm-80) cc_final: 0.7146 (ttt-90) REVERT: B 556 TYR cc_start: 0.8997 (p90) cc_final: 0.8730 (p90) REVERT: B 578 TYR cc_start: 0.7754 (t80) cc_final: 0.7250 (t80) REVERT: B 583 LYS cc_start: 0.8514 (OUTLIER) cc_final: 0.7971 (tmmt) REVERT: B 681 LYS cc_start: 0.8394 (mptt) cc_final: 0.8021 (mptt) REVERT: B 705 GLN cc_start: 0.8610 (tt0) cc_final: 0.8269 (tt0) REVERT: B 714 ARG cc_start: 0.7405 (mtm-85) cc_final: 0.7178 (mtm-85) outliers start: 38 outliers final: 26 residues processed: 323 average time/residue: 0.1194 time to fit residues: 51.0002 Evaluate side-chains 332 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 298 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ARG Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 259 GLU Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 583 LYS Chi-restraints excluded: chain A residue 682 GLU Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 713 ILE Chi-restraints excluded: chain A residue 715 LYS Chi-restraints excluded: chain A residue 716 ASP Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain B residue 73 ASP Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 383 GLN Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 404 THR Chi-restraints excluded: chain B residue 463 MET Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain B residue 583 LYS Chi-restraints excluded: chain B residue 690 VAL Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 699 VAL Chi-restraints excluded: chain B residue 703 MET Chi-restraints excluded: chain B residue 713 ILE Chi-restraints excluded: chain B residue 716 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 67 optimal weight: 0.7980 chunk 83 optimal weight: 0.9990 chunk 104 optimal weight: 0.8980 chunk 107 optimal weight: 0.8980 chunk 123 optimal weight: 2.9990 chunk 46 optimal weight: 0.6980 chunk 31 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 50 optimal weight: 0.6980 chunk 94 optimal weight: 0.9980 chunk 101 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 446 GLN A 457 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.116154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.098813 restraints weight = 21186.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.101943 restraints weight = 10525.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.103790 restraints weight = 6231.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.105290 restraints weight = 4299.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.106041 restraints weight = 3246.078| |-----------------------------------------------------------------------------| r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.5674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10390 Z= 0.196 Angle : 0.754 12.065 14120 Z= 0.381 Chirality : 0.046 0.268 1714 Planarity : 0.004 0.043 1756 Dihedral : 6.001 89.276 1440 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 15.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 3.56 % Allowed : 25.80 % Favored : 70.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.97 (0.23), residues: 1316 helix: 0.34 (0.18), residues: 832 sheet: 2.30 (1.15), residues: 20 loop : -2.63 (0.28), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 440 TYR 0.030 0.002 TYR B 323 PHE 0.030 0.002 PHE B 128 TRP 0.012 0.002 TRP B 83 HIS 0.005 0.001 HIS A 728 Details of bonding type rmsd covalent geometry : bond 0.00436 (10390) covalent geometry : angle 0.75436 (14120) hydrogen bonds : bond 0.03774 ( 576) hydrogen bonds : angle 4.04739 ( 1683) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 308 time to evaluate : 0.