Starting phenix.real_space_refine on Wed Sep 25 11:08:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wle_32583/09_2024/7wle_32583.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wle_32583/09_2024/7wle_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wle_32583/09_2024/7wle_32583.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wle_32583/09_2024/7wle_32583.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wle_32583/09_2024/7wle_32583.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wle_32583/09_2024/7wle_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 10188 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 662, 5094 Classifications: {'peptide': 662} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 26, 'TRANS': 635} Chain breaks: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'ARG:plan': 3} Unresolved non-hydrogen planarities: 15 Chain: "B" Number of atoms: 5094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 662, 5094 Classifications: {'peptide': 662} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 26, 'TRANS': 635} Chain breaks: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'ARG:plan': 3} Unresolved non-hydrogen planarities: 15 Time building chain proxies: 6.43, per 1000 atoms: 0.63 Number of scatterers: 10188 At special positions: 0 Unit cell: (84.056, 125.552, 123.424, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 42 16.00 O 1806 8.00 N 1690 7.00 C 6650 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.80 Conformation dependent library (CDL) restraints added in 1.5 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: 0.97 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: 2.74 Time building geometry restraints manager: 3.25 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.880 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: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 25.280 Find NCS groups from input model: 0.270 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:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 10390 Z= 0.198 Angle : 0.499 9.614 14120 Z= 0.305 Chirality : 0.038 0.275 1714 Planarity : 0.004 0.039 1756 Dihedral : 9.906 85.978 3718 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 5.25 % Allowed : 6.41 % Favored : 88.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.62 (0.19), residues: 1316 helix: -1.46 (0.16), residues: 808 sheet: -2.61 (0.85), residues: 20 loop : -4.00 (0.21), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 83 HIS 0.002 0.000 HIS B 535 PHE 0.008 0.001 PHE B 555 TYR 0.005 0.001 TYR B 20 ARG 0.001 0.000 ARG A 213 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 409 time to evaluate : 1.185 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: 0.2652 time to fit residues: 156.8507 Evaluate side-chains 341 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 313 time to evaluate : 1.148 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.3152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 10390 Z= 0.266 Angle : 0.663 8.048 14120 Z= 0.346 Chirality : 0.043 0.262 1714 Planarity : 0.004 0.033 1756 Dihedral : 6.863 101.158 1465 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 5.25 % Allowed : 17.26 % Favored : 77.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.07 (0.22), residues: 1316 helix: -0.30 (0.18), residues: 818 sheet: -0.09 (0.98), residues: 20 loop : -3.39 (0.24), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 83 HIS 0.005 0.001 HIS B 728 PHE 0.028 0.002 PHE A 130 TYR 0.021 0.002 TYR B 323 ARG 0.007 0.001 ARG A 674 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 326 time to evaluate : 0.989 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 ARG cc_start: 0.7226 (mtm-85) cc_final: 0.6852 (mtt90) REVERT: A 37 GLU cc_start: 0.7986 (OUTLIER) cc_final: 0.6857 (pm20) REVERT: A 77 LYS cc_start: 0.8085 (ttpt) cc_final: 0.7656 (ttpt) REVERT: A 90 SER cc_start: 0.8576 (t) cc_final: 0.8096 (p) REVERT: A 94 THR cc_start: 0.8423 (t) cc_final: 0.8144 (p) REVERT: A 118 TYR cc_start: 0.6995 (m-10) cc_final: 0.6754 (m-10) REVERT: A 128 PHE cc_start: 0.8616 (t80) cc_final: 0.8363 (t80) REVERT: A 195 LEU cc_start: 0.8712 (OUTLIER) cc_final: 0.8293 (tm) REVERT: A 207 GLN cc_start: 0.7809 (tm-30) cc_final: 0.7489 (tm-30) REVERT: A 230 GLN cc_start: 0.8122 (tp40) cc_final: 0.7871 (tm-30) REVERT: A 250 ILE cc_start: 0.8609 (pt) cc_final: 0.8376 (mm) REVERT: A 259 GLU cc_start: 0.7775 (OUTLIER) cc_final: 0.7221 (tm-30) REVERT: A 260 ILE cc_start: 0.8531 (mt) cc_final: 0.7882 (mt) REVERT: A 263 ASN cc_start: 0.8393 (t0) cc_final: 0.7663 (t0) REVERT: A 350 LEU cc_start: 0.8597 (tp) cc_final: 0.8269 (tt) REVERT: A 385 PHE cc_start: 0.8706 (OUTLIER) cc_final: 0.8428 (t80) REVERT: A 432 MET cc_start: 0.7424 (tmm) cc_final: 0.7078 (tmm) REVERT: A 466 CYS cc_start: 0.7820 (t) cc_final: 0.7391 (t) REVERT: A 473 LYS cc_start: 0.8413 (mttp) cc_final: 0.8169 (mttp) REVERT: A 530 TYR cc_start: 0.8401 (m-80) cc_final: 0.8035 (m-80) REVERT: A 580 LYS cc_start: 0.8157 (mmmt) cc_final: 0.7882 (tttt) REVERT: A 581 ARG cc_start: 0.8282 (tpt170) cc_final: 0.8061 (tpt170) REVERT: A 583 LYS cc_start: 0.8635 (OUTLIER) cc_final: 0.8087 (tmmt) REVERT: A 714 ARG cc_start: 0.7231 (mpt180) cc_final: 0.6694 (mtm-85) REVERT: B 80 VAL cc_start: 0.9377 (OUTLIER) cc_final: 0.8853 (t) REVERT: B 90 SER cc_start: 0.8837 (t) cc_final: 0.8265 (p) REVERT: B 94 THR cc_start: 0.8702 (t) cc_final: 0.8279 (p) REVERT: B 132 THR cc_start: 0.7277 (OUTLIER) cc_final: 0.6532 (t) REVERT: B 150 SER cc_start: 0.8364 (t) cc_final: 0.8084 (p) REVERT: B 195 LEU cc_start: 0.8697 (tp) cc_final: 0.8480 (tp) REVERT: B 230 GLN cc_start: 0.8289 (tm-30) cc_final: 0.7991 (tm-30) REVERT: B 237 LYS cc_start: 0.8580 (pttt) cc_final: 0.8145 (ptpt) REVERT: B 239 VAL cc_start: 0.8367 (OUTLIER) cc_final: 0.8145 (p) REVERT: B 250 ILE cc_start: 0.8615 (pt) cc_final: 0.8312 (mm) REVERT: B 259 GLU cc_start: 0.7665 (OUTLIER) cc_final: 0.6835 (tm-30) REVERT: B 384 GLU cc_start: 0.7667 (mm-30) cc_final: 0.7256 (tp30) REVERT: B 388 PHE cc_start: 0.7048 (m-80) cc_final: 0.6816 (m-80) REVERT: B 394 PHE cc_start: 0.8255 (t80) cc_final: 0.7927 (t80) REVERT: B 400 CYS cc_start: 0.7641 (m) cc_final: 0.7369 (m) REVERT: B 426 ILE cc_start: 0.8014 (tt) cc_final: 0.7773 (tp) REVERT: B 431 VAL cc_start: 0.8956 (t) cc_final: 0.8708 (p) REVERT: B 432 MET cc_start: 0.7316 (tmm) cc_final: 0.7105 (tmm) REVERT: B 462 PHE cc_start: 0.8586 (m-80) cc_final: 0.8369 (m-80) REVERT: B 463 MET cc_start: 0.7578 (tmm) cc_final: 0.7233 (tmm) REVERT: B 466 CYS cc_start: 0.8125 (t) cc_final: 0.7576 (t) REVERT: B 470 ARG cc_start: 0.6700 (mtp180) cc_final: 0.6373 (mtp180) REVERT: B 473 LYS cc_start: 0.8383 (mttp) cc_final: 0.8138 (mtpp) REVERT: B 486 CYS cc_start: 0.8829 (t) cc_final: 0.8577 (t) REVERT: B 488 MET cc_start: 0.7530 (tpp) cc_final: 0.7032 (tpp) REVERT: B 492 LEU cc_start: 0.8796 (mt) cc_final: 0.8594 (mt) REVERT: B 513 VAL cc_start: 0.9134 (OUTLIER) cc_final: 0.8912 (p) REVERT: B 531 LYS cc_start: 0.8606 (mmtm) cc_final: 0.8294 (mmmm) REVERT: B 537 LYS cc_start: 0.8261 (mmmm) cc_final: 0.7254 (ttpp) REVERT: B 556 TYR cc_start: 0.8990 (p90) cc_final: 0.8728 (p90) REVERT: B 578 TYR cc_start: 0.7673 (t80) cc_final: 0.7036 (t80) REVERT: B 581 ARG cc_start: 0.8287 (tpp-160) cc_final: 0.7853 (tpp-160) REVERT: B 583 LYS cc_start: 0.8397 (OUTLIER) cc_final: 0.7886 (tmmt) REVERT: B 681 LYS cc_start: 0.8372 (mptt) cc_final: 0.8051 (mptt) REVERT: B 715 LYS cc_start: 0.8730 (ptpt) cc_final: 0.8467 (ptpp) outliers start: 59 outliers final: 23 residues processed: 361 average time/residue: 0.2396 time to fit residues: 116.2239 Evaluate side-chains 336 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 302 time to evaluate : 1.009 ------------------------------------------------------------------------------- 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 66 optimal weight: 0.0370 chunk 37 optimal weight: 0.7980 chunk 99 optimal weight: 0.6980 chunk 81 optimal weight: 9.9990 chunk 33 optimal weight: 2.9990 chunk 120 optimal weight: 0.7980 chunk 129 optimal weight: 0.5980 chunk 106 optimal weight: 1.9990 chunk 119 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 overall best weight: 0.5858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN ** A 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 457 ASN B 35 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.3916 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= 0.231 Angle : 0.628 7.972 14120 Z= 0.326 Chirality : 0.042 0.164 1714 Planarity : 0.004 0.039 1756 Dihedral : 6.649 96.190 1452 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 5.43 % Allowed : 17.35 % Favored : 77.22 % 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: -1.56 (0.23), residues: 1316 helix: -0.00 (0.18), residues: 826 sheet: 0.81 (1.02), residues: 20 loop : -3.04 (0.26), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 83 HIS 0.006 0.001 HIS B 728 PHE 0.023 0.001 PHE A 130 TYR 0.018 0.002 TYR B 323 ARG 0.005 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 321 time to evaluate : 1.103 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: 0.7403 (mtm-85) cc_final: 0.7083 (mtt90) REVERT: A 77 LYS cc_start: 0.8046 (ttpt) cc_final: 0.7644 (ttpt) REVERT: A 90 SER cc_start: 0.8588 (t) cc_final: 0.8040 (p) REVERT: A 94 THR cc_start: 0.8394 (t) cc_final: 0.8104 (p) REVERT: A 155 MET cc_start: 0.8142 (ptp) cc_final: 0.7764 (ptm) REVERT: A 195 LEU cc_start: 0.8862 (OUTLIER) cc_final: 0.8513 (tp) REVERT: A 230 GLN cc_start: 0.8217 (tp40) cc_final: 0.7872 (tm-30) REVERT: A 237 LYS cc_start: 0.8693 (pttt) cc_final: 0.8281 (ptmm) REVERT: A 259 GLU cc_start: 0.7832 (OUTLIER) cc_final: 0.7150 (tm-30) REVERT: A 260 ILE cc_start: 0.8549 (mt) cc_final: 0.7871 (mt) REVERT: A 263 ASN cc_start: 0.8354 (t0) cc_final: 0.7696 (t0) REVERT: A 350 LEU cc_start: 0.8560 (tp) cc_final: 0.8218 (tt) REVERT: A 385 PHE cc_start: 0.8820 (OUTLIER) cc_final: 0.8578 (t80) REVERT: A 414 GLU cc_start: 0.7521 (tm-30) cc_final: 0.7121 (tp30) REVERT: A 425 LEU cc_start: 0.8516 (tp) cc_final: 0.8224 (tt) REVERT: A 432 MET cc_start: 0.7501 (tmm) cc_final: 0.7110 (tmm) REVERT: A 463 MET cc_start: 0.7654 (tmm) cc_final: 0.7323 (tmm) REVERT: A 466 CYS cc_start: 0.7915 (t) cc_final: 0.7364 (t) REVERT: A 473 LYS cc_start: 0.8443 (mttp) cc_final: 0.8079 (ttmm) REVERT: A 546 LYS cc_start: 0.6778 (ptmm) cc_final: 0.6298 (ptmm) REVERT: A 580 LYS cc_start: 0.8183 (mmmt) cc_final: 0.7908 (mtpt) REVERT: A 581 ARG cc_start: 0.8309 (tpt170) cc_final: 0.8081 (tpt170) REVERT: A 583 LYS cc_start: 0.8647 (OUTLIER) cc_final: 0.8089 (tmmt) REVERT: B 66 LYS cc_start: 0.8471 (tptt) cc_final: 0.8095 (tppt) REVERT: B 77 LYS cc_start: 0.8383 (ttpt) cc_final: 0.8014 (ttpt) REVERT: B 80 VAL cc_start: 0.9303 (OUTLIER) cc_final: 0.9038 (t) REVERT: B 90 SER cc_start: 0.8756 (t) cc_final: 0.8191 (p) REVERT: B 94 THR cc_start: 0.8609 (t) cc_final: 0.8308 (p) REVERT: B 125 LEU cc_start: 0.9060 (tp) cc_final: 0.8844 (tp) REVERT: B 127 TYR cc_start: 0.8625 (t80) cc_final: 0.8356 (t80) REVERT: B 150 SER cc_start: 0.8364 (t) cc_final: 0.8079 (p) REVERT: B 213 ARG cc_start: 0.8225 (mtp180) cc_final: 0.7936 (mtp180) REVERT: B 230 GLN cc_start: 0.8345 (tm-30) cc_final: 0.7855 (tm-30) REVERT: B 237 LYS cc_start: 0.8613 (pttt) cc_final: 0.8285 (ttpp) REVERT: B 250 ILE cc_start: 0.8652 (pt) cc_final: 0.8308 (mm) REVERT: B 259 GLU cc_start: 0.7658 (OUTLIER) cc_final: 0.6838 (tm-30) REVERT: B 260 ILE cc_start: 0.8657 (mt) cc_final: 0.8164 (mt) REVERT: B 349 MET cc_start: 0.6198 (mmm) cc_final: 0.5861 (mmm) REVERT: B 354 PHE cc_start: 0.7292 (OUTLIER) cc_final: 0.7029 (t80) REVERT: B 384 GLU cc_start: 0.7768 (mm-30) cc_final: 0.7482 (mm-30) REVERT: B 394 PHE cc_start: 0.8237 (t80) cc_final: 0.7901 (t80) REVERT: B 400 CYS cc_start: 0.7519 (m) cc_final: 0.7217 (m) REVERT: B 409 ARG cc_start: 0.7682 (mtm180) cc_final: 0.7469 (ttm110) REVERT: B 432 MET cc_start: 0.7440 (tmm) cc_final: 0.7170 (tmm) REVERT: B 462 PHE cc_start: 0.8565 (m-80) cc_final: 0.8330 (m-80) REVERT: B 463 MET cc_start: 0.7547 (tmm) cc_final: 0.7271 (tmm) REVERT: B 466 CYS cc_start: 0.8152 (t) cc_final: 0.7675 (t) REVERT: B 470 ARG cc_start: 0.6715 (mtp180) cc_final: 0.6400 (mtp180) REVERT: B 473 LYS cc_start: 0.8409 (mttp) cc_final: 0.8150 (mtpp) REVERT: B 486 CYS cc_start: 0.8812 (t) cc_final: 0.8558 (t) REVERT: B 488 MET cc_start: 0.7537 (tpp) cc_final: 0.7169 (tpp) REVERT: B 513 VAL cc_start: 0.9137 (OUTLIER) cc_final: 0.8908 (p) REVERT: B 531 LYS cc_start: 0.8617 (mmtm) cc_final: 0.8280 (mmmm) REVERT: B 556 TYR cc_start: 0.8996 (p90) cc_final: 0.8695 (p90) REVERT: B 578 TYR cc_start: 0.7748 (t80) cc_final: 0.7170 (t80) REVERT: B 581 ARG cc_start: 0.8227 (tpp-160) cc_final: 0.7867 (tpp-160) REVERT: B 583 LYS cc_start: 0.8473 (OUTLIER) cc_final: 0.7944 (tmmt) REVERT: B 681 LYS cc_start: 0.8360 (mptt) cc_final: 0.7970 (mptt) REVERT: B 705 GLN cc_start: 0.8671 (tt0) cc_final: 0.8364 (tt0) REVERT: B 714 ARG cc_start: 0.7406 (mtm-85) cc_final: 0.7105 (mtm-85) REVERT: B 715 LYS cc_start: 0.8519 (ptpt) cc_final: 0.8260 (ptpp) outliers start: 61 outliers final: 26 residues processed: 354 average time/residue: 0.2509 time to fit residues: 118.7625 Evaluate side-chains 333 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 298 time to evaluate : 1.014 ------------------------------------------------------------------------------- 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 187 LEU Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 203 PHE Chi-restraints excluded: chain A residue 259 GLU Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 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 80 VAL Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 259 GLU Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 354 PHE Chi-restraints excluded: chain B residue 405 THR Chi-restraints excluded: chain B residue 449 VAL Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain B residue 583 LYS Chi-restraints excluded: chain B residue 688 VAL Chi-restraints excluded: chain B residue 690 VAL Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 699 VAL Chi-restraints excluded: chain B residue 713 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 1.9990 chunk 90 optimal weight: 0.4980 chunk 62 optimal weight: 0.0030 chunk 13 optimal weight: 0.6980 chunk 57 optimal weight: 0.9980 chunk 80 optimal weight: 4.9990 chunk 120 optimal weight: 0.9990 chunk 127 optimal weight: 1.9990 chunk 114 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 106 optimal weight: 0.7980 overall best weight: 0.