Starting phenix.real_space_refine on Fri Feb 14 12:49:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wle_32583/02_2025/7wle_32583.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wle_32583/02_2025/7wle_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_32583/02_2025/7wle_32583.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wle_32583/02_2025/7wle_32583.map" model { file = "/net/cci-nas-00/data/ceres_data/7wle_32583/02_2025/7wle_32583.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wle_32583/02_2025/7wle_32583.cif" } resolution = 3.62 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 6.17, per 1000 atoms: 0.61 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: 2.76 Conformation dependent library (CDL) restraints added in 1.3 seconds 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: 1.00 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: 3.08 Time building geometry restraints manager: 3.13 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: 0.05 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: 1.510 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: 0.020 Extract box with map and model: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 25.110 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.040 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:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.140 ------------------------------------------------------------------------------- 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= 0.198 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.010 0.001 TRP B 83 HIS 0.002 0.000 HIS B 535 PHE 0.008 0.001 PHE B 555 TYR 0.005 0.001 TYR B 20 ARG 0.001 0.000 ARG A 213 *********************** 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 : 1.052 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: 0.8153 (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: 0.7749 (OUTLIER) cc_final: 0.7158 (m-80) REVERT: A 230 GLN cc_start: 0.8128 (tp40) cc_final: 0.7651 (tm-30) REVERT: A 237 LYS cc_start: 0.8406 (pttt) cc_final: 0.8042 (pttt) REVERT: A 244 THR cc_start: 0.7634 (t) cc_final: 0.7183 (p) REVERT: A 259 GLU cc_start: 0.7598 (OUTLIER) cc_final: 0.7106 (tm-30) REVERT: A 260 ILE cc_start: 0.8451 (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: 0.6270 (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: 0.7469 (OUTLIER) cc_final: 0.7131 (t80) REVERT: A 356 ILE cc_start: 0.7419 (mt) cc_final: 0.6244 (mt) REVERT: A 473 LYS cc_start: 0.8261 (mttp) cc_final: 0.7988 (mttp) REVERT: A 573 ASP cc_start: 0.7470 (t0) cc_final: 0.6926 (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: 0.8172 (p) cc_final: 0.7941 (p) REVERT: B 130 PHE cc_start: 0.7357 (m-80) cc_final: 0.7120 (m-80) REVERT: B 132 THR cc_start: 0.6746 (OUTLIER) cc_final: 0.6262 (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: 0.8132 (pt) cc_final: 0.7925 (pp) REVERT: B 213 ARG cc_start: 0.7768 (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: 0.7220 (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: 0.7161 (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: 0.8400 (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: 0.2765 time to fit residues: 163.5045 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 : 1.097 ------------------------------------------------------------------------------- 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 111 optimal weight: 0.3980 chunk 100 optimal weight: 0.8980 chunk 55 optimal weight: 0.8980 chunk 34 optimal weight: 0.9990 chunk 67 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 119 optimal weight: 0.1980 overall best weight: 0.6782 ------------------------------------------------------------------------------- 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 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: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.131360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.114257 restraints weight = 20942.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.117613 restraints weight = 10511.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.119771 restraints weight = 6248.292| |-----------------------------------------------------------------------------| r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.3152 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= 0.266 Angle : 0.663 8.048 14120 Z= 0.346 Chirality : 0.043 0.262 1714 Planarity : 0.004 0.033 1756 Dihedral : 6.863 101.158 1465 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 5.25 % Allowed : 17.26 % Favored : 77.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.07 (0.22), residues: 1316 helix: -0.30 (0.18), residues: 818 sheet: -0.09 (0.98), residues: 20 loop : -3.39 (0.24), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 83 HIS 0.005 0.001 HIS B 728 PHE 0.028 0.002 PHE A 130 TYR 0.021 0.002 TYR B 323 ARG 0.007 0.001 ARG A 674 *********************** 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 385 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 326 time to evaluate : 1.207 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 ARG cc_start: 0.7243 (mtm-85) cc_final: 0.6849 (mtt90) REVERT: A 37 GLU cc_start: 0.8088 (OUTLIER) cc_final: 0.6851 (pm20) REVERT: A 77 LYS cc_start: 0.8035 (ttpt) cc_final: 0.7610 (ttpt) REVERT: A 90 SER cc_start: 0.8470 (t) cc_final: 0.8022 (p) REVERT: A 94 THR cc_start: 0.8412 (t) cc_final: 0.8144 (p) REVERT: A 118 TYR cc_start: 0.7074 (m-10) cc_final: 0.6836 (m-10) REVERT: A 128 PHE cc_start: 0.8578 (t80) cc_final: 0.8332 (t80) REVERT: A 195 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.8291 (tm) REVERT: A 207 GLN cc_start: 0.7722 (tm-30) cc_final: 0.7403 (tm-30) REVERT: A 230 GLN cc_start: 0.8096 (tp40) cc_final: 0.7885 (tm-30) REVERT: A 259 GLU cc_start: 0.7671 (OUTLIER) cc_final: 0.7202 (tm-30) REVERT: A 260 ILE cc_start: 0.8569 (mt) cc_final: 0.7952 (mt) REVERT: A 263 ASN cc_start: 0.8344 (t0) cc_final: 0.7677 (t0) REVERT: A 350 LEU cc_start: 0.8596 (tp) cc_final: 0.8236 (tt) REVERT: A 385 PHE cc_start: 0.8690 (OUTLIER) cc_final: 0.8418 (t80) REVERT: A 432 MET cc_start: 0.7370 (tmm) cc_final: 0.7031 (tmm) REVERT: A 466 CYS cc_start: 0.7746 (t) cc_final: 0.7360 (t) REVERT: A 473 LYS cc_start: 0.8418 (mttp) cc_final: 0.8165 (mttp) REVERT: A 530 TYR cc_start: 0.8393 (m-80) cc_final: 0.8033 (m-80) REVERT: A 580 LYS cc_start: 0.8170 (mmmt) cc_final: 0.7912 (tttt) REVERT: A 583 LYS cc_start: 0.8579 (OUTLIER) cc_final: 0.8023 (tmmt) REVERT: A 714 ARG cc_start: 0.7254 (mpt180) cc_final: 0.6711 (mtm-85) REVERT: B 80 VAL cc_start: 0.9380 (OUTLIER) cc_final: 0.8858 (t) REVERT: B 90 SER cc_start: 0.8751 (t) cc_final: 0.8217 (p) REVERT: B 94 THR cc_start: 0.8670 (t) cc_final: 0.8266 (p) REVERT: B 132 THR cc_start: 0.7184 (OUTLIER) cc_final: 0.6504 (t) REVERT: B 150 SER cc_start: 0.8364 (t) cc_final: 0.8096 (p) REVERT: B 195 LEU cc_start: 0.8794 (tp) cc_final: 0.8584 (tp) REVERT: B 230 GLN cc_start: 0.8255 (tm-30) cc_final: 0.7949 (tm-30) REVERT: B 237 LYS cc_start: 0.8545 (pttt) cc_final: 0.8113 (ptpt) REVERT: B 239 VAL cc_start: 0.8480 (OUTLIER) cc_final: 0.8263 (p) REVERT: B 250 ILE cc_start: 0.8587 (pt) cc_final: 0.8313 (mm) REVERT: B 259 GLU cc_start: 0.7539 (OUTLIER) cc_final: 0.6785 (tm-30) REVERT: B 384 GLU cc_start: 0.7581 (mm-30) cc_final: 0.7216 (tp30) REVERT: B 394 PHE cc_start: 0.8255 (t80) cc_final: 0.7964 (t80) REVERT: B 400 CYS cc_start: 0.7573 (m) cc_final: 0.7359 (m) REVERT: B 426 ILE cc_start: 0.8088 (tt) cc_final: 0.7850 (tp) REVERT: B 431 VAL cc_start: 0.8952 (t) cc_final: 0.8728 (p) REVERT: B 463 MET cc_start: 0.7495 (tmm) cc_final: 0.7169 (tmm) REVERT: B 466 CYS cc_start: 0.8020 (t) cc_final: 0.7527 (t) REVERT: B 470 ARG cc_start: 0.6652 (mtp180) cc_final: 0.6376 (mtp180) REVERT: B 473 LYS cc_start: 0.8407 (mttp) cc_final: 0.8151 (mtpp) REVERT: B 486 CYS cc_start: 0.8736 (t) cc_final: 0.8489 (t) REVERT: B 488 MET cc_start: 0.7441 (tpp) cc_final: 0.6988 (tpp) REVERT: B 513 VAL cc_start: 0.9127 (OUTLIER) cc_final: 0.8898 (p) REVERT: B 531 LYS cc_start: 0.8617 (mmtm) cc_final: 0.8292 (mmmm) REVERT: B 537 LYS cc_start: 0.8281 (mmmm) cc_final: 0.7205 (ttpp) REVERT: