Starting phenix.real_space_refine on Thu Mar 14 22:50:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8opq_17085/03_2024/8opq_17085.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8opq_17085/03_2024/8opq_17085.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.28 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8opq_17085/03_2024/8opq_17085.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8opq_17085/03_2024/8opq_17085.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8opq_17085/03_2024/8opq_17085.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8opq_17085/03_2024/8opq_17085.pdb" } resolution = 3.28 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= 0.024 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: 5 Type Number sf(0) Gaussians S 38 5.16 5 Cl 2 4.86 5 C 6532 2.51 5 N 1668 2.21 5 O 1766 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 538": "NH1" <-> "NH2" Residue "B ARG 66": "NH1" <-> "NH2" Residue "B ARG 538": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 10006 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 648, 5002 Classifications: {'peptide': 648} Link IDs: {'PTRANS': 28, 'TRANS': 619} Chain breaks: 2 Chain: "B" Number of atoms: 5002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 648, 5002 Classifications: {'peptide': 648} Link IDs: {'PTRANS': 28, 'TRANS': 619} Chain breaks: 2 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CL': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CL': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.70, per 1000 atoms: 0.57 Number of scatterers: 10006 At special positions: 0 Unit cell: (100.905, 121.737, 106.764, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 2 17.00 S 38 16.00 O 1766 8.00 N 1668 7.00 C 6532 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 - 3.50 Amino acid : False - 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: 4.13 Conformation dependent library (CDL) restraints added in 1.8 seconds 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2412 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 4 sheets defined 72.7% alpha, 3.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.03 Creating SS restraints... Processing helix chain 'A' and resid 37 through 46 Processing helix chain 'A' and resid 63 through 75 Processing helix chain 'A' and resid 76 through 81 Processing helix chain 'A' and resid 85 through 116 removed outlier: 5.327A pdb=" N LEU A 91 " --> pdb=" O ARG A 87 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N GLY A 92 " --> pdb=" O ASP A 88 " (cutoff:3.500A) Proline residue: A 106 - end of helix removed outlier: 3.715A pdb=" N LEU A 109 " --> pdb=" O LEU A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 126 removed outlier: 4.212A pdb=" N GLY A 122 " --> pdb=" O PRO A 118 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU A 123 " --> pdb=" O PRO A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 137 removed outlier: 4.103A pdb=" N PHE A 131 " --> pdb=" O PHE A 127 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU A 135 " --> pdb=" O PHE A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 162 Processing helix chain 'A' and resid 170 through 201 Processing helix chain 'A' and resid 205 through 210 Processing helix chain 'A' and resid 211 through 236 removed outlier: 4.024A pdb=" N LYS A 232 " --> pdb=" O VAL A 228 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N TYR A 233 " --> pdb=" O SER A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 258 Processing helix chain 'A' and resid 259 through 262 Processing helix chain 'A' and resid 263 through 287 Processing helix chain 'A' and resid 296 through 313 Processing helix chain 'A' and resid 337 through 339 No H-bonds generated for 'chain 'A' and resid 337 through 339' Processing helix chain 'A' and resid 340 through 371 removed outlier: 4.798A pdb=" N GLY A 346 " --> pdb=" O SER A 342 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N SER A 347 " --> pdb=" O LYS A 343 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N THR A 350 " --> pdb=" O GLY A 346 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ILE A 351 " --> pdb=" O SER A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 393 Processing helix chain 'A' and resid 401 through 412 removed outlier: 3.598A pdb=" N GLY A 412 " --> pdb=" O GLN A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 432 removed outlier: 4.436A pdb=" N GLY A 419 " --> pdb=" O SER A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 438 removed outlier: 3.691A pdb=" N PHE A 437 " --> pdb=" O GLY A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 452 removed outlier: 4.058A pdb=" N LEU A 445 " --> pdb=" O PRO A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 470 removed outlier: 4.428A pdb=" N LEU A 460 " --> pdb=" O MET A 456 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N SER A 461 " --> pdb=" O LEU A 457 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ASP A 462 " --> pdb=" O ARG A 458 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N TRP A 467 " --> pdb=" O MET A 463 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N LYS A 468 " --> pdb=" O ARG A 464 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ALA A 469 " --> pdb=" O SER A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 470 through 487 Processing helix chain 'A' and resid 487 through 509 removed outlier: 3.946A pdb=" N LEU A 491 " --> pdb=" O LEU A 487 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL A 494 " --> pdb=" O ASP A 490 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR A 508 " --> pdb=" O VAL A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 553 through 565 Processing helix chain 'A' and resid 568 through 594 Processing helix chain 'A' and resid 656 through 661 Processing helix chain 'A' and resid 681 through 698 Processing helix chain 'A' and resid 708 through 718 removed outlier: 3.619A pdb=" N VAL A 712 " --> pdb=" O HIS A 708 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER A 713 " --> pdb=" O SER A 709 " (cutoff:3.500A) Processing helix chain 'A' and resid 726 through 728 No H-bonds generated for 'chain 'A' and resid 726 through 728' Processing helix chain 'A' and resid 733 through 744 Processing helix chain 'B' and resid 37 through 46 Processing helix chain 'B' and resid 63 through 75 Processing helix chain 'B' and resid 76 through 81 Processing helix chain 'B' and resid 85 through 116 removed outlier: 5.328A pdb=" N LEU B 91 " --> pdb=" O ARG B 87 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N GLY B 92 " --> pdb=" O ASP B 