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 289 ASN A 322 ASN A 457 ASN B 35 GLN ** B 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 567 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.4469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 10390 Z= 0.235 Angle : 0.640 8.989 14120 Z= 0.330 Chirality : 0.043 0.235 1714 Planarity : 0.004 0.040 1756 Dihedral : 6.586 95.475 1448 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 5.69 % Allowed : 20.02 % Favored : 74.29 % 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: -1.33 (0.23), residues: 1316 helix: 0.14 (0.18), residues: 830 sheet: 1.35 (1.02), residues: 20 loop : -2.90 (0.27), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 83 HIS 0.007 0.001 HIS B 728 PHE 0.030 0.002 PHE B 128 TYR 0.032 0.002 TYR A 578 ARG 0.005 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 324 time to evaluate : 1.107 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 ARG cc_start: 0.7608 (mtm-85) cc_final: 0.7272 (mtt90) REVERT: A 66 LYS cc_start: 0.8420 (tptp) cc_final: 0.8052 (tppt) REVERT: A 77 LYS cc_start: 0.8052 (ttpt) cc_final: 0.7643 (ttpt) REVERT: A 90 SER cc_start: 0.8595 (t) cc_final: 0.8033 (p) REVERT: A 94 THR cc_start: 0.8447 (t) cc_final: 0.8049 (p) REVERT: A 125 LEU cc_start: 0.8959 (tp) cc_final: 0.8705 (tt) REVERT: A 155 MET cc_start: 0.8158 (ptp) cc_final: 0.7929 (ptp) REVERT: A 195 LEU cc_start: 0.8887 (OUTLIER) cc_final: 0.8474 (tm) REVERT: A 230 GLN cc_start: 0.8221 (tp40) cc_final: 0.7869 (tm-30) REVERT: A 237 LYS cc_start: 0.8748 (pttt) cc_final: 0.8436 (ttpp) REVERT: A 238 ILE cc_start: 0.8847 (tp) cc_final: 0.8587 (tp) REVERT: A 259 GLU cc_start: 0.7870 (OUTLIER) cc_final: 0.7245 (tm-30) REVERT: A 260 ILE cc_start: 0.8555 (mt) cc_final: 0.7919 (mt) REVERT: A 263 ASN cc_start: 0.8325 (t0) cc_final: 0.8077 (t0) REVERT: A 350 LEU cc_start: 0.8478 (tp) cc_final: 0.8143 (tt) REVERT: A 385 PHE cc_start: 0.8841 (OUTLIER) cc_final: 0.8586 (t80) REVERT: A 404 THR cc_start: 0.7432 (OUTLIER) cc_final: 0.6995 (t) REVERT: A 414 GLU cc_start: 0.7538 (tm-30) cc_final: 0.7165 (tp30) REVERT: A 432 MET cc_start: 0.7571 (tmm) cc_final: 0.7146 (tmm) REVERT: A 463 MET cc_start: 0.7679 (tmm) cc_final: 0.7118 (tmm) REVERT: A 466 CYS cc_start: 0.8034 (t) cc_final: 0.7498 (t) REVERT: A 473 LYS cc_start: 0.8464 (mttp) cc_final: 0.8022 (mtpp) REVERT: A 564 LYS cc_start: 0.8434 (OUTLIER) cc_final: 0.8178 (ttmm) REVERT: A 573 ASP cc_start: 0.7711 (t0) cc_final: 0.6771 (p0) REVERT: A 580 LYS cc_start: 0.8185 (mmmt) cc_final: 0.7942 (mmmm) REVERT: A 581 ARG cc_start: 0.8308 (tpt170) cc_final: 0.8085 (tpt170) REVERT: A 583 LYS cc_start: 0.8600 (OUTLIER) cc_final: 0.8068 (tmmt) REVERT: B 66 LYS cc_start: 0.8405 (tptt) cc_final: 0.7925 (tppt) REVERT: B 77 LYS cc_start: 0.8404 (ttpt) cc_final: 0.8025 (ttpt) REVERT: B 90 SER cc_start: 0.8748 (t) cc_final: 0.8262 (p) REVERT: B 125 LEU cc_start: 0.8992 (tp) cc_final: 0.8609 (tp) REVERT: B 150 SER cc_start: 0.8407 (t) cc_final: 0.8126 (p) REVERT: B 230 GLN cc_start: 0.8412 (tm-30) cc_final: 0.7586 (tm-30) REVERT: B 237 LYS cc_start: 0.8655 (pttt) cc_final: 0.8324 (ttpp) REVERT: B 238 ILE cc_start: 0.8853 (tp) cc_final: 0.8398 (pt) REVERT: B 250 ILE cc_start: 0.8705 (pt) cc_final: 0.8351 (mm) REVERT: B 255 TYR cc_start: 0.7969 (m-10) cc_final: 0.7482 (m-10) REVERT: B 259 GLU cc_start: 0.7593 (OUTLIER) cc_final: 0.6859 (tm-30) REVERT: B 260 ILE cc_start: 0.8719 (mt) cc_final: 0.8191 (mt) REVERT: B 354 PHE cc_start: 0.7306 (OUTLIER) cc_final: 0.7026 (t80) REVERT: B 384 GLU cc_start: 0.7734 (mm-30) cc_final: 0.7495 (mm-30) REVERT: B 394 PHE cc_start: 0.8245 (t80) cc_final: 0.7896 (t80) REVERT: B 400 CYS cc_start: 0.7249 (m) cc_final: 0.6889 (m) REVERT: B 414 GLU cc_start: 0.7691 (tm-30) cc_final: 0.7124 (tp30) REVERT: B 432 MET cc_start: 0.7529 (tmm) cc_final: 0.7297 (tmm) REVERT: B 458 LEU cc_start: 0.8597 (OUTLIER) cc_final: 0.8346 (mt) REVERT: B 462 PHE cc_start: 0.8561 (m-80) cc_final: 0.8303 (m-10) REVERT: B 463 MET cc_start: 0.7563 (tmm) cc_final: 0.7265 (tmm) REVERT: B 466 CYS cc_start: 0.8166 (t) cc_final: 0.7718 (t) REVERT: B 470 ARG cc_start: 0.6743 (mtp180) cc_final: 0.6425 (mtp180) REVERT: B 473 LYS cc_start: 0.8442 (mttp) cc_final: 0.8190 (mtpp) REVERT: B 486 CYS cc_start: 0.8815 (t) cc_final: 0.8564 (t) REVERT: B 488 MET cc_start: 0.7524 (tpp) cc_final: 0.7195 (tpp) REVERT: B 513 VAL cc_start: 0.9162 (OUTLIER) cc_final: 0.8933 (p) REVERT: B 531 LYS cc_start: 0.8626 (mmtm) cc_final: 0.8323 (mmmm) REVERT: B 537 LYS cc_start: 0.8325 (tmtt) cc_final: 0.8019 (tptp) REVERT: B 556 TYR cc_start: 0.8997 (p90) cc_final: 0.8646 (p90) REVERT: B 578 TYR cc_start: 0.7739 (t80) cc_final: 0.7222 (t80) REVERT: B 580 LYS cc_start: 0.7842 (mmmm) cc_final: 0.7606 (mmmm) REVERT: B 581 ARG cc_start: 0.8204 (tpp-160) cc_final: 0.7862 (tpp-160) REVERT: B 583 LYS cc_start: 0.8491 (OUTLIER) cc_final: 0.7946 (tmmt) REVERT: B 705 GLN cc_start: 0.8664 (tt0) cc_final: 0.8329 (tt0) REVERT: B 714 ARG cc_start: 0.7417 (mtm-85) cc_final: 0.7160 (mtm-85) REVERT: B 715 LYS cc_start: 0.8404 (ptpt) cc_final: 0.8015 (ptpp) outliers start: 64 outliers final: 35 residues processed: 363 average time/residue: 0.2542 time to fit residues: 124.9413 Evaluate side-chains 355 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 309 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 GLU Chi-restraints excluded: chain A residue 43 ARG Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 203 PHE Chi-restraints excluded: chain A residue 259 GLU Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 397 PHE Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 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 75 LEU Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 259 GLU Chi-restraints excluded: chain B residue 283 MET Chi-restraints excluded: chain B residue 298 VAL 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 72 optimal weight: 1.9990 chunk 1 optimal weight: 0.0970 chunk 95 optimal weight: 0.9990 chunk 52 optimal weight: 0.9980 chunk 108 optimal weight: 0.8980 chunk 88 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 65 optimal weight: 0.8980 chunk 114 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 42 optimal weight: 0.5980 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 GLN A 322 ASN ** A 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 457 ASN ** B 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.4881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 10390 Z= 0.257 Angle : 0.679 11.178 14120 Z= 0.346 Chirality : 0.043 0.182 1714 Planarity : 0.004 0.041 1756 Dihedral : 6.610 96.895 1445 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 12.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 5.52 % Allowed : 22.15 % Favored : 72.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.23), residues: 1316 helix: 0.28 (0.18), residues: 830 sheet: 1.76 (1.08), residues: 20 loop : -2.77 (0.27), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 83 HIS 0.007 0.001 HIS B 728 PHE 0.028 0.002 PHE B 272 TYR 0.031 0.002 TYR B 323 ARG 0.007 0.001 ARG B 409 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 330 time to evaluate : 1.116 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: 0.7763 (mtm-85) cc_final: 0.7495 (mtt90) REVERT: A 77 LYS cc_start: 0.8127 (ttpt) cc_final: 0.7682 (ttpt) REVERT: A 90 SER cc_start: 0.8668 (t) cc_final: 0.8028 (p) REVERT: A 94 THR cc_start: 0.8517 (t) cc_final: 0.8164 (p) REVERT: A 125 LEU cc_start: 0.8968 (tp) cc_final: 0.8720 (tt) REVERT: A 134 ARG cc_start: 0.7973 (mpp80) cc_final: 0.7085 (mpp80) REVERT: A 195 LEU cc_start: 0.8966 (OUTLIER) cc_final: 0.8724 (tp) REVERT: A 230 GLN cc_start: 0.8229 (tp40) cc_final: 0.7882 (tm-30) REVERT: A 237 LYS cc_start: 0.8789 (pttt) cc_final: 0.8384 (ttpp) REVERT: A 238 ILE cc_start: 0.8931 (tp) cc_final: 0.8686 (tp) REVERT: A 255 TYR cc_start: 0.7740 (m-10) cc_final: 0.7478 (m-10) REVERT: A 259 GLU cc_start: 0.7786 (tm-30) cc_final: 0.7149 (tm-30) REVERT: A 260 ILE cc_start: 0.8629 (mt) cc_final: 0.8035 (mt) REVERT: A 322 ASN cc_start: 0.7190 (OUTLIER) cc_final: 0.5962 (t0) REVERT: A 350 LEU cc_start: 0.8520 (tp) cc_final: 0.8161 (tt) REVERT: A 358 VAL cc_start: 0.8857 (t) cc_final: 0.8645 (p) REVERT: A 377 TYR cc_start: 0.6293 (t80) cc_final: 0.5851 (t80) REVERT: A 404 THR cc_start: 0.7351 (OUTLIER) cc_final: 0.6862 (t) REVERT: A 414 GLU cc_start: 0.7638 (tm-30) cc_final: 0.7313 (tp30) REVERT: A 432 MET cc_start: 0.7606 (tmm) cc_final: 0.7157 (tmm) REVERT: A 463 MET cc_start: 0.7672 (tmm) cc_final: 0.7163 (tmm) REVERT: A 466 CYS cc_start: 0.8124 (t) cc_final: 0.7579 (t) REVERT: A 473 LYS cc_start: 0.8520 (mttp) cc_final: 0.8101 (ttmm) REVERT: A 537 LYS cc_start: 