B 556 TYR cc_start: 0.8991 (p90) cc_final: 0.8722 (p90) REVERT: B 578 TYR cc_start: 0.7732 (t80) cc_final: 0.7086 (t80) REVERT: B 581 ARG cc_start: 0.8264 (tpp-160) cc_final: 0.7837 (tpp-160) REVERT: B 583 LYS cc_start: 0.8353 (OUTLIER) cc_final: 0.7833 (tmmt) REVERT: B 681 LYS cc_start: 0.8386 (mptt) cc_final: 0.8059 (mptt) REVERT: B 715 LYS cc_start: 0.8714 (ptpt) cc_final: 0.8439 (ptpp) outliers start: 59 outliers final: 23 residues processed: 361 average time/residue: 0.2552 time to fit residues: 123.9305 Evaluate side-chains 334 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 300 time to evaluate : 1.071 ------------------------------------------------------------------------------- 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 135 HIS 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 385 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 458 LEU 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 A residue 716 ASP 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 259 GLU Chi-restraints excluded: chain B residue 298 VAL 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 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 61 optimal weight: 0.9990 chunk 39 optimal weight: 0.7980 chunk 1 optimal weight: 0.9990 chunk 102 optimal weight: 0.6980 chunk 51 optimal weight: 2.9990 chunk 75 optimal weight: 0.6980 chunk 93 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 15 optimal weight: 10.0000 chunk 115 optimal weight: 0.0770 chunk 0 optimal weight: 1.9990 overall best weight: 0.6540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN ** A 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 457 ASN B 35 GLN B 382 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.129992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.112959 restraints weight = 21274.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.116344 restraints weight = 10572.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.118369 restraints weight = 6216.092| |-----------------------------------------------------------------------------| r_work (final): 0.3589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.3972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 10390 Z= 0.255 Angle : 0.641 7.863 14120 Z= 0.332 Chirality : 0.042 0.166 1714 Planarity : 0.004 0.039 1756 Dihedral : 6.674 96.546 1452 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 12.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 5.69 % Allowed : 17.70 % Favored : 76.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.23), residues: 1316 helix: 0.07 (0.18), residues: 806 sheet: 0.77 (1.02), residues: 20 loop : -2.88 (0.26), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 83 HIS 0.005 0.001 HIS B 728 PHE 0.023 0.002 PHE A 130 TYR 0.018 0.002 TYR B 323 ARG 0.008 0.000 ARG B 134 *********************** 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 380 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 316 time to evaluate : 1.148 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 36 ARG cc_start: 0.7472 (mtm-85) cc_final: 0.7113 (mtt90) REVERT: A 77 LYS cc_start: 0.8075 (ttpt) cc_final: 0.7666 (ttpt) REVERT: A 90 SER cc_start: 0.8508 (t) cc_final: 0.7973 (p) REVERT: A 94 THR cc_start: 0.8412 (t) cc_final: 0.8124 (p) REVERT: A 195 LEU cc_start: 0.8879 (OUTLIER) cc_final: 0.8529 (tp) REVERT: A 230 GLN cc_start: 0.8208 (tp40) cc_final: 0.7905 (tm-30) REVERT: A 237 LYS cc_start: 0.8665 (pttt) cc_final: 0.8340 (ptmm) REVERT: A 238 ILE cc_start: 0.8693 (tp) cc_final: 0.8418 (tp) REVERT: A 259 GLU cc_start: 0.7758 (OUTLIER) cc_final: 0.7144 (tm-30) REVERT: A 260 ILE cc_start: 0.8597 (mt) cc_final: 0.7932 (mt) REVERT: A 263 ASN cc_start: 0.8328 (t0) cc_final: 0.7727 (t0) REVERT: A 350 LEU cc_start: 0.8555 (tp) cc_final: 0.8196 (tt) REVERT: A 385 PHE cc_start: 0.8831 (OUTLIER) cc_final: 0.8597 (t80) REVERT: A 414 GLU cc_start: 0.7451 (tm-30) cc_final: 0.7092 (tp30) REVERT: A 425 LEU cc_start: 0.8543 (tp) cc_final: 0.8234 (tt) REVERT: A 432 MET cc_start: 0.7502 (tmm) cc_final: 0.7115 (tmm) REVERT: A 463 MET cc_start: 0.7597 (tmm) cc_final: 0.7084 (tmm) REVERT: A 466 CYS cc_start: 0.7878 (t) cc_final: 0.7269 (t) REVERT: A 473 LYS cc_start: 0.8455 (mttp) cc_final: 0.8085 (ttmm) REVERT: A 546 LYS cc_start: 0.6793 (ptmm) cc_final: 0.6486 (ptmm) REVERT: A 580 LYS cc_start: 0.8208 (mmmt) cc_final: 0.7933 (mtpt) REVERT: A 583 LYS cc_start: 0.8482 (OUTLIER) cc_final: 0.7903 (tmmt) REVERT: B 66 LYS cc_start: 0.8474 (tptt) cc_final: 0.8099 (tppt) REVERT: B 77 LYS cc_start: 0.8380 (ttpt) cc_final: 0.8010 (ttpt) REVERT: B 80 VAL cc_start: 0.9315 (OUTLIER) cc_final: 0.9014 (t) REVERT: B 90 SER cc_start: 0.8665 (t) cc_final: 0.8127 (p) REVERT: B 94 THR cc_start: 0.8618 (t) cc_final: 0.8309 (p) REVERT: B 125 LEU cc_start: 0.9045 (tp) cc_final: 0.8801 (tp) REVERT: B 127 TYR cc_start: 0.8583 (t80) cc_final: 0.8305 (t80) REVERT: B 134 ARG cc_start: 0.7229 (mtm-85) cc_final: 0.6993 (mtm-85) REVERT: B 150 SER cc_start: 0.8372 (t) cc_final: 0.8102 (p) REVERT: B 213 ARG cc_start: 0.8228 (mtp180) cc_final: 0.7945 (mtp180) REVERT: B 230 GLN cc_start: 0.8324 (tm-30) cc_final: 0.7840 (tm-30) REVERT: B 237 LYS cc_start: 0.8580 (pttt) cc_final: 0.8278 (ttpp) REVERT: B 250 ILE cc_start: 0.8618 (pt) cc_final: 0.8329 (mm) REVERT: B 259 GLU cc_start: 0.7547 (OUTLIER) cc_final: 0.6802 (tm-30) REVERT: B 260 ILE cc_start: 0.8700 (mt) cc_final: 0.8200 (mt) REVERT: B 287 GLU cc_start: 0.8056 (tp30) cc_final: 0.7562 (tm-30) REVERT: B 349 MET cc_start: 0.6101 (mmm) cc_final: 0.5804 (mmm) REVERT: B 354 PHE cc_start: 0.7280 (OUTLIER) cc_final: 0.7068 (t80) REVERT: B 384 GLU cc_start: 0.7689 (mm-30) cc_final: 0.7447 (mm-30) REVERT: B 394 PHE cc_start: 0.8241 (t80) cc_final: 0.7938 (t80) REVERT: B 400 CYS cc_start: 0.7430 (m) cc_final: 0.7102 (m) REVERT: B 409 ARG cc_start: 0.7748 (mtm180) cc_final: 0.7515 (ttm110) REVERT: B 463 MET cc_start: 0.7459 (tmm) cc_final: 0.7245 (tmm) REVERT: B 466 CYS cc_start: 0.8073 (t) cc_final: 0.7629 (t) REVERT: B 470 ARG cc_start: 0.6675 (mtp180) cc_final: 0.6407 (mtp180) REVERT: B 473 LYS cc_start: 0.8436 (mttp) cc_final: 0.8161 (mtpp) REVERT: B 486 CYS cc_start: 0.8755 (t) cc_final: 0.8494 (t) REVERT: B 488 MET cc_start: 0.7487 (tpp) cc_final: 0.7107 (tpp) REVERT: B 513 VAL cc_start: 0.9141 (OUTLIER) cc_final: 0.8903 (p) REVERT: B 531 LYS cc_start: 0.8634 (mmtm) cc_final: 0.8279 (mmmm) REVERT: B 556 TYR cc_start: 0.8998 (p90) cc_final: 0.8689 (p90) REVERT: B 578 TYR cc_start: 0.7781 (t80) cc_final: 0.7190 (t80) REVERT: B 581 ARG cc_start: 0.8215 (tpp-160) cc_final: 0.7865 (tpp-160) REVERT: B 583 LYS cc_start: 0.8455 (OUTLIER) cc_final: 0.7924 (tmmt) REVERT: B 681 LYS cc_start: 0.8390 (mptt) cc_final: 0.8000 (mptt) REVERT: B 705 GLN cc_start: 0.8672 (tt0) cc_final: 0.8363 (tt0) REVERT: B 714 ARG cc_start: 0.7418 (mtm-85) cc_final: 0.7109 (mtm-85) outliers start: 64 outliers final: 29 residues processed: 350 average time/residue: 0.2653 time to fit residues: 123.7393 Evaluate side-chains 337 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 299 time to evaluate : 1.199 ------------------------------------------------------------------------------- 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 135 HIS 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 349 MET Chi-restraints excluded: chain A residue 385 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 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 30 LEU Chi-restraints excluded: chain B residue 73 ASP Chi-restraints excluded: chain B residue 80 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 298 VAL 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 449 VAL 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 105 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 52 optimal weight: 0.9990 chunk 1 optimal weight: 0.0770 chunk 125 optimal weight: 1.9990 chunk 10 optimal weight: 0.0070 chunk 60 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 90 optimal weight: 0.9980 chunk 83 optimal weight: 1.9990 chunk 70 optimal weight: 4.9990 overall best weight: 0.5356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 289 ASN A 457 ASN B 35 GLN ** B 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.124624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.108004 restraints weight = 21158.