88 " (cutoff:3.500A) Proline residue: B 106 - end of helix removed outlier: 3.716A pdb=" N LEU B 109 " --> pdb=" O LEU B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 126 removed outlier: 4.212A pdb=" N GLY B 122 " --> pdb=" O PRO B 118 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU B 123 " --> pdb=" O PRO B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 137 removed outlier: 4.103A pdb=" N PHE B 131 " --> pdb=" O PHE B 127 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU B 135 " --> pdb=" O PHE B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 162 Processing helix chain 'B' and resid 170 through 201 Processing helix chain 'B' and resid 205 through 210 Processing helix chain 'B' and resid 211 through 236 removed outlier: 4.023A pdb=" N LYS B 232 " --> pdb=" O VAL B 228 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N TYR B 233 " --> pdb=" O SER B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 258 Processing helix chain 'B' and resid 259 through 262 Processing helix chain 'B' and resid 263 through 287 Processing helix chain 'B' and resid 296 through 313 Processing helix chain 'B' and resid 337 through 339 No H-bonds generated for 'chain 'B' and resid 337 through 339' Processing helix chain 'B' and resid 340 through 371 removed outlier: 4.797A pdb=" N GLY B 346 " --> pdb=" O SER B 342 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N SER B 347 " --> pdb=" O LYS B 343 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N THR B 350 " --> pdb=" O GLY B 346 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ILE B 351 " --> pdb=" O SER B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 375 through 393 Processing helix chain 'B' and resid 401 through 412 removed outlier: 3.599A pdb=" N GLY B 412 " --> pdb=" O GLN B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 432 removed outlier: 4.436A pdb=" N GLY B 419 " --> pdb=" O SER B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 434 through 438 removed outlier: 3.691A pdb=" N PHE B 437 " --> pdb=" O GLY B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 441 through 452 removed outlier: 4.057A pdb=" N LEU B 445 " --> pdb=" O PRO B 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 453 through 470 removed outlier: 4.427A pdb=" N LEU B 460 " --> pdb=" O MET B 456 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N SER B 461 " --> pdb=" O LEU B 457 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ASP B 462 " --> pdb=" O ARG B 458 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N TRP B 467 " --> pdb=" O MET B 463 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N LYS B 468 " --> pdb=" O ARG B 464 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ALA B 469 " --> pdb=" O SER B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 470 through 487 Processing helix chain 'B' and resid 487 through 509 removed outlier: 3.946A pdb=" N LEU B 491 " --> pdb=" O LEU B 487 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL B 494 " --> pdb=" O ASP B 490 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR B 508 " --> pdb=" O VAL B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 553 through 565 Processing helix chain 'B' and resid 568 through 594 Processing helix chain 'B' and resid 656 through 661 Processing helix chain 'B' and resid 681 through 698 Processing helix chain 'B' and resid 708 through 718 removed outlier: 3.619A pdb=" N VAL B 712 " --> pdb=" O HIS B 708 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER B 713 " --> pdb=" O SER B 709 " (cutoff:3.500A) Processing helix chain 'B' and resid 726 through 728 No H-bonds generated for 'chain 'B' and resid 726 through 728' Processing helix chain 'B' and resid 733 through 744 Processing sheet with id=AA1, first strand: chain 'A' and resid 144 through 145 Processing sheet with id=AA2, first strand: chain 'A' and resid 525 through 527 removed outlier: 4.430A pdb=" N VAL A 542 " --> pdb=" O LEU A 516 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N GLN A 518 " --> pdb=" O VAL A 540 " (cutoff:3.500A) removed outlier: 12.076A pdb=" N VAL A 540 " --> pdb=" O GLN A 518 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N LYS A 541 " --> pdb=" O ILE A 671 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N ASP A 673 " --> pdb=" O LYS A 541 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N PHE A 543 " --> pdb=" O ASP A 673 " (cutoff:3.500A) removed outlier: 8.062A pdb=" N PHE A 731 " --> pdb=" O VAL A 702 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N MET A 704 " --> pdb=" O PHE A 731 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 144 through 145 Processing sheet with id=AA4, first strand: chain 'B' and resid 525 through 527 removed outlier: 4.431A pdb=" N VAL B 542 " --> pdb=" O LEU B 516 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N GLN B 518 " --> pdb=" O VAL B 540 " (cutoff:3.500A) removed outlier: 12.076A pdb=" N VAL B 540 " --> pdb=" O GLN B 518 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N LYS B 541 " --> pdb=" O ILE B 671 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N ASP B 673 " --> pdb=" O LYS B 541 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N PHE B 543 " --> pdb=" O ASP B 673 " (cutoff:3.500A) removed outlier: 8.063A pdb=" N PHE B 731 " --> pdb=" O VAL B 702 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N MET B 704 " --> pdb=" O PHE B 731 " (cutoff:3.500A) 664 hydrogen bonds defined for protein. 1950 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: 2.85 Time building geometry restraints manager: 4.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3163 1.34 - 1.46: 2037 1.46 - 1.58: 4958 1.58 - 1.69: 0 1.69 - 1.81: 62 Bond restraints: 10220 Sorted by residual: bond pdb=" N VAL A 79 " pdb=" CA VAL A 79 " ideal model delta sigma weight residual 1.452 1.493 -0.041 1.18e-02 7.18e+03 1.20e+01 bond pdb=" N VAL B 79 " pdb=" CA VAL B 79 " ideal model delta sigma weight residual 1.452 1.492 -0.040 1.18e-02 7.18e+03 1.13e+01 bond pdb=" N LEU B 90 " pdb=" CA LEU B 90 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.17e-02 7.31e+03 6.56e+00 bond pdb=" N CYS B 565 " pdb=" CA CYS B 565 " ideal model delta sigma weight residual 1.456 1.490 -0.033 1.31e-02 5.83e+03 6.52e+00 bond pdb=" N ILE B 102 " pdb=" CA ILE B 102 " ideal model delta sigma weight residual 1.461 1.491 -0.030 1.19e-02 7.06e+03 6.52e+00 ... (remaining 10215 not shown) Histogram of bond angle deviations from ideal: 100.45 - 107.16: 311 107.16 - 113.88: 5988 113.88 - 120.59: 4113 120.59 - 127.31: 3372 127.31 - 134.02: 112 Bond angle