0.8041 (ttmt) cc_final: 0.7450 (ptmm) REVERT: A 577 VAL cc_start: 0.8612 (OUTLIER) cc_final: 0.8408 (p) REVERT: A 580 LYS cc_start: 0.8184 (mmmt) cc_final: 0.7843 (mmmt) REVERT: A 583 LYS cc_start: 0.8631 (OUTLIER) cc_final: 0.7942 (tmmt) REVERT: A 681 LYS cc_start: 0.8378 (mptt) cc_final: 0.8015 (mptt) REVERT: A 714 ARG cc_start: 0.7382 (mpt180) cc_final: 0.6857 (mtm-85) REVERT: B 77 LYS cc_start: 0.8458 (ttpt) cc_final: 0.8105 (ttpt) REVERT: B 90 SER cc_start: 0.8676 (t) cc_final: 0.8236 (p) REVERT: B 126 THR cc_start: 0.8549 (OUTLIER) cc_final: 0.8333 (t) REVERT: B 150 SER cc_start: 0.8335 (t) cc_final: 0.8063 (p) REVERT: B 230 GLN cc_start: 0.8446 (tm-30) cc_final: 0.8069 (tm-30) REVERT: B 236 LEU cc_start: 0.8936 (tp) cc_final: 0.8695 (tp) REVERT: B 237 LYS cc_start: 0.8667 (pttt) cc_final: 0.8219 (ptmm) REVERT: B 238 ILE cc_start: 0.8936 (tp) cc_final: 0.8491 (pt) REVERT: B 250 ILE cc_start: 0.8729 (pt) cc_final: 0.8411 (mm) REVERT: B 255 TYR cc_start: 0.7987 (m-10) cc_final: 0.7571 (m-10) REVERT: B 260 ILE cc_start: 0.8740 (mt) cc_final: 0.8417 (mt) REVERT: B 354 PHE cc_start: 0.7342 (OUTLIER) cc_final: 0.7122 (t80) REVERT: B 384 GLU cc_start: 0.7765 (mm-30) cc_final: 0.7508 (mm-30) REVERT: B 394 PHE cc_start: 0.8256 (t80) cc_final: 0.7678 (t80) REVERT: B 400 CYS cc_start: 0.7265 (m) cc_final: 0.6953 (m) REVERT: B 414 GLU cc_start: 0.7718 (tm-30) cc_final: 0.7151 (tp30) REVERT: B 432 MET cc_start: 0.7550 (tmm) cc_final: 0.7299 (tmm) REVERT: B 442 LEU cc_start: 0.7883 (mt) cc_final: 0.7673 (mm) REVERT: B 447 LYS cc_start: 0.8797 (ttmt) cc_final: 0.8560 (ttmm) REVERT: B 458 LEU cc_start: 0.8636 (OUTLIER) cc_final: 0.8393 (mt) REVERT: B 462 PHE cc_start: 0.8579 (m-80) cc_final: 0.8322 (m-10) REVERT: B 463 MET cc_start: 0.7562 (tmm) cc_final: 0.7287 (tmm) REVERT: B 466 CYS cc_start: 0.8211 (t) cc_final: 0.7773 (t) REVERT: B 470 ARG cc_start: 0.6737 (mtp180) cc_final: 0.6424 (mtp180) REVERT: B 473 LYS cc_start: 0.8449 (mttp) cc_final: 0.8194 (ttmm) REVERT: B 486 CYS cc_start: 0.8810 (t) cc_final: 0.8557 (t) REVERT: B 488 MET cc_start: 0.7549 (tpp) cc_final: 0.7217 (tpp) REVERT: B 513 VAL cc_start: 0.9186 (OUTLIER) cc_final: 0.8953 (p) REVERT: B 556 TYR cc_start: 0.9011 (p90) cc_final: 0.8727 (p90) REVERT: B 578 TYR cc_start: 0.7704 (t80) cc_final: 0.7218 (t80) REVERT: B 580 LYS cc_start: 0.7871 (mmmm) cc_final: 0.7609 (mmmm) REVERT: B 581 ARG cc_start: 0.8215 (tpp-160) cc_final: 0.7876 (tpp-160) REVERT: B 583 LYS cc_start: 0.8494 (OUTLIER) cc_final: 0.7962 (tmmt) REVERT: B 681 LYS cc_start: 0.8442 (mptt) cc_final: 0.8029 (mptt) REVERT: B 705 GLN cc_start: 0.8650 (tt0) cc_final: 0.8300 (tt0) REVERT: B 714 ARG cc_start: 0.7452 (mtm-85) cc_final: 0.7251 (mtm-85) outliers start: 62 outliers final: 35 residues processed: 366 average time/residue: 0.2705 time to fit residues: 129.8171 Evaluate side-chains 362 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 317 time to evaluate : 1.085 ------------------------------------------------------------------------------- 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 195 LEU Chi-restraints excluded: chain A residue 322 ASN 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 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 75 LEU Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 259 GLU Chi-restraints excluded: chain B residue 283 MET Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 354 PHE Chi-restraints excluded: chain B residue 397 PHE 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 703 MET Chi-restraints excluded: chain B residue 704 GLU Chi-restraints excluded: chain B residue 713 ILE Chi-restraints excluded: chain B residue 716 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 114 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 127 optimal weight: 0.9980 chunk 106 optimal weight: 0.5980 chunk 59 optimal weight: 0.6980 chunk 10 optimal weight: 0.5980 chunk 42 optimal weight: 0.7980 chunk 67 optimal weight: 1.9990 chunk 123 optimal weight: 4.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN A 535 HIS A 538 ASN ** B 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.5233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 10390 Z= 0.267 Angle : 0.687 8.776 14120 Z= 0.354 Chirality : 0.044 0.216 1714 Planarity : 0.005 0.081 1756 Dihedral : 6.149 95.788 1442 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 13.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 5.25 % Allowed : 23.75 % Favored : 71.00 % 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: -1.07 (0.23), residues: 1316 helix: 0.31 (0.18), residues: 828 sheet: 1.86 (1.11), residues: 20 loop : -2.74 (0.27), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 83 HIS 0.006 0.001 HIS B 728 PHE 0.029 0.002 PHE B 128 TYR 0.033 0.002 TYR B 323 ARG 0.009 0.001 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 329 time to evaluate : 1.289 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: 0.6980 (mp0) cc_final: 0.6542 (mp0) REVERT: A 77 LYS cc_start: 0.8181 (ttpt) cc_final: 0.7708 (ttpt) REVERT: A 90 SER cc_start: 0.8650 (t) cc_final: 0.8025 (p) REVERT: A 94 THR cc_start: 0.8572 (t) cc_final: 0.8178 (p) REVERT: A 125 LEU cc_start: 0.8948 (tp) cc_final: 0.8709 (tt) REVERT: A 155 MET cc_start: 0.8208 (ptp) cc_final: 0.7963 (ptp) REVERT: A 195 LEU cc_start: 0.8949 (OUTLIER) cc_final: 0.8699 (tp) REVERT: A 207 GLN cc_start: 0.7866 (mp10) cc_final: 0.7666 (mp10) REVERT: A 230 GLN cc_start: 0.8269 (tp40) cc_final: 0.7891 (tm-30) REVERT: A 237 LYS cc_start: 0.8815 (pttt) cc_final: 0.8383 (ttpp) REVERT: A 238 ILE cc_start: 0.8962 (tp) cc_final: 0.8705 (tp) REVERT: A 251 LEU cc_start: 0.8741 (mm) cc_final: 0.8379 (mm) REVERT: A 255 TYR cc_start: 0.7759 (m-10) cc_final: 0.7531 (m-10) REVERT: A 259 GLU cc_start: 0.7850 (tm-30) cc_final: 0.7208 (tm-30) REVERT: A 260 ILE cc_start: 0.8649 (mt) cc_final: 0.8389 (mt) REVERT: A 263 ASN cc_start: 0.8279 (t0) cc_final: 0.7785 (t0) REVERT: A 350 LEU cc_start: 0.8496 (tp) cc_final: 0.8128 (tt) REVERT: A 358 VAL cc_start: 0.8869 (t) cc_final: 0.8605 (p) REVERT: A 385 PHE cc_start: 0.8947 (OUTLIER) cc_final: 0.8633 (t80) REVERT: A 404 THR cc_start: 0.7400 (OUTLIER) cc_final: 0.6899 (t) REVERT: A 409 ARG cc_start: 0.8244 (mtm180) cc_final: 0.7818 (mtm110) REVERT: A 414 GLU cc_start: 0.7632 (tm-30) cc_final: 0.7047 (tm-30) REVERT: A 432 MET cc_start: 0.7606 (tmm) cc_final: 0.7190 (tmm) REVERT: A 463 MET cc_start: 0.7649 (tmm) cc_final: 0.7121 (tmm) REVERT: A 466 CYS cc_start: 0.8142 (t) cc_final: 0.7602 (t) REVERT: A 473 LYS cc_start: 0.8541 (mttp) cc_final: 0.8110 (ttmm) REVERT: A 475 ASN cc_start: 0.8361 (t0) cc_final: 0.7997 (t0) REVERT: A 540 GLU cc_start: 0.8164 (pm20) cc_final: 0.7871 (pm20) REVERT: A 580 LYS cc_start: 0.8182 (mmmt) cc_final: 0.7850 (mmmt) REVERT: A 583 LYS cc_start: 0.8634 (OUTLIER) cc_final: 0.7948 (tmmt) REVERT: B 66 LYS cc_start: 0.8450 (tptt) cc_final: 0.8039 (tppt) REVERT: B 77 LYS cc_start: 0.8457 (ttpt) cc_final: 0.8086 (ttpt) REVERT: B 90 SER cc_start: 0.8656 (t) cc_final: 0.8222 (p) REVERT: B 150 SER cc_start: 0.8360 (t) cc_final: 0.8076 (p) REVERT: B 230 GLN cc_start: 0.8483 (tm-30) cc_final: 0.8095 (tm-30) REVERT: B 235 GLN cc_start: 0.8219 (mm-40) cc_final: 0.7986 (mm110) REVERT: B 236 LEU cc_start: 0.8985 (tp) cc_final: 0.8731 (tp) REVERT: B 237 LYS cc_start: 0.8664 (pttt) cc_final: 0.8364 (ttpp) REVERT: B 250 ILE cc_start: 0.8743 (pt) cc_final: 0.8435 (mm) REVERT: B 255 TYR cc_start: 0.8021 (m-10) cc_final: 0.7670 (m-10) REVERT: B 259 GLU cc_start: 0.7615 (OUTLIER) cc_final: 0.7400 (tm-30) REVERT: B 260 ILE cc_start: 0.8741 (mt) cc_final: 0.8399 (mt) REVERT: B 354 PHE cc_start: 0.7365 (OUTLIER) cc_final: 0.7009 (t80) REVERT: B 400 CYS cc_start: 0.7237 (m) cc_final: 0.6892 (m) REVERT: B 414 GLU