Starting phenix.real_space_refine on Sat Nov 16 04:47:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sea_40408/11_2024/8sea_40408.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sea_40408/11_2024/8sea_40408.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sea_40408/11_2024/8sea_40408.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sea_40408/11_2024/8sea_40408.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sea_40408/11_2024/8sea_40408.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sea_40408/11_2024/8sea_40408.cif" } resolution = 3.4 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= -0.000 sd= 0.020 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 P 1 5.49 5 S 37 5.16 5 C 6490 2.51 5 N 1792 2.21 5 O 1888 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 10208 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 7712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 992, 7712 Classifications: {'peptide': 992} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 65, 'TRANS': 926} Chain: "B" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 627 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 4, 'TRANS': 74} Chain: "C" Number of atoms: 1243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 1243 Classifications: {'peptide': 152} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 133} Chain: "D" Number of atoms: 603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 603 Classifications: {'peptide': 76} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 72} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'GLY%COO:oxt': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Classifications: {'RNA': 1} Modifications used: {'rna2p': 1} Time building chain proxies: 6.36, per 1000 atoms: 0.62 Number of scatterers: 10208 At special positions: 0 Unit cell: (91.652, 104.983, 117.481, 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) S 37 16.00 P 1 15.00 O 1888 8.00 N 1792 7.00 C 6490 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.68 Conformation dependent library (CDL) restraints added in 1.4 seconds 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2426 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 13 sheets defined 44.9% alpha, 13.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.50 Creating SS restraints... Processing helix chain 'A' and resid 23 through 32 removed outlier: 4.059A pdb=" N ARG A 29 " --> pdb=" O PRO A 25 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLN A 31 " --> pdb=" O MET A 27 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLY A 32 " --> pdb=" O GLN A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 55 Processing helix chain 'A' and resid 69 through 74 removed outlier: 3.527A pdb=" N ALA A 74 " --> pdb=" O ASP A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 99 removed outlier: 4.077A pdb=" N GLU A 93 " --> pdb=" O GLU A 89 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N LEU A 94 " --> pdb=" O ALA A 90 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ASN A 99 " --> pdb=" O LEU A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 119 Processing helix chain 'A' and resid 128 through 142 Processing helix chain 'A' and resid 197 through 203 removed outlier: 4.031A pdb=" N HIS A 201 " --> pdb=" O GLY A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 221 removed outlier: 3.517A pdb=" N ASN A 221 " --> pdb=" O VAL A 218 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 218 through 221' Processing helix chain 'A' and resid 266 through 273 removed outlier: 4.330A pdb=" N LEU A 272 " --> pdb=" O ASP A 268 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLN A 273 " --> pdb=" O THR A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 305 Processing helix chain 'A' and resid 312 through 326 Processing helix chain 'A' and resid 327 through 331 Processing helix chain 'A' and resid 342 through 352 Processing helix chain 'A' and resid 357 through 378 Processing helix chain 'A' and resid 392 through 395 Processing helix chain 'A' and resid 404 through 409 Processing helix chain 'A' and resid 415 through 423 removed outlier: 4.640A pdb=" N VAL A 421 " --> pdb=" O GLY A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 433 Processing helix chain 'A' and resid 442 through 455 Processing helix chain 'A' and resid 473 through 478 Processing helix chain 'A' and resid 484 through 488 removed outlier: 4.128A pdb=" N VAL A 488 " --> pdb=" O SER A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 491 through 504 Processing helix chain 'A' and resid 517 through 521 removed outlier: 3.951A pdb=" N GLU A 521 " --> pdb=" O PRO A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 532 removed outlier: 3.522A pdb=" N VAL A 532 " --> pdb=" O PHE A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 556 removed outlier: 3.554A pdb=" N ARG A 545 " --> pdb=" O SER A 541 " (cutoff:3.500A) Processing helix chain 'A' and resid 585 through 593 removed outlier: 4.306A pdb=" N ASP A 593 " --> pdb=" O ALA A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 603 Processing helix chain 'A' and resid 607 through 631 removed outlier: 3.870A pdb=" N LEU A 625 " --> pdb=" O GLU A 621 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N SER A 626 " --> pdb=" O LEU A 622 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA A 627 " --> pdb=" O PHE A 623 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N GLU A 628 " --> pdb=" O ARG A 624 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASN A 631 " --> pdb=" O ALA A 627 " (cutoff:3.500A) Processing helix chain 'A' and resid 631 through 637 removed outlier: 3.554A pdb=" N HIS A 637 " --> pdb=" O HIS A 633 " (cutoff:3.500A) Processing helix chain 'A' and resid 644 through 651 removed outlier: 4.000A pdb=" N THR A 648 " --> pdb=" O ASP A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 657 Processing helix chain 'A' and resid 672 through 681 Processing helix chain 'A' and resid 681 through 692 Processing helix chain 'A' and resid 721 through 740 removed outlier: 3.518A pdb=" N LEU A 725 " --> pdb=" O GLN A 721 " (cutoff:3.500A) Processing helix chain 'A' and resid 749 through 757 Processing helix chain 'A' and resid 761 through 765 removed outlier: 4.070A pdb=" N MET A 765 " --> pdb=" O PRO A 762 " (cutoff:3.500A) Processing