restraints: 13896 Sorted by residual: angle pdb=" N VAL B 451 " pdb=" CA VAL B 451 " pdb=" C VAL B 451 " ideal model delta sigma weight residual 112.80 108.60 4.20 1.15e+00 7.56e-01 1.33e+01 angle pdb=" N VAL A 451 " pdb=" CA VAL A 451 " pdb=" C VAL A 451 " ideal model delta sigma weight residual 112.80 108.65 4.15 1.15e+00 7.56e-01 1.30e+01 angle pdb=" N ASP B 462 " pdb=" CA ASP B 462 " pdb=" C ASP B 462 " ideal model delta sigma weight residual 111.36 107.46 3.90 1.09e+00 8.42e-01 1.28e+01 angle pdb=" N GLN A 575 " pdb=" CA GLN A 575 " pdb=" C GLN A 575 " ideal model delta sigma weight residual 111.07 107.53 3.54 1.07e+00 8.73e-01 1.10e+01 angle pdb=" N VAL A 79 " pdb=" CA VAL A 79 " pdb=" C VAL A 79 " ideal model delta sigma weight residual 112.96 109.83 3.13 1.00e+00 1.00e+00 9.80e+00 ... (remaining 13891 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.56: 5482 11.56 - 23.11: 398 23.11 - 34.67: 128 34.67 - 46.23: 47 46.23 - 57.79: 9 Dihedral angle restraints: 6064 sinusoidal: 2324 harmonic: 3740 Sorted by residual: dihedral pdb=" CA ASP A 736 " pdb=" CB ASP A 736 " pdb=" CG ASP A 736 " pdb=" OD1 ASP A 736 " ideal model delta sinusoidal sigma weight residual -30.00 -87.79 57.79 1 2.00e+01 2.50e-03 1.12e+01 dihedral pdb=" CA ASP B 736 " pdb=" CB ASP B 736 " pdb=" CG ASP B 736 " pdb=" OD1 ASP B 736 " ideal model delta sinusoidal sigma weight residual -30.00 -87.49 57.49 1 2.00e+01 2.50e-03 1.11e+01 dihedral pdb=" CA ARG A 140 " pdb=" C ARG A 140 " pdb=" N HIS A 141 " pdb=" CA HIS A 141 " ideal model delta harmonic sigma weight residual -180.00 -164.26 -15.74 0 5.00e+00 4.00e-02 9.90e+00 ... (remaining 6061 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 1243 0.042 - 0.084: 314 0.084 - 0.126: 93 0.126 - 0.168: 15 0.168 - 0.210: 3 Chirality restraints: 1668 Sorted by residual: chirality pdb=" CA ILE A 102 " pdb=" N ILE A 102 " pdb=" C ILE A 102 " pdb=" CB ILE A 102 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" CA ILE B 102 " pdb=" N ILE B 102 " pdb=" C ILE B 102 " pdb=" CB ILE B 102 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.10e+00 chirality pdb=" CA LEU A 491 " pdb=" N LEU A 491 " pdb=" C LEU A 491 " pdb=" CB LEU A 491 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.16e-01 ... (remaining 1665 not shown) Planarity restraints: 1730 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG B 64 " 0.017 2.00e-02 2.50e+03 3.56e-02 1.27e+01 pdb=" C ARG B 64 " -0.062 2.00e-02 2.50e+03 pdb=" O ARG B 64 " 0.023 2.00e-02 2.50e+03 pdb=" N ALA B 65 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 537 " -0.013 2.00e-02 2.50e+03 2.67e-02 7.13e+00 pdb=" C VAL A 537 " 0.046 2.00e-02 2.50e+03 pdb=" O VAL A 537 " -0.017 2.00e-02 2.50e+03 pdb=" N ARG A 538 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 537 " 0.013 2.00e-02 2.50e+03 2.55e-02 6.48e+00 pdb=" C VAL B 537 " -0.044 2.00e-02 2.50e+03 pdb=" O VAL B 537 " 0.016 2.00e-02 2.50e+03 pdb=" N ARG B 538 " 0.015 2.00e-02 2.50e+03 ... (remaining 1727 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1941 2.78 - 3.31: 10162 3.31 - 3.84: 16914 3.84 - 4.37: 18453 4.37 - 4.90: 33014 Nonbonded interactions: 80484 Sorted by model distance: nonbonded pdb=" OG SER A 185 " pdb=" O GLY A 391 " model vdw 2.245 2.440 nonbonded pdb=" OG SER B 185 " pdb=" O GLY B 391 " model vdw 2.245 2.440 nonbonded pdb=" OG1 THR A 508 " pdb=" OH TYR A 550 " model vdw 2.255 2.440 nonbonded pdb=" OG1 THR B 508 " pdb=" OH TYR B 550 " model vdw 2.255 2.440 nonbonded pdb=" O ALA B 420 " pdb=" OG SER B 423 " model vdw 2.258 2.440 ... (remaining 80479 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.810 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: 16.140 Check model and map are aligned: 0.140 Set scattering table: 0.080 Process input model: 29.300 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.050 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:2.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7387 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 0.041 10220 Z= 0.195 Angle : 0.524 6.514 13896 Z= 0.338 Chirality : 0.041 0.210 1668 Planarity : 0.005 0.070 1730 Dihedral : 9.908 57.785 3652 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % 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: 1.64 (0.25), residues: 1284 helix: 1.55 (0.19), residues: 902 sheet: 0.87 (0.74), residues: 54 loop : -0.01 (0.33), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 80 HIS 0.004 0.000 HIS A 40 PHE 0.011 0.001 PHE A 356 TYR 0.012 0.001 TYR A 550 ARG 0.002 0.000 ARG A 176 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 269 time to evaluate : 1.113 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 68 TYR cc_start: 0.7383 (t80) cc_final: 0.7107 (t80) REVERT: A 159 GLU cc_start: 0.7666 (mm-30) cc_final: 0.6855 (mm-30) REVERT: A 240 SER cc_start: 0.8479 (m) cc_final: 0.8171 (t) REVERT: A 334 VAL cc_start: 0.8213 (t) cc_final: 0.7954 (p) REVERT: A 410 SER cc_start: 0.8677 (t) cc_final: 0.8398 (m) REVERT: A 535 LYS cc_start: 0.8020 (mttp) cc_final: 0.7708 (mtpp) REVERT: A 568 ASP cc_start: 0.6702 (t0) cc_final: 0.6461 (t0) REVERT: A 728 LYS cc_start: 0.7454 (mttp) cc_final: 0.7177 (mttm) REVERT: B 263 LYS cc_start: 0.7661 (mttt) cc_final: 0.7327 (mttt) REVERT: B 308 ILE cc_start: 0.7923 (mt) cc_final: 0.7700 (mm) REVERT: B 309 SER cc_start: 0.8020 (t) cc_final: 0.7711 (p) REVERT: B 334 VAL cc_start: 0.8334 (t) cc_final: 0.8123 (m) REVERT: B 369 ARG cc_start: 0.7999 (ttm170) cc_final: 0.7737 (mtm-85) REVERT: B 409 GLU cc_start: 0.6836 (tt0) cc_final: 0.6441 (tt0) REVERT: B 410 SER cc_start: 0.8646 (t) cc_final: 0.8440 (p) REVERT: B 521 ASP cc_start: 0.7408 (t0) cc_final: 0.7096 (t0) REVERT: B 673 ASP cc_start: 0.7617 (t0) cc_final: 0.7393 (t0) REVERT: B 728 LYS cc_start: 0.7287 (mttp) cc_final: 0.7023 (ttmm) outliers start: 0 outliers final: 0 residues processed: 269 average time/residue: 0.2650 time to fit residues: 96.0143 Evaluate side-chains 214 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 214 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 108 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 0.6980 chunk 51 optimal weight: 0.9990 chunk 100 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 74 optimal weight: 0.8980 chunk 116 optimal weight: 0.0470 overall best weight: 0.6878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 182 GLN A 394 GLN A 488 ASN A 563 GLN B 104 GLN B 182 GLN B 452 ASN B 563 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.1500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10220 Z= 0.274 Angle : 0.567 11.010 