Starting phenix.real_space_refine on Mon Jun 9 03:17:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wle_32583/06_2025/7wle_32583.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wle_32583/06_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_32583/06_2025/7wle_32583.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wle_32583/06_2025/7wle_32583.map" model { file = "/net/cci-nas-00/data/ceres_data/7wle_32583/06_2025/7wle_32583.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wle_32583/06_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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 7.56, per 1000 atoms: 0.74 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: 3.00 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: 1.16 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: 2.76 Time building geometry restraints manager: 3.49 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: 0.010 Normalize map: mean=0, sd=1: 3.320 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: 0.680 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 29.010 Find NCS groups from input model: 0.340 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:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 10390 Z= 0.207 Angle : 0.499 9.614 14120 Z= 0.305 Chirality : 0.038 0.275 1714 Planarity : 0.004 0.039 1756 Dihedral : 9.906 85.978 3718 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 5.25 % Allowed : 6.41 % Favored : 88.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 Details of bonding type rmsd hydrogen bonds : bond 0.13515 ( 576) hydrogen bonds : angle 5.32232 ( 1683) covalent geometry : bond 0.00312 (10390) covalent geometry : angle 0.49894 (14120) *********************** 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 : 1.063 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: 0.2696 time to fit residues: 159.4333 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 : 1.054 ------------------------------------------------------------------------------- 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 = 0.131361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.114242 restraints weight = 20942.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.117579 restraints weight = 10525.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.119790 restraints weight = 6287.868| |-----------------------------------------------------------------------------| r_work (final): 0.3638 ------------------------------------------------------------------------------- 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= 0.190 Angle : 0.663 8.048 14120 Z= 0.346 Chirality : 0.043 0.262 1714 Planarity : 0.004 0.033 1756 Dihedral : 6.863 101.159 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 Details of bonding type rmsd hydrogen bonds : bond 0.03806 ( 576) hydrogen bonds : angle 3.99899 ( 1683) covalent geometry : bond 0.00413 (10390) covalent geometry : angle 0.66322 (14120) *********************** 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 : 1.084 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 ARG cc_start: 0.7242 (mtm-85) cc_final: 0.6847 (mtt90) REVERT: A 37 GLU cc_start: 0.8088 (OUTLIER) cc_final: 0.6850 (pm20) REVERT: A 77 LYS cc_start: 0.8036 (ttpt) cc_final: 0.7610 (ttpt) REVERT: A 90 SER cc_start: 0.8470 (t) cc_final: 0.8024 (p) REVERT: A 94 THR cc_start: 0.8413 (t) cc_final: 0.8145 (p) REVERT: A 118 TYR cc_start: 0.7075 (m-10) cc_final: 0.6835 (m-10) REVERT: A 128 PHE cc_start: 0.8578 (t80) cc_final: 0.8333 (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: 0.7402 (tm-30) REVERT: A 230 GLN cc_start: 0.8098 (tp40) cc_final: 0.7886 (tm-30) REVERT: A 259 GLU cc_start: 0.7672 (OUTLIER) cc_final: 0.7203 (tm-30) REVERT: A 260 ILE cc_start: 0.8570 (mt) cc_final: 0.7953 (mt) REVERT: A 263 ASN cc_start: 0.8346 (t0) cc_final: 0.7676 (t0) REVERT: A 350 LEU cc_start: 0.8598 (tp) cc_final: 0.8238 (tt) REVERT: A 385 PHE cc_start: 0.8692 (OUTLIER) cc_final: 0.8420 (t80) REVERT: A 432 MET cc_start: 0.7372 (tmm) cc_final: 0.7032 (tmm) REVERT: A 466 CYS cc_start: 0.7744 (t) cc_final: 0.7361 (t) REVERT: A 473 LYS cc_start: 0.8418 (mttp) cc_final: 0.8164 (mttp) REVERT: A 530 TYR cc_start: 0.8394 (m-80) cc_final: 0.8032 (m-80) REVERT: A 580 LYS cc_start: 0.8169 (mmmt) cc_final: 0.7912 (tttt) REVERT: A 583 LYS cc_start: 0.8578 (OUTLIER) cc_final: 0.8020 (tmmt) REVERT: A 714 ARG cc_start: 0.7254 (mpt180) cc_final: 0.6710 (mtm-85) REVERT: B 80 VAL cc_start: 0.9380 (OUTLIER) cc_final: 0.8857 (t) REVERT: B 90 SER cc_start: 0.8753 (t) cc_final: 0.8219 (p) REVERT: B 94 THR cc_start: 0.8675 (t) cc_final: 0.8271 (p) REVERT: B 132 THR cc_start: 0.7183 (OUTLIER) cc_final: 0.6506 (t) REVERT: B 150 SER cc_start: 0.8363 (t) cc_final: 0.8093 (p) REVERT: B 195 LEU cc_start: 0.8795 (tp) cc_final: 0.8583 (tp) REVERT: B 230 GLN cc_start: 0.8255 (tm-30) cc_final: 0.7950 (tm-30) REVERT: B 237 LYS cc_start: 0.8546 (pttt) cc_final: 0.8114 (ptpt) REVERT: B 239 VAL cc_start: 0.8480 (OUTLIER) cc_final: 0.8263 (p) REVERT: B 250 ILE cc_start: 0.8586 (pt) cc_final: 0.8313 (mm) REVERT: B 259 GLU cc_start: 0.7542 (OUTLIER) cc_final: 0.6788 (tm-30) REVERT: B 384 GLU cc_start: 0.7579 (mm-30) cc_final: 0.7220 (tp30) REVERT: B 394 PHE cc_start: 0.8254 (t80) cc_final: 0.7962 (t80) REVERT: B 400 CYS cc_start: 0.7576 (m) cc_final: 0.7358 (m) REVERT: B 426 ILE cc_start: 0.8087 (tt) cc_final: 0.7849 (tp) REVERT: B 431 VAL cc_start: 0.8953 (t) cc_final: 0.8728 (p) REVERT: B 432 MET cc_start: 0.7292 (tmm) cc_final: 0.7088 (tmm) REVERT: B 463 MET cc_start: 0.7495 (tmm) cc_final: 0.7171 (tmm) REVERT: B 466 CYS cc_start: 0.8016 (t) cc_final: 0.7525 (t) REVERT: B 470 ARG cc_start: 0.6650 (mtp180) cc_final: 0.6376 (mtp180) REVERT: B 473 LYS cc_start: 0.8406 (mttp) cc_final: 0.8149 (mtpp) REVERT: B 486 CYS cc_start: 0.8739 (t) cc_final: 0.8495 (t) REVERT: B 488 MET cc_start: 0.7445 (tpp) cc_final: 0.6992 (tpp) REVERT: B 513 VAL cc_start: 0.9129 (OUTLIER) cc_final: 0.8900 (p) REVERT: B 531 LYS cc_start: 0.8618 (mmtm) cc_final: 0.8290 (mmmm) REVERT: B 537 LYS cc_start: 0.8279 (mmmm) cc_final: 0.7205 (ttpp) REVERT: B 556 TYR cc_start: 0.8990 (p90) cc_final: 0.8721 (p90) REVERT: B 578 TYR cc_start: 0.7732 (t80) cc_final: 0.7084 (t80) REVERT: B 581 ARG cc_start: 0.8264 (tpp-160) cc_final: 0.7836 (tpp-160) REVERT: B 583 LYS cc_start: 0.8354 (OUTLIER) cc_final: 0.7834 (tmmt) REVERT: B 681 LYS cc_start: 0.8388 (mptt) cc_final: 0.8060 (mptt) REVERT: B 715 LYS cc_start: 0.8714 (ptpt) cc_final: 0.8440 (ptpp) outliers start: 59 outliers final: 23 residues processed: 361 average time/residue: 0.2474 time to fit residues: 120.4433 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 : 1.153 ------------------------------------------------------------------------------- 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: 0.8980 chunk 1 optimal weight: 0.9990 chunk 102 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 75 optimal weight: 0.5980 chunk 93 optimal weight: 7.9990 chunk 2 optimal weight: 2.9990 chunk 15 optimal weight: 9.9990 chunk 115 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 289 ASN A 457 ASN B 35 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.127517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.110422 restraints weight = 21250.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.113740 restraints weight = 10565.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.115767 restraints weight = 6233.421| |-----------------------------------------------------------------------------| r_work (final): 0.3555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.4218 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= 0.203 Angle : 0.663 8.257 14120 Z= 0.347 Chirality : 0.043 0.171 1714 Planarity : 0.004 0.039 1756 Dihedral : 6.788 95.744 1452 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 12.