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.111143 restraints weight = 10361.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.113284 restraints weight = 6078.141| |-----------------------------------------------------------------------------| r_work (final): 0.3571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.4425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.093 10390 Z= 0.232 Angle : 0.645 9.040 14120 Z= 0.330 Chirality : 0.043 0.236 1714 Planarity : 0.004 0.040 1756 Dihedral : 6.579 95.774 1448 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 5.34 % Allowed : 20.20 % Favored : 74.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.23), residues: 1316 helix: 0.15 (0.18), residues: 830 sheet: 1.34 (1.02), residues: 20 loop : -2.90 (0.27), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 83 HIS 0.006 0.001 HIS B 728 PHE 0.029 0.002 PHE B 128 TYR 0.033 0.002 TYR A 578 ARG 0.006 0.000 ARG B 134 *********************** 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 373 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 313 time to evaluate : 1.119 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 ARG cc_start: 0.7539 (mtm-85) cc_final: 0.7212 (mtt90) REVERT: A 66 LYS cc_start: 0.8475 (tptp) cc_final: 0.8115 (tppt) REVERT: A 77 LYS cc_start: 0.7971 (ttpt) cc_final: 0.7577 (ttpt) REVERT: A 90 SER cc_start: 0.8451 (t) cc_final: 0.7928 (p) REVERT: A 94 THR cc_start: 0.8445 (t) cc_final: 0.8067 (p) REVERT: A 103 MET cc_start: 0.7359 (mmp) cc_final: 0.7150 (mmp) REVERT: A 195 LEU cc_start: 0.8899 (OUTLIER) cc_final: 0.8499 (tp) REVERT: A 230 GLN cc_start: 0.8164 (tp40) cc_final: 0.7895 (tm-30) REVERT: A 237 LYS cc_start: 0.8691 (pttt) cc_final: 0.8411 (ttpp) REVERT: A 238 ILE cc_start: 0.8792 (tp) cc_final: 0.8551 (tp) REVERT: A 259 GLU cc_start: 0.7745 (OUTLIER) cc_final: 0.7222 (tm-30) REVERT: A 260 ILE cc_start: 0.8603 (mt) cc_final: 0.7969 (mt) REVERT: A 273 ILE cc_start: 0.8167 (mp) cc_final: 0.7949 (mp) REVERT: A 350 LEU cc_start: 0.8528 (tp) cc_final: 0.8147 (tt) REVERT: A 385 PHE cc_start: 0.8837 (OUTLIER) cc_final: 0.8593 (t80) REVERT: A 404 THR cc_start: 0.7404 (OUTLIER) cc_final: 0.7004 (t) REVERT: A 414 GLU cc_start: 0.7465 (tm-30) cc_final: 0.7118 (tp30) REVERT: A 432 MET cc_start: 0.7506 (tmm) cc_final: 0.7095 (tmm) REVERT: A 463 MET cc_start: 0.7580 (tmm) cc_final: 0.7071 (tmm) REVERT: A 466 CYS cc_start: 0.7922 (t) cc_final: 0.7467 (t) REVERT: A 473 LYS cc_start: 0.8460 (mttp) cc_final: 0.8017 (mtpp) REVERT: A 564 LYS cc_start: 0.8426 (OUTLIER) cc_final: 0.8165 (ttmm) REVERT: A 573 ASP cc_start: 0.7788 (t0) cc_final: 0.6887 (p0) REVERT: A 580 LYS cc_start: 0.8205 (mmmt) cc_final: 0.7947 (tttt) REVERT: A 581 ARG cc_start: 0.8208 (tpt170) cc_final: 0.7831 (tpt170) REVERT: A 583 LYS cc_start: 0.8445 (OUTLIER) cc_final: 0.7914 (tmmt) REVERT: B 66 LYS cc_start: 0.8396 (tptt) cc_final: 0.7940 (tppt) REVERT: B 77 LYS cc_start: 0.8326 (ttpt) cc_final: 0.7945 (ttpt) REVERT: B 90 SER cc_start: 0.8640 (t) cc_final: 0.8173 (p) REVERT: B 125 LEU cc_start: 0.8912 (tp) cc_final: 0.8495 (tp) REVERT: B 150 SER cc_start: 0.8381 (t) cc_final: 0.8125 (p) REVERT: B 230 GLN cc_start: 0.8356 (tm-30) cc_final: 0.7543 (tm-30) REVERT: B 237 LYS cc_start: 0.8550 (pttt) cc_final: 0.8252 (ttpp) REVERT: B 238 ILE cc_start: 0.8794 (tp) cc_final: 0.8409 (pt) REVERT: B 250 ILE cc_start: 0.8674 (pt) cc_final: 0.8405 (mm) REVERT: B 260 ILE cc_start: 0.8773 (mt) cc_final: 0.8468 (mt) REVERT: B 354 PHE cc_start: 0.7217 (OUTLIER) cc_final: 0.6998 (t80) REVERT: B 384 GLU cc_start: 0.7627 (mm-30) cc_final: 0.7406 (mm-30) REVERT: B 394 PHE cc_start: 0.8245 (t80) cc_final: 0.7905 (t80) REVERT: B 400 CYS cc_start: 0.7227 (m) cc_final: 0.6928 (m) REVERT: B 414 GLU cc_start: 0.7552 (tm-30) cc_final: 0.7017 (tp30) REVERT: B 463 MET cc_start: 0.7460 (tmm) cc_final: 0.7238 (tmm) REVERT: B 466 CYS cc_start: 0.8050 (t) cc_final: 0.7650 (t) REVERT: B 470 ARG cc_start: 0.6699 (mtp180) cc_final: 0.6429 (mtp180) REVERT: B 473 LYS cc_start: 0.8453 (mttp) cc_final: 0.8195 (mtpp) REVERT: B 486 CYS cc_start: 0.8729 (t) cc_final: 0.8473 (t) REVERT: B 488 MET cc_start: 0.7443 (tpp) cc_final: 0.7092 (tpp) REVERT: B 513 VAL cc_start: 0.9155 (OUTLIER) cc_final: 0.8923 (p) REVERT: B 531 LYS cc_start: 0.8617 (mmtm) cc_final: 0.8305 (mmmm) REVERT: B 537 LYS cc_start: 0.8239 (tmtt) cc_final: 0.7899 (tptp) REVERT: B 556 TYR cc_start: 0.8983 (p90) cc_final: 0.8626 (p90) REVERT: B 578 TYR cc_start: 0.7819 (t80) cc_final: 0.7286 (t80) REVERT: B 580 LYS cc_start: 0.7869 (mmmm) cc_final: 0.7614 (mmmm) REVERT: B 581 ARG cc_start: 0.8154 (tpp-160) cc_final: 0.7823 (tpp-160) REVERT: B 583 LYS cc_start: 0.8422 (OUTLIER) cc_final: 0.7871 (tmmt) REVERT: B 705 GLN cc_start: 0.8651 (tt0) cc_final: 0.8348 (tt0) REVERT: B 714 ARG cc_start: 0.7380 (mtm-85) cc_final: 0.7141 (mtm-85) outliers start: 60 outliers final: 35 residues processed: 350 average time/residue: 0.2463 time to fit residues: 116.1349 Evaluate side-chains 347 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 303 time to evaluate : 1.194 ------------------------------------------------------------------------------- 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 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 397 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 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 30 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 187 LEU Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 283 MET Chi-restraints excluded: chain B residue 298 VAL 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 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 15 optimal weight: 6.9990 chunk 109 optimal weight: 0.9990 chunk 69 optimal weight: 0.0060 chunk 66 optimal weight: 0.8980 chunk 120 optimal weight: 0.5980 chunk 22 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 37 optimal weight: 0.7980 chunk 112 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 110 optimal weight: 0.6980 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 457 ASN ** B 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 567 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.118154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.101212 restraints weight = 21104.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.104387 restraints weight = 10425.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.106327 restraints weight = 6125.041| |-----------------------------------------------------------------------------| r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.4839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 10390 Z= 0.234 Angle : 0.663 10.780 14120 Z= 0.337 Chirality : 0.043 0.186 1714 Planarity : 0.004 0.044 1756 Dihedral : 6.017 97.057 1442 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 4.98 % Allowed : 21.89 % Favored : 73.