13896 Z= 0.283 Chirality : 0.042 0.147 1668 Planarity : 0.004 0.033 1730 Dihedral : 3.770 15.522 1376 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.00 % Allowed : 12.73 % Favored : 85.27 % 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: 2.19 (0.24), residues: 1284 helix: 2.03 (0.18), residues: 900 sheet: 0.70 (0.73), residues: 54 loop : 0.04 (0.34), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 80 HIS 0.004 0.001 HIS B 735 PHE 0.016 0.002 PHE A 127 TYR 0.016 0.002 TYR A 128 ARG 0.003 0.000 ARG A 544 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 242 time to evaluate : 1.335 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 MET cc_start: 0.5844 (tmm) cc_final: 0.5478 (tmm) REVERT: A 209 TYR cc_start: 0.8045 (m-10) cc_final: 0.7820 (m-10) REVERT: A 240 SER cc_start: 0.8544 (m) cc_final: 0.8251 (t) REVERT: A 293 MET cc_start: 0.6805 (ptp) cc_final: 0.6602 (ptp) REVERT: A 334 VAL cc_start: 0.8081 (t) cc_final: 0.7854 (p) REVERT: A 410 SER cc_start: 0.8756 (t) cc_final: 0.8431 (m) REVERT: A 535 LYS cc_start: 0.8082 (mttp) cc_final: 0.7747 (mtpp) REVERT: A 568 ASP cc_start: 0.6668 (t0) cc_final: 0.6336 (t0) REVERT: A 698 ILE cc_start: 0.8646 (tt) cc_final: 0.8434 (tt) REVERT: A 728 LYS cc_start: 0.7443 (mttp) cc_final: 0.7108 (mttm) REVERT: B 293 MET cc_start: 0.6665 (ptp) cc_final: 0.6416 (ptp) REVERT: B 308 ILE cc_start: 0.7983 (mt) cc_final: 0.7740 (mm) REVERT: B 309 SER cc_start: 0.8068 (t) cc_final: 0.7731 (p) REVERT: B 334 VAL cc_start: 0.8322 (t) cc_final: 0.8066 (m) REVERT: B 521 ASP cc_start: 0.7466 (t0) cc_final: 0.7186 (t0) REVERT: B 673 ASP cc_start: 0.7699 (t0) cc_final: 0.7484 (t0) REVERT: B 699 GLU cc_start: 0.7419 (mm-30) cc_final: 0.7177 (mm-30) REVERT: B 728 LYS cc_start: 0.7462 (mttp) cc_final: 0.6954 (ttmm) outliers start: 22 outliers final: 14 residues processed: 254 average time/residue: 0.2415 time to fit residues: 82.9698 Evaluate side-chains 246 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 232 time to evaluate : 1.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 415 SER Chi-restraints excluded: chain A residue 485 ILE Chi-restraints excluded: chain A residue 678 SER Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 401 SER Chi-restraints excluded: chain B residue 432 LYS Chi-restraints excluded: chain B residue 485 ILE Chi-restraints excluded: chain B residue 726 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 64 optimal weight: 0.6980 chunk 36 optimal weight: 0.9980 chunk 96 optimal weight: 0.9990 chunk 79 optimal weight: 1.9990 chunk 32 optimal weight: 0.5980 chunk 116 optimal weight: 1.9990 chunk 125 optimal weight: 0.3980 chunk 103 optimal weight: 0.7980 chunk 115 optimal weight: 0.7980 chunk 39 optimal weight: 0.0770 chunk 93 optimal weight: 0.9980 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 452 ASN A 488 ASN B 182 GLN B 563 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.1883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10220 Z= 0.225 Angle : 0.526 11.494 13896 Z= 0.260 Chirality : 0.040 0.147 1668 Planarity : 0.004 0.034 1730 Dihedral : 3.779 16.339 1376 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.73 % Allowed : 14.55 % Favored : 82.73 % 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: 2.22 (0.24), residues: 1284 helix: 2.04 (0.18), residues: 912 sheet: 0.55 (0.72), residues: 54 loop : 0.06 (0.35), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 80 HIS 0.003 0.000 HIS B 735 PHE 0.024 0.002 PHE A 731 TYR 0.011 0.001 TYR A 209 ARG 0.003 0.000 ARG B 696 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 247 time to evaluate : 1.138 Fit side-chains revert: symmetry clash REVERT: A 31 MET cc_start: 0.5823 (tmm) cc_final: 0.5536 (tmm) REVERT: A 75 LEU cc_start: 0.7962 (mt) cc_final: 0.7741 (mt) REVERT: A 102 ILE cc_start: 0.8386 (mm) cc_final: 0.8122 (tp) REVERT: A 240 SER cc_start: 0.8545 (m) cc_final: 0.8262 (t) REVERT: A 293 MET cc_start: 0.6808 (ptp) cc_final: 0.6590 (ptp) REVERT: A 309 SER cc_start: 0.8112 (t) cc_final: 0.7874 (m) REVERT: A 334 VAL cc_start: 0.8061 (t) cc_final: 0.7819 (p) REVERT: A 358 ILE cc_start: 0.7828 (OUTLIER) cc_final: 0.7585 (mt) REVERT: A 394 GLN cc_start: 0.8526 (mt0) cc_final: 0.8219 (mt0) REVERT: A 410 SER cc_start: 0.8751 (t) cc_final: 0.8420 (m) REVERT: A 535 LYS cc_start: 0.8079 (mttp) cc_final: 0.7734 (mtpp) REVERT: A 568 ASP cc_start: 0.6623 (t0) cc_final: 0.6296 (t0) REVERT: A 686 LYS cc_start: 0.7724 (OUTLIER) cc_final: 0.7420 (mttm) REVERT: A 698 ILE cc_start: 0.8632 (tt) cc_final: 0.8400 (tt) REVERT: A 728 LYS cc_start: 0.7637 (mttp) cc_final: 0.7372 (mttm) REVERT: B 247 SER cc_start: 0.8109 (p) cc_final: 0.7875 (t) REVERT: B 309 SER cc_start: 0.8077 (t) cc_final: 0.7743 (p) REVERT: B 334 VAL cc_start: 0.8285 (t) cc_final: 0.8032 (m) REVERT: B 358 ILE cc_start: 0.7783 (OUTLIER) cc_final: 0.7572 (mt) REVERT: B 699 GLU cc_start: 0.7415 (mm-30) cc_final: 0.7178 (mm-30) REVERT: B 728 LYS cc_start: 0.7549 (mttp) cc_final: 0.7236 (ttmm) outliers start: 30 outliers final: 17 residues processed: 261 average time/residue: 0.2447 time to fit residues: 86.5846 Evaluate side-chains 251 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 231 time to evaluate : 1.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 409 GLU Chi-restraints excluded: chain A residue 426 ILE Chi-restraints excluded: chain A residue 432 LYS Chi-restraints excluded: chain A residue 678 SER Chi-restraints excluded: chain A residue 686 LYS Chi-restraints excluded: chain A residue 701 GLU Chi-restraints excluded: chain A residue 719 HIS Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 401 SER Chi-restraints excluded: chain B residue 426 ILE Chi-restraints excluded: chain B residue 432 LYS Chi-restraints excluded: chain B residue 572 LEU Chi-restraints excluded: chain B residue 726 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 115 optimal weight: 0.8980 chunk 87 optimal weight: 2.9990 chunk 60 optimal weight: 0.3980 chunk 12 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 78 optimal weight: 0.9990 chunk 116 optimal weight: 0.9980 chunk 123 optimal weight: 0.5980 chunk 61 optimal weight: 0.8980 chunk 110 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 416 GLN A 664 GLN B 370 HIS B 664 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 moved from start: 0.2177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10220 Z= 0.280 Angle : 0.540 12.148 13896 Z= 0.268 Chirality : 0.041 0.146 1668 Planarity : 0.004 0.034 1730 Dihedral : 3.864 16.525 1376 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 