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 5.96 % Allowed : 17.62 % Favored : 76.42 % 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: -1.62 (0.23), residues: 1316 helix: -0.03 (0.18), residues: 820 sheet: 0.79 (1.01), residues: 20 loop : -3.06 (0.26), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 83 HIS 0.005 0.001 HIS B 728 PHE 0.023 0.002 PHE A 130 TYR 0.017 0.002 TYR B 323 ARG 0.006 0.001 ARG B 134 Details of bonding type rmsd hydrogen bonds : bond 0.03795 ( 576) hydrogen bonds : angle 3.98256 ( 1683) covalent geometry : bond 0.00441 (10390) covalent geometry : angle 0.66315 (14120) *********************** 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 389 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 322 time to evaluate : 1.338 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 36 ARG cc_start: 0.7600 (mtm-85) cc_final: 0.7237 (mtt90) REVERT: A 77 LYS cc_start: 0.8108 (ttpt) cc_final: 0.7695 (ttpt) REVERT: A 90 SER cc_start: 0.8515 (t) cc_final: 0.7953 (p) REVERT: A 94 THR cc_start: 0.8460 (t) cc_final: 0.8149 (p) REVERT: A 195 LEU cc_start: 0.8956 (OUTLIER) cc_final: 0.8640 (tp) REVERT: A 207 GLN cc_start: 0.7896 (tm-30) cc_final: 0.7575 (tm-30) REVERT: A 230 GLN cc_start: 0.8269 (tp40) cc_final: 0.7927 (tm-30) REVERT: A 237 LYS cc_start: 0.8683 (pttt) cc_final: 0.8366 (ptmm) REVERT: A 238 ILE cc_start: 0.8814 (tp) cc_final: 0.8552 (tp) REVERT: A 259 GLU cc_start: 0.7812 (OUTLIER) cc_final: 0.7221 (tm-30) REVERT: A 260 ILE cc_start: 0.8625 (mt) cc_final: 0.7939 (mt) REVERT: A 350 LEU cc_start: 0.8581 (tp) cc_final: 0.8212 (tt) REVERT: A 369 LYS cc_start: 0.8646 (mmmm) cc_final: 0.8354 (mmmm) REVERT: A 385 PHE cc_start: 0.8855 (OUTLIER) cc_final: 0.8603 (t80) REVERT: A 414 GLU cc_start: 0.7489 (tm-30) cc_final: 0.7155 (tp30) REVERT: A 425 LEU cc_start: 0.8562 (tp) cc_final: 0.8256 (tt) REVERT: A 432 MET cc_start: 0.7539 (tmm) cc_final: 0.7164 (tmm) REVERT: A 463 MET cc_start: 0.7594 (tmm) cc_final: 0.7104 (tmm) REVERT: A 466 CYS cc_start: 0.7944 (t) cc_final: 0.7325 (t) REVERT: A 473 LYS cc_start: 0.8487 (mttp) cc_final: 0.8115 (ttmm) REVERT: A 573 ASP cc_start: 0.7703 (t0) cc_final: 0.6973 (p0) REVERT: A 580 LYS cc_start: 0.8215 (mmmt) cc_final: 0.7871 (mmmt) REVERT: A 583 LYS cc_start: 0.8468 (OUTLIER) cc_final: 0.7771 (tmmt) REVERT: B 27 TYR cc_start: 0.7131 (m-10) cc_final: 0.6867 (m-10) REVERT: B 66 LYS cc_start: 0.8479 (tptt) cc_final: 0.8092 (tppt) REVERT: B 77 LYS cc_start: 0.8405 (ttpt) cc_final: 0.8032 (ttpt) REVERT: B 80 VAL cc_start: 0.9350 (OUTLIER) cc_final: 0.9072 (t) REVERT: B 90 SER cc_start: 0.8672 (t) cc_final: 0.8200 (p) REVERT: B 127 TYR cc_start: 0.8592 (t80) cc_final: 0.8357 (t80) REVERT: B 134 ARG cc_start: 0.7275 (mtm-85) cc_final: 0.7046 (mtm-85) REVERT: B 150 SER cc_start: 0.8370 (t) cc_final: 0.8106 (p) REVERT: B 230 GLN cc_start: 0.8351 (tm-30) cc_final: 0.7867 (tm-30) REVERT: B 237 LYS cc_start: 0.8615 (pttt) cc_final: 0.8340 (ttpp) REVERT: B 250 ILE cc_start: 0.8691 (pt) cc_final: 0.8407 (mm) REVERT: B 259 GLU cc_start: 0.7580 (OUTLIER) cc_final: 0.6841 (tm-30) REVERT: B 260 ILE cc_start: 0.8711 (mt) cc_final: 0.8212 (mt) REVERT: B 287 GLU cc_start: 0.8088 (tp30) cc_final: 0.7562 (tm-30) REVERT: B 349 MET cc_start: 0.6072 (mmm) cc_final: 0.5786 (mmm) REVERT: B 354 PHE cc_start: 0.7286 (OUTLIER) cc_final: 0.7052 (t80) REVERT: B 384 GLU cc_start: 0.7652 (mm-30) cc_final: 0.7414 (mm-30) REVERT: B 394 PHE cc_start: 0.8257 (t80) cc_final: 0.7737 (t80) REVERT: B 400 CYS cc_start: 0.7417 (m) cc_final: 0.7096 (m) REVERT: B 414 GLU cc_start: 0.7575 (tm-30) cc_final: 0.7030 (tp30) REVERT: B 432 MET cc_start: 0.7502 (tmm) cc_final: 0.7246 (tmm) REVERT: B 463 MET cc_start: 0.7487 (tmm) cc_final: 0.7282 (tmm) REVERT: B 466 CYS cc_start: 0.8107 (t) cc_final: 0.7716 (t) REVERT: B 470 ARG cc_start: 0.6668 (mtp180) cc_final: 0.6393 (mtp180) REVERT: B 473 LYS cc_start: 0.8466 (mttp) cc_final: 0.8193 (mtpp) REVERT: B 486 CYS cc_start: 0.8761 (t) cc_final: 0.8501 (t) REVERT: B 488 MET cc_start: 0.7501 (tpp) cc_final: 0.7138 (tpp) REVERT: B 513 VAL cc_start: 0.9152 (OUTLIER) cc_final: 0.8911 (p) REVERT: B 531 LYS cc_start: 0.8639 (mmtm) cc_final: 0.8295 (mmmm) REVERT: B 556 TYR cc_start: 0.9000 (p90) cc_final: 0.8661 (p90) REVERT: B 578 TYR cc_start: 0.7782 (t80) cc_final: 0.7192 (t80) REVERT: B 581 ARG cc_start: 0.8217 (tpp-160) cc_final: 0.7863 (tpp-160) REVERT: B 583 LYS cc_start: 0.8476 (OUTLIER) cc_final: 0.7943 (tmmt) REVERT: B 705 GLN cc_start: 0.8672 (tt0) cc_final: 0.8376 (tt0) REVERT: B 714 ARG cc_start: 0.7441 (mtm-85) cc_final: 0.7117 (mtm-85) REVERT: B 715 LYS cc_start: 0.8533 (ptpt) cc_final: 0.8243 (ptpp) outliers start: 67 outliers final: 30 residues processed: 360 average time/residue: 0.2697 time to fit residues: 129.9938 Evaluate side-chains 335 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 296 time to evaluate : 1.202 ------------------------------------------------------------------------------- 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 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 458 LEU Chi-restraints excluded: chain A residue 564 LYS Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 583 LYS Chi-restraints excluded: chain A residue 682 GLU Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 715 LYS Chi-restraints excluded: chain A residue 716 ASP Chi-restraints excluded: chain B residue 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 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 713 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 105 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 1 optimal weight: 0.5980 chunk 125 optimal weight: 0.7980 chunk 10 optimal weight: 0.5980 chunk 60 optimal weight: 0.9980 chunk 11 optimal weight: 3.9990 chunk 90 optimal weight: 0.0970 chunk 83 optimal weight: 1.9990 chunk 70 optimal weight: 5.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN A 457 ASN B 35 GLN B 567 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.125833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.108752 restraints weight = 21072.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.112043 restraints weight = 10418.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.114095 restraints weight = 6128.303| |-----------------------------------------------------------------------------| r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.4625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 10390 Z= 0.164 Angle : 0.654 10.649 14120 Z= 0.336 Chirality : 0.043 0.222 1714 Planarity : 0.004 0.041 1756 Dihedral : 6.653 95.998 1447 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 12.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 5.60 % Allowed : 20.73 % Favored : 73.67 % 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: -1.28 (0.23), residues: 1316 helix: 0.20 (0.18), residues: 810 sheet: 1.21 (1.00), residues: 20 loop : -2.80 (0.26), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 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 181 Details of bonding type rmsd hydrogen bonds : bond 0.03594 ( 576) hydrogen bonds : angle 3.90763 ( 1683) covalent geometry : bond 0.00368 (10390) covalent geometry : angle 0.65421 (14120) *********************** 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 380 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 317 time to evaluate : 1.176 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: 0.7606 (mtm-85) cc_final: 0.7301 (mtt90) REVERT: A 66 LYS cc_start: 0.8483 (tptp) cc_final: 0.8130 (tppt) REVERT: A 77 LYS cc_start: 0.8057 (ttpt) cc_final: 0.7632 (ttpt) REVERT: A 90 SER cc_start: 0.8474 (t) cc_final: 0.7892 (p) REVERT: A 94 THR cc_start: 0.8448 (t) cc_final: 0.8037 (p) REVERT: A 153 LEU cc_start: 0.8915 (mt) cc_final: 0.8706 (mm) REVERT: A 195 LEU cc_start: 0.8920 (OUTLIER) cc_final: 0.8583 (tp) REVERT: A 230 GLN cc_start: 0.8192 (tp40) cc_final: 0.7896 (tm-30) REVERT: A 237 LYS cc_start: 0.8739 (pttt) cc_final: 0.8444 (ttpp) REVERT: A 238 ILE cc_start: 0.8854 (tp) cc_final: 0.8601 (tp) REVERT: A 255 TYR cc_start: 0.7650 (m-10) cc_final: 0.7351 (m-10) REVERT: A 259 GLU cc_start: 0.7784 (OUTLIER) cc_final: 0.7225 (tm-30) REVERT: A 260 ILE cc_start: 0.8649 (mt) cc_final: 0.8031 (mt) REVERT: A 350 LEU cc_start: 0.8563 (tp) cc_final: 0.8183 (tt) REVERT: A 385 PHE cc_start: 0.8866 (OUTLIER) cc_final: 0.8612 (t80) REVERT: A 404 THR cc_start: 0.7364 (OUTLIER) cc_final: 0.6952 (t) REVERT: A 414 GLU cc_start: 0.7463 (tm-30) cc_final: 0.7136 (tp30) REVERT: A 425 LEU cc_start: 0.8543 (tp) cc_final: 0.8236 (tt) REVERT: A 432 MET cc_start: 0.7542 (tmm) cc_final: 0.7131 (tmm) REVERT: A 463 MET cc_start: 0.7610 (tmm) cc_final: 0.7108 (tmm) REVERT: A 466 CYS cc_start: 0.7945 (t) cc_final: 0.7460 (t) REVERT: A 473 LYS cc_start: 0.8489 (mttp) cc_final: 0.8022 (mtpp) REVERT: A 564 LYS cc_start: 0.8457 (OUTLIER) cc_final: 0.8204 (ttmm) REVERT: A 580 LYS cc_start: 0.8205 (mmmt) cc_final: 0.7970 (mmmm) REVERT: A 583 LYS cc_start: 0.8443 (OUTLIER) cc_final: 0.7873 (tmmt) REVERT: A 714 ARG cc_start: 0.7405 (mpt180) cc_final: 0.7203 (mpt180) REVERT: B 77 LYS cc_start: 0.8384 (ttpt) cc_final: 0.8005 (ttpt) REVERT: B 90 SER cc_start: 0.8633 (t) cc_final: 0.8190 (p) REVERT: B 125 LEU cc_start: 0.8976 (tp) cc_final: 0.8616 (tp) REVERT: B 127 TYR cc_start: 0.8623 (t80) cc_final: 0.8405 (t80) REVERT: B 150 SER cc_start: 0.8380 (t) cc_final: 0.8110 (p) REVERT: B 182 ASP cc_start: 0.7433 (OUTLIER) cc_final: 0.7219 (p0) REVERT: B 213 ARG cc_start: 0.8214 (mtp180) cc_final: 0.7938 (mtp180) REVERT: B 230 GLN cc_start: 0.8387 (tm-30) cc_final: 0.7578 (tm-30) REVERT: B 237 LYS cc_start: 0.8615 (pttt) cc_final: 0.8222 (ptmm) REVERT: B 238 ILE cc_start: 0.8878 (tp) cc_final: 0.8427 (pt) REVERT: B 250 ILE cc_start: 0.8677 (pt) cc_final: 0.8380 (mm) REVERT: B 255 TYR cc_start: 0.7898 (m-10) cc_final: 0.7400 (m-10) REVERT: B 260 ILE cc_start: 0.8783 (mt) cc_final: 0.8456 (mt) REVERT: B 354 PHE cc_start: 0.7262 (OUTLIER) cc_final: 0.7026 (t80) REVERT: B 369 LYS cc_start: 0.8580 (mmtp) cc_final: 0.8328 (mmmm) REVERT: B 384 GLU cc_start: 0.7650 (mm-30) cc_final: 0.7393 (mm-30) REVERT: B 394 PHE cc_start: 0.8262 (t80) cc_final: 0.7911 (t80) REVERT: B 400 CYS cc_start: 0.7269 (m) cc_final: 0.6934 (m) REVERT: B 414 GLU cc_start: 0.7548 (tm-30) cc_final: 0.7021 (tp30) REVERT: B 432 MET cc_start: 0.7457 (tmm) cc_final: 0.7162 (tmm) REVERT: B 447 LYS cc_start: 0.8746 (ttmt) cc_final: 0.8534 (ttmm) REVERT: B 463 MET cc_start: 0.7501 (tmm) cc_final: 0.7281 (tmm) REVERT: B 466 CYS cc_start: 0.8138 (t) cc_final: 0.7706 (t) REVERT: B 470 ARG cc_start: 0.6713 (mtp180) cc_final: 0.6434 (mtp180) REVERT: B 473 LYS cc_start: 0.8466 (mttp) cc_final: 0.8192 (ttmm) REVERT: B 486 CYS cc_start: 0.8757 (t) cc_final: 0.8495 (t) REVERT: B 488 MET cc_start: 0.7515 (tpp) cc_final: 0.7146 (tpp) REVERT: B 513 VAL cc_start: 0.9158 (OUTLIER) cc_final: 0.8929 (p) REVERT: B 556 TYR cc_start: 0.8995 (p90) cc_final: 0.8604 (p90) REVERT: B 578 TYR cc_start: 0.7817 (t80) cc_final: 0.7270 (t80) REVERT: B 581 ARG cc_start: 0.8183 (tpp-160) cc_final: 0.7861 (tpp-160) REVERT: B 583 LYS cc_start: 0.8464 (OUTLIER) cc_final: 0.7918 (tmmt) REVERT: B 681 LYS cc_start: 0.8384 (mptt) cc_final: 0.8027 (mptt) REVERT: B 705 GLN cc_start: 0.8667 (tt0) cc_final: 0.8365 (tt0) REVERT: B 714 ARG cc_start: 0.7421 (mtm-85) cc_final: 0.7167 (mtm-85) outliers start: 63 outliers final: 37 residues processed: 358 average time/residue: 0.2589 time to fit residues: 123.8109 Evaluate side-chains 355 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 308 time to evaluate : 1.210 ------------------------------------------------------------------------------- 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 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 73 ASP Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 182 ASP Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 259 GLU Chi-restraints excluded: chain B residue 283 MET Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 354 PHE Chi-restraints excluded: chain B residue 383 GLN Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 405 THR Chi-restraints excluded: chain B residue 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 713 ILE Chi-restraints excluded: chain B residue 715 LYS Chi-restraints excluded: chain B residue 716 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 15 optimal weight: 9.9990 chunk 109 optimal weight: 1.9990 chunk 69 optimal weight: 30.0000 chunk 66 optimal weight: 0.9980 chunk 120 optimal weight: 0.6980 chunk 22 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 37 optimal weight: 0.9980 chunk 112 optimal weight: 0.8980 chunk 72 optimal weight: 1.9990 chunk 110 optimal weight: 0.5980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 GLN A 289 ASN ** A 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 457 ASN A 535 HIS B 35 GLN B 382 ASN B 457 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.116282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.099268 restraints weight = 21026.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.102335 restraints weight = 10412.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.104425 restraints weight = 6195.713| |-----------------------------------------------------------------------------| r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.5038 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= 0.201 Angle : 0.682 8.204 14120 Z= 0.352 Chirality : 0.044 0.202 1714 Planarity : 0.004 0.046 1756 Dihedral : 6.658 97.196 1444 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer: Outliers : 5.52 % Allowed : 22.33 % Favored : 72.15 % 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: -1.14 (0.23), residues: 1316 helix: 0.30 (0.18), residues: 810 sheet: 1.46 (1.00), residues: 20 loop : -2.73 (0.27), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 83 HIS 0.005 0.001 HIS B 728 PHE 0.028 0.002 PHE B 128 TYR 0.027 0.002 TYR B 323 ARG 0.005 0.000 ARG B 134 Details of bonding type rmsd hydrogen bonds : bond 0.03719 ( 576) hydrogen bonds : angle 3.99993 ( 1683) covalent geometry : bond 0.00442 (10390) covalent geometry : angle 0.68234 (14120) *********************** 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 394 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 332 time to evaluate : 1.059 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 ARG cc_start: 0.7709 (mtm-85) cc_final: 0.7350 (ttm110) REVERT: A 90 SER cc_start: 0.8627 (t) cc_final: 0.7963 (p) REVERT: A 94 THR cc_start: 0.8542 (t) cc_final: 0.8192 (p) REVERT: A 195 LEU cc_start: 0.8981 (OUTLIER) cc_final: 0.8539 (tm) REVERT: A 230 GLN cc_start: 0.8224 (tp40) cc_final: 0.7913 (tm-30) REVERT: A 237 LYS cc_start: 0.8765 (pttt) cc_final: 0.8409 (ttpp) REVERT: A 238 ILE cc_start: 0.8937 (tp) cc_final: 0.8690 (tp) REVERT: A 251 LEU cc_start: 0.8781 (mm) cc_final: 0.8429 (mm) REVERT: A 255 TYR cc_start: 0.7647 (m-10) cc_final: 0.7437 (m-10) REVERT: A 259 GLU cc_start: 0.7698 (tm-30) cc_final: 0.7136 (tm-30) REVERT: A 260 ILE cc_start: 0.8705 (mt) cc_final: 0.8133 (mt) REVERT: A 263 ASN cc_start: 0.8221 (t0) cc_final: 0.7617 (t0) REVERT: A 350 LEU cc_start: 0.8520 (tp) cc_final: 0.8177 (tt) REVERT: A 358 VAL cc_start: 0.8883 (t) cc_final: 0.8646 (p) REVERT: A 377 TYR cc_start: 0.6315 (t80) cc_final: 0.6012 (t80) REVERT: A 385 PHE cc_start: 0.8937 (OUTLIER) cc_final: 0.8653 (t80) REVERT: A 392 ASN cc_start: 0.7731 (t0) cc_final: 0.7326 (t0) REVERT: A 404 THR cc_start: 0.7403 (OUTLIER) cc_final: 0.6942 (t) REVERT: A 414 GLU cc_start: 0.7571 (tm-30) cc_final: 0.7272 (tp30) REVERT: A 432 MET cc_start: 0.7548 (tmm) cc_final: 0.7174 (tmm) REVERT: A 463 MET cc_start: 0.7601 (tmm) cc_final: 0.7149 (tmm) REVERT: A 466 CYS cc_start: 0.8007 (t) cc_final: 0.7578 (t) REVERT: A 473 LYS cc_start: 0.8537 (mttp) cc_final: 0.8113 (ttmm) REVERT: A 577 VAL