cc_start: 0.7748 (tm-30) cc_final: 0.7192 (tp30) REVERT: B 432 MET cc_start: 0.7606 (tmm) cc_final: 0.7351 (tmm) REVERT: B 458 LEU cc_start: 0.8700 (OUTLIER) cc_final: 0.8472 (mt) REVERT: B 462 PHE cc_start: 0.8576 (m-80) cc_final: 0.8319 (m-10) REVERT: B 463 MET cc_start: 0.7594 (tmm) cc_final: 0.7313 (tmm) REVERT: B 466 CYS cc_start: 0.8261 (t) cc_final: 0.7863 (t) REVERT: B 467 ASP cc_start: 0.7337 (OUTLIER) cc_final: 0.6972 (t0) REVERT: B 473 LYS cc_start: 0.8436 (mttp) cc_final: 0.8165 (mtpp) REVERT: B 486 CYS cc_start: 0.8800 (t) cc_final: 0.8555 (t) REVERT: B 488 MET cc_start: 0.7574 (tpp) cc_final: 0.7229 (tpp) REVERT: B 513 VAL cc_start: 0.9201 (OUTLIER) cc_final: 0.8974 (p) REVERT: B 531 LYS cc_start: 0.8642 (mmtm) cc_final: 0.8417 (mmmm) REVERT: B 556 TYR cc_start: 0.9016 (p90) cc_final: 0.8712 (p90) REVERT: B 578 TYR cc_start: 0.7720 (t80) cc_final: 0.7222 (t80) REVERT: B 580 LYS cc_start: 0.7956 (mmmm) cc_final: 0.7692 (mmmm) REVERT: B 581 ARG cc_start: 0.8207 (tpp-160) cc_final: 0.7847 (tpp-160) REVERT: B 583 LYS cc_start: 0.8540 (OUTLIER) cc_final: 0.7996 (tmmt) REVERT: B 681 LYS cc_start: 0.8425 (mptt) cc_final: 0.8178 (mptt) REVERT: B 705 GLN cc_start: 0.8692 (tt0) cc_final: 0.8385 (tt0) REVERT: B 724 ASP cc_start: 0.7828 (OUTLIER) cc_final: 0.7505 (t70) outliers start: 59 outliers final: 33 residues processed: 362 average time/residue: 0.2664 time to fit residues: 127.8247 Evaluate side-chains 351 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 307 time to evaluate : 1.073 ------------------------------------------------------------------------------- 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 144 VAL Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 397 PHE Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 564 LYS Chi-restraints excluded: chain A residue 583 LYS Chi-restraints excluded: chain A residue 682 GLU Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 715 LYS Chi-restraints excluded: chain A residue 716 ASP Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 73 ASP Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 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 329 LYS Chi-restraints excluded: chain B residue 348 ASP Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 354 PHE Chi-restraints excluded: chain B residue 383 GLN Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 405 THR Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 467 ASP Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain B residue 583 LYS Chi-restraints excluded: chain B residue 690 VAL Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 699 VAL Chi-restraints excluded: chain B residue 713 ILE Chi-restraints excluded: chain B residue 716 ASP Chi-restraints excluded: chain B residue 724 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 14 optimal weight: 0.6980 chunk 72 optimal weight: 0.6980 chunk 93 optimal weight: 0.0030 chunk 107 optimal weight: 1.9990 chunk 71 optimal weight: 0.2980 chunk 127 optimal weight: 0.6980 chunk 79 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 78 optimal weight: 0.7980 chunk 50 optimal weight: 0.6980 overall best weight: 0.4790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 324 ASN ** B 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.5381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 10390 Z= 0.229 Angle : 0.685 9.314 14120 Z= 0.352 Chirality : 0.043 0.239 1714 Planarity : 0.004 0.047 1756 Dihedral : 6.129 95.522 1441 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 13.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 5.34 % Allowed : 24.11 % 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: -0.99 (0.23), residues: 1316 helix: 0.36 (0.18), residues: 828 sheet: 2.06 (1.14), residues: 20 loop : -2.68 (0.27), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 83 HIS 0.004 0.001 HIS A 728 PHE 0.028 0.001 PHE B 128 TYR 0.029 0.002 TYR B 323 ARG 0.010 0.001 ARG B 134 *********************** 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 365 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 305 time to evaluate : 1.159 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: 0.6931 (mp0) cc_final: 0.6555 (mp0) REVERT: A 77 LYS cc_start: 0.8137 (ttpt) cc_final: 0.7678 (ttpt) REVERT: A 90 SER cc_start: 0.8623 (t) cc_final: 0.8008 (p) REVERT: A 94 THR cc_start: 0.8570 (t) cc_final: 0.8164 (p) REVERT: A 125 LEU cc_start: 0.8950 (tp) cc_final: 0.8709 (tt) REVERT: A 155 MET cc_start: 0.8212 (ptp) cc_final: 0.7983 (ptp) REVERT: A 195 LEU cc_start: 0.8976 (OUTLIER) cc_final: 0.8763 (tp) REVERT: A 207 GLN cc_start: 0.7851 (mp10) cc_final: 0.7640 (mp10) REVERT: A 230 GLN cc_start: 0.8245 (tp40) cc_final: 0.7897 (tm-30) REVERT: A 237 LYS cc_start: 0.8801 (pttt) cc_final: 0.8369 (ttpp) REVERT: A 238 ILE cc_start: 0.8951 (tp) cc_final: 0.8700 (tp) REVERT: A 251 LEU cc_start: 0.8711 (mm) cc_final: 0.8407 (mm) REVERT: A 259 GLU cc_start: 0.7826 (tm-30) cc_final: 0.7126 (tm-30) REVERT: A 260 ILE cc_start: 0.8650 (mt) cc_final: 0.8371 (mt) REVERT: A 350 LEU cc_start: 0.8480 (tp) cc_final: 0.8128 (tt) REVERT: A 358 VAL cc_start: 0.8867 (t) cc_final: 0.8602 (p) REVERT: A 404 THR cc_start: 0.7407 (OUTLIER) cc_final: 0.6814 (p) REVERT: A 409 ARG cc_start: 0.8217 (mtm180) cc_final: 0.7790 (mtm110) REVERT: A 414 GLU cc_start: 0.7619 (tm-30) cc_final: 0.7030 (tm-30) REVERT: A 432 MET cc_start: 0.7592 (tmm) cc_final: 0.7160 (tmm) REVERT: A 463 MET cc_start: 0.7627 (tmm) cc_final: 0.7085 (tmm) REVERT: A 466 CYS cc_start: 0.8113 (t) cc_final: 0.7592 (t) REVERT: A 473 LYS cc_start: 0.8513 (mttp) cc_final: 0.8103 (ttmm) REVERT: A 537 LYS cc_start: 0.8084 (ttmt) cc_final: 0.7520 (ttpp) REVERT: A 540 GLU cc_start: 0.8149 (pm20) cc_final: 0.7806 (pm20) REVERT: A 580 LYS cc_start: 0.8178 (mmmt) cc_final: 0.7840 (mmmt) REVERT: A 583 LYS cc_start: 0.8611 (OUTLIER) cc_final: 0.7925 (tmmt) REVERT: A 681 LYS cc_start: 0.8308 (mptt) cc_final: 0.8020 (mptt) REVERT: B 66 LYS cc_start: 0.8388 (tptt) cc_final: 0.7927 (tppt) REVERT: B 77 LYS cc_start: 0.8446 (ttpt) cc_final: 0.8076 (ttpt) REVERT: B 90 SER cc_start: 0.8610 (t) cc_final: 0.8182 (p) REVERT: B 150 SER cc_start: 0.8359 (t) cc_final: 0.8076 (p) REVERT: B 230 GLN cc_start: 0.8476 (tm-30) cc_final: 0.8104 (tm-30) REVERT: B 235 GLN cc_start: 0.8223 (mm-40) cc_final: 0.7999 (mm110) REVERT: B 236 LEU cc_start: 0.8957 (tp) cc_final: 0.8706 (tp) REVERT: B 237 LYS cc_start: 0.8664 (pttt) cc_final: 0.8326 (ttpp) REVERT: B 250 ILE cc_start: 0.8758 (pt) cc_final: 0.8488 (mm) REVERT: B 255 TYR cc_start: 0.8015 (m-10) cc_final: 0.7685 (m-10) REVERT: B 404 THR cc_start: 0.7705 (OUTLIER) cc_final: 0.7164 (p) REVERT: B 414 GLU cc_start: 0.7740 (tm-30) cc_final: 0.7384 (tp30) REVERT: B 432 MET cc_start: 0.7599 (tmm) cc_final: 0.7362 (tmm) REVERT: B 458 LEU cc_start: 0.8639 (OUTLIER) cc_final: 0.8401 (mt) REVERT: B 462 PHE cc_start: 0.8561 (m-80) cc_final: 0.8284 (m-10) REVERT: B 463 MET cc_start: 0.7555 (tmm) cc_final: 0.7282 (tmm) REVERT: B 466 CYS cc_start: 0.8249 (t) cc_final: 0.7880 (t) REVERT: B 473 LYS cc_start: 0.8351 (mttp) cc_final: 0.8088 (mtpp) REVERT: B 486 CYS cc_start: 0.8802 (t) cc_final: 0.8549 (t) REVERT: B 488 MET cc_start: 0.7562 (tpp) cc_final: 0.7215 (tpp) REVERT: B 513 VAL cc_start: 0.9199 (OUTLIER) cc_final: 0.8968 (p) REVERT: B 531 LYS cc_start: 0.8637 (mmtm) cc_final: 0.8397 (mmmm) REVERT: B 549 ARG cc_start: 0.7615 (ttm-80) cc_final: 0.7157 (ttt-90) REVERT: B 556 TYR cc_start: 0.9012 (p90) cc_final: 0.8728 (p90) REVERT: B 578 TYR cc_start: 0.7693 (t80) cc_final: 0.7192 (t80) REVERT: B 580 LYS cc_start: 0.7983 (mmmm) cc_final: 0.7710 (mmmm) REVERT: B 581 ARG cc_start: 0.8208 (tpp-160) cc_final: 0.7843 (tpp-160) REVERT: B 583 LYS cc_start: 0.8533 (OUTLIER) cc_final: 0.7989 (tmmt) REVERT: B 677 ARG cc_start: 0.7915 (ttp-110) cc_final: 0.7629 (ttp-110) REVERT: B 681 LYS cc_start: 0.8497 (mptt) cc_final: 0.8206 (mptt) REVERT: B 705 GLN cc_start: 0.8640 (tt0) cc_final: 0.8312 (tt0) REVERT: B 724 ASP cc_start: 0.7790 (OUTLIER) cc_final: 0.7537 (t70) outliers start: 60 outliers final: 34 residues processed: 340 average time/residue: 0.2673 time to fit residues: 119.7279 Evaluate side-chains 340 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 298 time to evaluate : 1.258 ------------------------------------------------------------------------------- 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 195 LEU Chi-restraints excluded: chain A residue 276 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 564 LYS Chi-restraints excluded: chain A residue 583 LYS Chi-restraints excluded: chain A residue 682 GLU Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 715 LYS Chi-restraints excluded: chain A residue 716 ASP Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 73 ASP Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 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 404 THR Chi-restraints excluded: chain B residue 405 THR Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 461 MET Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain B residue 583 LYS Chi-restraints excluded: chain B residue 690 VAL Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 699 VAL Chi-restraints excluded: chain B residue 713 ILE Chi-restraints excluded: chain B residue 716 ASP Chi-restraints excluded: chain B residue 724 ASP 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 75 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 chunk 24 optimal weight: 0.0040 chunk 80 optimal weight: 6.9990 chunk 86 optimal weight: 0.5980 chunk 62 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 100 optimal weight: 0.6980 chunk 115 optimal weight: 0.6980 chunk 121 optimal weight: 0.7980 chunk 111 optimal weight: 0.0670 overall best weight: 0.4130 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.5472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10390 Z= 0.217 Angle : 0.700 11.604 14120 Z= 0.355 Chirality : 0.043 0.166 1714 Planarity : 0.004 0.047 1756 Dihedral : 5.515 44.981 1438 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 13.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 4.09 % Allowed : 25.80 % Favored : 70.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.93 (0.23), residues: 1316 helix: 0.38 (0.18), residues: 828 sheet: 2.30 (1.16), residues: 20 loop : -2.63 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 83 HIS 0.005 0.001 HIS A 728 PHE 0.029 0.002 PHE B 394 TYR 0.027 0.002 TYR B 323 ARG 0.013 0.001 ARG A 36 *********************** 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 340 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 294 time to evaluate : 1.010 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: 0.6901 (mp0) cc_final: 0.6543 (mp0) REVERT: A 36 ARG cc_start: 0.7432 (mtt90) cc_final: 0.7095 (mtt90) REVERT: A 77 LYS cc_start: 0.8134 (ttpt) cc_final: 0.7677 (ttpt) REVERT: A 90 SER cc_start: 0.8623 (t) cc_final: 0.7968 (p) REVERT: A 94 THR cc_start: 0.8567 (t) cc_final: 0.8165 (p) REVERT: A 125 LEU cc_start: 0.8938 (tp) cc_final: 0.8696 (tt) REVERT: A 195 LEU cc_start: 0.8968 (OUTLIER) cc_final: 0.8613 (tp) REVERT: A 207 GLN cc_start: 0.7953 (mp10) cc_final: 0.7728 (mp10) REVERT: A 230 GLN cc_start: 0.8201 (tp40) cc_final: 0.7899 (tm-30) REVERT: A 235 GLN cc_start: 0.8295 (mm-40) cc_final: 0.8084 (mm-40) REVERT: A 237 LYS cc_start: 0.8782 (pttt) cc_final: 0.8390 (ttpp) REVERT: A 238 ILE cc_start: 0.8949 (tp) cc_final: 0.8686 (tp) REVERT: A 251 LEU cc_start: 0.8685 (mm) cc_final: 0.8453 (mm) REVERT: A 259 GLU cc_start: 0.7870 (tm-30) cc_final: 0.7044 (tm-30) REVERT: A 260 ILE cc_start: 0.8643 (mt) cc_final: 0.8361 (mt) REVERT: A 303 GLU cc_start: 0.8085 (mp0) cc_final: 0.7802 (mp0) REVERT: A 350 LEU cc_start: 0.8424 (tp) cc_final: 0.8081 (tt) REVERT: A 358 VAL cc_start: 0.8817 (t) cc_final: 0.8568 (p) REVERT: A 404 THR cc_start: 0.7418 (OUTLIER) cc_final: 0.6832 (p) REVERT: A 409 ARG cc_start: 0.8200 (mtm180) cc_final: 0.7773 (mtm110) REVERT: A 414 GLU cc_start: 0.7617 (tm-30) cc_final: 0.7033 (tm-30) REVERT: A 432 MET cc_start: 0.7587 (tmm) cc_final: 0.7162 (tmm) REVERT: A 463 MET cc_start: 0.7610 (tmm) cc_final: 0.7042 (tmm) REVERT: A 473 LYS cc_start: 0.8538 (mttp) cc_final: 0.8134 (ttmm) REVERT: A 476 LYS cc_start: 0.9129 (mtmm) cc_final: 0.8870 (mtmm) REVERT: A 537 LYS cc_start: 0.8112 (ttmt) cc_final: 0.7577 (ttpp) REVERT: A 540 GLU cc_start: 0.8174 (pm20) cc_final: 0.7827 (pm20) REVERT: A 580 LYS cc_start: 0.8176 (mmmt) cc_final: 0.7847 (mmmt) REVERT: A 583 LYS cc_start: 0.8590 (OUTLIER) cc_final: 0.7882 (tmmt) REVERT: B 30 LEU cc_start: 0.8226 (OUTLIER) cc_final: 0.7853 (tp) REVERT: B 66 LYS cc_start: 0.8391 (tptt) cc_final: 0.7918 (tppt) REVERT: B 77 LYS cc_start: 0.8451 (ttpt) cc_final: 0.8077 (ttpt) REVERT: B 90 SER cc_start: 0.8580 (t) cc_final: 0.8201 (p) REVERT: B 150 SER cc_start: 0.8378 (t) cc_final: 0.8052 (p) REVERT: B 192 LEU cc_start: 0.8358 (tp) cc_final: 0.8136 (tp) REVERT: B 230 GLN cc_start: 0.8483 (tm-30) cc_final: 0.8117 (tm-30) REVERT: B 236 LEU cc_start: 0.8951 (tp) cc_final: 0.8693 (tp) REVERT: B 237 LYS cc_start: 0.8699 (pttt) cc_final: 0.8247 (ttmt) REVERT: B 245 LYS cc_start: 0.8224 (mmtm) cc_final: 0.8017 (mppt) REVERT: B 250 ILE cc_start: 0.8735 (pt) cc_final: 0.8491 (mm) REVERT: B 255 TYR cc_start: 0.8042 (m-10) cc_final: 0.7697 (m-10) REVERT: B 384 GLU cc_start: 0.7812 (mm-30) cc_final: 0.7541 (mm-30) REVERT: B 404 THR cc_start: 0.7700 (OUTLIER) cc_final: 0.7162 (p) REVERT: B 414 GLU cc_start: 0.7730 (tm-30) cc_final: 0.7131 (tp30) REVERT: B 426 ILE cc_start: 0.8112 (tt) cc_final: 0.7729 (pt) REVERT: B 432 MET cc_start: 0.7632 (tmm) cc_final: 0.7401 (tmm) REVERT: B 462 PHE cc_start: 0.8550 (m-80) cc_final: 0.8251 (m-10) REVERT: B 463 MET cc_start: 0.7538 (tmm) cc_final: 0.7260 (tmm) REVERT: B 466 CYS cc_start: 0.8245 (t) cc_final: 0.7867 (t) REVERT: B 473 LYS cc_start: 0.8332 (mttp) cc_final: 0.8063 (mtpp) REVERT: B 486 CYS cc_start: 0.8801 (t) cc_final: 0.8543 (t) REVERT: B 488 MET cc_start: 0.7554 (tpp) cc_final: 0.7204 (tpp) REVERT: B 513 VAL cc_start: 0.9209 (OUTLIER) cc_final: 0.8989 (p) REVERT: B 531 LYS cc_start: 0.8597 (mmtm) cc_final: 0.8362 (mmmm) REVERT: B 549 ARG cc_start: 0.7579 (ttm-80) cc_final: 0.7125 (ttt-90) REVERT: B 556 TYR cc_start: 0.8990 (p90) cc_final: 0.8725 (p90) REVERT: B 578 TYR cc_start: 0.7683 (t80) cc_final: 0.7249 (t80) REVERT: B 580 LYS cc_start: 0.7998 (mmmm) cc_final: 0.7793 (mmmm) REVERT: B 581 ARG cc_start: 0.8206 (tpp-160) cc_final: 0.7825 (tpp-160) REVERT: B 583 LYS cc_start: 0.8555 (OUTLIER) cc_final: 0.8033 (tmmt) REVERT: B 677 ARG cc_start: 0.7912 (ttp-110) cc_final: 0.7617 (ttp-110) REVERT: B 681 LYS cc_start: 0.8453 (mptt) cc_final: 0.8189 (mptt) REVERT: B 705 GLN cc_start: 0.8635 (tt0) cc_final: 0.8294 (tt0) REVERT: B 724 ASP cc_start: 0.7786 (OUTLIER) cc_final: 0.7552 (t70) outliers start: 46 outliers final: 30 residues processed: 323 average time/residue: 0.2716 time to fit residues: 115.8956 Evaluate side-chains 328 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 290 time to evaluate : 1.191 ------------------------------------------------------------------------------- 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 195 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 682 GLU Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 715 LYS Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 73 ASP Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 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 404 THR Chi-restraints excluded: chain B residue 405 THR Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain B residue 583 LYS Chi-restraints excluded: chain B residue 690 VAL Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 699 VAL Chi-restraints excluded: chain B residue 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 118 optimal weight: 1.9990 chunk 121 optimal weight: 0.4980 chunk 71 optimal weight: 0.9990 chunk 51 optimal weight: 0.0570 chunk 93 optimal weight: 0.0070 chunk 36 optimal weight: 0.2980 chunk 107 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 chunk 77 optimal weight: 0.8980 chunk 125 optimal weight: 0.9990 chunk 76 optimal weight: 0.8980 overall best weight: 0.3516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 446 GLN B 246 ASN ** B 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.5531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10390 Z= 0.209 Angle : 0.700 9.761 14120 Z= 0.355 Chirality : 0.044 0.164 1714 Planarity : 0.004 0.048 1756 Dihedral : 5.431 44.823 1436 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 13.