3.64 % Allowed : 15.09 % Favored : 81.27 % 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: 2.14 (0.24), residues: 1284 helix: 2.02 (0.18), residues: 910 sheet: 0.21 (0.68), residues: 54 loop : -0.05 (0.35), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 80 HIS 0.009 0.001 HIS B 708 PHE 0.020 0.002 PHE A 720 TYR 0.012 0.002 TYR A 29 ARG 0.006 0.000 ARG A 544 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 238 time to evaluate : 1.143 Fit side-chains REVERT: A 31 MET cc_start: 0.5782 (tmm) cc_final: 0.5548 (tmm) REVERT: A 240 SER cc_start: 0.8573 (m) cc_final: 0.8278 (t) REVERT: A 293 MET cc_start: 0.6833 (ptp) cc_final: 0.6595 (ptp) REVERT: A 309 SER cc_start: 0.8165 (t) cc_final: 0.7927 (m) REVERT: A 334 VAL cc_start: 0.8059 (t) cc_final: 0.7830 (p) REVERT: A 358 ILE cc_start: 0.7848 (OUTLIER) cc_final: 0.7617 (mt) REVERT: A 535 LYS cc_start: 0.8025 (mttp) cc_final: 0.7711 (mtpp) REVERT: A 568 ASP cc_start: 0.6651 (t0) cc_final: 0.6323 (t0) REVERT: A 698 ILE cc_start: 0.8642 (tt) cc_final: 0.8416 (tt) REVERT: A 728 LYS cc_start: 0.7623 (mttp) cc_final: 0.7373 (mttm) REVERT: B 247 SER cc_start: 0.8130 (p) cc_final: 0.7903 (t) REVERT: B 309 SER cc_start: 0.8093 (t) cc_final: 0.7750 (p) REVERT: B 334 VAL cc_start: 0.8285 (t) cc_final: 0.8013 (m) REVERT: B 358 ILE cc_start: 0.7833 (OUTLIER) cc_final: 0.7618 (mt) REVERT: B 498 ILE cc_start: 0.8082 (mm) cc_final: 0.7677 (mt) REVERT: B 699 GLU cc_start: 0.7417 (mm-30) cc_final: 0.7183 (mm-30) REVERT: B 728 LYS cc_start: 0.7605 (mttp) cc_final: 0.7334 (ttmm) outliers start: 40 outliers final: 30 residues processed: 257 average time/residue: 0.2428 time to fit residues: 86.0901 Evaluate side-chains 262 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 230 time to evaluate : 1.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 316 HIS Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 409 GLU Chi-restraints excluded: chain A residue 426 ILE Chi-restraints excluded: chain A residue 432 LYS Chi-restraints excluded: chain A residue 485 ILE Chi-restraints excluded: chain A residue 678 SER Chi-restraints excluded: chain A residue 701 GLU Chi-restraints excluded: chain A residue 719 HIS Chi-restraints excluded: chain A residue 726 THR Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 401 SER Chi-restraints excluded: chain B residue 426 ILE Chi-restraints excluded: chain B residue 432 LYS Chi-restraints excluded: chain B residue 485 ILE Chi-restraints excluded: chain B residue 572 LEU Chi-restraints excluded: chain B residue 701 GLU Chi-restraints excluded: chain B residue 719 HIS Chi-restraints excluded: chain B residue 726 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 103 optimal weight: 0.9980 chunk 70 optimal weight: 0.1980 chunk 1 optimal weight: 4.9990 chunk 92 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 chunk 105 optimal weight: 0.2980 chunk 85 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 63 optimal weight: 0.9980 chunk 111 optimal weight: 0.6980 chunk 31 optimal weight: 0.5980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 708 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.2364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10220 Z= 0.220 Angle : 0.527 12.986 13896 Z= 0.259 Chirality : 0.040 0.145 1668 Planarity : 0.004 0.044 1730 Dihedral : 3.869 16.811 1376 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 3.82 % Allowed : 17.36 % Favored : 78.82 % 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: 2.21 (0.24), residues: 1284 helix: 2.07 (0.18), residues: 910 sheet: 0.24 (0.68), residues: 54 loop : 0.01 (0.36), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 80 HIS 0.015 0.001 HIS A 708 PHE 0.016 0.001 PHE A 720 TYR 0.010 0.001 TYR B 550 ARG 0.003 0.000 ARG B 507 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 234 time to evaluate : 1.183 Fit side-chains REVERT: A 240 SER cc_start: 0.8581 (m) cc_final: 0.8282 (t) REVERT: A 293 MET cc_start: 0.6815 (ptp) cc_final: 0.6585 (ptp) REVERT: A 301 THR cc_start: 0.8290 (t) cc_final: 0.8052 (p) REVERT: A 309 SER cc_start: 0.8173 (t) cc_final: 0.7931 (m) REVERT: A 334 VAL cc_start: 0.8046 (t) cc_final: 0.7790 (p) REVERT: A 358 ILE cc_start: 0.7845 (OUTLIER) cc_final: 0.7628 (mt) REVERT: A 535 LYS cc_start: 0.8014 (mttp) cc_final: 0.7687 (mtpp) REVERT: A 568 ASP cc_start: 0.6628 (t0) cc_final: 0.6287 (t0) REVERT: A 662 LEU cc_start: 0.8652 (mt) cc_final: 0.8405 (mp) REVERT: A 728 LYS cc_start: 0.7633 (mttp) cc_final: 0.7341 (mttm) REVERT: A 730 LEU cc_start: 0.8069 (OUTLIER) cc_final: 0.7765 (mp) REVERT: B 247 SER cc_start: 0.8090 (p) cc_final: 0.7856 (t) REVERT: B 309 SER cc_start: 0.8082 (t) cc_final: 0.7746 (p) REVERT: B 334 VAL cc_start: 0.8277 (t) cc_final: 0.8005 (m) REVERT: B 358 ILE cc_start: 0.7806 (OUTLIER) cc_final: 0.7600 (mt) REVERT: B 498 ILE cc_start: 0.8076 (mm) cc_final: 0.7666 (mt) REVERT: B 699 GLU cc_start: 0.7375 (mm-30) cc_final: 0.7154 (mm-30) REVERT: B 728 LYS cc_start: 0.7626 (mttp) cc_final: 0.7293 (ttmm) outliers start: 42 outliers final: 25 residues processed: 258 average time/residue: 0.2237 time to fit residues: 79.6981 Evaluate side-chains 256 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 228 time to evaluate : 1.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 103 MET Chi-restraints excluded: chain A residue 160 SER Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 409 GLU Chi-restraints excluded: chain A residue 426 ILE Chi-restraints excluded: chain A residue 432 LYS Chi-restraints excluded: chain A residue 485 ILE Chi-restraints excluded: chain A residue 532 SER Chi-restraints excluded: chain A residue 701 GLU Chi-restraints excluded: chain A residue 719 HIS Chi-restraints excluded: chain A residue 726 THR Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 401 SER Chi-restraints excluded: chain B residue 426 ILE Chi-restraints excluded: chain B residue 432 LYS Chi-restraints excluded: chain B residue 485 ILE Chi-restraints excluded: chain B residue 582 LYS Chi-restraints excluded: chain B residue 701 GLU Chi-restraints excluded: chain B residue 719 HIS Chi-restraints excluded: chain B residue 726 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 41 optimal weight: 0.9990 chunk 111 optimal weight: 0.0170 chunk 24 optimal weight: 0.9990 chunk 72 optimal weight: 0.9980 chunk 30 optimal weight: 0.8980 chunk 123 optimal weight: 0.9990 chunk 102 optimal weight: 2.9990 chunk 57 optimal weight: 0.7980 chunk 10 optimal weight: 0.8980 chunk 40 optimal weight: 0.5980 chunk 65 optimal weight: 0.6980 overall best weight: 