cc_start: 0.8679 (OUTLIER) cc_final: 0.8470 (p) REVERT: A 580 LYS cc_start: 0.8203 (mmmt) cc_final: 0.7864 (mmmt) REVERT: A 583 LYS cc_start: 0.8480 (OUTLIER) cc_final: 0.7793 (tmmt) REVERT: A 702 LYS cc_start: 0.7978 (ttmm) cc_final: 0.7773 (ttmm) REVERT: B 38 ARG cc_start: 0.8206 (mtp85) cc_final: 0.7945 (mtp-110) REVERT: B 66 LYS cc_start: 0.8423 (tptt) cc_final: 0.8070 (tppt) REVERT: B 77 LYS cc_start: 0.8398 (ttpt) cc_final: 0.8021 (ttpt) REVERT: B 90 SER cc_start: 0.8622 (t) cc_final: 0.8176 (p) REVERT: B 125 LEU cc_start: 0.8996 (tp) cc_final: 0.8791 (tp) REVERT: B 150 SER cc_start: 0.8328 (t) cc_final: 0.8097 (p) REVERT: B 230 GLN cc_start: 0.8424 (tm-30) cc_final: 0.8051 (tm-30) REVERT: B 237 LYS cc_start: 0.8628 (pttt) cc_final: 0.8324 (ttpp) REVERT: B 250 ILE cc_start: 0.8713 (pt) cc_final: 0.8449 (mm) REVERT: B 255 TYR cc_start: 0.7885 (m-10) cc_final: 0.7549 (m-10) REVERT: B 260 ILE cc_start: 0.8806 (mt) cc_final: 0.8498 (mt) REVERT: B 384 GLU cc_start: 0.7683 (mm-30) cc_final: 0.7453 (mm-30) REVERT: B 398 PHE cc_start: 0.6940 (m-80) cc_final: 0.6691 (m-10) REVERT: B 400 CYS cc_start: 0.7247 (m) cc_final: 0.6987 (m) REVERT: B 414 GLU cc_start: 0.7621 (tm-30) cc_final: 0.7096 (tp30) REVERT: B 432 MET cc_start: 0.7492 (tmm) cc_final: 0.7292 (tmm) REVERT: B 458 LEU cc_start: 0.8801 (OUTLIER) cc_final: 0.8583 (mt) REVERT: B 466 CYS cc_start: 0.8144 (t) cc_final: 0.7753 (t) REVERT: B 470 ARG cc_start: 0.6774 (mtp180) cc_final: 0.6488 (mtp180) REVERT: B 473 LYS cc_start: 0.8494 (mttp) cc_final: 0.8190 (mtpp) REVERT: B 486 CYS cc_start: 0.8722 (t) cc_final: 0.8472 (t) REVERT: B 488 MET cc_start: 0.7484 (tpp) cc_final: 0.7140 (tpp) REVERT: B 513 VAL cc_start: 0.9197 (OUTLIER) cc_final: 0.8970 (p) REVERT: B 531 LYS cc_start: 0.8654 (mmtm) cc_final: 0.8347 (mmmm) REVERT: B 556 TYR cc_start: 0.8995 (p90) cc_final: 0.8673 (p90) REVERT: B 578 TYR cc_start: 0.7777 (t80) cc_final: 0.7321 (t80) REVERT: B 583 LYS cc_start: 0.8520 (OUTLIER) cc_final: 0.7980 (tmmt) REVERT: B 681 LYS cc_start: 0.8395 (mptt) cc_final: 0.8036 (mptt) REVERT: B 687 ASP cc_start: 0.7390 (t0) cc_final: 0.6945 (t0) REVERT: B 705 GLN cc_start: 0.8702 (tt0) cc_final: 0.8383 (tt0) REVERT: B 714 ARG cc_start: 0.7450 (mtm-85) cc_final: 0.7184 (mtm-85) REVERT: B 715 LYS cc_start: 0.8286 (OUTLIER) cc_final: 0.7891 (ptpp) outliers start: 62 outliers final: 38 residues processed: 369 average time/residue: 0.2590 time to fit residues: 127.3574 Evaluate side-chains 372 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 325 time to evaluate : 1.142 ------------------------------------------------------------------------------- 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 129 VAL Chi-restraints excluded: chain A residue 144 VAL 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 385 PHE Chi-restraints excluded: chain A residue 404 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 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 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 113 VAL Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 329 LYS Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 382 ASN 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 449 VAL 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 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 713 ILE Chi-restraints excluded: chain B residue 715 LYS 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: 0.7980 chunk 43 optimal weight: 0.8980 chunk 84 optimal weight: 0.7980 chunk 31 optimal weight: 0.5980 chunk 14 optimal weight: 10.0000 chunk 78 optimal weight: 0.5980 chunk 83 optimal weight: 0.8980 chunk 85 optimal weight: 0.6980 chunk 117 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 chunk 82 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 457 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.116537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.099350 restraints weight = 21144.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.102467 restraints weight = 10446.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.104578 restraints weight = 6164.066| |-----------------------------------------------------------------------------| r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.5334 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= 0.182 Angle : 0.695 8.493 14120 Z= 0.360 Chirality : 0.044 0.226 1714 Planarity : 0.004 0.049 1756 Dihedral : 5.527 50.320 1437 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 14.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 5.78 % Allowed : 23.93 % Favored : 70.28 % 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: -1.04 (0.23), residues: 1316 helix: 0.38 (0.18), residues: 808 sheet: 1.26 (0.99), residues: 20 loop : -2.67 (0.27), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 83 HIS 0.004 0.001 HIS A 728 PHE 0.029 0.002 PHE B 128 TYR 0.023 0.002 TYR B 27 ARG 0.008 0.001 ARG B 134 Details of bonding type rmsd hydrogen bonds : bond 0.03717 ( 576) hydrogen bonds : angle 3.99734 ( 1683) covalent geometry : bond 0.00408 (10390) covalent geometry : angle 0.69454 (14120) *********************** 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 390 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 325 time to evaluate : 1.261 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 GLU cc_start: 0.6941 (mp0) cc_final: 0.6555 (mp0) REVERT: A 36 ARG cc_start: 0.7772 (mtm-85) cc_final: 0.7536 (ttm110) REVERT: A 90 SER cc_start: 0.8555 (t) cc_final: 0.7923 (p) REVERT: A 94 THR cc_start: 0.8584 (t) cc_final: 0.8206 (p) REVERT: A 195 LEU cc_start: 0.8976 (OUTLIER) cc_final: 0.8754 (tp) REVERT: A 230 GLN cc_start: 0.8204 (tp40) cc_final: 0.7909 (tm-30) REVERT: A 237 LYS cc_start: 0.8767 (pttt) cc_final: 0.8384 (ttpp) REVERT: A 238 ILE cc_start: 0.8973 (tp) cc_final: 0.8729 (tp) REVERT: A 251 LEU cc_start: 0.8764 (mm) cc_final: 0.8469 (mm) REVERT: A 259 GLU cc_start: 0.7718 (tm-30) cc_final: 0.7148 (tm-30) REVERT: A 260 ILE cc_start: 0.8717 (mt) cc_final: 0.8163 (mt) REVERT: A 350 LEU cc_start: 0.8534 (tp) cc_final: 0.8155 (tt) REVERT: A 358 VAL cc_start: 0.8891 (t) cc_final: 0.8655 (p) REVERT: A 385 PHE cc_start: 0.8949 (OUTLIER) cc_final: 0.8649 (t80) REVERT: A 404 THR cc_start: 0.7446 (OUTLIER) cc_final: 0.6887 (p) REVERT: A 409 ARG cc_start: 0.8322 (mtm180) cc_final: 0.7923 (mtm110) REVERT: A 414 GLU cc_start: 0.7567 (tm-30) cc_final: 0.6965 (tm-30) REVERT: A 425 LEU cc_start: 0.8526 (tp) cc_final: 0.8192 (tt) REVERT: A 432 MET cc_start: 0.7541 (tmm) cc_final: 0.7172 (tmm) REVERT: A 463 MET cc_start: 0.7543 (tmm) cc_final: 0.7096 (tmm) REVERT: A 466 CYS cc_start: 0.8029 (t) cc_final: 0.7569 (t) REVERT: A 473 LYS cc_start: 0.8510 (mttp) cc_final: 0.8153 (ttmm) REVERT: A 475 ASN cc_start: 0.8424 (t0) cc_final: 0.8161 (t0) REVERT: A 476 LYS cc_start: 0.9159 (mtmm) cc_final: 0.8839 (mtmm) REVERT: A 537 LYS cc_start: 0.8133 (ttmt) cc_final: 0.7777 (ttpp) REVERT: A 580 LYS cc_start: 0.8202 (mmmt) cc_final: 0.7857 (mmmt) REVERT: A 583 LYS cc_start: 0.8472 (OUTLIER) cc_final: 0.7777 (tmmt) REVERT: A 681 LYS cc_start: 0.8280 (mptt) cc_final: 0.8023 (mptt) REVERT: A 702 LYS cc_start: 0.7961 (ttmm) cc_final: 0.7751 (ttmm) REVERT: B 77 LYS cc_start: 0.8408 (ttpt) cc_final: 0.8050 (ttpt) REVERT: B 90 SER cc_start: 0.8593 (t) cc_final: 0.8088 (p) REVERT: B 150 SER cc_start: 0.8327 (t) cc_final: 0.8068 (p) REVERT: B 230 GLN cc_start: 0.8423 (tm-30) cc_final: 0.8072 (tm-30) REVERT: B 236 LEU cc_start: 0.9017 (tp) cc_final: 0.8751 (tp) REVERT: B 237 LYS cc_start: 0.8615 (pttt) cc_final: 0.8264 (ptmm) REVERT: B 250 ILE cc_start: 0.8701 (pt) cc_final: 0.8450 (mm) REVERT: B 255 TYR cc_start: 0.7918 (m-10) cc_final: 0.7579 (m-10) REVERT: B 260 ILE cc_start: 0.8797 (mt) cc_final: 0.8481 (mt) REVERT: B 384 GLU cc_start: 0.7751 (mm-30) cc_final: 0.7428 (mm-30) REVERT: B 398 PHE cc_start: 0.6952 (m-80) cc_final: 0.6609 (m-10) REVERT: B 400 CYS cc_start: 0.7266 (m) cc_final: 0.6994 (m) REVERT: B 447 LYS cc_start: 0.8778 (ttmt) cc_final: 0.8542 (ttmm) REVERT: B 466 CYS cc_start: 0.8134 (t) cc_final: 0.7789 (t) REVERT: B 467 ASP cc_start: 0.7174 (OUTLIER) cc_final: 0.6875 (t0) REVERT: B 473 LYS cc_start: 0.8453 (mttp) cc_final: 0.8213 (ttmm) REVERT: B 476 LYS cc_start: 0.9066 (OUTLIER) cc_final: 0.8685 (mtmm) REVERT: B 486 CYS cc_start: 0.8717 (t) cc_final: 0.8460 (t) REVERT: B 488 MET cc_start: 0.7471 (tpp) cc_final: 0.7116 (tpp) REVERT: B 513 VAL cc_start: 0.9204 (OUTLIER) cc_final: 0.8979 (p) REVERT: B 537 LYS cc_start: 0.8397 (tmtt) cc_final: 0.7988 (tptp) REVERT: B 549 ARG cc_start: 0.7525 (ttm-80) cc_final: 0.7178 (ttt-90) REVERT: B 556 TYR cc_start: 0.8998 (p90) cc_final: 0.8659 (p90) REVERT: B 578 TYR cc_start: 0.7765 (t80) cc_final: 0.7314 (t80) REVERT: B 583 LYS cc_start: 0.8515 (OUTLIER) cc_final: 0.7981 (tmmt) REVERT: B 705 GLN cc_start: 0.8654 (tt0) cc_final: 0.8389 (tt0) REVERT: B 724 ASP cc_start: 0.7782 (OUTLIER) cc_final: 0.7467 (t70) outliers start: 65 outliers final: 40 residues processed: 357 average time/residue: 0.2778 time to fit residues: 130.6616 Evaluate side-chains 368 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 319 time to evaluate : 1.087 ------------------------------------------------------------------------------- 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 111 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 276 LEU Chi-restraints excluded: chain A residue 346 PHE 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 441 LEU 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 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 329 LYS 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 441 LEU Chi-restraints excluded: chain B residue 461 MET Chi-restraints excluded: chain B residue 467 ASP Chi-restraints excluded: chain B residue 476 LYS 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 Chi-restraints excluded: chain B residue 727 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 66 optimal weight: 0.5980 chunk 83 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 chunk 115 optimal weight: 0.6980 chunk 7 optimal weight: 0.8980 chunk 81 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 99 optimal weight: 0.5980 chunk 61 optimal weight: 0.9980 chunk 48 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 ** A 392 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 = 0.3695 r_free = 0.3695 target = 0.116173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.098824 restraints weight = 21201.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.102029 restraints weight = 10472.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.104092 restraints weight = 6140.678| |-----------------------------------------------------------------------------| r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.5518 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= 0.180 Angle : 0.713 9.658 14120 Z= 0.366 Chirality : 0.044 0.169 1714 Planarity : 0.004 0.049 1756 Dihedral : 5.597 53.772 1437 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 13.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 5.69 % Allowed : 23.75 % Favored : 70.55 % 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: -1.12 (0.23), residues: 1316 helix: 0.33 (0.18), residues: 828 sheet: 1.41 (0.99), residues: 20 loop : -2.86 (0.27), residues: 468 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 0.030 0.002 PHE B 128 TYR 0.035 0.002 TYR B 361 ARG 0.006 0.001 ARG B 440 Details of bonding type rmsd hydrogen bonds : bond 0.03737 ( 576) hydrogen bonds : angle 3.98524 ( 1683) covalent geometry : bond 0.00409 (10390) covalent geometry : angle 0.71282 (14120) *********************** 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 386 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 322 time to evaluate : 1.280 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 GLU cc_start: 0.6952 (mp0) cc_final: 0.6537 (mp0) REVERT: A 85 LEU cc_start: 0.6668 (tp) cc_final: 0.6429 (tp) REVERT: A 90 SER cc_start: 0.8535 (t) cc_final: 0.7917 (p) REVERT: A 94 THR cc_start: 0.8556 (t) cc_final: 0.8181 (p) REVERT: A 134 ARG cc_start: 0.8086 (mpp80) cc_final: 0.7843 (mpp80) REVERT: A 182 ASP cc_start: 0.7748 (OUTLIER) cc_final: 0.7485 (p0) REVERT: A 195 LEU cc_start: 0.8993 (OUTLIER) cc_final: 0.8612 (tp) REVERT: A 230 GLN cc_start: 0.8216 (tp40) cc_final: 0.7929 (tm-30) REVERT: A 237 LYS cc_start: 0.8766 (pttt) cc_final: 0.8382 (ttpp) REVERT: A 238 ILE cc_start: 0.8990 (tp) cc_final: 0.8731 (tp) REVERT: A 251 LEU cc_start: 0.8710 (mm) cc_final: 0.8506 (mt) REVERT: A 259 GLU cc_start: 0.7723 (tm-30) cc_final: 0.7164 (tm-30) REVERT: A 260 ILE cc_start: 0.8776 (mt) cc_final: 0.8509 (mt) REVERT: A 263 ASN cc_start: 0.8274 (t0) cc_final: 0.7511 (t0) REVERT: A 350 LEU cc_start: 0.8491 (tp) cc_final: 0.8124 (tt) REVERT: A 358 VAL cc_start: 0.8928 (t) cc_final: 0.8655 (p) REVERT: A 385 PHE cc_start: 0.9017 (OUTLIER) cc_final: 0.8697 (t80) REVERT: A 404 THR cc_start: 0.7479 (OUTLIER) cc_final: 0.6943 (p) REVERT: A 409 ARG cc_start: 0.8320 (mtm180) cc_final: 0.7938 (mtm110) REVERT: A 414 GLU cc_start: 0.7562 (tm-30) cc_final: 0.6943 (tm-30) REVERT: A 425 LEU cc_start: 0.8513 (tp) cc_final: 0.8205 (tt) REVERT: A 432 MET cc_start: 0.7548 (tmm) cc_final: 0.7184 (tmm) REVERT: A 463 MET cc_start: 0.7520 (tmm) cc_final: 0.7056 (tmm) REVERT: A 466 CYS cc_start: 0.8028 (t) cc_final: 0.7590 (t) REVERT: A 473 LYS cc_start: 0.8506 (mttp) cc_final: 0.8113 (ttmm) REVERT: A 537 LYS cc_start: 0.8049 (ttmt) cc_final: 0.7586 (ptmm) REVERT: A 546 LYS cc_start: 0.7584 (mmtt) cc_final: 0.7298 (mmmm) REVERT: A 580 LYS cc_start: 0.8201 (mmmt) cc_final: 0.7857 (mmmt) REVERT: A 583 LYS cc_start: 0.8460 (OUTLIER) cc_final: 0.7766 (tmmt) REVERT: B 66 LYS cc_start: 0.8379 (tptt) cc_final: 0.7976 (tppt) REVERT: B 77 LYS cc_start: 0.8395 (ttpt) cc_final: 0.8029 (ttpt) REVERT: B 90 SER cc_start: 0.8541 (t) cc_final: 0.8125 (p) REVERT: B 125 LEU cc_start: 0.8862 (tp) cc_final: 0.8585 (tp) REVERT: B 150 SER cc_start: 0.8329 (t) cc_final: 0.8075 (p) REVERT: B 230 GLN cc_start: 0.8450 (tm-30) cc_final: 0.8090 (tm-30) REVERT: B 235 GLN cc_start: 0.8147 (mm-40) cc_final: 0.7841 (mm110) REVERT: B 236 LEU cc_start: 0.9023 (tp) cc_final: 0.8770 (tp) REVERT: B 237 LYS cc_start: 0.8701 (pttt) cc_final: 0.8368 (ttpt) REVERT: B 250 ILE cc_start: 0.8735 (pt) cc_final: 0.8519 (mm) REVERT: B 255 TYR cc_start: 0.7934 (m-10) cc_final: 0.7619 (m-10) REVERT: B 260 ILE cc_start: 0.8811 (mt) cc_final: 0.8494 (mt) REVERT: B 384 GLU cc_start: 0.7756 (mm-30) cc_final: 0.7477 (mm-30) REVERT: B 398 PHE cc_start: 0.6946 (m-80) cc_final: 0.6531 (m-10) REVERT: B 400 CYS cc_start: 0.7266 (m) cc_final: 0.7033 (m) REVERT: B 414 GLU cc_start: 0.7601 (tm-30) cc_final: 0.7074 (tp30) REVERT: B 458 LEU cc_start: 0.8790 (OUTLIER) cc_final: 0.8571 (mt) REVERT: B 466 CYS cc_start: 0.8056 (t) cc_final: 0.7738 (t) REVERT: B 473 LYS cc_start: 0.8387 (mttp) cc_final: 0.8125 (mtpp) REVERT: B 486 CYS cc_start: 0.8718 (t) cc_final: 0.8452 (t) REVERT: B 488 MET cc_start: 0.7465 (tpp) cc_final: 0.7115 (tpp) REVERT: B 513 VAL cc_start: 0.9213 (OUTLIER) cc_final: 0.8989 (p) REVERT: B 537 LYS cc_start: 0.8366 (tmtt) cc_final: 0.7980 (tptp) REVERT: B 540 GLU cc_start: 0.8157 (pm20) cc_final: 0.7338 (pm20) REVERT: B 546 LYS cc_start: 0.7758 (mmtt) cc_final: 0.7352 (mmmm) REVERT: B 549 ARG cc_start: 0.7496 (ttm-80) cc_final: 0.7134 (ttt-90) REVERT: B 556 TYR cc_start: 0.9012 (p90) cc_final: 0.8751 (p90) REVERT: B 578 TYR cc_start: 0.7730 (t80) cc_final: 0.7346 (t80) REVERT: B 583 LYS cc_start: 0.8506 (OUTLIER) cc_final: 0.7983 (tmmt) REVERT: B 681 LYS cc_start: 0.8363 (mptt) cc_final: 0.8115 (mptt) REVERT: B 705 GLN cc_start: 0.8633 (tt0) cc_final: 0.8407 (tt0) REVERT: B 724 ASP cc_start: 0.7771 (OUTLIER) cc_final: 0.7510 (t70) outliers start: 64 outliers final: 42 residues processed: 359 