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 3.91 % Allowed : 25.89 % Favored : 70.20 % 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: -0.84 (0.23), residues: 1316 helix: 0.44 (0.18), residues: 828 sheet: 2.29 (1.17), residues: 20 loop : -2.56 (0.28), residues: 468 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 0.032 0.001 PHE B 394 TYR 0.025 0.002 TYR B 323 ARG 0.014 0.001 ARG A 36 *********************** 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 346 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 302 time to evaluate : 1.076 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: 0.6930 (mp0) cc_final: 0.6565 (mp0) REVERT: A 36 ARG cc_start: 0.7472 (mtt90) cc_final: 0.7187 (mtt90) REVERT: A 90 SER cc_start: 0.8614 (t) cc_final: 0.7960 (p) REVERT: A 94 THR cc_start: 0.8567 (t) cc_final: 0.8156 (p) REVERT: A 125 LEU cc_start: 0.8928 (tp) cc_final: 0.8688 (tt) REVERT: A 134 ARG cc_start: 0.7934 (mpp80) cc_final: 0.7305 (mtm-85) REVERT: A 195 LEU cc_start: 0.8961 (OUTLIER) cc_final: 0.8757 (tp) REVERT: A 207 GLN cc_start: 0.7959 (mp10) cc_final: 0.7723 (mp10) REVERT: A 230 GLN cc_start: 0.8184 (tp40) cc_final: 0.7898 (tm-30) REVERT: A 235 GLN cc_start: 0.8355 (mm-40) cc_final: 0.8134 (mm110) REVERT: A 237 LYS cc_start: 0.8784 (pttt) cc_final: 0.8396 (ttpp) REVERT: A 238 ILE cc_start: 0.8945 (tp) cc_final: 0.8690 (tp) REVERT: A 251 LEU cc_start: 0.8662 (mm) cc_final: 0.8325 (mp) REVERT: A 259 GLU cc_start: 0.7862 (tm-30) cc_final: 0.7068 (tm-30) REVERT: A 260 ILE cc_start: 0.8635 (mt) cc_final: 0.8345 (mt) REVERT: A 303 GLU cc_start: 0.8068 (mp0) cc_final: 0.7811 (mp0) REVERT: A 350 LEU cc_start: 0.8510 (tp) cc_final: 0.8184 (tt) REVERT: A 358 VAL cc_start: 0.8808 (t) cc_final: 0.8557 (p) REVERT: A 404 THR cc_start: 0.7386 (OUTLIER) cc_final: 0.6920 (t) REVERT: A 409 ARG cc_start: 0.8181 (mtm180) cc_final: 0.7756 (mtm110) REVERT: A 414 GLU cc_start: 0.7623 (tm-30) cc_final: 0.7024 (tm-30) REVERT: A 432 MET cc_start: 0.7587 (tmm) cc_final: 0.7150 (tmm) REVERT: A 463 MET cc_start: 0.7611 (tmm) cc_final: 0.7062 (tmm) REVERT: A 473 LYS cc_start: 0.8540 (mttp) cc_final: 0.8156 (ttmm) REVERT: A 476 LYS cc_start: 0.9126 (mtmm) cc_final: 0.8882 (mtmm) REVERT: A 540 GLU cc_start: 0.8213 (pm20) cc_final: 0.7854 (pm20) REVERT: A 580 LYS cc_start: 0.8179 (mmmt) cc_final: 0.7895 (mtpt) REVERT: A 583 LYS cc_start: 0.8592 (OUTLIER) cc_final: 0.8004 (tmmt) REVERT: A 681 LYS cc_start: 0.8309 (mptt) cc_final: 0.8033 (mptt) REVERT: B 30 LEU cc_start: 0.8210 (OUTLIER) cc_final: 0.7874 (tp) REVERT: B 66 LYS cc_start: 0.8392 (tptt) cc_final: 0.7897 (tppt) REVERT: B 77 LYS cc_start: 0.8426 (ttpt) cc_final: 0.8060 (ttpt) REVERT: B 90 SER cc_start: 0.8576 (t) cc_final: 0.8199 (p) REVERT: B 150 SER cc_start: 0.8365 (t) cc_final: 0.8032 (p) REVERT: B 203 PHE cc_start: 0.8264 (m-80) cc_final: 0.7991 (m-80) REVERT: B 208 ILE cc_start: 0.8662 (OUTLIER) cc_final: 0.8395 (pt) REVERT: B 230 GLN cc_start: 0.8479 (tm-30) cc_final: 0.7716 (tm-30) REVERT: B 236 LEU cc_start: 0.8927 (tp) cc_final: 0.8671 (tp) REVERT: B 237 LYS cc_start: 0.8713 (pttt) cc_final: 0.8358 (ttpt) REVERT: B 250 ILE cc_start: 0.8767 (pt) cc_final: 0.8512 (mm) REVERT: B 255 TYR cc_start: 0.8041 (m-10) cc_final: 0.7704 (m-10) REVERT: B 259 GLU cc_start: 0.8320 (tp30) cc_final: 0.7296 (tp30) REVERT: B 384 GLU cc_start: 0.7794 (mm-30) cc_final: 0.7556 (mm-30) REVERT: B 404 THR cc_start: 0.7683 (OUTLIER) cc_final: 0.7163 (p) REVERT: B 414 GLU cc_start: 0.7712 (tm-30) cc_final: 0.7150 (tp30) REVERT: B 426 ILE cc_start: 0.8131 (tt) cc_final: 0.7729 (pt) REVERT: B 432 MET cc_start: 0.7640 (tmm) cc_final: 0.7406 (tmm) REVERT: B 462 PHE cc_start: 0.8542 (m-80) cc_final: 0.8232 (m-10) REVERT: B 463 MET cc_start: 0.7524 (tmm) cc_final: 0.7244 (tmm) REVERT: B 466 CYS cc_start: 0.8226 (t) cc_final: 0.7828 (t) REVERT: B 473 LYS cc_start: 0.8331 (mttp) cc_final: 0.8063 (mtpp) REVERT: B 486 CYS cc_start: 0.8795 (t) cc_final: 0.8535 (t) REVERT: B 488 MET cc_start: 0.7547 (tpp) cc_final: 0.7181 (tpp) REVERT: B 513 VAL cc_start: 0.9218 (OUTLIER) cc_final: 0.9006 (p) REVERT: B 531 LYS cc_start: 0.8625 (mmtm) cc_final: 0.8397 (mmmm) REVERT: B 549 ARG cc_start: 0.7565 (ttm-80) cc_final: 0.7107 (ttt-90) REVERT: B 556 TYR cc_start: 0.8993 (p90) cc_final: 0.8767 (p90) REVERT: B 578 TYR cc_start: 0.7778 (t80) cc_final: 0.7388 (t80) REVERT: B 580 LYS cc_start: 0.8012 (mmmm) cc_final: 0.7796 (mmmm) REVERT: B 583 LYS cc_start: 0.8548 (OUTLIER) cc_final: 0.8034 (tmmt) REVERT: B 677 ARG cc_start: 0.7911 (ttp-110) cc_final: 0.7621 (ttp-110) REVERT: B 681 LYS cc_start: 0.8447 (mptt) cc_final: 0.8188 (mptt) REVERT: B 705 GLN cc_start: 0.8648 (tt0) cc_final: 0.8319 (tt0) outliers start: 44 outliers final: 29 residues processed: 328 average time/residue: 0.2752 time to fit residues: 118.9268 Evaluate side-chains 325 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 288 time to evaluate : 1.109 ------------------------------------------------------------------------------- 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 195 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 583 LYS Chi-restraints excluded: chain A residue 682 GLU Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 715 LYS Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 73 ASP Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 208 ILE 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 503 LEU Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain B residue 583 LYS Chi-restraints excluded: chain B residue 690 VAL Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 699 VAL Chi-restraints excluded: chain B residue 713 ILE Chi-restraints excluded: chain B residue 727 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 59 optimal weight: 0.0980 chunk 87 optimal weight: 1.9990 chunk 131 optimal weight: 1.9990 chunk 121 optimal weight: 0.9990 chunk 104 optimal weight: 0.7980 chunk 10 optimal weight: 0.7980 chunk 80 optimal weight: 7.9990 chunk 64 optimal weight: 1.9990 chunk 83 optimal weight: 0.6980 chunk 111 optimal weight: 0.9980 chunk 32 optimal weight: 0.0050 overall best weight: 0.4794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN A 538 ASN B 268 ASN ** B 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.5673 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= 0.226 Angle : 0.732 11.558 14120 Z= 0.368 Chirality : 0.045 0.201 1714 Planarity : 0.004 0.050 1756 Dihedral : 5.425 44.619 1435 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 13.