0.6018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 708 HIS B 509 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.2501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 10220 Z= 0.251 Angle : 0.550 13.166 13896 Z= 0.269 Chirality : 0.041 0.145 1668 Planarity : 0.004 0.063 1730 Dihedral : 3.905 16.847 1376 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 4.73 % Allowed : 16.27 % Favored : 79.00 % 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: 2.13 (0.24), residues: 1284 helix: 2.02 (0.18), residues: 908 sheet: 0.22 (0.67), residues: 54 loop : -0.05 (0.36), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 80 HIS 0.014 0.001 HIS B 708 PHE 0.017 0.001 PHE A 720 TYR 0.011 0.001 TYR B 29 ARG 0.006 0.000 ARG A 544 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 242 time to evaluate : 1.138 Fit side-chains REVERT: A 31 MET cc_start: 0.5766 (tmm) cc_final: 0.5380 (tmm) REVERT: A 240 SER cc_start: 0.8597 (m) cc_final: 0.8295 (t) REVERT: A 293 MET cc_start: 0.6842 (ptp) cc_final: 0.6611 (ptp) REVERT: A 301 THR cc_start: 0.8303 (t) cc_final: 0.8080 (p) REVERT: A 309 SER cc_start: 0.8186 (t) cc_final: 0.7941 (m) REVERT: A 334 VAL cc_start: 0.8009 (t) cc_final: 0.7777 (p) REVERT: A 358 ILE cc_start: 0.7840 (OUTLIER) cc_final: 0.7612 (mt) REVERT: A 498 ILE cc_start: 0.8241 (mm) cc_final: 0.7917 (mt) REVERT: A 535 LYS cc_start: 0.8014 (mttp) cc_final: 0.7687 (mtpp) REVERT: A 568 ASP cc_start: 0.6623 (t0) cc_final: 0.6284 (t0) REVERT: A 662 LEU cc_start: 0.8672 (mt) cc_final: 0.8442 (mp) REVERT: A 728 LYS cc_start: 0.7615 (mttp) cc_final: 0.7327 (mttm) REVERT: A 730 LEU cc_start: 0.8111 (OUTLIER) cc_final: 0.7806 (mp) REVERT: B 247 SER cc_start: 0.8078 (p) cc_final: 0.7844 (t) REVERT: B 309 SER cc_start: 0.8095 (t) cc_final: 0.7747 (p) REVERT: B 334 VAL cc_start: 0.8237 (t) cc_final: 0.7976 (m) REVERT: B 498 ILE cc_start: 0.8077 (mm) cc_final: 0.7676 (mt) REVERT: B 699 GLU cc_start: 0.7369 (mm-30) cc_final: 0.7138 (mm-30) REVERT: B 728 LYS cc_start: 0.7629 (mttp) cc_final: 0.7299 (ttmm) outliers start: 52 outliers final: 39 residues processed: 272 average time/residue: 0.2238 time to fit residues: 84.2452 Evaluate side-chains 276 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 235 time to evaluate : 1.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 103 MET Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 160 SER Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 316 HIS Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 409 GLU Chi-restraints excluded: chain A residue 426 ILE Chi-restraints excluded: chain A residue 432 LYS Chi-restraints excluded: chain A residue 485 ILE Chi-restraints excluded: chain A residue 532 SER Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 678 SER Chi-restraints excluded: chain A residue 681 ASP Chi-restraints excluded: chain A residue 701 GLU Chi-restraints excluded: chain A residue 719 HIS Chi-restraints excluded: chain A residue 726 THR Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 240 SER Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 401 SER Chi-restraints excluded: chain B residue 426 ILE Chi-restraints excluded: chain B residue 432 LYS Chi-restraints excluded: chain B residue 485 ILE Chi-restraints excluded: chain B residue 532 SER Chi-restraints excluded: chain B residue 572 LEU Chi-restraints excluded: chain B residue 582 LYS Chi-restraints excluded: chain B residue 701 GLU Chi-restraints excluded: chain B residue 719 HIS Chi-restraints excluded: chain B residue 726 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 119 optimal weight: 0.5980 chunk 13 optimal weight: 0.0570 chunk 70 optimal weight: 0.0170 chunk 90 optimal weight: 0.8980 chunk 104 optimal weight: 0.9980 chunk 69 optimal weight: 3.9990 chunk 123 optimal weight: 0.9980 chunk 77 optimal weight: 0.7980 chunk 75 optimal weight: 0.9990 chunk 56 optimal weight: 0.2980 chunk 76 optimal weight: 0.9990 overall best weight: 0.3536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 370 HIS ** A 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 708 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.2575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10220 Z= 0.182 Angle : 0.534 14.051 13896 Z= 0.258 Chirality : 0.040 0.161 1668 Planarity : 0.004 0.070 1730 Dihedral : 3.858 16.926 1376 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 4.00 % Allowed : 17.64 % Favored : 78.36 % 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: 2.29 (0.24), residues: 1284 helix: 2.13 (0.18), residues: 908 sheet: 0.41 (0.68), residues: 54 loop : 0.01 (0.36), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 80 HIS 0.012 0.001 HIS B 708 PHE 0.022 0.001 PHE A 720 TYR 0.010 0.001 TYR B 550 ARG 0.006 0.000 ARG A 544 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 245 time to evaluate : 1.089 Fit side-chains REVERT: A 31 MET cc_start: 0.5817 (tmm) cc_final: 0.5466 (tmm) REVERT: A 240 SER cc_start: 0.8595 (m) cc_final: 0.8292 (t) REVERT: A 293 MET cc_start: 0.6822 (ptp) cc_final: 0.6572 (ptp) REVERT: A 309 SER cc_start: 0.8141 (t) cc_final: 0.7908 (m) REVERT: A 334 VAL cc_start: 0.8032 (t) cc_final: 0.7781 (p) REVERT: A 358 ILE cc_start: 0.7849 (OUTLIER) cc_final: 0.7619 (mt) REVERT: A 662 LEU cc_start: 0.8656 (mt) cc_final: 0.8427 (mp) REVERT: A 728 LYS cc_start: 0.7630 (mttp) cc_final: 0.7340 (mttm) REVERT: A 730 LEU cc_start: 0.8040 (OUTLIER) cc_final: 0.7726 (mp) REVERT: B 209 TYR cc_start: 0.8043 (m-10) cc_final: 0.7743 (m-10) REVERT: B 247 SER cc_start: 0.8044 (p) cc_final: 0.7803 (t) REVERT: B 293 MET cc_start: 0.6716 (ptp) cc_final: 0.6461 (ptp) REVERT: B 309 SER cc_start: 0.8044 (t) cc_final: 0.7833 (m) REVERT: B 334 VAL cc_start: 0.8250 (t) cc_final: 0.7987 (m) REVERT: B 498 ILE cc_start: 0.8048 (mm) cc_final: 0.7635 (mt) REVERT: B 728 LYS cc_start: 0.7640 (mttp) cc_final: 0.7312 (ttmm) outliers start: 44 outliers final: 36 residues processed: 270 average time/residue: 0.2197 time to fit residues: 82.6898 Evaluate side-chains 275 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 237 time to evaluate : 1.