average time/residue: 0.3284 time to fit residues: 157.9177 Evaluate side-chains 363 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 312 time to evaluate : 1.763 ------------------------------------------------------------------------------- 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 111 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 144 VAL 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 239 VAL Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 345 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 523 SER Chi-restraints excluded: chain A residue 583 LYS Chi-restraints excluded: chain A residue 658 LEU 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 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 329 LYS Chi-restraints excluded: chain B residue 405 THR Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 476 LYS 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 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 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: 2.9990 chunk 6 optimal weight: 0.7980 chunk 30 optimal weight: 0.9990 chunk 53 optimal weight: 0.9980 chunk 124 optimal weight: 3.9990 chunk 15 optimal weight: 0.7980 chunk 111 optimal weight: 0.4980 chunk 112 optimal weight: 0.6980 chunk 100 optimal weight: 0.6980 chunk 102 optimal weight: 1.9990 chunk 128 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN B 246 ASN B 268 ASN ** B 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 514 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.115765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.098223 restraints weight = 21353.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.101342 restraints weight = 10507.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.103390 restraints weight = 6202.841| |-----------------------------------------------------------------------------| r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.5736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10390 Z= 0.185 Angle : 0.756 17.908 14120 Z= 0.379 Chirality : 0.045 0.175 1714 Planarity : 0.005 0.051 1756 Dihedral : 5.639 55.822 1435 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 14.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 5.16 % Allowed : 24.91 % Favored : 69.93 % 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: -1.12 (0.23), residues: 1316 helix: 0.32 (0.18), residues: 828 sheet: 1.37 (1.03), residues: 20 loop : -2.84 (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 0.030 0.002 PHE B 128 TYR 0.023 0.002 TYR B 323 ARG 0.007 0.001 ARG A 36 Details of bonding type rmsd hydrogen bonds : bond 0.03731 ( 576) hydrogen bonds : angle 4.01001 ( 1683) covalent geometry : bond 0.00416 (10390) covalent geometry : angle 0.75603 (14120) *********************** 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 375 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 317 time to evaluate : 1.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 GLU cc_start: 0.6969 (mp0) cc_final: 0.6578 (mp0) REVERT: A 35 GLN cc_start: 0.7755 (OUTLIER) cc_final: 0.7349 (pt0) REVERT: A 36 ARG cc_start: 0.7726 (mmt90) cc_final: 0.7405 (mtt90) REVERT: A 85 LEU cc_start: 0.6762 (tp) cc_final: 0.6526 (tp) REVERT: A 90 SER cc_start: 0.8517 (t) cc_final: 0.7900 (p) REVERT: A 94 THR cc_start: 0.8554 (t) cc_final: 0.8171 (p) REVERT: A 118 TYR cc_start: 0.7248 (m-10) cc_final: 0.6964 (m-80) REVERT: A 134 ARG cc_start: 0.8072 (mpp80) cc_final: 0.7561 (mpp80) REVERT: A 182 ASP cc_start: 0.7751 (OUTLIER) cc_final: 0.7482 (p0) REVERT: A 195 LEU cc_start: 0.8999 (OUTLIER) cc_final: 0.8674 (tp) REVERT: A 230 GLN cc_start: 0.8230 (tp40) cc_final: 0.7935 (tm-30) REVERT: A 237 LYS cc_start: 0.8775 (pttt) cc_final: 0.8399 (ttpp) REVERT: A 238 ILE cc_start: 0.9011 (tp) cc_final: 0.8765 (tp) REVERT: A 259 GLU cc_start: 0.7726 (tm-30) cc_final: 0.7088 (tm-30) REVERT: A 260 ILE cc_start: 0.8778 (mt) cc_final: 0.8496 (mt) REVERT: A 263 ASN cc_start: 0.8249 (t0) cc_final: 0.7627 (t0) REVERT: A 350 LEU cc_start: 0.8505 (tp) cc_final: 0.8208 (tt) REVERT: A 358 VAL cc_start: 0.8872 (t) cc_final: 0.8609 (p) REVERT: A 385 PHE cc_start: 0.9008 (OUTLIER) cc_final: 0.8674 (t80) REVERT: A 404 THR cc_start: 0.7460 (OUTLIER) cc_final: 0.6909 (p) REVERT: A 409 ARG cc_start: 0.8318 (mtm180) cc_final: 0.7959 (mtm110) REVERT: A 414 GLU cc_start: 0.7549 (tm-30) cc_final: 0.6935 (tm-30) REVERT: A 432 MET cc_start: 0.7549 (tmm) cc_final: 0.7192 (tmm) REVERT: A 463 MET cc_start: 0.7540 (tmm) cc_final: 0.7065 (tmm) REVERT: A 466 CYS cc_start: 0.8042 (t) cc_final: 0.7613 (t) REVERT: A 473 LYS cc_start: 0.8555 (mttp) cc_final: 0.8123 (ttmm) REVERT: A 476 LYS cc_start: 0.9162 (mtmm) cc_final: 0.8943 (mtmm) REVERT: A 537 LYS cc_start: 0.8092 (ttmt) cc_final: 0.7505 (ttpp) REVERT: A 540 GLU cc_start: 0.8382 (pm20) cc_final: 0.7674 (pm20) REVERT: A 546 LYS cc_start: 0.7629 (mmtt) cc_final: 0.7398 (mmmm) REVERT: A 580 LYS cc_start: 0.8208 (mmmt) cc_final: 0.7864 (mmmt) REVERT: A 583 LYS cc_start: 0.8468 (OUTLIER) cc_final: 0.7775 (tmmt) REVERT: A 681 LYS cc_start: 0.8302 (mptt) cc_final: 0.8051 (mptt) REVERT: B 66 LYS cc_start: 0.8350 (tptt) cc_final: 0.7941 (tppt) REVERT: B 77 LYS cc_start: 0.8444 (ttpt) cc_final: 0.8082 (ttpt) REVERT: B 90 SER cc_start: 0.8532 (t) cc_final: 0.8113 (p) REVERT: B 125 LEU cc_start: 0.8875 (tp) cc_final: 0.8557 (tp) REVERT: B 150 SER cc_start: 0.8340 (t) cc_final: 0.8047 (p) REVERT: B 230 GLN cc_start: 0.8463 (tm-30) cc_final: 0.8111 (tm-30) REVERT: B 235 GLN cc_start: 0.8177 (mm-40) cc_final: 0.7957 (mm110) REVERT: B 236 LEU cc_start: 0.8997 (tp) cc_final: 0.8766 (tp) REVERT: B 237 LYS cc_start: 0.8683 (pttt) cc_final: 0.8390 (ttpt) REVERT: B 255 TYR cc_start: 0.7951 (m-10) cc_final: 0.7626 (m-10) REVERT: B 260 ILE cc_start: 0.8820 (mt) cc_final: 0.8530 (mt) REVERT: B 329 LYS cc_start: 0.8149 (OUTLIER) cc_final: 0.7937 (mtmm) REVERT: B 384 GLU cc_start: 0.7687 (mm-30) cc_final: 0.7405 (mm-30) REVERT: B 398 PHE cc_start: 0.6952 (m-80) cc_final: 0.6553 (m-10) REVERT: B 400 CYS cc_start: 0.7277 (m) cc_final: 0.7067 (m) REVERT: B 404 THR cc_start: 0.7669 (OUTLIER) cc_final: 0.7244 (p) REVERT: B 414 GLU cc_start: 0.7611 (tm-30) cc_final: 0.7059 (tp30) REVERT: B 458 LEU cc_start: 0.8797 (OUTLIER) cc_final: 0.8584 (mt) REVERT: B 466 CYS cc_start: 0.8086 (t) cc_final: 0.7764 (t) REVERT: B 473 LYS cc_start: 0.8389 (mttp) cc_final: 0.8128 (mtpp) REVERT: B 486 CYS cc_start: 0.8718 (t) cc_final: 0.8457 (t) REVERT: B 488 MET cc_start: 0.7464 (tpp) cc_final: 0.7115 (tpp) REVERT: B 513 VAL cc_start: 0.9222 (OUTLIER) cc_final: 0.8996 (p) REVERT: B 537 LYS cc_start: 0.8435 (tmtt) cc_final: 0.8052 (tmtt) REVERT: B 540 GLU cc_start: 0.8105 (pm20) cc_final: 0.7729 (pm20) REVERT: B 549 ARG cc_start: 0.7525 (ttm-80) cc_final: 0.7136 (ttt-90) REVERT: B 556 TYR cc_start: 0.8997 (p90) cc_final: 0.8708 (p90) REVERT: B 578 TYR cc_start: 0.7761 (t80) cc_final: 0.7311 (t80) REVERT: B 583 LYS cc_start: 0.8520 (OUTLIER) cc_final: 0.7990 (tmmt) REVERT: B 705 GLN cc_start: 0.8616 (tt0) cc_final: 0.8323 (tt0) REVERT: B 724 ASP cc_start: 0.7762 (OUTLIER) cc_final: 0.7430 (t0) outliers start: 58 outliers final: 33 residues processed: 356 average time/residue: 0.2617 time to fit residues: 124.7605 Evaluate side-chains 346 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 301 time to evaluate : 1.073 ------------------------------------------------------------------------------- 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 239 VAL Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 345 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 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 283 MET Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 329 LYS 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 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 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: 1.9990 chunk 102 optimal weight: 0.0970 chunk 89 optimal weight: 0.0370 chunk 50 optimal weight: 0.3980 chunk 54 optimal weight: 0.7980 chunk 88 optimal weight: 0.7980 chunk 62 optimal weight: 0.8980 chunk 61 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 129 optimal weight: 0.7980 overall best weight: 0.4256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.116794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.099556 restraints weight = 21357.