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.23), residues: 1316 helix: 0.28 (0.18), residues: 830 sheet: 1.72 (1.05), residues: 20 loop : -2.77 (0.27), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 83 HIS 0.007 0.001 HIS B 728 PHE 0.028 0.001 PHE B 272 TYR 0.018 0.002 TYR B 247 ARG 0.009 0.001 ARG B 409 *********************** 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 372 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 316 time to evaluate : 1.122 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 36 ARG cc_start: 0.7646 (mtm-85) cc_final: 0.7417 (mtt90) REVERT: A 77 LYS cc_start: 0.8045 (ttpt) cc_final: 0.7598 (ttpt) REVERT: A 79 ARG cc_start: 0.7079 (ptt-90) cc_final: 0.6709 (ptt-90) REVERT: A 90 SER cc_start: 0.8566 (t) cc_final: 0.7959 (p) REVERT: A 94 THR cc_start: 0.8529 (t) cc_final: 0.8198 (p) REVERT: A 134 ARG cc_start: 0.7959 (mpp80) cc_final: 0.7043 (mpp80) REVERT: A 182 ASP cc_start: 0.7668 (OUTLIER) cc_final: 0.7352 (p0) REVERT: A 195 LEU cc_start: 0.8953 (OUTLIER) cc_final: 0.8645 (tp) REVERT: A 230 GLN cc_start: 0.8170 (tp40) cc_final: 0.7897 (tm-30) REVERT: A 237 LYS cc_start: 0.8735 (pttt) cc_final: 0.8374 (ttpp) REVERT: A 238 ILE cc_start: 0.8883 (tp) cc_final: 0.8632 (tp) REVERT: A 255 TYR cc_start: 0.7614 (m-10) cc_final: 0.7369 (m-10) REVERT: A 259 GLU cc_start: 0.7652 (tm-30) cc_final: 0.7099 (tm-30) REVERT: A 260 ILE cc_start: 0.8721 (mt) cc_final: 0.8112 (mt) REVERT: A 273 ILE cc_start: 0.8122 (OUTLIER) cc_final: 0.7904 (mp) REVERT: A 350 LEU cc_start: 0.8478 (tp) cc_final: 0.8113 (tt) REVERT: A 358 VAL cc_start: 0.8942 (t) cc_final: 0.8701 (p) REVERT: A 377 TYR cc_start: 0.6243 (t80) cc_final: 0.5815 (t80) REVERT: A 404 THR cc_start: 0.7311 (OUTLIER) cc_final: 0.6885 (t) REVERT: A 414 GLU cc_start: 0.7571 (tm-30) cc_final: 0.7271 (tp30) REVERT: A 432 MET cc_start: 0.7521 (tmm) cc_final: 0.7103 (tmm) REVERT: A 463 MET cc_start: 0.7573 (tmm) cc_final: 0.7128 (tmm) REVERT: A 466 CYS cc_start: 0.7996 (t) cc_final: 0.7528 (t) REVERT: A 473 LYS cc_start: 0.8513 (mttp) cc_final: 0.8085 (ttmm) REVERT: A 476 LYS cc_start: 0.9154 (mtmm) cc_final: 0.8925 (mtmm) REVERT: A 577 VAL cc_start: 0.8648 (OUTLIER) cc_final: 0.8437 (p) REVERT: A 580 LYS cc_start: 0.8185 (mmmt) cc_final: 0.7845 (mmmt) REVERT: A 581 ARG cc_start: 0.8287 (tpt170) cc_final: 0.7880 (tpt170) REVERT: A 583 LYS cc_start: 0.8469 (OUTLIER) cc_final: 0.7780 (tmmt) REVERT: B 66 LYS cc_start: 0.8393 (tptt) cc_final: 0.7937 (tppt) REVERT: B 77 LYS cc_start: 0.8367 (ttpt) cc_final: 0.7984 (ttpt) REVERT: B 90 SER cc_start: 0.8581 (t) cc_final: 0.8150 (p) REVERT: B 126 THR cc_start: 0.8497 (t) cc_final: 0.8260 (t) REVERT: B 150 SER cc_start: 0.8304 (t) cc_final: 0.8047 (p) REVERT: B 230 GLN cc_start: 0.8388 (tm-30) cc_final: 0.7597 (tm-30) REVERT: B 236 LEU cc_start: 0.8977 (tp) cc_final: 0.8741 (tp) REVERT: B 237 LYS cc_start: 0.8615 (pttt) cc_final: 0.8213 (ttpt) REVERT: B 238 ILE cc_start: 0.8876 (tp) cc_final: 0.8478 (pt) REVERT: B 250 ILE cc_start: 0.8681 (pt) cc_final: 0.8420 (mm) REVERT: B 255 TYR cc_start: 0.7862 (m-10) cc_final: 0.7481 (m-10) REVERT: B 394 PHE cc_start: 0.8251 (t80) cc_final: 0.7675 (t80) REVERT: B 398 PHE cc_start: 0.6893 (m-80) cc_final: 0.6586 (m-10) REVERT: B 400 CYS cc_start: 0.7285 (m) cc_final: 0.7035 (m) REVERT: B 414 GLU cc_start: 0.7574 (tm-30) cc_final: 0.7028 (tp30) REVERT: B 466 CYS cc_start: 0.8069 (t) cc_final: 0.7714 (t) REVERT: B 470 ARG cc_start: 0.6664 (mtp180) cc_final: 0.6406 (mtp180) REVERT: B 473 LYS cc_start: 0.8439 (mttp) cc_final: 0.8163 (mtpp) REVERT: B 486 CYS cc_start: 0.8700 (t) cc_final: 0.8447 (t) REVERT: B 488 MET cc_start: 0.7429 (tpp) cc_final: 0.7090 (tpp) REVERT: B 513 VAL cc_start: 0.9180 (OUTLIER) cc_final: 0.8948 (p) REVERT: B 556 TYR cc_start: 0.8987 (p90) cc_final: 0.8634 (p90) REVERT: B 578 TYR cc_start: 0.7771 (t80) cc_final: 0.7301 (t80) REVERT: B 580 LYS cc_start: 0.7878 (mmmm) cc_final: 0.7598 (mmmm) REVERT: B 581 ARG cc_start: 0.8160 (tpp-160) cc_final: 0.7840 (tpp-160) REVERT: B 583 LYS cc_start: 0.8434 (OUTLIER) cc_final: 0.7900 (tmmt) REVERT: B 681 LYS cc_start: 0.8447 (mptt) cc_final: 0.8076 (mptt) REVERT: B 705 GLN cc_start: 0.8669 (tt0) cc_final: 0.8372 (tt0) REVERT: B 714 ARG cc_start: 0.7397 (mtm-85) cc_final: 0.7145 (mtm-85) outliers start: 56 outliers final: 32 residues processed: 348 average time/residue: 0.2719 time to fit residues: 124.9151 Evaluate side-chains 341 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 301 time to evaluate : 1.056 ------------------------------------------------------------------------------- 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 69 LEU Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 182 ASP Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 273 ILE 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 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 30 LEU Chi-restraints excluded: chain B residue 75 LEU 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 298 VAL Chi-restraints excluded: chain B residue 350 LEU 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 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 Chi-restraints excluded: chain B residue 716 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 111 optimal weight: 0.1980 chunk 43 optimal weight: 0.9990 chunk 84 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 78 optimal weight: 0.9990 chunk 83 optimal weight: 0.9980 chunk 85 optimal weight: 0.6980 chunk 117 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 82 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN A 101 GLN A 324 ASN ** B 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.116312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.099259 restraints weight = 21299.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.102485 restraints weight = 10482.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.104305 restraints weight = 6125.291| |-----------------------------------------------------------------------------| r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.5248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 10390 Z= 0.261 Angle : 0.686 9.294 14120 Z= 0.351 Chirality : 0.044 0.225 1714 Planarity : 0.004 0.044 1756 Dihedral : 5.469 45.249 1439 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 5.69 % Allowed : 23.13 % Favored : 71.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.23), residues: 1316 helix: 0.37 (0.18), residues: 828 sheet: 1.88 (1.12), residues: 20 loop : -2.73 (0.27), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 83 HIS 0.008 0.001 HIS B 728 PHE 0.033 0.002 PHE A 272 TYR 0.026 0.002 TYR B 323 ARG 0.008 0.001 ARG B 134 *********************** 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 384 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 320 time to evaluate : 1.181 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 GLU cc_start: 0.6940 (mp0) cc_final: 0.6513 (mp0) REVERT: A 36 ARG cc_start: 0.7770 (mtm-85) cc_final: 0.7529 (mtt90) REVERT: A 77 LYS cc_start: 0.8115 (ttpt) cc_final: 0.7655 (ttpt) REVERT: A 79 ARG cc_start: 0.7046 (ptt-90) cc_final: 0.6676 (ptt-90) REVERT: A 82 GLU cc_start: 0.7278 (pm20) cc_final: 0.6748 (pm20) REVERT: A 90 SER cc_start: 0.8564 (t) cc_final: 0.7946 (p) REVERT: A 94 THR cc_start: 0.8589 (t) cc_final: 0.8210 (p) REVERT: A 155 MET cc_start: 0.7937 (ptm) cc_final: 0.7607 (ptp) REVERT: A 182 ASP cc_start: 0.7737 (OUTLIER) cc_final: 0.7458 (p0) REVERT: A 195 LEU cc_start: 0.8980 (OUTLIER) cc_final: 0.8707 (tp) REVERT: A 207 GLN cc_start: 0.7960 (mp10) cc_final: 0.7665 (mp10) REVERT: A 230 GLN cc_start: 0.8227 (tp40) cc_final: 0.7926 (tm-30) REVERT: A 237 LYS cc_start: 0.8753 (pttt) cc_final: 0.8388 (ttpp) REVERT: A 238 ILE cc_start: 0.8952 (tp) cc_final: 0.8700 (tp) REVERT: A 251 LEU cc_start: 0.8763 (mm) cc_final: 0.8426 (mm) REVERT: A 255 TYR cc_start: 0.7669 (m-10) cc_final: 0.7462 (m-10) REVERT: A 259 GLU cc_start: 0.7743 (tm-30) cc_final: 0.7170 (tm-30) REVERT: A 260 ILE cc_start: 0.8745 (mt) cc_final: 0.8508 (mt) REVERT: A 350 LEU cc_start: 0.8529 (tp) cc_final: 0.8144 (tt) REVERT: A 358 VAL cc_start: 0.8922 (t) cc_final: 0.8645 (p) REVERT: A 385 PHE cc_start: 0.8928 (OUTLIER) cc_final: 0.8637 (t80) REVERT: A 404 THR cc_start: 0.7403 (OUTLIER) cc_final: 0.6935 (t) REVERT: A 409 ARG cc_start: 0.8271 (mtm180) cc_final: 0.8069 (mtm110) REVERT: A 414 GLU cc_start: 0.7568 (tm-30) cc_final: 0.6970 (tm-30) REVERT: A 432 MET cc_start: 0.7533 (tmm) cc_final: 0.7152 (tmm) REVERT: A 463 MET cc_start: 0.7545 (tmm) cc_final: 0.7080 (tmm) REVERT: A 466 CYS cc_start: 0.8032 (t) cc_final: 0.7584 (t) REVERT: A 473 LYS cc_start: 0.8525 (mttp) cc_final: 0.8083 (ttmm) REVERT: A 476 LYS cc_start: 0.9158 (mtmm) cc_final: 0.8931 (mtmm) REVERT: A 580 LYS cc_start: 0.8195 (mmmt) cc_final: 0.7859 (mmmt) REVERT: A 583 LYS cc_start: 0.8476 (OUTLIER) cc_final: 0.7786 (tmmt) REVERT: A 681 LYS cc_start: 0.8290 (mptt) cc_final: 0.8029 (mptt) REVERT: B 66 LYS cc_start: 0.8426 (tptt) cc_final: 0.7887 (tppt) REVERT: B 77 LYS cc_start: 0.8385 (ttpt) cc_final: 0.8015 (ttpt) REVERT: B 90 SER cc_start: 0.8601 (t) cc_final: 0.8163 (p) REVERT: B 150 SER cc_start: 0.8312 (t) cc_final: 0.8070 (p) REVERT: B 192 LEU cc_start: 0.8486 (OUTLIER) cc_final: 0.8269 (tp) REVERT: B 202 VAL cc_start: 0.8631 (p) cc_final: 0.8420 (p) REVERT: B 208 ILE cc_start: 0.8952 (OUTLIER) cc_final: 0.8737 (pt) REVERT: B 230 GLN cc_start: 0.8416 (tm-30) cc_final: 0.8037 (tm-30) REVERT: B 235 GLN cc_start: 0.8121 (mm-40) cc_final: 0.7878 (mm110) REVERT: B 236 LEU cc_start: 0.9023 (tp) cc_final: 0.8746 (tp) REVERT: B 237 LYS cc_start: 0.8613 (pttt) cc_final: 0.8235 (ttmt) REVERT: B 250 ILE cc_start: 0.8697 (pt) cc_final: 0.8461 (mm) REVERT: B 255 TYR cc_start: 0.7915 (m-10) cc_final: 0.7610 (m-10) REVERT: B 271 ASP cc_start: 0.7875 (t0) cc_final: 0.7661 (t0) REVERT: B 356 ILE cc_start: 0.7397 (mt) cc_final: 0.7168 (mt) REVERT: B 398 PHE cc_start: 0.6951 (m-80) cc_final: 0.6658 (m-10) REVERT: B 400 CYS cc_start: 0.7261 (m) cc_final: 0.7006 (m) REVERT: B 414 GLU cc_start: 0.7632 (tm-30) cc_final: 0.7082 (tp30) REVERT: B 463 MET cc_start: 0.7610 (tmm) cc_final: 0.7220 (tmm) REVERT: B 466 CYS cc_start: 0.8086 (t) cc_final: 0.7625 (t) REVERT: B 467 ASP cc_start: 0.7171 (OUTLIER) cc_final: 0.6852 (t0) REVERT: B 473 LYS cc_start: 0.8486 (mttp) cc_final: 0.8203 (mtpp) REVERT: B 486 CYS cc_start: 0.8710 (t) cc_final: 0.8457 (t) REVERT: B 488 MET cc_start: 0.7482 (tpp) cc_final: 0.7135 (tpp) REVERT: B 513 VAL cc_start: 0.9205 (OUTLIER) cc_final: 0.8980 (p) REVERT: B 556 TYR cc_start: 0.9002 (p90) cc_final: 0.8702 (p90) REVERT: B 578 TYR cc_start: 0.7735 (t80) cc_final: 0.7277 (t80) REVERT: B 580 LYS cc_start: 0.7948 (mmmm) cc_final: 0.7660 (mmmm) REVERT: B 581 ARG cc_start: 0.8158 (tpp-160) cc_final: 0.7805 (tpp-160) REVERT: B 583 LYS cc_start: 0.8440 (OUTLIER) cc_final: 0.7903 (tmmt) REVERT: B 681 LYS cc_start: 0.8457 (mptt) cc_final: 0.8220 (mptt) REVERT: B 705 GLN cc_start: 0.8660 (tt0) cc_final: 0.8338 (tt0) REVERT: B 714 ARG cc_start: 0.7428 (mtm-85) cc_final: 0.7175 (mtm-85) REVERT: B 724 ASP cc_start: 0.7748 (OUTLIER) cc_final: 0.7511 (t70) outliers start: 64 outliers final: 41 residues processed: 355 average time/residue: 0.2647 time to fit residues: 124.8572 Evaluate side-chains 365 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 313 time to evaluate : 1.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLN 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 144 VAL Chi-restraints excluded: chain A residue 182 ASP Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 397 PHE Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 427 SER 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 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 30 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 151 VAL Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 348 ASP 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 467 ASP 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 Chi-restraints excluded: chain B residue 716 ASP Chi-restraints excluded: chain B residue 724 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 66 optimal weight: 0.2980 chunk 83 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 chunk 115 optimal weight: 0.6980 chunk 7 optimal weight: 0.9980 chunk 81 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 0 optimal weight: 0.9990 chunk 99 optimal weight: 0.8980 chunk 61 optimal weight: 0.5980 chunk 48 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN A 324 ASN ** B 382 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 = 0.3703 r_free = 0.3703 target = 0.116792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.099544 restraints weight = 21259.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.102741 restraints weight = 10447.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.104730 restraints weight = 6137.682| |-----------------------------------------------------------------------------| r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.5420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 10390 Z= 0.249 Angle : 0.683 9.358 14120 Z= 0.350 Chirality : 0.043 0.223 1714 Planarity : 0.004 0.044 1756 Dihedral : 5.478 45.394 1439 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 13.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 4.98 % Allowed : 24.11 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.23), residues: 1316 helix: 0.38 (0.18), residues: 828 sheet: 2.02 (1.14), residues: 20 loop : -2.71 (0.27), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 83 HIS 0.007 0.001 HIS B 728 PHE 0.023 0.001 PHE A 128 TYR 0.022 0.002 TYR B 323 ARG 0.005 0.000 ARG B 38 *********************** 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 366 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 310 time to evaluate : 1.072 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 GLU cc_start: 0.6923 (mp0) cc_final: 0.6532 (mp0) REVERT: A 36 ARG cc_start: 0.7803 (mtm-85) cc_final: 0.7585 (mtm-85) REVERT: A 77 LYS cc_start: 0.8081 (ttpt) cc_final: 0.7629 (ttpt) REVERT: A 79 ARG cc_start: 0.6975 (ptt-90) cc_final: 0.6679 (ptt-90) REVERT: A 82 GLU cc_start: 0.7220 (pm20) cc_final: 0.6841 (pm20) REVERT: A 90 SER cc_start: 0.8547 (t) cc_final: 0.7947 (p) REVERT: A 94 THR cc_start: 0.8597 (t) cc_final: 0.8206 (p) REVERT: A 134 ARG cc_start: 0.7968 (mpp80) cc_final: 0.7328 (mpp80) REVERT: A 195 LEU cc_start: 0.9014 (OUTLIER) cc_final: 0.8648 (tp) REVERT: A 207 GLN cc_start: 0.8024 (mp10) cc_final: 0.7672 (mp10) REVERT: A 230 GLN cc_start: 0.8229 (tp40) cc_final: 0.7937 (tm-30) REVERT: A 237 LYS cc_start: 0.8770 (pttt) cc_final: 0.8387 (ttpp) REVERT: A 238 ILE cc_start: 0.8980 (tp) cc_final: 0.8706 (tp) REVERT: A 251 LEU cc_start: 0.8745 (mm) cc_final: 0.8462 (mm) REVERT: A 259 GLU cc_start: 0.7725 (tm-30) cc_final: 0.7167 (tm-30) REVERT: A 260 ILE cc_start: 0.8740 (mt) cc_final: 0.8496 (mt) REVERT: A 263 ASN cc_start: 0.8206 (t0) cc_final: 0.7374 (t0) REVERT: A 350 LEU cc_start: 0.8472 (tp) cc_final: 0.8094 (tt) REVERT: A 358 VAL cc_start: 0.8915 (t) cc_final: 0.8641 (p) REVERT: A 377 TYR cc_start: 0.6275 (t80) cc_final: 0.5948 (t80) REVERT: A 385 PHE cc_start: 0.8943 (OUTLIER) cc_final: 0.8666 (t80) REVERT: A 404 THR cc_start: 0.7423 (OUTLIER) cc_final: 0.6891 (p) REVERT: A 409 ARG cc_start: 0.8291 (mtm180) cc_final: 0.7900 (mtm110) REVERT: A 414 GLU cc_start: 0.7566 (tm-30) cc_final: 0.6963 (tm-30) REVERT: A 432 MET cc_start: 0.7540 (tmm) cc_final: 0.7166 (tmm) REVERT: A 463 MET cc_start: 0.7525 (tmm) cc_final: 0.7042 (tmm) REVERT: A 466 CYS cc_start: 0.8024 (t) cc_final: 0.7578 (t) REVERT: A 473 LYS cc_start: 0.8526 (mttp) cc_final: 0.8077 (ttmm) REVERT: A 476 LYS cc_start: 0.9159 (mtmm) cc_final: 0.8920 (mtmm) REVERT: A 537 LYS cc_start: 0.8143 (ttmt) cc_final: 0.7762 (ttpp) REVERT: A 580 LYS cc_start: 0.8185 (mmmt) cc_final: 0.7839 (mmmt) REVERT: A 583 LYS cc_start: 0.8465 (OUTLIER) cc_final: 0.7766 (tmmt) REVERT: B 66 LYS cc_start: 0.8407 (tptt) cc_final: 0.7841 (tppt) REVERT: B 77 LYS cc_start: 0.8395 (ttpt) cc_final: 0.8025 (ttpt) REVERT: B 90 SER cc_start: 0.8574 (t) cc_final: 0.8136 (p) REVERT: B 150 SER cc_start: 0.8345 (t) cc_final: 0.8079 (p) REVERT: B 230 GLN cc_start: 0.8434 (tm-30) cc_final: 0.8064 (tm-30) REVERT: B 235 GLN cc_start: 0.8146 (mm-40) cc_final: 0.7911 (mm110) REVERT: B 236 LEU cc_start: 0.9003 (tp) cc_final: 0.8749 (tp) REVERT: B 237 LYS cc_start: 0.8636 (pttt) cc_final: 0.8255 (ttmt) REVERT: B 250 ILE cc_start: 0.8687 (pt) cc_final: 0.8480 (mm) REVERT: B 255 TYR cc_start: 0.7919 (m-10) cc_final: 0.7590 (m-10) REVERT: B 256 THR cc_start: 0.8649 (m) cc_final: 0.8435 (m) REVERT: B 394 PHE cc_start: 0.8214 (t80) cc_final: 0.7955 (t80) REVERT: B 398 PHE cc_start: 0.6964 (m-80) cc_final: 0.6550 (m-10) REVERT: B 400 CYS cc_start: 0.7261 (m) cc_final: 0.7014 (m) REVERT: B 414 GLU cc_start: 0.7642 (tm-30) cc_final: 0.7094 (tp30) REVERT: B 458 LEU cc_start: 0.8774 (OUTLIER) cc_final: 0.8551 (mt) REVERT: B 466 CYS cc_start: 0.8112 (t) cc_final: 0.7823 (t) REVERT: B 473 LYS cc_start: 0.8385 (mttp) cc_final: 0.8116 (mtpp) REVERT: B 486 CYS cc_start: 0.8714 (t) cc_final: 0.8451 (t) REVERT: B 488 MET cc_start: 0.7478 (tpp) cc_final: 0.7125 (tpp) REVERT: B 513 VAL cc_start: 0.9212 (OUTLIER) cc_final: 0.8977 (p) REVERT: B 549 ARG cc_start: 0.7616 (ttm-80) cc_final: 0.7177 (ttt-90) REVERT: B 556 TYR cc_start: 