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 103 MET Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 426 ILE Chi-restraints excluded: chain A residue 432 LYS Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 485 ILE Chi-restraints excluded: chain A residue 532 SER Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 666 ASP Chi-restraints excluded: chain A residue 678 SER Chi-restraints excluded: chain A residue 681 ASP Chi-restraints excluded: chain A residue 701 GLU Chi-restraints excluded: chain A residue 719 HIS Chi-restraints excluded: chain A residue 726 THR Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain A residue 734 VAL Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 240 SER Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 401 SER Chi-restraints excluded: chain B residue 426 ILE Chi-restraints excluded: chain B residue 432 LYS Chi-restraints excluded: chain B residue 485 ILE Chi-restraints excluded: chain B residue 532 SER Chi-restraints excluded: chain B residue 582 LYS Chi-restraints excluded: chain B residue 701 GLU Chi-restraints excluded: chain B residue 719 HIS Chi-restraints excluded: chain B residue 726 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 49 optimal weight: 0.0870 chunk 73 optimal weight: 0.5980 chunk 37 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 60 optimal weight: 0.0670 chunk 11 optimal weight: 0.9990 chunk 96 optimal weight: 0.9990 chunk 112 optimal weight: 0.9980 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 230 GLN ** A 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 459 GLN B 182 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 moved from start: 0.2700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 10220 Z= 0.240 Angle : 0.563 14.428 13896 Z= 0.273 Chirality : 0.042 0.218 1668 Planarity : 0.004 0.050 1730 Dihedral : 3.899 17.337 1376 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 4.00 % Allowed : 18.45 % Favored : 77.55 % 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: 2.17 (0.24), residues: 1284 helix: 2.04 (0.18), residues: 908 sheet: 0.33 (0.66), residues: 54 loop : -0.03 (0.36), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 80 HIS 0.016 0.001 HIS B 708 PHE 0.033 0.002 PHE B 720 TYR 0.010 0.001 TYR B 550 ARG 0.005 0.000 ARG A 538 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 234 time to evaluate : 1.020 Fit side-chains REVERT: A 31 MET cc_start: 0.5879 (tmm) cc_final: 0.5483 (tmm) REVERT: A 240 SER cc_start: 0.8607 (m) cc_final: 0.8298 (t) REVERT: A 293 MET cc_start: 0.6843 (ptp) cc_final: 0.6591 (ptp) REVERT: A 301 THR cc_start: 0.8296 (t) cc_final: 0.8090 (p) REVERT: A 309 SER cc_start: 0.8142 (t) cc_final: 0.7909 (m) REVERT: A 334 VAL cc_start: 0.8008 (t) cc_final: 0.7768 (p) REVERT: A 358 ILE cc_start: 0.7847 (OUTLIER) cc_final: 0.7628 (mt) REVERT: A 498 ILE cc_start: 0.8248 (mm) cc_final: 0.7924 (mt) REVERT: A 662 LEU cc_start: 0.8668 (mt) cc_final: 0.8454 (mp) REVERT: A 728 LYS cc_start: 0.7620 (mttp) cc_final: 0.7329 (mttm) REVERT: A 730 LEU cc_start: 0.8066 (OUTLIER) cc_final: 0.7766 (mp) REVERT: B 209 TYR cc_start: 0.8061 (m-10) cc_final: 0.7787 (m-10) REVERT: B 247 SER cc_start: 0.8058 (p) cc_final: 0.7828 (t) REVERT: B 293 MET cc_start: 0.6755 (ptp) cc_final: 0.6507 (ptp) REVERT: B 309 SER cc_start: 0.8066 (t) cc_final: 0.7858 (m) REVERT: B 334 VAL cc_start: 0.8243 (t) cc_final: 0.7981 (m) REVERT: B 498 ILE cc_start: 0.8073 (mm) cc_final: 0.7663 (mt) REVERT: B 728 LYS cc_start: 0.7657 (mttp) cc_final: 0.7314 (ttmm) outliers start: 44 outliers final: 36 residues processed: 258 average time/residue: 0.2193 time to fit residues: 78.9339 Evaluate side-chains 267 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 229 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 103 MET Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 426 ILE Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 485 ILE Chi-restraints excluded: chain A residue 532 SER Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 678 SER Chi-restraints excluded: chain A residue 681 ASP Chi-restraints excluded: chain A residue 701 GLU Chi-restraints excluded: chain A residue 719 HIS Chi-restraints excluded: chain A residue 726 THR Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain A residue 734 VAL Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 240 SER Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 401 SER Chi-restraints excluded: chain B residue 426 ILE Chi-restraints excluded: chain B residue 432 LYS Chi-restraints excluded: chain B residue 485 ILE Chi-restraints excluded: chain B residue 572 LEU Chi-restraints excluded: chain B residue 582 LYS Chi-restraints excluded: chain B residue 701 GLU Chi-restraints excluded: chain B residue 719 HIS Chi-restraints excluded: chain B residue 726 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 118 optimal weight: 4.9990 chunk 107 optimal weight: 0.9990 chunk 114 optimal weight: 0.7980 chunk 69 optimal weight: 0.9990 chunk 50 optimal weight: 0.8980 chunk 90 optimal weight: 0.5980 chunk 35 optimal weight: 0.7980 chunk 103 optimal weight: 1.9990 chunk 108 optimal weight: 0.8980 chunk 75 optimal weight: 0.9990 chunk 121 optimal weight: 0.4980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.2813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 10220 Z= 0.287 Angle : 0.589 14.573 13896 Z= 0.286 Chirality : 0.043 0.219 1668 Planarity : 0.004 0.056 1730 Dihedral : 3.995 17.992 1376 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 4.00 % Allowed : 18.18 % Favored : 77.82 % 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: 2.11 (0.24), residues: 1284 helix: 2.04 (0.18), residues: 894 sheet: 0.24 (0.67), residues: 54 loop : -0.11 (0.35), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 80 HIS 0.016 0.001 HIS B 708 PHE 0.030 0.002 PHE B 720 TYR 0.011 0.001 TYR B 550 ARG 0.008 0.000 ARG A 538 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 240 time to evaluate : 1.193 Fit side-chains REVERT: A 31 MET cc_start: 0.5860 (tmm) cc_final: 0.5448 (tmm) REVERT: A 240 SER cc_start: 0.8621 (m) cc_final: 0.8317 (t) REVERT: A 293 MET cc_start: 0.6893 (ptp) cc_final: 0.6643 (ptp) REVERT: A 301 THR cc_start: 0.8341 (t) cc_final: 0.8140 (p) REVERT: A 309 SER cc_start: 0.8168 (t) cc_final: 0.7913 (m) REVERT: A 334 VAL cc_start: 0.7989 (t) cc_final: 0.7761 (p) REVERT: A 358 ILE cc_start: 0.7861 (OUTLIER) cc_final: 0.7636 (mt) REVERT: A 432 LYS cc_start: 0.8572 (mtmm) cc_final: 0.8299 (mtpp) REVERT: A 498 ILE cc_start: 0.8249 (mm) cc_final: 0.7916 (mt) REVERT: A 568 ASP cc_start: 0.6640 (t0) cc_final: 0.6333 (t0) REVERT: A 728 LYS cc_start: 0.7615 (mttp) cc_final: 0.7327 (mttm) REVERT: A 730 LEU cc_start: 0.8094 (OUTLIER) cc_final: 0.7809 (mp) REVERT: A 742 LEU cc_start: 0.8354 (mt) cc_final: 0.8137 (mp) REVERT: B 293 MET cc_start: 0.6786 (ptp) cc_final: 0.6538 (ptp) REVERT: B 309 SER cc_start: 0.8098 (t) cc_final: 0.7746 (p) REVERT: B 334 VAL cc_start: 0.8234 (t) cc_final: 0.7968 (m) REVERT: B 498 ILE cc_start: 0.8076 (mm) cc_final: 0.7697 (mt) REVERT: B 728 LYS cc_start: 0.7654 (mttp) cc_final: 0.7316 (ttmm) outliers start: 44 outliers final: 37 residues processed: 266 average time/residue: 0.2296 time to fit residues: 85.0322 Evaluate side-chains 277 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 238 time to evaluate : 1.