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 3.74 % Allowed : 26.33 % 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: -0.81 (0.23), residues: 1316 helix: 0.44 (0.18), residues: 830 sheet: 2.20 (1.19), residues: 20 loop : -2.49 (0.28), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 83 HIS 0.010 0.001 HIS B 728 PHE 0.029 0.001 PHE B 128 TYR 0.025 0.002 TYR B 323 ARG 0.010 0.001 ARG A 36 ********************** 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 345 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 303 time to evaluate : 1.191 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: 0.6907 (mp0) cc_final: 0.6585 (mp0) REVERT: A 36 ARG cc_start: 0.7449 (mtt90) cc_final: 0.7171 (mtt90) REVERT: A 90 SER cc_start: 0.8614 (t) cc_final: 0.7965 (p) REVERT: A 94 THR cc_start: 0.8567 (t) cc_final: 0.8149 (p) REVERT: A 105 TYR cc_start: 0.7351 (m-80) cc_final: 0.7044 (m-80) REVERT: A 125 LEU cc_start: 0.8932 (tp) cc_final: 0.8710 (tt) REVERT: A 134 ARG cc_start: 0.8168 (mpp80) cc_final: 0.7967 (mpp80) REVERT: A 207 GLN cc_start: 0.7920 (mp10) cc_final: 0.7688 (mp10) REVERT: A 230 GLN cc_start: 0.8189 (tp40) cc_final: 0.7903 (tm-30) REVERT: A 235 GLN cc_start: 0.8377 (mm-40) cc_final: 0.8120 (mm-40) REVERT: A 237 LYS cc_start: 0.8812 (pttt) cc_final: 0.8416 (ttpp) REVERT: A 238 ILE cc_start: 0.8975 (tp) cc_final: 0.8710 (tp) REVERT: A 251 LEU cc_start: 0.8639 (mm) cc_final: 0.8332 (mp) REVERT: A 259 GLU cc_start: 0.7860 (tm-30) cc_final: 0.7068 (tm-30) REVERT: A 260 ILE cc_start: 0.8688 (mt) cc_final: 0.8394 (mt) REVERT: A 263 ASN cc_start: 0.8231 (t0) cc_final: 0.7710 (t0) REVERT: A 303 GLU cc_start: 0.8058 (mp0) cc_final: 0.7813 (mp0) REVERT: A 358 VAL cc_start: 0.8814 (t) cc_final: 0.8555 (p) REVERT: A 404 THR cc_start: 0.7392 (OUTLIER) cc_final: 0.6796 (p) REVERT: A 409 ARG cc_start: 0.8184 (mtm180) cc_final: 0.7783 (mtm110) REVERT: A 414 GLU cc_start: 0.7620 (tm-30) cc_final: 0.7033 (tm-30) REVERT: A 432 MET cc_start: 0.7599 (tmm) cc_final: 0.7167 (tmm) REVERT: A 463 MET cc_start: 0.7608 (tmm) cc_final: 0.7009 (tmm) REVERT: A 473 LYS cc_start: 0.8558 (mttp) cc_final: 0.8185 (ttmm) REVERT: A 475 ASN cc_start: 0.8331 (t0) cc_final: 0.7992 (t0) REVERT: A 540 GLU cc_start: 0.8272 (pm20) cc_final: 0.7080 (pm20) REVERT: A 580 LYS cc_start: 0.8176 (mmmt) cc_final: 0.7853 (mmmt) REVERT: A 583 LYS cc_start: 0.8590 (OUTLIER) cc_final: 0.7883 (tmmt) REVERT: A 681 LYS cc_start: 0.8290 (mptt) cc_final: 0.8070 (mptt) REVERT: B 30 LEU cc_start: 0.8268 (OUTLIER) cc_final: 0.7921 (tp) REVERT: B 66 LYS cc_start: 0.8394 (tptt) cc_final: 0.7907 (tppt) REVERT: B 77 LYS cc_start: 0.8452 (ttpt) cc_final: 0.8085 (ttpt) REVERT: B 90 SER cc_start: 0.8566 (t) cc_final: 0.8206 (p) REVERT: B 125 LEU cc_start: 0.8789 (tp) cc_final: 0.8525 (tt) REVERT: B 150 SER cc_start: 0.8355 (t) cc_final: 0.8025 (p) REVERT: B 203 PHE cc_start: 0.8290 (m-80) cc_final: 0.8004 (m-80) REVERT: B 208 ILE cc_start: 0.8730 (OUTLIER) cc_final: 0.8473 (pt) REVERT: B 230 GLN cc_start: 0.8485 (tm-30) cc_final: 0.8130 (tm-30) REVERT: B 236 LEU cc_start: 0.8938 (tp) cc_final: 0.8679 (tp) REVERT: B 237 LYS cc_start: 0.8709 (pttt) cc_final: 0.8409 (ttpp) REVERT: B 250 ILE cc_start: 0.8763 (pt) cc_final: 0.8514 (mm) REVERT: B 255 TYR cc_start: 0.8074 (m-10) cc_final: 0.7771 (m-10) REVERT: B 260 ILE cc_start: 0.8895 (mt) cc_final: 0.8600 (mt) REVERT: B 329 LYS cc_start: 0.8083 (OUTLIER) cc_final: 0.7635 (ptpt) REVERT: B 384 GLU cc_start: 0.7811 (mm-30) cc_final: 0.7574 (mm-30) REVERT: B 404 THR cc_start: 0.7678 (OUTLIER) cc_final: 0.7141 (p) REVERT: B 405 THR cc_start: 0.8911 (OUTLIER) cc_final: 0.8452 (p) REVERT: B 414 GLU cc_start: 0.7738 (tm-30) cc_final: 0.7407 (tp30) REVERT: B 426 ILE cc_start: 0.8134 (tt) cc_final: 0.7739 (pt) REVERT: B 432 MET cc_start: 0.7669 (tmm) cc_final: 0.7428 (tmm) REVERT: B 458 LEU cc_start: 0.8552 (OUTLIER) cc_final: 0.8286 (mt) REVERT: B 462 PHE cc_start: 0.8555 (m-80) cc_final: 0.8267 (m-10) REVERT: B 463 MET cc_start: 0.7519 (OUTLIER) cc_final: 0.7270 (tmm) REVERT: B 466 CYS cc_start: 0.8235 (t) cc_final: 0.7844 (t) REVERT: B 473 LYS cc_start: 0.8341 (mttp) cc_final: 0.8070 (mtpp) REVERT: B 486 CYS cc_start: 0.8792 (t) cc_final: 0.8541 (t) REVERT: B 488 MET cc_start: 0.7545 (tpp) cc_final: 0.7199 (tpp) REVERT: B 513 VAL cc_start: 0.9230 (OUTLIER) cc_final: 0.9016 (p) REVERT: B 531 LYS cc_start: 0.8597 (mmtm) cc_final: 0.8382 (mmmm) REVERT: B 549 ARG cc_start: 0.7571 (ttm-80) cc_final: 0.7157 (ttt-90) REVERT: B 556 TYR cc_start: 0.9005 (p90) cc_final: 0.8761 (p90) REVERT: B 578 TYR cc_start: 0.7795 (t80) cc_final: 0.7340 (t80) REVERT: B 580 LYS cc_start: 0.8012 (mmmm) cc_final: 0.7801 (mmmm) REVERT: B 581 ARG cc_start: 0.8270 (tpt170) cc_final: 0.7839 (tpp-160) REVERT: B 583 LYS cc_start: 0.8548 (OUTLIER) cc_final: 0.8023 (tmmt) REVERT: B 677 ARG cc_start: 0.7919 (ttp-110) cc_final: 0.7619 (ttp-110) REVERT: B 681 LYS cc_start: 0.8505 (mptt) cc_final: 0.8186 (mptt) REVERT: B 705 GLN cc_start: 0.8643 (tt0) cc_final: 0.8320 (tt0) outliers start: 42 outliers final: 26 residues processed: 327 average time/residue: 0.2750 time to fit residues: 119.9197 Evaluate side-chains 336 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 299 time to evaluate : 1.057 ------------------------------------------------------------------------------- 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 404 THR Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 427 SER Chi-restraints excluded: chain A residue 583 LYS Chi-restraints excluded: chain A residue 682 GLU Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 715 LYS Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 73 ASP Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 208 ILE 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 463 MET Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain B residue 583 LYS Chi-restraints excluded: chain B residue 690 VAL Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 699 VAL Chi-restraints excluded: chain B residue 713 ILE Chi-restraints excluded: chain B residue 727 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 96 optimal weight: 0.0050 chunk 15 optimal weight: 0.2980 chunk 29 optimal weight: 0.5980 chunk 104 optimal weight: 0.8980 chunk 43 optimal weight: 0.8980 chunk 107 optimal weight: 0.8980 chunk 13 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 92 optimal weight: 0.7980 chunk 5 optimal weight: 0.5980 chunk 75 optimal weight: 0.3980 overall best weight: 0.3794 ------------------------------------------------------------------------------- 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 246 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 = 0.3718 r_free = 0.3718 target = 0.117554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.100473 restraints weight = 21100.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.103602 restraints weight = 10359.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.105557 restraints weight = 6093.029| |-----------------------------------------------------------------------------| r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.5710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.214 10390 Z= 0.333 Angle : 0.973 59.200 14120 Z= 0.553 Chirality : 0.046 0.505 1714 Planarity : 0.004 0.049 1756 Dihedral : 5.352 44.622 1433 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 16.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 3.91 % Allowed : 26.69 % Favored : 69.40 % 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: -0.81 (0.23), residues: 1316 helix: 0.43 (0.18), residues: 830 sheet: 2.18 (1.19), residues: 20 loop : -2.49 (0.28), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 83 HIS 0.009 0.001 HIS B 728 PHE 0.027 0.001 PHE B 128 TYR 0.024 0.002 TYR B 323 ARG 0.010 0.001 ARG B 134 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2821.37 seconds wall clock time: 50 minutes 46.43 seconds (3046.43 seconds total)