helix chain 'A' and resid 782 through 800 removed outlier: 3.914A pdb=" N GLN A 786 " --> pdb=" O PHE A 782 " (cutoff:3.500A) Processing helix chain 'A' and resid 817 through 832 Processing helix chain 'A' and resid 838 through 845 removed outlier: 3.557A pdb=" N SER A 842 " --> pdb=" O ASN A 838 " (cutoff:3.500A) Processing helix chain 'A' and resid 853 through 873 Processing helix chain 'A' and resid 877 through 881 Processing helix chain 'A' and resid 927 through 940 Processing helix chain 'A' and resid 959 through 967 Processing helix chain 'A' and resid 970 through 980 Processing helix chain 'B' and resid 103 through 116 removed outlier: 3.511A pdb=" N LEU B 107 " --> pdb=" O THR B 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 17 removed outlier: 3.701A pdb=" N LYS C 16 " --> pdb=" O GLU C 12 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N LYS C 17 " --> pdb=" O ASP C 13 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 47 No H-bonds generated for 'chain 'C' and resid 45 through 47' Processing helix chain 'C' and resid 100 through 114 removed outlier: 3.873A pdb=" N VAL C 104 " --> pdb=" O LYS C 100 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 132 Processing helix chain 'C' and resid 132 through 148 Processing helix chain 'D' and resid 103 through 116 removed outlier: 3.726A pdb=" N LEU D 107 " --> pdb=" O THR D 103 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLN D 110 " --> pdb=" O HIS D 106 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 122 Processing helix chain 'D' and resid 136 through 141 removed outlier: 4.430A pdb=" N TYR D 140 " --> pdb=" O PRO D 136 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 103 through 106 removed outlier: 6.301A pdb=" N VAL A 35 " --> pdb=" O THR A 60 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N HIS A 62 " --> pdb=" O VAL A 35 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N VAL A 37 " --> pdb=" O HIS A 62 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL A 121 " --> pdb=" O ARG A 34 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N VAL A 155 " --> pdb=" O ARG A 152 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 103 through 106 removed outlier: 6.301A pdb=" N VAL A 35 " --> pdb=" O THR A 60 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N HIS A 62 " --> pdb=" O VAL A 35 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N VAL A 37 " --> pdb=" O HIS A 62 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL A 121 " --> pdb=" O ARG A 34 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 166 through 168 Processing sheet with id=AA4, first strand: chain 'A' and resid 178 through 179 removed outlier: 4.492A pdb=" N LEU A 208 " --> pdb=" O VAL A 256 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 181 through 184 removed outlier: 3.739A pdb=" N LEU A 236 " --> pdb=" O LEU A 192 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 214 through 216 Processing sheet with id=AA7, first strand: chain 'A' and resid 511 through 512 removed outlier: 6.083A pdb=" N VAL A 466 " --> pdb=" O LEU A 512 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N LEU A 437 " --> pdb=" O VAL A 467 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N VAL A 535 " --> pdb=" O LEU A 560 " (cutoff:3.500A) removed outlier: 8.528A pdb=" N ALA A 562 " --> pdb=" O VAL A 535 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N ALA A 537 " --> pdb=" O ALA A 562 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU A 559 " --> pdb=" O PHE A 574 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 904 through 906 Processing sheet with id=AA9, first strand: chain 'A' and resid 917 through 919 removed outlier: 6.502A pdb=" N LEU A 917 " --> pdb=" O HIS A1009 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N GLU A1011 " --> pdb=" O LEU A 917 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N VAL A 919 " --> pdb=" O GLU A1011 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N LEU A 946 " --> pdb=" O LEU A 953 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 93 through 98 removed outlier: 9.051A pdb=" N VAL B 148 " --> pdb=" O SER B 83 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N LEU B 85 " --> pdb=" O VAL B 148 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N MET B 150 " --> pdb=" O LEU B 85 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ARG B 87 " --> pdb=" O MET B 150 " (cutoff:3.500A) removed outlier: 8.369A pdb=" N LEU B 152 " --> pdb=" O ARG B 87 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 22 through 26 removed outlier: 6.029A pdb=" N ASN C 24 " --> pdb=" O LEU C 38 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N LEU C 38 " --> pdb=" O ASN C 24 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 22 through 26 removed outlier: 6.029A pdb=" N ASN C 24 " --> pdb=" O LEU C 38 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N LEU C 38 " --> pdb=" O ASN C 24 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL C 149 " --> pdb=" O ALA C 50 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 124 through 126 removed outlier: 3.508A pdb=" N THR D 125 " --> pdb=" O PHE D 149 " (cutoff:3.500A) 455 hydrogen bonds defined for protein. 1281 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.90 Time building geometry restraints manager: 3.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3420 1.34 - 1.46: 1327 1.46 - 1.57: 5653 1.57 - 1.69: 4 1.69 - 1.81: 56 Bond restraints: 10460 Sorted by residual: bond pdb=" C1' AMP B1101 " pdb=" O4' AMP B1101 " ideal model delta sigma weight residual 1.415 1.624 -0.209 1.50e-02 4.44e+03 1.94e+02 bond pdb=" C1' AMP B1101 " pdb=" C2' AMP B1101 " ideal model delta sigma weight residual 1.526 1.366 0.160 1.50e-02 4.44e+03 1.13e+02 bond pdb=" C4' AMP B1101 " pdb=" O4' AMP B1101 " ideal model delta sigma weight residual 1.454 1.295 0.159 1.50e-02 4.44e+03 1.13e+02 bond pdb=" C6 AMP B1101 " pdb=" N6 AMP B1101 " ideal model delta sigma weight residual 1.355 1.497 -0.142 2.00e-02 2.50e+03 5.08e+01 bond pdb=" C4 AMP B1101 " pdb=" C5 AMP B1101 " ideal model delta sigma weight residual 1.490 1.374 0.116 2.00e-02 2.50e+03 3.36e+01 ... (remaining 10455 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.71: 14137 2.71 - 5.41: 94 5.41 - 8.12: 6 8.12 - 10.82: 1 10.82 - 13.53: 4 Bond