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 LYS cc_start: 0.8379 (tptt) cc_final: 0.8141 (tptt) REVERT: A 85 LEU cc_start: 0.6733 (tp) cc_final: 0.6485 (tp) REVERT: A 90 SER cc_start: 0.8431 (t) cc_final: 0.7862 (p) REVERT: A 94 THR cc_start: 0.8548 (t) cc_final: 0.8136 (p) REVERT: A 105 TYR cc_start: 0.7624 (m-80) cc_final: 0.7214 (m-80) REVERT: A 195 LEU cc_start: 0.9013 (OUTLIER) cc_final: 0.8683 (tp) REVERT: A 210 PHE cc_start: 0.6769 (p90) cc_final: 0.6544 (p90) REVERT: A 230 GLN cc_start: 0.8222 (tp40) cc_final: 0.7948 (tm-30) REVERT: A 237 LYS cc_start: 0.8773 (pttt) cc_final: 0.8438 (ttpp) REVERT: A 238 ILE cc_start: 0.8999 (tp) cc_final: 0.8740 (tp) REVERT: A 259 GLU cc_start: 0.7739 (OUTLIER) cc_final: 0.7207 (tm-30) REVERT: A 322 ASN cc_start: 0.7639 (OUTLIER) cc_final: 0.6758 (t0) REVERT: A 404 THR cc_start: 0.7556 (OUTLIER) cc_final: 0.7014 (p) REVERT: A 414 GLU cc_start: 0.7495 (tm-30) cc_final: 0.6899 (tm-30) REVERT: A 425 LEU cc_start: 0.8517 (tp) cc_final: 0.8184 (tt) REVERT: A 426 ILE cc_start: 0.8149 (tp) cc_final: 0.7906 (mm) REVERT: A 432 MET cc_start: 0.7573 (tmm) cc_final: 0.7172 (tmm) REVERT: A 463 MET cc_start: 0.7489 (tmm) cc_final: 0.6994 (tmm) REVERT: A 466 CYS cc_start: 0.8016 (t) cc_final: 0.7602 (t) REVERT: A 473 LYS cc_start: 0.8558 (mttp) cc_final: 0.8114 (ttmm) REVERT: A 540 GLU cc_start: 0.8378 (pm20) cc_final: 0.7444 (pm20) REVERT: A 573 ASP cc_start: 0.7856 (t0) cc_final: 0.7100 (p0) REVERT: A 580 LYS cc_start: 0.8153 (mmmt) cc_final: 0.7843 (mmmt) REVERT: A 583 LYS cc_start: 0.8477 (OUTLIER) cc_final: 0.7787 (tmmt) REVERT: B 66 LYS cc_start: 0.8440 (tptt) cc_final: 0.7919 (tppt) REVERT: B 77 LYS cc_start: 0.8431 (ttpt) cc_final: 0.8064 (ttpt) REVERT: B 90 SER cc_start: 0.8523 (t) cc_final: 0.7980 (p) REVERT: B 125 LEU cc_start: 0.8835 (tp) cc_final: 0.8543 (tp) REVERT: B 127 TYR cc_start: 0.8531 (t80) cc_final: 0.8274 (t80) REVERT: B 150 SER cc_start: 0.8340 (t) cc_final: 0.8014 (p) REVERT: B 202 VAL cc_start: 0.8626 (p) cc_final: 0.8420 (p) REVERT: B 230 GLN cc_start: 0.8479 (tm-30) cc_final: 0.8118 (tm-30) REVERT: B 236 LEU cc_start: 0.9004 (tp) cc_final: 0.8747 (tp) REVERT: B 237 LYS cc_start: 0.8687 (pttt) cc_final: 0.8360 (ttmt) REVERT: B 255 TYR cc_start: 0.7985 (m-10) cc_final: 0.7693 (m-10) REVERT: B 256 THR cc_start: 0.8641 (m) cc_final: 0.8426 (m) REVERT: B 260 ILE cc_start: 0.8820 (mt) cc_final: 0.8528 (mt) REVERT: B 384 GLU cc_start: 0.7665 (mm-30) cc_final: 0.7062 (tp30) REVERT: B 394 PHE cc_start: 0.8239 (t80) cc_final: 0.7970 (t80) REVERT: B 398 PHE cc_start: 0.6976 (m-80) cc_final: 0.6540 (m-10) REVERT: B 400 CYS cc_start: 0.7315 (m) cc_final: 0.6968 (m) REVERT: B 404 THR cc_start: 0.7654 (OUTLIER) cc_final: 0.7223 (p) REVERT: B 409 ARG cc_start: 0.8013 (mtm180) cc_final: 0.7752 (ttm110) REVERT: B 414 GLU cc_start: 0.7518 (tm-30) cc_final: 0.7230 (tp30) REVERT: B 463 MET cc_start: 0.7398 (OUTLIER) cc_final: 0.7186 (tmm) REVERT: B 466 CYS cc_start: 0.8154 (t) cc_final: 0.7837 (t) REVERT: B 470 ARG cc_start: 0.6715 (mtp180) cc_final: 0.6469 (mtp180) REVERT: B 473 LYS cc_start: 0.8426 (mttp) cc_final: 0.8164 (mtpp) REVERT: B 486 CYS cc_start: 0.8678 (t) cc_final: 0.8444 (t) REVERT: B 488 MET cc_start: 0.7404 (tpp) cc_final: 0.7070 (tpp) REVERT: B 513 VAL cc_start: 0.9239 (OUTLIER) cc_final: 0.9008 (p) REVERT: B 537 LYS cc_start: 0.8456 (tmtt) cc_final: 0.7951 (tmtt) REVERT: B 549 ARG cc_start: 0.7511 (ttm-80) cc_final: 0.7111 (ttt-90) REVERT: B 556 TYR cc_start: 0.9012 (p90) cc_final: 0.8768 (p90) REVERT: B 578 TYR cc_start: 0.7809 (t80) cc_final: 0.7298 (t80) REVERT: B 581 