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 103 MET Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 160 SER Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 316 HIS Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 426 ILE Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 485 ILE Chi-restraints excluded: chain A residue 532 SER Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 678 SER Chi-restraints excluded: chain A residue 681 ASP Chi-restraints excluded: chain A residue 701 GLU Chi-restraints excluded: chain A residue 726 THR Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain A residue 734 VAL Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 240 SER Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 401 SER Chi-restraints excluded: chain B residue 426 ILE Chi-restraints excluded: chain B residue 485 ILE Chi-restraints excluded: chain B residue 532 SER Chi-restraints excluded: chain B residue 572 LEU Chi-restraints excluded: chain B residue 582 LYS Chi-restraints excluded: chain B residue 701 GLU Chi-restraints excluded: chain B residue 719 HIS Chi-restraints excluded: chain B residue 726 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 74 optimal weight: 0.9980 chunk 57 optimal weight: 0.0670 chunk 84 optimal weight: 0.7980 chunk 127 optimal weight: 0.9980 chunk 117 optimal weight: 1.9990 chunk 101 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 78 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 80 optimal weight: 0.2980 chunk 108 optimal weight: 0.7980 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.2872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 10220 Z= 0.243 Angle : 0.587 14.991 13896 Z= 0.283 Chirality : 0.042 0.181 1668 Planarity : 0.004 0.055 1730 Dihedral : 3.985 17.802 1376 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 3.64 % Allowed : 19.00 % Favored : 77.36 % 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: 2.08 (0.24), residues: 1284 helix: 1.99 (0.18), residues: 906 sheet: 0.21 (0.67), residues: 54 loop : -0.08 (0.36), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 80 HIS 0.015 0.001 HIS B 708 PHE 0.033 0.002 PHE B 720 TYR 0.011 0.001 TYR B 550 ARG 0.006 0.000 ARG A 538 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 240 time to evaluate : 1.154 Fit side-chains REVERT: A 31 MET cc_start: 0.5896 (tmm) cc_final: 0.5477 (tmm) REVERT: A 102 ILE cc_start: 0.8442 (mm) cc_final: 0.8176 (tp) REVERT: A 293 MET cc_start: 0.6893 (ptp) cc_final: 0.6651 (ptp) REVERT: A 301 THR cc_start: 0.8325 (t) cc_final: 0.8122 (p) REVERT: A 309 SER cc_start: 0.8160 (t) cc_final: 0.7929 (m) REVERT: A 334 VAL cc_start: 0.7981 (t) cc_final: 0.7754 (p) REVERT: A 358 ILE cc_start: 0.7850 (OUTLIER) cc_final: 0.7634 (mt) REVERT: A 432 LYS cc_start: 0.8551 (mtmm) cc_final: 0.8272 (mtpp) REVERT: A 498 ILE cc_start: 0.8247 (mm) cc_final: 0.7910 (mt) REVERT: A 728 LYS cc_start: 0.7588 (mttp) cc_final: 0.7312 (mttm) REVERT: A 730 LEU cc_start: 0.8073 (OUTLIER) cc_final: 0.7763 (mp) REVERT: B 247 SER cc_start: 0.8068 (p) cc_final: 0.7858 (t) REVERT: B 293 MET cc_start: 0.6773 (ptp) cc_final: 0.6530 (ptp) REVERT: B 309 SER cc_start: 0.8082 (t) cc_final: 0.7735 (p) REVERT: B 334 VAL cc_start: 0.8227 (t) cc_final: 0.7959 (m) REVERT: B 498 ILE cc_start: 0.8085 (mm) cc_final: 0.7684 (mt) REVERT: B 728 LYS cc_start: 0.7674 (mttp) cc_final: 0.7322 (ttmm) outliers start: 40 outliers final: 36 residues processed: 266 average time/residue: 0.2216 time to fit residues: 81.5964 Evaluate side-chains 280 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 242 time to evaluate : 1.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 103 MET Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 160 SER Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 426 ILE Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 485 ILE Chi-restraints excluded: chain A residue 532 SER Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 678 SER Chi-restraints excluded: chain A residue 681 ASP Chi-restraints excluded: chain A residue 701 GLU Chi-restraints excluded: chain A residue 726 THR Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain A residue 734 VAL Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 240 SER Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 401 SER Chi-restraints excluded: chain B residue 426 ILE Chi-restraints excluded: chain B residue 485 ILE Chi-restraints excluded: chain B residue 532 SER Chi-restraints excluded: chain B residue 572 LEU Chi-restraints excluded: chain B residue 701 GLU Chi-restraints excluded: chain B residue 719 HIS Chi-restraints excluded: chain B residue 725 ILE Chi-restraints excluded: chain B residue 726 THR Chi-restraints excluded: chain B residue 734 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 31 optimal weight: 0.8980 chunk 93 optimal weight: 0.0060 chunk 14 optimal weight: 0.9990 chunk 28 optimal weight: 0.0170 chunk 101 optimal weight: 3.9990 chunk 42 optimal weight: 0.9980 chunk 104 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 89 optimal weight: 0.7980 chunk 5 optimal weight: 0.6980 overall best weight: 0.4634 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 575 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.135195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.118141 restraints weight = 13805.792| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 2.13 r_work: 0.3363 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3199 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.2905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10220 Z= 0.220 Angle : 0.579 15.028 13896 Z= 0.280 Chirality : 0.041 0.166 1668 Planarity : 0.004 0.045 1730 Dihedral : 3.981 19.871 1376 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 3.73 % Allowed : 19.09 % Favored : 77.18 % 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: 2.20 (0.24), residues: 1284 helix: 2.11 (0.18), residues: 894 sheet: 0.26 (0.67), residues: 54 loop : -0.06 (0.35), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 80 HIS 0.010 0.001 HIS B 708 PHE 0.038 0.002 PHE B 571 TYR 0.011 0.001 TYR B 550 ARG 0.006 0.000 ARG A 538 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2679.62 seconds wall clock time: 48 minutes 39.94 seconds (2919.94 seconds total)