angle restraints: 14242 Sorted by residual: angle pdb=" C2' AMP B1101 " pdb=" C1' AMP B1101 " pdb=" N9 AMP B1101 " ideal model delta sigma weight residual 114.00 127.43 -13.43 1.50e+00 4.44e-01 8.02e+01 angle pdb=" N9 AMP B1101 " pdb=" C1' AMP B1101 " pdb=" O4' AMP B1101 " ideal model delta sigma weight residual 108.20 95.38 12.82 1.50e+00 4.44e-01 7.30e+01 angle pdb=" C1' AMP B1101 " pdb=" O4' AMP B1101 " pdb=" C4' AMP B1101 " ideal model delta sigma weight residual 109.70 104.33 5.37 1.00e+00 1.00e+00 2.88e+01 angle pdb=" O2P AMP B1101 " pdb=" P AMP B1101 " pdb=" O3P AMP B1101 " ideal model delta sigma weight residual 119.90 106.37 13.53 3.00e+00 1.11e-01 2.03e+01 angle pdb=" C1' AMP B1101 " pdb=" C2' AMP B1101 " pdb=" C3' AMP B1101 " ideal model delta sigma weight residual 101.50 105.75 -4.25 1.00e+00 1.00e+00 1.81e+01 ... (remaining 14237 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.84: 5680 13.84 - 27.68: 436 27.68 - 41.52: 142 41.52 - 55.36: 27 55.36 - 69.21: 14 Dihedral angle restraints: 6299 sinusoidal: 2548 harmonic: 3751 Sorted by residual: dihedral pdb=" C1' AMP B1101 " pdb=" C4' AMP B1101 " pdb=" O4' AMP B1101 " pdb=" C5' AMP B1101 " ideal model delta sinusoidal sigma weight residual -123.00 -152.80 29.80 1 8.00e+00 1.56e-02 1.98e+01 dihedral pdb=" N PHE A 211 " pdb=" CA PHE A 211 " pdb=" CB PHE A 211 " pdb=" CG PHE A 211 " ideal model delta sinusoidal sigma weight residual -60.00 -0.14 -59.86 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" CA ARG A 895 " pdb=" CB ARG A 895 " pdb=" CG ARG A 895 " pdb=" CD ARG A 895 " ideal model delta sinusoidal sigma weight residual -60.00 -118.15 58.15 3 1.50e+01 4.44e-03 9.46e+00 ... (remaining 6296 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 979 0.028 - 0.057: 427 0.057 - 0.085: 98 0.085 - 0.114: 75 0.114 - 0.142: 12 Chirality restraints: 1591 Sorted by residual: chirality pdb=" CA GLN A 385 " pdb=" N GLN A 385 " pdb=" C GLN A 385 " pdb=" CB GLN A 385 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.06e-01 chirality pdb=" CA ILE A 834 " pdb=" N ILE A 834 " pdb=" C ILE A 834 " pdb=" CB ILE A 834 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 5.00e-01 chirality pdb=" CA ILE A 214 " pdb=" N ILE A 214 " pdb=" C ILE A 214 " pdb=" CB ILE A 214 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.19e-01 ... (remaining 1588 not shown) Planarity restraints: 1867 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS C 76 " 0.022 5.00e-02 4.00e+02 3.37e-02 1.81e+00 pdb=" N PRO C 77 " -0.058 5.00e-02 4.00e+02 pdb=" CA PRO C 77 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO C 77 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 876 " -0.018 5.00e-02 4.00e+02 2.67e-02 1.14e+00 pdb=" N PRO A 877 " 0.046 5.00e-02 4.00e+02 pdb=" CA PRO A 877 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 877 " -0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN A 759 " -0.017 5.00e-02 4.00e+02 2.59e-02 1.07e+00 pdb=" N PRO A 760 " 0.045 5.00e-02 4.00e+02 pdb=" CA PRO A 760 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO A 760 " -0.014 5.00e-02 4.00e+02 ... (remaining 1864 not shown) Histogram of nonbonded interaction distances: 1.27 - 2.00: 2 2.00 - 2.72: 415 2.72 - 3.45: 14994 3.45 - 4.17: 23096 4.17 - 4.90: 42039 Nonbonded interactions: 80546 Sorted by model distance: nonbonded pdb=" NZ LYS C 121 " pdb=" OXT GLY D 157 " model vdw 1.270 3.120 nonbonded pdb=" NZ LYS C 121 " pdb=" C GLY D 157 " model vdw 1.332 3.350 nonbonded pdb=" O GLY A 39 " pdb=" OG1 THR A 125 " model vdw 2.213 3.040 nonbonded pdb=" O ASN A 695 " pdb=" OG SER A 706 " model vdw 2.219 3.040 nonbonded pdb=" OE2 GLU A 592 " pdb=" NH1 ARG B 155 " model vdw 2.233 3.120 ... (remaining 80541 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 'B' and resid 82 through 157) selection = chain 'D' } 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: 2.850 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: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 26.310 Find NCS groups from input model: 0.140 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: 0.010 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7317 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 : 0.005 0.209 10460 Z= 0.343 Angle : 0.565 13.528 14242 Z= 0.280 Chirality : 0.038 0.142 1591 Planarity : 0.004 0.034 1867 Dihedral : 11.768 69.205 3873 Min Nonbonded Distance : 1.270 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 3.00 % Allowed : 7.08 % Favored : 89.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 0.54 (0.24), residues: 1291 helix: 1.74 (0.24), residues: 476 sheet: -1.21 (0.38), residues: 185 loop : -0.12 (0.26), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 95 HIS 0.003 0.001 HIS A 948 PHE 0.007 0.001 PHE A 146 TYR 0.011 0.001 TYR A 603 ARG 0.002 0.000 ARG A 87 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 144 time to evaluate : 1.062 Fit side-chains REVERT: A 244 PHE cc_start: 0.5585 (OUTLIER) cc_final: 0.4391 (m-80) REVERT: A 272 LEU cc_start: 0.8684 (mt) cc_final: 0.8304 (mm) REVERT: A 282 GLN cc_start: 0.8504 (tt0) cc_final: 0.8097 (tp40) REVERT: A 325 ASP cc_start: 0.8016 (t0) cc_final: 0.7807 (t0) REVERT: A 643 MET cc_start: 0.0794 (mmm) cc_final: 0.0458 (mmm) REVERT: A 710 GLN cc_start: 0.2452 (OUTLIER) cc_final: 0.1485 (pp30) REVERT: A 715 LEU cc_start: 0.6883 (tt) cc_final: 0.6603 (tt) REVERT: A 738 MET cc_start: 0.6749 (mtp) cc_final: 0.6539 (mtp) REVERT: A 791 ASN cc_start: 0.7878 (m-40) cc_final: 0.7541 (m-40) REVERT: B 114 LEU cc_start: 0.8305 (OUTLIER) cc_final: 0.8027 (mp) REVERT: B 140 TYR cc_start: 0.8531 (m-10) cc_final: 0.8260 (m-10) REVERT: C 21 TYR cc_start: 0.8274 (p90) cc_final: 0.7656 (p90) REVERT: C 47 HIS cc_start: 0.7016 (OUTLIER) cc_final: 0.6331 (p90) REVERT: C 67 MET cc_start: 0.7942 (mtt) cc_final: 0.7707 (mtp) REVERT: C 76 HIS cc_start: 0.8354 (t70) cc_final: 0.7837 (t-90) REVERT: C 81 GLU cc_start: 0.8014 (tt0) cc_final: 0.7205 (pt0) REVERT: C 114 ARG cc_start: 0.7093 (tmm160) cc_final: 0.6758 (tmt170) outliers start: 33 outliers final: 15 residues processed: 171 average time/residue: 0.2321 time to fit residues: 55.7644 Evaluate side-chains 132 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 113 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 211 PHE Chi-restraints