0.9009 (p90) cc_final: 0.8728 (p90) REVERT: B 578 TYR cc_start: 0.7733 (t80) cc_final: 0.7292 (t80) REVERT: B 580 LYS cc_start: 0.7971 (mmmm) cc_final: 0.7711 (mmmm) REVERT: B 583 LYS cc_start: 0.8426 (OUTLIER) cc_final: 0.7910 (tmmt) REVERT: B 681 LYS cc_start: 0.8434 (mptt) cc_final: 0.8204 (mptt) REVERT: B 705 GLN cc_start: 0.8664 (tt0) cc_final: 0.8335 (tt0) REVERT: B 714 ARG cc_start: 0.7423 (mtm-85) cc_final: 0.7169 (mtm-85) REVERT: B 724 ASP cc_start: 0.7743 (OUTLIER) cc_final: 0.7511 (t70) outliers start: 56 outliers final: 34 residues processed: 343 average time/residue: 0.2724 time to fit residues: 123.7728 Evaluate side-chains 348 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 306 time to evaluate : 1.132 ------------------------------------------------------------------------------- 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 195 LEU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 397 PHE Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 427 SER 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 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 30 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 187 LEU Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 283 MET Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 383 GLN Chi-restraints excluded: chain B residue 405 THR Chi-restraints excluded: chain B residue 458 LEU 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 Chi-restraints excluded: chain B residue 724 ASP Chi-restraints excluded: chain B residue 727 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 40 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 53 optimal weight: 0.5980 chunk 124 optimal weight: 0.7980 chunk 15 optimal weight: 9.9990 chunk 111 optimal weight: 0.5980 chunk 112 optimal weight: 0.5980 chunk 100 optimal weight: 0.5980 chunk 102 optimal weight: 0.8980 chunk 128 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN B 268 ASN ** B 382 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 = 0.3700 r_free = 0.3700 target = 0.116442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.099238 restraints weight = 21431.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.102437 restraints weight = 10523.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.104250 restraints weight = 6171.557| |-----------------------------------------------------------------------------| r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.5591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10390 Z= 0.251 Angle : 0.713 9.414 14120 Z= 0.361 Chirality : 0.044 0.233 1714 Planarity : 0.004 0.043 1756 Dihedral : 5.506 45.119 1439 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 13.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 4.80 % Allowed : 25.18 % Favored : 70.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.23), residues: 1316 helix: 0.35 (0.18), residues: 828 sheet: 2.01 (1.14), residues: 20 loop : -2.67 (0.27), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 83 HIS 0.004 0.001 HIS A 728 PHE 0.027 0.001 PHE B 272 TYR 0.036 0.002 TYR B 361 ARG 0.006 0.001 ARG B 134 *********************** 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 358 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 304 time to evaluate : 1.185 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 GLU cc_start: 0.6964 (mp0) cc_final: 0.6627 (mp0) REVERT: A 36 ARG cc_start: 0.7832 (mtm-85) cc_final: 0.7612 (mtm-85) REVERT: A 79 ARG cc_start: 0.7007 (ptt-90) cc_final: 0.6694 (ptt-90) REVERT: A 82 GLU cc_start: 0.7272 (pm20) cc_final: 0.6924 (pm20) REVERT: A 90 SER cc_start: 0.8534 (t) cc_final: 0.7906 (p) REVERT: A 94 THR cc_start: 0.8603 (t) cc_final: 0.8209 (p) REVERT: A 133 SER cc_start: 0.8711 (t) cc_final: 0.7980 (m) REVERT: A 182 ASP cc_start: 0.7792 (OUTLIER) cc_final: 0.7559 (p0) REVERT: A 195 LEU cc_start: 0.9017 (OUTLIER) cc_final: 0.8681 (tp) REVERT: A 207 GLN cc_start: 0.8040 (mp10) cc_final: 0.7707 (mp10) REVERT: A 230 GLN cc_start: 0.8241 (tp40) cc_final: 0.7947 (tm-30) REVERT: A 237 LYS cc_start: 0.8776 (pttt) cc_final: 0.8389 (ttpp) REVERT: A 238 ILE cc_start: 0.8969 (tp) cc_final: 0.8699 (tp) REVERT: A 251 LEU cc_start: 0.8709 (mm) cc_final: 0.8506 (mt) REVERT: A 259 GLU cc_start: 0.7725 (tm-30) cc_final: 0.7078 (tm-30) REVERT: A 260 ILE cc_start: 0.8783 (mt) cc_final: 0.8511 (mt) REVERT: A 263 ASN cc_start: 0.8284 (t0) cc_final: 0.7567 (t0) REVERT: A 350 LEU cc_start: 0.8496 (tp) cc_final: 0.8118 (tt) REVERT: A 358 VAL cc_start: 0.8867 (t) cc_final: 0.8602 (p) REVERT: A 385 PHE cc_start: 0.8941 (OUTLIER) cc_final: 0.8637 (t80) REVERT: A 404 THR cc_start: 0.7403 (OUTLIER) cc_final: 0.6867 (p) REVERT: A 409 ARG cc_start: 0.8308 (mtm180) cc_final: 0.7891 (mtm110) REVERT: A 414 GLU cc_start: 0.7553 (tm-30) cc_final: 0.6942 (tm-30) REVERT: A 432 MET cc_start: 0.7535 (tmm) cc_final: 0.7182 (tmm) REVERT: A 463 MET cc_start: 0.7518 (tmm) cc_final: 0.7028 (tmm) REVERT: A 466 CYS cc_start: 0.8033 (t) cc_final: 0.7604 (t) REVERT: A 473 LYS cc_start: 0.8562 (mttp) cc_final: 0.8126 (ttmm) REVERT: A 476 LYS cc_start: 0.9165 (mtmm) cc_final: 0.8924 (mtmm) REVERT: A 540 GLU cc_start: 0.8281 (pm20) cc_final: 0.7356 (pm20) REVERT: A 573 ASP cc_start: 0.7852 (t0) cc_final: 0.7067 (p0) REVERT: A 580 LYS cc_start: 0.8193 (mmmt) cc_final: 0.7856 (mmmt) REVERT: A 583 LYS cc_start: 0.8474 (OUTLIER) cc_final: 0.7777 (tmmt) REVERT: A 681 LYS cc_start: 0.8284 (mptt) cc_final: 0.8054 (mptt) REVERT: B 66 LYS cc_start: 0.8422 (tptt) cc_final: 0.7864 (tppt) REVERT: B 77 LYS cc_start: 0.8428 (ttpt) cc_final: 0.8060 (ttpt) REVERT: B 90 SER cc_start: 0.8566 (t) cc_final: 0.8136 (p) REVERT: B 150 SER cc_start: 0.8362 (t) cc_final: 0.8050 (p) REVERT: B 203 PHE cc_start: 0.8460 (m-80) cc_final: 0.8196 (m-80) REVERT: B 230 GLN cc_start: 0.8446 (tm-30) cc_final: 0.8089 (tm-30) REVERT: B 235 GLN cc_start: 0.8159 (mm-40) cc_final: 0.7913 (mm110) REVERT: B 236 LEU cc_start: 0.9000 (tp) cc_final: 0.8756 (tp) REVERT: B 237 LYS cc_start: 0.8691 (pttt) cc_final: 0.8297 (ttmt) REVERT: B 255 TYR cc_start: 0.7949 (m-10) cc_final: 0.7613 (m-10) REVERT: B 361 TYR cc_start: 0.8451 (t80) cc_final: 0.7896 (t80) REVERT: B 394 PHE cc_start: 0.8184 (t80) cc_final: 0.7909 (t80) REVERT: B 398 PHE cc_start: 0.6976 (m-80) cc_final: 0.6549 (m-10) REVERT: B 404 THR cc_start: 0.7694 (OUTLIER) cc_final: 0.7233 (p) REVERT: B 414 GLU cc_start: 0.7653 (tm-30) cc_final: 0.7085 (tp30) REVERT: B 458 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8548 (mt) REVERT: B 466 CYS cc_start: 0.8076 (t) cc_final: 0.7762 (t) REVERT: B 473 LYS cc_start: 0.8385 (mttp) cc_final: 0.8119 (mtpp) REVERT: B 486 CYS cc_start: 0.8718 (t) cc_final: 0.8458 (t) REVERT: B 488 MET cc_start: 0.7472 (tpp) cc_final: 0.7129 (tpp) REVERT: B 513 VAL cc_start: 0.9233 (OUTLIER) cc_final: 0.9017 (p) REVERT: B 546 LYS cc_start: 0.7866 (mmtt) cc_final: 0.7634 (mmmm) REVERT: B 549 ARG cc_start: 0.7605 (ttm-80) cc_final: 0.7173 (ttt-90) REVERT: B 556 TYR cc_start: 0.9000 (p90) cc_final: 0.8767 (p90) REVERT: B 578 TYR cc_start: 0.7702 (t80) cc_final: 0.7227 (t80) REVERT: B 580 LYS cc_start: 0.7983 (mmmm) cc_final: 0.7771 (mmmm) REVERT: B 581 ARG cc_start: 0.8243 (tpt170) cc_final: 0.7827 (tpp-160) REVERT: B 583 LYS cc_start: 0.8458 (OUTLIER) cc_final: 0.7926 (tmmt) REVERT: B 681 LYS cc_start: 0.8425 (mptt) cc_final: 0.8197 (mptt) REVERT: B 705 GLN cc_start: 0.8664 (tt0) cc_final: 0.8328 (tt0) REVERT: B 714 ARG cc_start: 0.7437 (mtm-85) cc_final: 0.7162 (mtm-85) REVERT: B 720 LEU cc_start: 0.8581 (mp) cc_final: 0.8285 (mp) REVERT: B 724 ASP cc_start: 0.7754 (OUTLIER) cc_final: 0.7517 (t70) outliers start: 54 outliers final: 35 residues processed: 337 average time/residue: 0.2728 time to fit residues: 121.9771 Evaluate side-chains 348 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 303 time to evaluate : 1.