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.102640 restraints weight = 10568.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.104728 restraints weight = 6251.299| |-----------------------------------------------------------------------------| r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.5802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 10390 Z= 0.159 Angle : 0.756 9.575 14120 Z= 0.385 Chirality : 0.045 0.206 1714 Planarity : 0.005 0.076 1756 Dihedral : 5.626 57.424 1433 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 14.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 4.45 % Allowed : 26.78 % Favored : 68.77 % 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: -1.10 (0.23), residues: 1316 helix: 0.32 (0.18), residues: 832 sheet: 1.29 (1.03), residues: 20 loop : -2.80 (0.27), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 83 HIS 0.005 0.001 HIS A 728 PHE 0.031 0.001 PHE B 394 TYR 0.021 0.002 TYR B 323 ARG 0.015 0.001 ARG A 36 Details of bonding type rmsd hydrogen bonds : bond 0.03721 ( 576) hydrogen bonds : angle 4.01839 ( 1683) covalent geometry : bond 0.00369 (10390) covalent geometry : angle 0.75619 (14120) *********************** 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 350 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 300 time to evaluate : 1.143 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 GLU cc_start: 0.6976 (mp0) cc_final: 0.6597 (mp0) REVERT: A 36 ARG cc_start: 0.7684 (mmt90) cc_final: 0.7415 (mtt90) REVERT: A 85 LEU cc_start: 0.6745 (tp) cc_final: 0.6501 (tp) REVERT: A 90 SER cc_start: 0.8502 (t) cc_final: 0.7860 (p) REVERT: A 94 THR cc_start: 0.8548 (t) cc_final: 0.8164 (p) REVERT: A 182 ASP cc_start: 0.7784 (OUTLIER) cc_final: 0.7475 (p0) REVERT: A 195 LEU cc_start: 0.8978 (OUTLIER) cc_final: 0.8641 (tp) REVERT: A 230 GLN cc_start: 0.8180 (tp40) cc_final: 0.7938 (tm-30) REVERT: A 235 GLN cc_start: 0.8311 (mm-40) cc_final: 0.8052 (mm-40) REVERT: A 237 LYS cc_start: 0.8754 (pttt) cc_final: 0.8370 (ttpp) REVERT: A 238 ILE cc_start: 0.8996 (tp) cc_final: 0.8735 (tp) REVERT: A 251 LEU cc_start: 0.8658 (mt) cc_final: 0.8428 (mp) REVERT: A 259 GLU cc_start: 0.7691 (tm-30) cc_final: 0.7119 (tm-30) REVERT: A 260 ILE cc_start: 0.8763 (mt) cc_final: 0.8507 (mt) REVERT: A 263 ASN cc_start: 0.8221 (t0) cc_final: 0.7573 (t0) REVERT: A 345 LEU cc_start: 0.8742 (OUTLIER) cc_final: 0.8379 (mm) REVERT: A 350 LEU cc_start: 0.8488 (tp) cc_final: 0.8153 (tt) REVERT: A 404 THR cc_start: 0.7438 (OUTLIER) cc_final: 0.6838 (p) REVERT: A 409 ARG cc_start: 0.8278 (mtm180) cc_final: 0.7918 (mtm110) REVERT: A 414 GLU cc_start: 0.7513 (tm-30) cc_final: 0.6901 (tm-30) REVERT: A 432 MET cc_start: 0.7526 (tmm) cc_final: 0.7172 (tmm) REVERT: A 463 MET cc_start: 0.7517 (tmm) cc_final: 0.7002 (tmm) REVERT: A 473 LYS cc_start: 0.8543 (mttp) cc_final: 0.8173 (ttmm) REVERT: A 476 LYS cc_start: 0.9162 (mtmm) cc_final: 0.8909 (mtmm) REVERT: A 537 LYS cc_start: 0.8105 (ttmt) cc_final: 0.7515 (ttpp) REVERT: A 540 GLU cc_start: 0.8372 (pm20) cc_final: 0.7622 (pm20) REVERT: A 546 LYS cc_start: 0.7623 (mmtt) cc_final: 0.7413 (mmmm) REVERT: A 580 LYS cc_start: 0.8196 (mmmt) cc_final: 0.7856 (mmmt) REVERT: A 583 LYS cc_start: 0.8460 (OUTLIER) cc_final: 0.7776 (tmmt) REVERT: B 30 LEU cc_start: 0.8283 (OUTLIER) cc_final: 0.7918 (tp) REVERT: B 66 LYS cc_start: 0.8345 (tptt) cc_final: 0.7907 (tppt) REVERT: B 77 LYS cc_start: 0.8429 (ttpt) cc_final: 0.8063 (ttpt) REVERT: B 90 SER cc_start: 0.8495 (t) cc_final: 0.8118 (p) REVERT: B 125 LEU cc_start: 0.8832 (tp) cc_final: 0.8491 (tp) REVERT: B 134 ARG cc_start: 0.7381 (mtm-85) cc_final: 0.7119 (mtm-85) REVERT: B 150 SER cc_start: 0.8341 (t) cc_final: 0.8046 (p) REVERT: B 230 GLN cc_start: 0.8461 (tm-30) cc_final: 0.8107 (tm-30) REVERT: B 235 GLN cc_start: 0.8173 (mm-40) cc_final: 0.7863 (mm110) REVERT: B 236 LEU cc_start: 0.8982 (tp) cc_final: 0.8745 (tp) REVERT: B 237 LYS cc_start: 0.8671 (pttt) cc_final: 0.8368 (ttpt) REVERT: B 255 TYR cc_start: 0.7959 (m-10) cc_final: 0.7639 (m-10) REVERT: B 260 ILE cc_start: 0.8849 (mt) cc_final: 0.8564 (mt) REVERT: B 329 LYS cc_start: 0.8102 (OUTLIER) cc_final: 0.7868 (mtmm) REVERT: B 384 GLU cc_start: 0.7724 (mm-30) cc_final: 0.7417 (mm-30) REVERT: B 398 PHE cc_start: 0.6879 (m-80) cc_final: 0.6488 (m-10) REVERT: B 404 THR cc_start: 0.7632 (OUTLIER) cc_final: 0.7183 (p) REVERT: B 414 GLU cc_start: 0.7588 (tm-30) cc_final: 0.7019 (tp30) REVERT: B 426 ILE cc_start: 0.8239 (tt) cc_final: 0.7790 (pt) REVERT: B 458 LEU cc_start: 0.8724 (OUTLIER) cc_final: 0.8483 (mt) REVERT: B 466 CYS cc_start: 0.8040 (t) cc_final: 0.7637 (t) REVERT: B 473 LYS cc_start: 0.8367 (mttp) cc_final: 0.8098 (mtpp) REVERT: B 486 CYS cc_start: 0.8711 (t) cc_final: 0.8448 (t) REVERT: B 488 MET cc_start: 0.7443 (tpp) cc_final: 0.7110 (tpp) REVERT: B 513 VAL cc_start: 0.9212 (OUTLIER) cc_final: 0.8988 (p) REVERT: B 537 LYS cc_start: 0.8445 (tmtt) cc_final: 0.7986 (tptp) REVERT: B 549 ARG cc_start: 0.7511 (ttm-80) cc_final: 0.7093 (ttt-90) REVERT: B 556 TYR cc_start: 0.8992 (p90) cc_final: 0.8758 (p90) REVERT: B 578 TYR cc_start: 0.7699 (t80) cc_final: 0.7310 (t80) REVERT: B 583 LYS cc_start: 0.8503 (OUTLIER) cc_final: 0.7974 (tmmt) REVERT: B 677 ARG cc_start: 0.7853 (ttp-110) cc_final: 0.7623 (ttp-110) REVERT: B 681 LYS cc_start: 0.8488 (mptt) cc_final: 0.8264 (mptt) REVERT: B 714 ARG cc_start: 0.6678 (mmp-170) cc_final: 0.6451 (mmp-170) REVERT: B 724 ASP cc_start: 0.7722 (OUTLIER) cc_final: 0.7403 (t0) outliers start: 50 outliers final: 31 residues processed: 334 average time/residue: 0.2703 time to fit residues: 120.8372 Evaluate side-chains 331 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 288 time to evaluate : 1.041 ------------------------------------------------------------------------------- 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 182 ASP Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 345 LEU 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 583 LYS Chi-restraints excluded: chain A residue 658 LEU 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 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 329 LYS Chi-restraints excluded: chain B residue 340 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 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 716 ASP Chi-restraints excluded: chain B residue 724 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 5 optimal weight: 0.0970 chunk 15 optimal weight: 9.9990 chunk 121 optimal weight: 0.6980 chunk 119 optimal weight: 1.9990 chunk 98 optimal weight: 0.7980 chunk 39 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 2 optimal weight: 3.9990 chunk 127 optimal weight: 0.5980 chunk 40 optimal weight: 0.6980 overall best weight: 0.5778 ------------------------------------------------------------------------------- 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 = 0.3692 r_free = 0.3692 target = 0.115830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.098606 restraints weight = 21380.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.101736 restraints weight = 10592.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.103554 restraints weight = 6236.401| |-----------------------------------------------------------------------------| r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.5960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10390 Z= 0.174 Angle : 0.765 10.075 14120 Z= 0.391 Chirality : 0.045 0.226 1714 Planarity : 0.005 0.055 1756 Dihedral : 5.615 58.904 1433 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 14.