excluded: chain A residue 229 HIS Chi-restraints excluded: chain A residue 244 PHE Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 468 ASP Chi-restraints excluded: chain A residue 619 PHE Chi-restraints excluded: chain A residue 710 GLN Chi-restraints excluded: chain A residue 919 VAL Chi-restraints excluded: chain A residue 943 VAL Chi-restraints excluded: chain A residue 972 THR Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain C residue 47 HIS Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 117 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 108 optimal weight: 0.9990 chunk 97 optimal weight: 2.9990 chunk 53 optimal weight: 0.1980 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 6.9990 chunk 51 optimal weight: 0.9980 chunk 100 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 0.9980 chunk 74 optimal weight: 30.0000 chunk 116 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN A 41 GLN A 385 GLN A 476 ASN A 522 HIS A 631 ASN A 981 GLN B 102 GLN B 110 GLN C 43 GLN C 103 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7327 moved from start: 0.1051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 10460 Z= 0.215 Angle : 0.578 6.957 14242 Z= 0.282 Chirality : 0.040 0.150 1591 Planarity : 0.004 0.039 1867 Dihedral : 6.518 56.106 1441 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 3.27 % Allowed : 9.99 % Favored : 86.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 0.54 (0.24), residues: 1291 helix: 1.64 (0.23), residues: 498 sheet: -0.99 (0.39), residues: 185 loop : -0.20 (0.26), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 614 HIS 0.003 0.001 HIS A 264 PHE 0.009 0.001 PHE A 146 TYR 0.016 0.002 TYR D 96 ARG 0.006 0.000 ARG C 23 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 123 time to evaluate : 1.296 Fit side-chains REVERT: A 170 ASP cc_start: 0.8145 (OUTLIER) cc_final: 0.7915 (p0) REVERT: A 244 PHE cc_start: 0.5659 (OUTLIER) cc_final: 0.4628 (m-80) REVERT: A 272 LEU cc_start: 0.8633 (mt) cc_final: 0.8430 (mm) REVERT: A 282 GLN cc_start: 0.8518 (tt0) cc_final: 0.8111 (tp40) REVERT: A 715 LEU cc_start: 0.6727 (tt) cc_final: 0.6409 (tt) REVERT: A 791 ASN cc_start: 0.7878 (m-40) cc_final: 0.7535 (m-40) REVERT: B 114 LEU cc_start: 0.8311 (OUTLIER) cc_final: 0.8011 (mp) REVERT: B 143 LYS cc_start: 0.8929 (tppp) cc_final: 0.8725 (tppt) REVERT: B 151 ASN cc_start: 0.9338 (m110) cc_final: 0.9115 (m110) REVERT: C 5 MET cc_start: 0.8661 (tpp) cc_final: 0.8240 (mmm) REVERT: C 21 TYR cc_start: 0.8245 (p90) cc_final: 0.7575 (p90) REVERT: C 47 HIS cc_start: 0.7132 (OUTLIER) cc_final: 0.6430 (p90) REVERT: C 67 MET cc_start: 0.7859 (mtt) cc_final: 0.7643 (mtp) REVERT: C 80 ASP cc_start: 0.7850 (m-30) cc_final: 0.7644 (m-30) REVERT: C 114 ARG cc_start: 0.7278 (tmm160) cc_final: 0.6077 (tmm160) outliers start: 36 outliers final: 17 residues processed: 150 average time/residue: 0.2360 time to fit residues: 51.0761 Evaluate side-chains 132 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 111 time to evaluate : 1.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 211 PHE Chi-restraints excluded: chain A residue 229 HIS Chi-restraints excluded: chain A residue 244 PHE Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 468 ASP Chi-restraints excluded: chain A residue 619 PHE Chi-restraints excluded: chain A residue 632 HIS Chi-restraints excluded: chain A residue 919 VAL Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain A residue 943 VAL Chi-restraints excluded: chain A residue 977 GLN Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain C residue 47 HIS Chi-restraints excluded: chain C residue 87 LEU Chi-restraints excluded: chain C residue 117 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 64 optimal weight: 8.9990 chunk 36 optimal weight: 0.6980 chunk 96 optimal weight: 0.5980 chunk 79 optimal weight: 10.0000 chunk 32 optimal weight: 0.9980 chunk 116 optimal weight: 2.9990 chunk 125 optimal weight: 10.0000 chunk 103 optimal weight: 2.9990 chunk 115 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 chunk 93 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 981 GLN ** B 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 43 GLN D 151 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7325 moved from start: 0.1302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10460 Z= 0.205 Angle : 0.571 8.068 14242 Z= 0.275 Chirality : 0.040 0.147 1591 Planarity : 0.004 0.045 1867 Dihedral : 6.340 57.426 1435 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 3.09 % Allowed : 11.53 % Favored : 85.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 0.55 (0.24), residues: 1291 helix: 1.72 (0.23), residues: 494 sheet: -0.99 (0.38), residues: 185 loop : -0.25 (0.26), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 614 HIS 0.004 0.001 HIS A 966 PHE 0.010 0.001 PHE A 146 TYR 0.016 0.002 TYR D 96 ARG 0.006 0.000 ARG C 23 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 119 time to evaluate : 0.998 Fit side-chains revert: symmetry clash REVERT: A 244 PHE cc_start: 0.5925 (OUTLIER) cc_final: 0.5341 (t80) REVERT: A 272 LEU cc_start: 0.8650 (mt) cc_final: 0.8445 (mm) REVERT: A 282 GLN cc_start: 0.8527 (tt0) cc_final: 0.8119 (tp40) REVERT: A 360 MET cc_start: 0.8862 (mmm) cc_final: 0.8654 (mmm) REVERT: A 715 LEU cc_start: 0.6736 (tt) cc_final: 0.6395 (tt) REVERT: A 765 MET cc_start: 0.0418 (tpt) cc_final: 0.0190 (tpt) REVERT: A 791 ASN cc_start: 0.7909 (m-40) cc_final: 0.7585 (m-40) REVERT: B 88 ASN cc_start: 0.8321 (t0) cc_final: 0.7898 (t0) REVERT: B 114 LEU cc_start: 0.8303 (OUTLIER) cc_final: 0.7984 (mp) REVERT: B 139 GLU cc_start: 0.7476 (tp30) cc_final: 0.7185 (tp30) REVERT: B 151 ASN cc_start: 0.9337 (m110) cc_final: 0.9122 (m110) REVERT: C 21 TYR cc_start: 0.8221 (p90) cc_final: 0.7544 (p90) REVERT: C 47 HIS cc_start: 0.7094 (OUTLIER) cc_final: 0.6452 (p90) REVERT: C 67 MET cc_start: 0.7918 (mtt) cc_final: 0.7701 (mtp) REVERT: C 75 TYR cc_start: 0.7189 (t80) cc_final: 0.6897 (t80) REVERT: C 80 ASP cc_start: 0.7846 (m-30) cc_final: 0.7613 (m-30) REVERT: C 114 ARG cc_start: 0.7377 (tmm160) cc_final: 0.7029 (tmm160) outliers start: 34 outliers final: 18 residues processed: 145 average time/residue: 0.2259 time to fit residues: 47.6871 Evaluate side-chains 129 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 108 time to evaluate : 1.