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLN 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 111 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 182 ASP Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 397 PHE Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 427 SER Chi-restraints excluded: chain A residue 449 VAL 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 30 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 187 LEU Chi-restraints excluded: chain B residue 283 MET Chi-restraints excluded: chain B residue 298 VAL 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 458 LEU 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 Chi-restraints excluded: chain B residue 724 ASP Chi-restraints excluded: chain B residue 727 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 14 optimal weight: 0.8980 chunk 102 optimal weight: 0.7980 chunk 89 optimal weight: 0.9980 chunk 50 optimal weight: 0.6980 chunk 54 optimal weight: 0.3980 chunk 88 optimal weight: 0.4980 chunk 62 optimal weight: 0.7980 chunk 61 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 57 optimal weight: 0.5980 chunk 129 optimal weight: 0.4980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN B 33 GLN B 246 ASN ** B 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.116129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.098967 restraints weight = 21413.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.102047 restraints weight = 10537.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.104193 restraints weight = 6233.900| |-----------------------------------------------------------------------------| r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.5694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10390 Z= 0.234 Angle : 0.709 9.786 14120 Z= 0.358 Chirality : 0.044 0.249 1714 Planarity : 0.004 0.047 1756 Dihedral : 5.486 45.071 1439 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 14.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 4.63 % Allowed : 25.62 % Favored : 69.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.23), residues: 1316 helix: 0.30 (0.18), residues: 842 sheet: 2.15 (1.17), residues: 20 loop : -2.61 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 83 HIS 0.005 0.001 HIS A 728 PHE 0.025 0.001 PHE A 128 TYR 0.034 0.002 TYR A 377 ARG 0.012 0.001 ARG B 134 *********************** 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 357 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 305 time to evaluate : 1.070 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 GLU cc_start: 0.6950 (mp0) cc_final: 0.6598 (mp0) REVERT: A 79 ARG cc_start: 0.6976 (ptt-90) cc_final: 0.6682 (ptt-90) REVERT: A 82 GLU cc_start: 0.7243 (pm20) cc_final: 0.6944 (pm20) REVERT: A 90 SER cc_start: 0.8507 (t) cc_final: 0.7875 (p) REVERT: A 94 THR cc_start: 0.8571 (t) cc_final: 0.8182 (p) REVERT: A 133 SER cc_start: 0.8793 (t) cc_final: 0.8062 (m) REVERT: A 182 ASP cc_start: 0.7712 (OUTLIER) cc_final: 0.7428 (p0) REVERT: A 195 LEU cc_start: 0.9029 (OUTLIER) cc_final: 0.8666 (tp) REVERT: A 207 GLN cc_start: 0.8030 (mp10) cc_final: 0.7699 (mp10) REVERT: A 230 GLN cc_start: 0.8225 (tp40) cc_final: 0.7941 (tm-30) REVERT: A 235 GLN cc_start: 0.8296 (mm-40) cc_final: 0.8019 (mm-40) REVERT: A 237 LYS cc_start: 0.8775 (pttt) cc_final: 0.8375 (ttpp) REVERT: A 238 ILE cc_start: 0.8982 (tp) cc_final: 0.8680 (tp) REVERT: A 259 GLU cc_start: 0.7705 (tm-30) cc_final: 0.7050 (tm-30) REVERT: A 260 ILE cc_start: 0.8771 (mt) cc_final: 0.8495 (mt) REVERT: A 263 ASN cc_start: 0.8265 (t0) cc_final: 0.7569 (t0) REVERT: A 350 LEU cc_start: 0.8450 (tp) cc_final: 0.8084 (tt) REVERT: A 358 VAL cc_start: 0.8853 (t) cc_final: 0.8585 (p) REVERT: A 385 PHE cc_start: 0.9004 (OUTLIER) cc_final: 0.8665 (t80) REVERT: A 404 THR cc_start: 0.7394 (OUTLIER) cc_final: 0.6837 (p) REVERT: A 409 ARG cc_start: 0.8299 (mtm180) cc_final: 0.7892 (mtm110) REVERT: A 414 GLU cc_start: 0.7540 (tm-30) cc_final: 0.6938 (tm-30) REVERT: A 432 MET cc_start: 0.7510 (tmm) cc_final: 0.7154 (tmm) REVERT: A 463 MET cc_start: 0.7514 (tmm) cc_final: 0.6989 (tmm) REVERT: A 466 CYS cc_start: 0.8025 (t) cc_final: 0.7604 (t) REVERT: A 473 LYS cc_start: 0.8561 (mttp) cc_final: 0.8120 (ttmm) REVERT: A 540 GLU cc_start: 0.8308 (pm20) cc_final: 0.7355 (pm20) REVERT: A 573 ASP cc_start: 0.7860 (t0) cc_final: 0.7098 (p0) REVERT: A 580 LYS cc_start: 0.8178 (mmmt) cc_final: 0.7842 (mmmt) REVERT: A 583 LYS cc_start: 0.8442 (OUTLIER) cc_final: 0.7744 (tmmt) REVERT: B 66 LYS cc_start: 0.8398 (tptt) cc_final: 0.7862 (tppt) REVERT: B 77 LYS cc_start: 0.8411 (ttpt) cc_final: 0.8032 (ttpt) REVERT: B 90 SER cc_start: 0.8527 (t) cc_final: 0.8147 (p) REVERT: B 150 SER cc_start: 0.8372 (t) cc_final: 0.8078 (p) REVERT: B 203 PHE cc_start: 0.8485 (m-80) cc_final: 0.8258 (m-80) REVERT: B 230 GLN cc_start: 0.8443 (tm-30) cc_final: 0.8096 (tm-30) REVERT: B 235 GLN cc_start: 0.8172 (mm-40) cc_final: 0.7901 (mm110) REVERT: B 236 LEU cc_start: 0.8981 (tp) cc_final: 0.8736 (tp) REVERT: B 237 LYS cc_start: 0.8697 (pttt) cc_final: 0.8290 (ttmt) REVERT: B 255 TYR cc_start: 0.7964 (m-10) cc_final: 0.7641 (m-10) REVERT: B 394 PHE cc_start: 0.8175 (t80) cc_final: 0.7847 (t80) REVERT: B 398 PHE cc_start: 0.6919 (m-80) cc_final: 0.6581 (m-10) REVERT: B 404 THR cc_start: 0.7655 (OUTLIER) cc_final: 0.7190 (p) REVERT: B 414 GLU cc_start: 0.7627 (tm-30) cc_final: 0.7059 (tp30) REVERT: B 426 ILE cc_start: 0.8242 (tt) cc_final: 0.7824 (pt) REVERT: B 458 LEU cc_start: 0.8703 (OUTLIER) cc_final: 0.8462 (mt) REVERT: B 466 CYS cc_start: 0.8060 (t) cc_final: 0.7751 (t) REVERT: B 473 LYS cc_start: 0.8371 (mttp) cc_final: 0.8107 (mtpp) REVERT: B 486 CYS cc_start: 0.8702 (t) cc_final: 0.8445 (t) REVERT: B 488 MET cc_start: 0.7438 (tpp) cc_final: 0.7108 (tpp) REVERT: B 513 VAL cc_start: 0.9235 (OUTLIER) cc_final: 0.9015 (p) REVERT: B 546 LYS cc_start: 0.7969 (mmtt) cc_final: 0.7530 (mmmm) REVERT: B 549 ARG cc_start: 0.7592 (ttm-80) cc_final: 0.7169 (ttt-90) REVERT: B 556 TYR cc_start: 0.8979 (p90) cc_final: 0.8722 (p90) REVERT: B 578 TYR cc_start: 0.7700 (t80) cc_final: 0.7266 (t80) REVERT: B 580 LYS cc_start: 0.7964 (mmmm) cc_final: 0.7745 (mmmm) REVERT: B 581 ARG cc_start: 0.8230 (tpt170) cc_final: 0.7826 (tpp-160) REVERT: B 583 LYS cc_start: 0.8445 (OUTLIER) cc_final: 0.7906 (tmmt) REVERT: B 681 LYS cc_start: 0.8434 (mptt) cc_final: 0.8215 (mptt) REVERT: B 705 GLN cc_start: 0.8656 (tt0) cc_final: 0.8297 (tt0) REVERT: B 714 ARG cc_start: 0.7419 (mtm-85) cc_final: 0.7165 (mtm-85) REVERT: B 720 LEU cc_start: 0.8540 (mp) cc_final: 0.8335 (mp) REVERT: B 724 ASP cc_start: 0.7735 (OUTLIER) cc_final: 0.7510 (t70) outliers start: 52 outliers final: 34 residues processed: 336 average time/residue: 0.2749 time to fit residues: 122.0500 Evaluate side-chains 341 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 297 time to evaluate : 1.189 ------------------------------------------------------------------------------- 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 111 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 182 ASP Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 397 PHE Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 427 SER Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 523 SER 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 727 LEU Chi-restraints excluded: chain B residue 30 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 147 MET 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 298 VAL 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 458 LEU Chi-restraints excluded: chain B residue 461 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 713 ILE Chi-restraints excluded: chain B residue 716 ASP Chi-restraints excluded: chain B residue 724 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 5 optimal weight: 1.9990 chunk 15 optimal weight: 0.3980 chunk 121 optimal weight: 0.9980 chunk 119 optimal weight: 0.9980 chunk 98 optimal weight: 0.9980 chunk 39 optimal weight: 0.5980 chunk 67 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 127 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN ** B 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.114943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.097571 restraints weight = 21462.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.100662 restraints weight = 10602.