ARG cc_start: 0.8194 (tpt170) cc_final: 0.7782 (tpp-160) REVERT: B 583 LYS cc_start: 0.8509 (OUTLIER) cc_final: 0.7926 (tmmt) REVERT: B 681 LYS cc_start: 0.8407 (mptt) cc_final: 0.8041 (mptt) REVERT: B 705 GLN cc_start: 0.8659 (tt0) cc_final: 0.8300 (tt0) REVERT: B 714 ARG cc_start: 0.7435 (mtm-85) cc_final: 0.7213 (mtm-85) outliers start: 40 outliers final: 26 residues processed: 331 average time/residue: 0.1179 time to fit residues: 51.8123 Evaluate side-chains 340 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 305 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ARG Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 259 GLU Chi-restraints excluded: chain A residue 322 ASN Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 583 LYS Chi-restraints excluded: chain A residue 682 GLU Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 715 LYS Chi-restraints excluded: chain A residue 716 ASP Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain B residue 73 ASP Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 383 GLN Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 404 THR Chi-restraints excluded: chain B residue 463 MET Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain B residue 583 LYS Chi-restraints excluded: chain B residue 690 VAL Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 699 VAL Chi-restraints excluded: chain B residue 703 MET Chi-restraints excluded: chain B residue 713 ILE Chi-restraints excluded: chain B residue 716 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 81 optimal weight: 3.9990 chunk 2 optimal weight: 0.7980 chunk 25 optimal weight: 0.8980 chunk 106 optimal weight: 0.9990 chunk 130 optimal weight: 0.4980 chunk 121 optimal weight: 0.0470 chunk 102 optimal weight: 0.9990 chunk 88 optimal weight: 0.5980 chunk 107 optimal weight: 0.9980 chunk 66 optimal weight: 0.9980 chunk 11 optimal weight: 3.9990 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 ASN B 322 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.116780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.099574 restraints weight = 21409.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.102699 restraints weight = 10553.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.104785 restraints weight = 6215.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.105867 restraints weight = 4189.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.106960 restraints weight = 3262.270| |-----------------------------------------------------------------------------| r_work (final): 0.3547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.5754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 10390 Z= 0.169 Angle : 0.757 11.244 14120 Z= 0.381 Chirality : 0.045 0.201 1714 Planarity : 0.004 0.045 1756 Dihedral : 6.014 87.431 1440 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 15.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 3.29 % Allowed : 26.60 % Favored : 70.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.92 (0.23), residues: 1316 helix: 0.36 (0.18), residues: 832 sheet: 2.00 (1.08), residues: 20 loop : -2.56 (0.28), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 181 TYR 0.026 0.002 TYR A 691 PHE 0.032 0.002 PHE B 272 TRP 0.013 0.002 TRP B 83 HIS 0.005 0.001 HIS A 728 Details of bonding type rmsd covalent geometry : bond 0.00389 (10390) covalent geometry : angle 0.75662 (14120) hydrogen bonds : bond 0.03712 ( 576) hydrogen bonds : angle 4.02426 ( 1683) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1934.50 seconds wall clock time: 34 minutes 7.15 seconds (2047.15 seconds total)