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 211 PHE Chi-restraints excluded: chain A residue 229 HIS Chi-restraints excluded: chain A residue 244 PHE Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 468 ASP Chi-restraints excluded: chain A residue 619 PHE Chi-restraints excluded: chain A residue 919 VAL Chi-restraints excluded: chain A residue 943 VAL Chi-restraints excluded: chain A residue 977 GLN Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain C residue 47 HIS Chi-restraints excluded: chain C residue 87 LEU Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 141 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 115 optimal weight: 2.9990 chunk 87 optimal weight: 0.5980 chunk 60 optimal weight: 9.9990 chunk 12 optimal weight: 3.9990 chunk 55 optimal weight: 0.0000 chunk 78 optimal weight: 7.9990 chunk 116 optimal weight: 0.7980 chunk 123 optimal weight: 0.9980 chunk 61 optimal weight: 0.0060 chunk 110 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 overall best weight: 0.4400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 631 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 43 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7297 moved from start: 0.1472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 10460 Z= 0.157 Angle : 0.555 7.563 14242 Z= 0.264 Chirality : 0.039 0.249 1591 Planarity : 0.004 0.037 1867 Dihedral : 6.275 58.376 1435 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 2.63 % Allowed : 12.99 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 0.60 (0.24), residues: 1291 helix: 1.75 (0.23), residues: 494 sheet: -0.95 (0.37), residues: 185 loop : -0.21 (0.26), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 614 HIS 0.002 0.000 HIS A 682 PHE 0.009 0.001 PHE A 808 TYR 0.011 0.001 TYR A1010 ARG 0.007 0.000 ARG C 23 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 117 time to evaluate : 1.116 Fit side-chains revert: symmetry clash REVERT: A 244 PHE cc_start: 0.5969 (OUTLIER) cc_final: 0.5395 (t80) REVERT: A 282 GLN cc_start: 0.8497 (tt0) cc_final: 0.8087 (tp40) REVERT: A 715 LEU cc_start: 0.6675 (tt) cc_final: 0.6253 (tt) REVERT: A 791 ASN cc_start: 0.7963 (m-40) cc_final: 0.7633 (m-40) REVERT: A 973 GLU cc_start: 0.8656 (OUTLIER) cc_final: 0.8228 (pp20) REVERT: B 114 LEU cc_start: 0.8321 (OUTLIER) cc_final: 0.7999 (mp) REVERT: B 139 GLU cc_start: 0.7398 (tp30) cc_final: 0.7190 (tp30) REVERT: C 21 TYR cc_start: 0.8226 (p90) cc_final: 0.7528 (p90) REVERT: C 47 HIS cc_start: 0.7075 (OUTLIER) cc_final: 0.6298 (p-80) REVERT: C 67 MET cc_start: 0.7881 (mtt) cc_final: 0.7656 (mtp) REVERT: C 75 TYR cc_start: 0.7162 (t80) cc_final: 0.6852 (t80) REVERT: C 80 ASP cc_start: 0.7800 (m-30) cc_final: 0.7582 (m-30) REVERT: C 114 ARG cc_start: 0.7354 (tmm160) cc_final: 0.6923 (tmt170) REVERT: D 125 THR cc_start: 0.2010 (m) cc_final: 0.1382 (p) outliers start: 29 outliers final: 22 residues processed: 138 average time/residue: 0.2360 time to fit residues: 47.2271 Evaluate side-chains 135 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 109 time to evaluate : 1.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 211 PHE Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 229 HIS Chi-restraints excluded: chain A residue 244 PHE Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 468 ASP Chi-restraints excluded: chain A residue 619 PHE Chi-restraints excluded: chain A residue 827 LEU Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 919 VAL Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain A residue 943 VAL Chi-restraints excluded: chain A residue 973 GLU Chi-restraints excluded: chain A residue 977 GLN Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain C residue 47 HIS Chi-restraints excluded: chain C residue 87 LEU Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 141 GLU Chi-restraints excluded: chain C residue 143 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 103 optimal weight: 0.8980 chunk 70 optimal weight: 10.0000 chunk 1 optimal weight: 2.9990 chunk 92 optimal weight: 0.5980 chunk 51 optimal weight: 2.9990 chunk 105 optimal weight: 3.9990 chunk 85 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 63 optimal weight: 9.9990 chunk 111 optimal weight: 0.8980 chunk 31 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 631 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 43 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7320 moved from start: 0.1576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 10460 Z= 0.210 Angle : 0.555 6.127 14242 Z= 0.265 Chirality : 0.040 0.206 1591 Planarity : 0.004 0.039 1867 Dihedral : 6.263 58.430 1434 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 3.45 % Allowed : 12.90 % Favored : 83.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 0.58 (0.24), residues: 1291 helix: 1.76 (0.23), residues: 493 sheet: -0.97 (0.37), residues: 185 loop : -0.23 (0.26), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 614 HIS 0.003 0.001 HIS A 682 PHE 0.011 0.001 PHE A 146 TYR 0.010 0.001 TYR A1010 ARG 0.009 0.000 ARG C 23 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 113 time to evaluate : 1.402 Fit side-chains revert: symmetry clash REVERT: A 244 PHE cc_start: 0.6034 (OUTLIER) cc_final: 0.5476 (t80) REVERT: A 282 GLN cc_start: 0.8528 (tt0) cc_final: 0.8129 (tp40) REVERT: A 360 MET cc_start: 0.8831 (mmm) cc_final: 0.8623 (mmm) REVERT: A 381 MET cc_start: 0.8285 (tpt) cc_final: 0.7991 (tpt) REVERT: A 715 LEU cc_start: 0.6669 (tt) cc_final: 0.6269 (tt) REVERT: A 765 MET cc_start: 0.0390 (tpt) cc_final: -0.0334 (tpt) REVERT: A 791 ASN cc_start: 0.7945 (m-40) cc_final: 0.7619 (m-40) REVERT: A 973 GLU cc_start: 0.8717 (OUTLIER) cc_final: 0.8276 (pp20) REVERT: B 114 LEU cc_start: 0.8381 (OUTLIER) cc_final: 0.7990 (mp) REVERT: C 47 HIS cc_start: 0.7123 (OUTLIER) cc_final: 0.6347 (p-80) REVERT: C 67 MET cc_start: 0.7852 (mtt) cc_final: 0.7619 (mtp) REVERT: C 75 TYR cc_start: 0.7175 (t80) cc_final: 0.6880 (t80) REVERT: C 80 ASP cc_start: 0.7801 (m-30) cc_final: 0.7578 (m-30) REVERT: C 81 GLU cc_start: 0.8036 (tt0) cc_final: 0.7236 (pt0) REVERT: C 114 ARG cc_start: 0.7468 (tmm160) cc_final: 0.7048 (tmt170) REVERT: C 118 ARG cc_start: 0.9056 (mmp80) cc_final: 0.8656 (mmp80) REVERT: D 125 THR cc_start: 0.2149 (m) cc_final: 0.1575 (p) outliers start: 38 outliers final: 22 residues processed: 141 average time/residue: 0.2236 time to fit residues: 45.6115 Evaluate side-chains 135 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 109 time to evaluate : 1.