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.102769 restraints weight = 6281.841| |-----------------------------------------------------------------------------| r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.5894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 10390 Z= 0.282 Angle : 0.748 10.429 14120 Z= 0.378 Chirality : 0.046 0.252 1714 Planarity : 0.004 0.060 1756 Dihedral : 5.512 44.861 1438 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 15.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 4.27 % Allowed : 26.16 % Favored : 69.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.23), residues: 1316 helix: 0.28 (0.18), residues: 838 sheet: 1.94 (1.16), residues: 20 loop : -2.66 (0.28), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 83 HIS 0.004 0.001 HIS A 728 PHE 0.026 0.001 PHE A 128 TYR 0.030 0.003 TYR A 377 ARG 0.008 0.001 ARG B 134 ********************** 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 355 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 307 time to evaluate : 1.201 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 GLU cc_start: 0.7066 (mp0) cc_final: 0.6715 (mp0) REVERT: A 35 GLN cc_start: 0.7844 (OUTLIER) cc_final: 0.7556 (pt0) REVERT: A 36 ARG cc_start: 0.7900 (mmt90) cc_final: 0.7600 (mtt90) REVERT: A 79 ARG cc_start: 0.7050 (ptt-90) cc_final: 0.6685 (ptt-90) REVERT: A 82 GLU cc_start: 0.7237 (pm20) cc_final: 0.6818 (pm20) REVERT: A 85 LEU cc_start: 0.6954 (tp) cc_final: 0.6700 (tp) REVERT: A 90 SER cc_start: 0.8544 (t) cc_final: 0.7845 (p) REVERT: A 94 THR cc_start: 0.8578 (t) cc_final: 0.8167 (p) REVERT: A 127 TYR cc_start: 0.8571 (t80) cc_final: 0.8285 (t80) REVERT: A 133 SER cc_start: 0.8878 (t) cc_final: 0.8143 (m) REVERT: A 134 ARG cc_start: 0.8094 (mpp80) cc_final: 0.7883 (mpp80) REVERT: A 182 ASP cc_start: 0.7737 (OUTLIER) cc_final: 0.7502 (p0) REVERT: A 195 LEU cc_start: 0.9062 (OUTLIER) cc_final: 0.8825 (tm) REVERT: A 207 GLN cc_start: 0.8139 (mp10) cc_final: 0.7870 (mp10) REVERT: A 230 GLN cc_start: 0.8259 (tp40) cc_final: 0.7875 (tm-30) REVERT: A 235 GLN cc_start: 0.8355 (mm-40) cc_final: 0.8064 (mm-40) REVERT: A 237 LYS cc_start: 0.8815 (pttt) cc_final: 0.8407 (ttpp) REVERT: A 238 ILE cc_start: 0.9005 (tp) cc_final: 0.8702 (tp) REVERT: A 259 GLU cc_start: 0.7716 (tm-30) cc_final: 0.7036 (tm-30) REVERT: A 260 ILE cc_start: 0.8786 (mt) cc_final: 0.8530 (mt) REVERT: A 263 ASN cc_start: 0.8257 (t0) cc_final: 0.7676 (t0) REVERT: A 303 GLU cc_start: 0.8028 (mp0) cc_final: 0.7790 (mp0) REVERT: A 350 LEU cc_start: 0.8545 (tp) cc_final: 0.8208 (tt) REVERT: A 358 VAL cc_start: 0.8847 (t) cc_final: 0.8582 (p) REVERT: A 385 PHE cc_start: 0.9017 (OUTLIER) cc_final: 0.8722 (t80) REVERT: A 404 THR cc_start: 0.7436 (OUTLIER) cc_final: 0.6908 (p) REVERT: A 409 ARG cc_start: 0.8344 (mtm180) cc_final: 0.7956 (mtm110) REVERT: A 414 GLU cc_start: 0.7568 (tm-30) cc_final: 0.6953 (tm-30) REVERT: A 432 MET cc_start: 0.7556 (tmm) cc_final: 0.7221 (tmm) REVERT: A 463 MET cc_start: 0.7541 (tmm) cc_final: 0.7013 (tmm) REVERT: A 466 CYS cc_start: 0.8061 (t) cc_final: 0.7640 (t) REVERT: A 473 LYS cc_start: 0.8584 (mttp) cc_final: 0.8172 (ttmm) REVERT: A 476 LYS cc_start: 0.9181 (mtmm) cc_final: 0.8945 (mtmm) REVERT: A 540 GLU cc_start: 0.8417 (pm20) cc_final: 0.7764 (pm20) REVERT: A 573 ASP cc_start: 0.7914 (t0) cc_final: 0.7226 (p0) REVERT: A 580 LYS cc_start: 0.8192 (mmmt) cc_final: 0.7863 (mmmt) REVERT: A 583 LYS cc_start: 0.8506 (OUTLIER) cc_final: 0.7782 (tmmt) REVERT: B 66 LYS cc_start: 0.8437 (tptt) cc_final: 0.7903 (tppt) REVERT: B 77 LYS cc_start: 0.8451 (ttpt) cc_final: 0.8071 (ttpt) REVERT: B 90 SER cc_start: 0.8526 (t) cc_final: 0.8102 (p) REVERT: B 150 SER cc_start: 0.8373 (t) cc_final: 0.8061 (p) REVERT: B 210 PHE cc_start: 0.6674 (p90) cc_final: 0.6342 (p90) REVERT: B 230 GLN cc_start: 0.8481 (tm-30) cc_final: 0.8127 (tm-30) REVERT: B 235 GLN cc_start: 0.8224 (mm-40) cc_final: 0.7892 (mm110) REVERT: B 236 LEU cc_start: 0.8990 (tp) cc_final: 0.8771 (tp) REVERT: B 237 LYS cc_start: 0.8753 (pttt) cc_final: 0.8388 (ttpp) REVERT: B 255 TYR cc_start: 0.7981 (m-10) cc_final: 0.7689 (m-10) REVERT: B 260 ILE cc_start: 0.8786 (mt) cc_final: 0.8487 (mt) REVERT: B 394 PHE cc_start: 0.8176 (t80) cc_final: 0.7902 (t80) REVERT: B 398 PHE cc_start: 0.7001 (m-80) cc_final: 0.6561 (m-10) REVERT: B 400 CYS cc_start: 0.7448 (m) cc_final: 0.7198 (m) REVERT: B 404 THR cc_start: 0.7563 (OUTLIER) cc_final: 0.7154 (p) REVERT: B 414 GLU cc_start: 0.7656 (tm-30) cc_final: 0.7087 (tp30) REVERT: B 458 LEU cc_start: 0.8764 (OUTLIER) cc_final: 0.8528 (mt) REVERT: B 466 CYS cc_start: 0.8107 (t) cc_final: 0.7692 (t) REVERT: B 473 LYS cc_start: 0.8387 (mttp) cc_final: 0.8129 (mtpp) REVERT: B 486 CYS cc_start: 0.8725 (t) cc_final: 0.8460 (t) REVERT: B 488 MET cc_start: 0.7453 (tpp) cc_final: 0.7124 (tpp) REVERT: B 513 VAL cc_start: 0.9248 (OUTLIER) cc_final: 0.9027 (p) REVERT: B 546 LYS cc_start: 0.7954 (mmtt) cc_final: 0.7699 (mmmm) REVERT: B 549 ARG cc_start: 0.7627 (ttm-80) cc_final: 0.7217 (ttt-90) REVERT: B 556 TYR cc_start: 0.8994 (p90) cc_final: 0.8740 (p90) REVERT: B 578 TYR cc_start: 0.7718 (t80) cc_final: 0.7277 (t80) REVERT: B 580 LYS cc_start: 0.7981 (mmmm) cc_final: 0.7752 (mmmm) REVERT: B 583 LYS cc_start: 0.8452 (OUTLIER) cc_final: 0.7921 (tmmt) REVERT: B 681 LYS cc_start: 0.8434 (mptt) cc_final: 0.8211 (mptt) REVERT: B 705 GLN cc_start: 0.8657 (tt0) cc_final: 0.8325 (tt0) REVERT: B 714 ARG cc_start: 0.7423 (mtm-85) cc_final: 0.7064 (mtm-85) outliers start: 48 outliers final: 33 residues processed: 339 average time/residue: 0.2946 time to fit residues: 134.1645 Evaluate side-chains 345 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 302 time to evaluate : 1.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLN Chi-restraints excluded: chain A residue 43 ARG Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 182 ASP Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 427 SER Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 523 SER 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 30 LEU Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 336 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 405 THR Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 461 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 713 ILE Chi-restraints excluded: chain B residue 716 ASP Chi-restraints excluded: chain B residue 727 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 57 optimal weight: 3.9990 chunk 85 optimal weight: 0.9980 chunk 86 optimal weight: 0.5980 chunk 35 optimal weight: 0.8980 chunk 131 optimal weight: 0.6980 chunk 89 optimal weight: 0.7980 chunk 99 optimal weight: 0.4980 chunk 53 optimal weight: 0.5980 chunk 111 optimal weight: 0.0370 chunk 36 optimal weight: 0.6980 chunk 100 optimal weight: 0.7980 overall best weight: 0.4858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN A 246 ASN ** B 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 382 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 = 0.3676 r_free = 0.3676 target = 0.114871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.097557 restraints weight = 21266.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.100591 restraints weight = 10526.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.102689 restraints weight = 6272.664| |-----------------------------------------------------------------------------| r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.5949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.216 10390 Z= 0.399 Angle : 1.008 59.198 14120 Z= 0.563 Chirality : 0.051 0.857 1714 Planarity : 0.005 0.057 1756 Dihedral : 5.442 44.871 1436 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 17.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 4.54 % Allowed : 26.87 % Favored : 68.59 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.23), residues: 1316 helix: 0.29 (0.18), residues: 838 sheet: 1.95 (1.16), residues: 20 loop : -2.65 (0.28), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 83 HIS 0.004 0.001 HIS A 728 PHE 0.023 0.001 PHE A 128 TYR 0.020 0.002 TYR B 323 ARG 0.007 0.000 ARG B 134 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3605.21 seconds wall clock time: 65 minutes 37.73 seconds (3937.73 seconds total)