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 4.36 % Allowed : 26.78 % Favored : 68.86 % 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: -1.02 (0.23), residues: 1316 helix: 0.35 (0.18), residues: 834 sheet: 1.20 (1.05), residues: 20 loop : -2.72 (0.28), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 518 HIS 0.004 0.001 HIS A 728 PHE 0.033 0.002 PHE B 394 TYR 0.025 0.002 TYR A 691 ARG 0.012 0.001 ARG B 134 Details of bonding type rmsd hydrogen bonds : bond 0.03773 ( 576) hydrogen bonds : angle 4.04968 ( 1683) covalent geometry : bond 0.00395 (10390) covalent geometry : angle 0.76529 (14120) ********************** 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 354 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 305 time to evaluate : 1.615 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 GLU cc_start: 0.7052 (mp0) cc_final: 0.6611 (mp0) REVERT: A 85 LEU cc_start: 0.6829 (tp) cc_final: 0.6585 (tp) REVERT: A 90 SER cc_start: 0.8503 (t) cc_final: 0.7848 (p) REVERT: A 94 THR cc_start: 0.8554 (t) cc_final: 0.8152 (p) REVERT: A 134 ARG cc_start: 0.8312 (mpp80) cc_final: 0.7932 (mpp80) REVERT: A 182 ASP cc_start: 0.7759 (OUTLIER) cc_final: 0.7484 (p0) REVERT: A 195 LEU cc_start: 0.8999 (OUTLIER) cc_final: 0.8644 (tp) REVERT: A 230 GLN cc_start: 0.8207 (tp40) cc_final: 0.7955 (tm-30) REVERT: A 237 LYS cc_start: 0.8771 (pttt) cc_final: 0.8390 (ttpp) REVERT: A 238 ILE cc_start: 0.9021 (tp) cc_final: 0.8771 (tp) REVERT: A 259 GLU cc_start: 0.7697 (tm-30) cc_final: 0.7070 (tm-30) REVERT: A 260 ILE cc_start: 0.8762 (mt) cc_final: 0.8496 (mt) REVERT: A 263 ASN cc_start: 0.8273 (t0) cc_final: 0.7649 (t0) REVERT: A 350 LEU cc_start: 0.8546 (tp) cc_final: 0.8222 (tt) REVERT: A 404 THR cc_start: 0.7402 (OUTLIER) cc_final: 0.6859 (p) REVERT: A 409 ARG cc_start: 0.8291 (mtm180) cc_final: 0.7958 (mtm110) REVERT: A 414 GLU cc_start: 0.7515 (tm-30) cc_final: 0.6930 (tm-30) REVERT: A 432 MET cc_start: 0.7572 (tmm) cc_final: 0.7196 (tmm) REVERT: A 463 MET cc_start: 0.7530 (tmm) cc_final: 0.7019 (tmm) REVERT: A 473 LYS cc_start: 0.8514 (mttp) cc_final: 0.8293 (ttmm) REVERT: A 476 LYS cc_start: 0.9175 (mtmm) cc_final: 0.8925 (mtmm) REVERT: A 537 LYS cc_start: 0.8087 (ttmt) cc_final: 0.7629 (ptmm) REVERT: A 540 GLU cc_start: 0.8412 (pm20) cc_final: 0.7663 (pm20) REVERT: A 546 LYS cc_start: 0.7701 (mmtt) cc_final: 0.7481 (mmmm) REVERT: A 580 LYS cc_start: 0.8190 (mmmt) cc_final: 0.7855 (mmmt) REVERT: A 583 LYS cc_start: 0.8543 (OUTLIER) cc_final: 0.7828 (tmmt) REVERT: A 681 LYS cc_start: 0.8313 (mptt) cc_final: 0.8094 (mptt) REVERT: B 30 LEU cc_start: 0.8298 (OUTLIER) cc_final: 0.7929 (tp) REVERT: B 66 LYS cc_start: 0.8348 (tptt) cc_final: 0.7919 (tppt) REVERT: B 77 LYS cc_start: 0.8462 (ttpt) cc_final: 0.8098 (ttpt) REVERT: B 90 SER cc_start: 0.8484 (t) cc_final: 0.8093 (p) REVERT: B 125 LEU cc_start: 0.8830 (tp) cc_final: 0.8435 (tp) REVERT: B 134 ARG cc_start: 0.7423 (mtm-85) cc_final: 0.7174 (mtm-85) REVERT: B 150 SER cc_start: 0.8405 (t) cc_final: 0.8100 (p) REVERT: B 230 GLN cc_start: 0.8463 (tm-30) cc_final: 0.8121 (tm-30) REVERT: B 235 GLN cc_start: 0.8208 (mm-40) cc_final: 0.7888 (mm110) REVERT: B 236 LEU cc_start: 0.8986 (tp) cc_final: 0.8762 (tp) REVERT: B 237 LYS cc_start: 0.8666 (pttt) cc_final: 0.8400 (ttpp) REVERT: B 255 TYR cc_start: 0.7962 (m-10) cc_final: 0.7680 (m-10) REVERT: B 260 ILE cc_start: 0.8896 (mt) cc_final: 0.8634 (mt) REVERT: B 329 LYS cc_start: 0.8106 (OUTLIER) cc_final: 0.7570 (ptpt) REVERT: B 384 GLU cc_start: 0.7707 (mm-30) cc_final: 0.7420 (mm-30) REVERT: B 398 PHE cc_start: 0.6843 (m-80) cc_final: 0.6617 (m-10) REVERT: B 404 THR cc_start: 0.7626 (OUTLIER) cc_final: 0.7211 (p) REVERT: B 414 GLU cc_start: 0.7579 (tm-30) cc_final: 0.7011 (tp30) REVERT: B 458 LEU cc_start: 0.8733 (OUTLIER) cc_final: 0.8491 (mt) REVERT: B 466 CYS cc_start: 0.8045 (t) cc_final: 0.7645 (t) REVERT: B 473 LYS cc_start: 0.8382 (mttp) cc_final: 0.8121 (mtpp) REVERT: B 486 CYS cc_start: 0.8714 (t) cc_final: 0.8451 (t) REVERT: B 488 MET cc_start: 0.7430 (tpp) cc_final: 0.7098 (tpp) REVERT: B 513 VAL cc_start: 0.9239 (OUTLIER) cc_final: 0.9017 (p) REVERT: B 537 LYS cc_start: 0.8469 (tmtt) cc_final: 0.8105 (tmtt) REVERT: B 546 LYS cc_start: 0.7795 (mmtt) cc_final: 0.7474 (mmmm) REVERT: B 549 ARG cc_start: 0.7510 (ttm-80) cc_final: 0.7097 (ttt-90) REVERT: B 556 TYR cc_start: 0.9006 (p90) cc_final: 0.8776 (p90) REVERT: B 578 TYR cc_start: 0.7784 (t80) cc_final: 0.7393 (t80) REVERT: B 583 LYS cc_start: 0.8512 (OUTLIER) cc_final: 0.7978 (tmmt) REVERT: B 677 ARG cc_start: 0.7893 (ttp-110) cc_final: 0.7628 (ttp-110) REVERT: B 681 LYS cc_start: 0.8472 (mptt) cc_final: 0.8250 (mptt) REVERT: B 714 ARG cc_start: 0.6770 (mmp-170) cc_final: 0.6494 (mmp-170) REVERT: B 724 ASP cc_start: 0.7730 (OUTLIER) cc_final: 0.7410 (t0) outliers start: 49 outliers final: 33 residues processed: 337 average time/residue: 0.3150 time to fit residues: 142.1016 Evaluate side-chains 339 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 295 time to evaluate : 1.139 ------------------------------------------------------------------------------- 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 182 ASP Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 336 LEU 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 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 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 329 LYS Chi-restraints excluded: chain B residue 340 LEU Chi-restraints excluded: chain B residue 349 MET Chi-restraints excluded: chain B residue 383 GLN Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 404 THR Chi-restraints excluded: chain B residue 405 THR Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 476 LYS 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 724 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: 2.9990 chunk 85 optimal weight: 0.7980 chunk 86 optimal weight: 0.9980 chunk 35 optimal weight: 0.2980 chunk 131 optimal weight: 0.9980 chunk 89 optimal weight: 0.0470 chunk 99 optimal weight: 2.9990 chunk 53 optimal weight: 0.7980 chunk 111 optimal weight: 0.6980 chunk 36 optimal weight: 0.9990 chunk 100 optimal weight: 0.5980 overall best weight: 0.4878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN ** A 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 33 GLN B 322 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 = 0.3688 r_free = 0.3688 target = 0.115634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.098362 restraints weight = 21187.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.101442 restraints weight = 10538.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.103469 restraints weight = 6240.917| |-----------------------------------------------------------------------------| r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.6035 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= 0.166 Angle : 0.779 11.534 14120 Z= 0.397 Chirality : 0.046 0.202 1714 Planarity : 0.005 0.060 1756 Dihedral : 5.606 58.839 1433 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 15.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 4.27 % Allowed : 27.14 % Favored : 68.59 % 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: -0.96 (0.23), residues: 1316 helix: 0.40 (0.18), residues: 832 sheet: 1.16 (1.04), residues: 20 loop : -2.69 (0.27), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 83 HIS 0.005 0.001 HIS A 728 PHE 0.034 0.001 PHE B 394 TYR 0.030 0.002 TYR A 691 ARG 0.013 0.001 ARG B 134 Details of bonding type rmsd hydrogen bonds : bond 0.03797 ( 576) hydrogen bonds : angle 4.02374 ( 1683) covalent geometry : bond 0.00382 (10390) covalent geometry : angle 0.77901 (14120) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4089.21 seconds wall clock time: 72 minutes 23.05 seconds (4343.05 seconds total)