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 229 HIS Chi-restraints excluded: chain A residue 244 PHE Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 468 ASP Chi-restraints excluded: chain A residue 619 PHE Chi-restraints excluded: chain A residue 919 VAL Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain A residue 943 VAL Chi-restraints excluded: chain A residue 973 GLU Chi-restraints excluded: chain A residue 977 GLN Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain C residue 47 HIS Chi-restraints excluded: chain C residue 87 LEU Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 141 GLU Chi-restraints excluded: chain C residue 143 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 41 optimal weight: 0.6980 chunk 111 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 72 optimal weight: 4.9990 chunk 30 optimal weight: 0.9990 chunk 123 optimal weight: 0.9990 chunk 102 optimal weight: 0.9990 chunk 57 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 40 optimal weight: 0.8980 chunk 65 optimal weight: 10.0000 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 631 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 43 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7325 moved from start: 0.1660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10460 Z= 0.212 Angle : 0.564 7.421 14242 Z= 0.269 Chirality : 0.040 0.185 1591 Planarity : 0.004 0.040 1867 Dihedral : 6.178 56.681 1432 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 3.27 % Allowed : 13.71 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 0.58 (0.24), residues: 1291 helix: 1.75 (0.23), residues: 493 sheet: -1.00 (0.37), residues: 185 loop : -0.21 (0.26), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 614 HIS 0.003 0.001 HIS A 264 PHE 0.011 0.001 PHE A 146 TYR 0.019 0.001 TYR C 21 ARG 0.009 0.000 ARG C 23 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 113 time to evaluate : 1.134 Fit side-chains revert: symmetry clash REVERT: A 244 PHE cc_start: 0.6020 (OUTLIER) cc_final: 0.5490 (t80) REVERT: A 282 GLN cc_start: 0.8535 (tt0) cc_final: 0.8127 (tp40) REVERT: A 381 MET cc_start: 0.8309 (tpt) cc_final: 0.7989 (tpt) REVERT: A 715 LEU cc_start: 0.6697 (tt) cc_final: 0.6244 (tt) REVERT: A 765 MET cc_start: 0.0430 (tpt) cc_final: -0.0242 (tpt) REVERT: A 791 ASN cc_start: 0.7935 (m-40) cc_final: 0.7599 (m-40) REVERT: A 973 GLU cc_start: 0.8710 (OUTLIER) cc_final: 0.8276 (pp20) REVERT: B 114 LEU cc_start: 0.8413 (OUTLIER) cc_final: 0.8038 (mp) REVERT: C 21 TYR cc_start: 0.8088 (p90) cc_final: 0.7776 (p90) REVERT: C 47 HIS cc_start: 0.7131 (OUTLIER) cc_final: 0.6351 (p-80) REVERT: C 75 TYR cc_start: 0.7166 (t80) cc_final: 0.6863 (t80) REVERT: C 80 ASP cc_start: 0.7797 (m-30) cc_final: 0.7564 (m-30) REVERT: C 81 GLU cc_start: 0.8043 (tt0) cc_final: 0.7242 (pt0) REVERT: C 114 ARG cc_start: 0.7474 (tmm160) cc_final: 0.7049 (tmt170) REVERT: D 125 THR cc_start: 0.2196 (m) cc_final: 0.1629 (p) outliers start: 36 outliers final: 24 residues processed: 140 average time/residue: 0.2235 time to fit residues: 45.3486 Evaluate side-chains 134 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 106 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 229 HIS Chi-restraints excluded: chain A residue 244 PHE Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 468 ASP Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 630 ILE Chi-restraints excluded: chain A residue 905 THR Chi-restraints excluded: chain A residue 919 VAL Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain A residue 943 VAL Chi-restraints excluded: chain A residue 973 GLU Chi-restraints excluded: chain A residue 977 GLN Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain C residue 47 HIS Chi-restraints excluded: chain C residue 87 LEU Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 141 GLU Chi-restraints excluded: chain C residue 143 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 119 optimal weight: 9.9990 chunk 13 optimal weight: 0.9990 chunk 70 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 69 optimal weight: 4.9990 chunk 123 optimal weight: 0.8980 chunk 77 optimal weight: 9.9990 chunk 75 optimal weight: 0.0040 chunk 56 optimal weight: 1.9990 chunk 76 optimal weight: 0.9990 overall best weight: 0.9798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 631 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 43 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7337 moved from start: 0.1752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10460 Z= 0.232 Angle : 0.576 7.422 14242 Z= 0.276 Chirality : 0.040 0.239 1591 Planarity : 0.004 0.042 1867 Dihedral : 6.090 57.776 1430 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 3.63 % Allowed : 14.08 % Favored : 82.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 0.55 (0.24), residues: 1291 helix: 1.72 (0.23), residues: 493 sheet: -1.05 (0.37), residues: 185 loop : -0.22 (0.26), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 614 HIS 0.003 0.001 HIS A 264 PHE 0.019 0.001 PHE D 126 TYR 0.015 0.001 TYR C 21 ARG 0.009 0.000 ARG C 23 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 112 time to evaluate : 1.175 Fit side-chains revert: symmetry clash REVERT: A 244 PHE cc_start: 0.6073 (OUTLIER) cc_final: 0.5560 (t80) REVERT: A 282 GLN cc_start: 0.8549 (tt0) cc_final: 0.8143 (tp40) REVERT: A 381 MET cc_start: 0.8314 (tpt) cc_final: 0.7951 (tpt) REVERT: A 715 LEU cc_start: 0.6676 (tt) cc_final: 0.6223 (tt) REVERT: A 765 MET cc_start: 0.0629 (tpt) cc_final: 0.0393 (tpt) REVERT: A 791 ASN cc_start: 0.7944 (m-40) cc_final: 0.7604 (m-40) REVERT: A 973 GLU cc_start: 0.8724 (OUTLIER) cc_final: 0.8294 (pp20) REVERT: B 114 LEU cc_start: 0.8444 (OUTLIER) cc_final: 0.8064 (mp) REVERT: C 21 TYR cc_start: 0.8160 (p90) cc_final: 0.7809 (p90) REVERT: C 75 TYR cc_start: 0.7200 (t80) cc_final: 0.6870 (t80) REVERT: C 80 ASP cc_start: 0.7839 (m-30) cc_final: 0.7580 (m-30) REVERT: C 81 GLU cc_start: 0.8054 (tt0) cc_final: 0.7255 (pt0) REVERT: C 114 ARG cc_start: 0.7508 (tmm160) cc_final: 0.7054 (tmt170) REVERT: C 118 ARG cc_start: 0.8984 (mmp80) cc_final: 0.8477 (mmp80) REVERT: D 125 THR cc_start: 0.2152 (m) cc_final: 0.1622 (p) outliers start: 40 outliers final: 29 residues processed: 143 average time/residue: 0.2498 time to fit residues: 51.9493 Evaluate side-chains 139 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 107 time to evaluate : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 229 HIS Chi-restraints excluded: chain A residue 244 PHE Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 468 ASP Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 630 ILE Chi-restraints excluded: chain A residue 905 THR Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 919 VAL Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain A residue 943 VAL Chi-restraints excluded: chain A residue 972 THR Chi-restraints excluded: chain A residue 973 GLU Chi-restraints excluded: chain A residue 977 GLN Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain C residue 47 HIS Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 87 LEU Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 141 GLU Chi-restraints excluded: chain C residue 143 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 49 optimal weight: 0.9990 chunk 73 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 24 optimal weight: 0.6980 chunk 23 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 84 optimal weight: 0.9990 chunk 60 optimal weight: 10.0000 chunk 11 optimal weight: 0.8980 chunk 96 optimal weight: 10.0000 chunk 112 optimal weight: 0.7980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 617 HIS ** A 631 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 43 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7330 moved from start: 0.1816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10460 Z= 0.212 Angle : 0.573 9.859 14242 Z= 0.272 Chirality : 0.040 0.360 1591 Planarity : 0.004 0.044 1867 Dihedral : 6.077 57.887 1430 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 3.27 % Allowed : 14.53 % Favored : 82.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 0.55 (0.24), residues: 1291 helix: 1.73 (0.23), residues: 493 sheet: -1.06 (0.37), residues: 185 loop : -0.23 (0.26), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 614 HIS 0.003 0.001 HIS A 817 PHE 0.015 0.001 PHE D 126 TYR 0.019 0.001 TYR A 735 ARG 0.010 0.000 ARG C 23 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 114 time to evaluate : 1.201 Fit side-chains revert: symmetry clash REVERT: A 244 PHE cc_start: 0.6071 (OUTLIER) cc_final: 0.5581 (t80) REVERT: A 282 GLN cc_start: 0.8540 (tt0) cc_final: 0.8129 (tp40) REVERT: A 381 MET cc_start: 0.8315 (tpt) cc_final: 0.7962 (tpt) REVERT: A 715 LEU cc_start: 0.6651 (tt) cc_final: 0.6214 (tt) REVERT: A 765 MET cc_start: 0.0529 (tpt) cc_final: 0.0324 (tpt) REVERT: A 791 ASN cc_start: 0.7943 (m-40) cc_final: 0.7301 (t0) REVERT: A 973 GLU cc_start: 0.8696 (OUTLIER) cc_final: 0.8293 (pp20) REVERT: B 114 LEU cc_start: 0.8428 (OUTLIER) cc_final: 0.7976 (mp) REVERT: C 21 TYR cc_start: 0.8207 (p90) cc_final: 0.7849 (p90) REVERT: C 75 TYR cc_start: 0.7178 (t80) cc_final: 0.6838 (t80) REVERT: C 80 ASP cc_start: 0.7854 (m-30) cc_final: 0.7539 (m-30) REVERT: C 81 GLU cc_start: 0.8076 (tt0) cc_final: 0.7273 (pt0) REVERT: C 114 ARG cc_start: 0.7511 (tmm160) cc_final: 0.6662 (tmt170) REVERT: D 125 THR cc_start: 0.2048 (m) cc_final: 0.1568 (p) outliers start: 36 outliers final: 29 residues processed: 143 average time/residue: 0.2609 time to fit residues: 53.3142 Evaluate side-chains 142 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 110 time to evaluate : 1.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 229 HIS Chi-restraints excluded: chain A residue 244 PHE Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 468 ASP Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 630 ILE Chi-restraints excluded: chain A residue 905 THR Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 919 VAL Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain A residue 943 VAL Chi-restraints excluded: chain A residue 972 THR Chi-restraints excluded: chain A residue 973 GLU Chi-restraints excluded: chain A residue 977 GLN Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain C residue 47 HIS Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 87 LEU Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 141 GLU Chi-restraints excluded: chain C residue 143 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 118 optimal weight: 8.9990 chunk 107 optimal weight: 3.9990 chunk 114 optimal weight: 0.0670 chunk 69 optimal weight: 5.9990 chunk 50 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 108 optimal weight: 3.9990 chunk 75 optimal weight: 20.0000 chunk 121 optimal weight: 4.9990 overall best weight: 1.8126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 GLN A 617 HIS ** A 631 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 43 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7387 moved from start: 0.1955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 10460 Z= 0.364 Angle : 0.643 8.693 14242 Z= 0.309 Chirality : 0.043 0.383 1591 Planarity : 0.004 0.045 1867 Dihedral : 6.321 56.543 1430 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 3.18 % Allowed : 15.08 % Favored : 81.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 0.26 (0.24), residues: 1291 helix: 1.44 (0.23), residues: 491 sheet: -1.30 (0.36), residues: 185 loop : -0.30 (0.26), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 614 HIS 0.006 0.001 HIS A 264 PHE 0.015 0.002 PHE A 881 TYR 0.019 0.002 TYR A 735 ARG 0.011 0.000 ARG C 23 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 114 time to evaluate : 1.266 Fit side-chains revert: symmetry clash REVERT: A 244 PHE cc_start: 0.6162 (OUTLIER) cc_final: 0.5719 (t80) REVERT: A 282 GLN cc_start: 0.8601 (tt0) cc_final: 0.8153 (tp40) REVERT: A 580 GLU cc_start: 0.8753 (OUTLIER) cc_final: 0.8284 (pm20) REVERT: A 715 LEU cc_start: 0.6758 (tt) cc_final: 0.6294 (tt) REVERT: A 791 ASN cc_start: 0.7954 (m-40) cc_final: 0.7471 (t0) REVERT: A 973 GLU cc_start: 0.8743 (OUTLIER) cc_final: 0.8329 (pp20) REVERT: B 114 LEU cc_start: 0.8425 (OUTLIER) cc_final: 0.8026 (mp) REVERT: C 21 TYR cc_start: 0.8293 (p90) cc_final: 0.7813 (p90) REVERT: C 47 HIS cc_start: 0.7165 (OUTLIER) cc_final: 0.6537 (p90) REVERT: C 75 TYR cc_start: 0.7308 (t80) cc_final: 0.6984 (t80) REVERT: C 80 ASP cc_start: 0.7828 (m-30) cc_final: 0.7551 (m-30) REVERT: C 81 GLU cc_start: 0.8129 (tt0) cc_final: 0.7299 (pt0) REVERT: C 114 ARG cc_start: 0.7548 (tmm160) cc_final: 0.6657 (tmt170) REVERT: C 118 ARG cc_start: 0.9016 (mmp80) cc_final: 0.8388 (mmp80) REVERT: D 125 THR cc_start: 0.2230 (m) cc_final: 0.1697 (p) outliers start: 35 outliers final: 26 residues processed: 142 average time/residue: 0.2340 time to fit residues: 47.1149 Evaluate side-chains 142 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 111 time to evaluate : 1.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 229 HIS Chi-restraints excluded: chain A residue 244 PHE Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 468 ASP Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 580 GLU Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 630 ILE Chi-restraints excluded: chain A residue 905 THR Chi-restraints excluded: chain A residue 919 VAL Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain A residue 943 VAL Chi-restraints excluded: chain A residue 972 THR Chi-restraints excluded: chain A residue 973 GLU Chi-restraints excluded: chain A residue 977 GLN Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain C residue 47 HIS Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 87 LEU Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 141 GLU Chi-restraints excluded: chain C residue 143 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 74 optimal weight: 6.9990 chunk 57 optimal weight: 1.9990 chunk 84 optimal weight: 0.5980 chunk 127 optimal weight: 0.0770 chunk 117 optimal weight: 1.9990 chunk 101 optimal weight: 4.9990 chunk 10 optimal weight: 0.9980 chunk 78 optimal weight: 5.9990 chunk 62 optimal weight: 0.9980 chunk 80 optimal weight: 5.9990 chunk 108 optimal weight: 3.9990 overall best weight: 0.9340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 617 HIS ** A 631 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 43 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7348 moved from start: 0.1976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10460 Z= 0.224 Angle : 0.589 8.785 14242 Z= 0.281 Chirality : 0.041 0.379 1591 Planarity : 0.004 0.043 1867 Dihedral : 6.128 56.813 1428 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 2.82 % Allowed : 15.99 % Favored : 81.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 0.44 (0.24), residues: 1291 helix: 1.64 (0.23), residues: 487 sheet: -1.25 (0.37), residues: 185 loop : -0.22 (0.26), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 614 HIS 0.005 0.001 HIS A 817 PHE 0.014 0.001 PHE D 126 TYR 0.018 0.001 TYR A 735 ARG 0.010 0.000 ARG C 23 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 110 time to evaluate : 1.252 Fit side-chains revert: symmetry clash REVERT: A 244 PHE cc_start: 0.6125 (OUTLIER) cc_final: 0.5716 (t80) REVERT: A 282 GLN cc_start: 0.8548 (tt0) cc_final: 0.8106 (tp40) REVERT: A 381 MET cc_start: 0.8357 (tpt) cc_final: 0.8129 (tpt) REVERT: A 715 LEU cc_start: 0.6712 (tt) cc_final: 0.6242 (tt) REVERT: A 738 MET cc_start: 0.6451 (mtp) cc_final: 0.6163 (mtp) REVERT: A 791 ASN cc_start: 0.7928 (m-40) cc_final: 0.7431 (t0) REVERT: A 973 GLU cc_start: 0.8738 (OUTLIER) cc_final: 0.8330 (pp20) REVERT: B 114 LEU cc_start: 0.8386 (OUTLIER) cc_final: 0.7926 (mp) REVERT: C 5 MET cc_start: 0.8690 (tpp) cc_final: 0.8252 (mmm) REVERT: C 21 TYR cc_start: 0.8227 (p90) cc_final: 0.7838 (p90) REVERT: C 47 HIS cc_start: 0.7089 (OUTLIER) cc_final: 0.6486 (p90) REVERT: C 75 TYR cc_start: 0.7197 (t80) cc_final: 0.6855 (t80) REVERT: C 80 ASP cc_start: 0.7850 (m-30) cc_final: 0.7551 (m-30) REVERT: C 81 GLU cc_start: 0.8124 (tt0) cc_final: 0.7306 (pt0) REVERT: C 114 ARG cc_start: 0.7526 (tmm160) cc_final: 0.7057 (tmt170) REVERT: C 118 ARG cc_start: 0.9000 (mmp80) cc_final: 0.8351 (mmp80) outliers start: 31 outliers final: 26 residues processed: 133 average time/residue: 0.2633 time to fit residues: 49.6161 Evaluate side-chains 136 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 106 time to evaluate : 1.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 229 HIS Chi-restraints excluded: chain A residue 244 PHE Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 407 ASP Chi-restraints excluded: chain A residue 468 ASP Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 630 ILE Chi-restraints excluded: chain A residue 905 THR Chi-restraints excluded: chain A residue 919 VAL Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain A residue 943 VAL Chi-restraints excluded: chain A residue 972 THR Chi-restraints excluded: chain A residue 973 GLU Chi-restraints excluded: chain A residue 977 GLN Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain C residue 47 HIS Chi-restraints excluded: chain C residue 87 LEU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 141 GLU Chi-restraints excluded: chain C residue 143 PHE 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: 2.9990 chunk 14 optimal weight: 3.9990 chunk 28 optimal weight: 0.9980 chunk 101 optimal weight: 4.9990 chunk 42 optimal weight: 0.9990 chunk 104 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 617 HIS ** A 631 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.177491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.115687 restraints weight = 13751.687| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 3.17 r_work: 0.3213 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.2079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 10460 Z= 0.333 Angle : 0.630 8.168 14242 Z= 0.304 Chirality : 0.042 0.375 1591 Planarity : 0.004 0.041 1867 Dihedral : 6.248 53.601 1428 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 3.45 % Allowed : 15.26 % Favored : 81.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 0.23 (0.24), residues: 1291 helix: 1.43 (0.23), residues: 491 sheet: -1.38 (0.36), residues: 185 loop : -0.31 (0.26), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 614 HIS 0.005 0.001 HIS A 817 PHE 0.013 0.002 PHE A 881 TYR 0.018 0.002 TYR A 735 ARG 0.010 0.001 ARG C 23 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2371.83 seconds wall clock time: 44 minutes 30.29 seconds (2670.29 seconds total)