Starting phenix.real_space_refine on Fri Jun 13 03:51:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7y3e_33592/06_2025/7y3e_33592.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y3e_33592/06_2025/7y3e_33592.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7y3e_33592/06_2025/7y3e_33592.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y3e_33592/06_2025/7y3e_33592.map" model { file = "/net/cci-nas-00/data/ceres_data/7y3e_33592/06_2025/7y3e_33592.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y3e_33592/06_2025/7y3e_33592.cif" } resolution = 2.8 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= -0.003 sd= 0.142 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 60 5.16 5 C 9522 2.51 5 N 2364 2.21 5 O 2626 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 45 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 14572 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 7254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 928, 7254 Classifications: {'peptide': 928} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 33, 'TRANS': 894} Chain breaks: 4 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 7254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 928, 7254 Classifications: {'peptide': 928} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 33, 'TRANS': 894} Chain breaks: 4 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {'R16': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {'R16': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 8.81, per 1000 atoms: 0.60 Number of scatterers: 14572 At special positions: 0 Unit cell: (115.44, 105.04, 127.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 60 16.00 O 2626 8.00 N 2364 7.00 C 9522 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.82 Conformation dependent library (CDL) restraints added in 1.8 seconds 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3456 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 8 sheets defined 69.9% alpha, 4.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.82 Creating SS restraints... Processing helix chain 'A' and resid 34 through 54 removed outlier: 3.625A pdb=" N LEU A 38 " --> pdb=" O VAL A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 78 removed outlier: 4.061A pdb=" N ALA A 64 " --> pdb=" O PRO A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 95 Processing helix chain 'A' and resid 97 through 116 Proline residue: A 107 - end of helix removed outlier: 4.568A pdb=" N GLU A 112 " --> pdb=" O ALA A 108 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N SER A 113 " --> pdb=" O LEU A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 151 removed outlier: 5.825A pdb=" N GLY A 127 " --> pdb=" O LYS A 123 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N GLN A 128 " --> pdb=" O ARG A 124 " (cutoff:3.500A) Proline residue: A 135 - end of helix Processing helix chain 'A' and resid 157 through 168 Processing helix chain 'A' and resid 172 through 184 removed outlier: 3.729A pdb=" N GLU A 182 " --> pdb=" O ALA A 178 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLY A 184 " --> pdb=" O LEU A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 216 removed outlier: 3.672A pdb=" N ASP A 201 " --> pdb=" O SER A 197 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N GLY A 202 " --> pdb=" O LEU A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 253 removed outlier: 3.955A pdb=" N ALA A 236 " --> pdb=" O VAL A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 278 removed outlier: 3.597A pdb=" N THR A 265 " --> pdb=" O GLU A 261 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N TYR A 274 " --> pdb=" O TYR A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 299 Processing helix chain 'A' and resid 306 through 339 removed outlier: 4.357A pdb=" N SER A 310 " --> pdb=" O ASP A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 347 removed outlier: 3.784A pdb=" N GLN A 347 " --> pdb=" O ILE A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 348 through 377 Proline residue: A 374 - end of helix Processing helix chain 'A' and resid 384 through 394 Processing helix chain 'A' and resid 398 through 411 Processing helix chain 'A' and resid 418 through 442 removed outlier: 3.752A pdb=" N SER A 442 " --> pdb=" O ILE A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 450 Processing helix chain 'A' and resid 451 through 453 No H-bonds generated for 'chain 'A' and resid 451 through 453' Processing helix chain 'A' and resid 457 through 482 Processing helix chain 'A' and resid 492 through 500 Processing helix chain 'A' and resid 527 through 549 Processing helix chain 'A' and resid 553 through 568 Processing helix chain 'A' and resid 581 through 585 Processing helix chain 'A' and resid 590 through 594 Processing helix chain 'A' and resid 603 through 638 removed outlier: 5.736A pdb=" N SER A 614 " --> pdb=" O GLU A 610 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N ALA A 615 " --> pdb=" O ARG A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 640 through 654 Processing helix chain 'A' and resid 654 through 668 removed outlier: 3.756A pdb=" N LYS A 658 " --> pdb=" O GLY A 654 " (cutoff:3.500A) Processing helix chain 'A' and resid 670 through 699 Processing helix chain 'A' and resid 704 through 723 Processing helix chain 'A' and resid 731 through 738 Processing helix chain 'A' and resid 739 through 744 removed outlier: 3.815A pdb=" N VAL A 743 " --> pdb=" O PRO A 740 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 751 Processing helix chain 'A' and resid 810 through 817 Processing helix chain 'A' and resid 837 through 842 Processing helix chain 'A' and resid 846 through 866 removed outlier: 3.654A pdb=" N PHE A 852 " --> pdb=" O THR A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 871 removed outlier: 3.525A pdb=" N GLU A 871 " --> pdb=" O PRO A 867 " (cutoff:3.500A) Processing helix chain 'A' and resid 876 through 884 Processing helix chain 'A' and resid 1012 through 1017 removed outlier: 3.682A pdb=" N ILE A1017 " --> pdb=" O TRP A1013 " (cutoff:3.500A) Processing helix chain 'A' and resid 1033 through 1042 Processing helix chain 'B' and resid 34 through 54 removed outlier: 3.625A pdb=" N LEU B 38 " --> pdb=" O VAL B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 60 through 78 removed outlier: 4.061A pdb=" N ALA B 64 " --> pdb=" O PRO B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 95 Processing helix chain 'B' and resid 97 through 116 Proline residue: B 107 - end of helix removed outlier: 4.568A pdb=" N GLU B 112 " --> pdb=" O ALA B 108 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N SER B 113 " --> pdb=" O LEU B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 151 removed outlier: 5.825A pdb=" N GLY B 127 " --> pdb=" O LYS B 123 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N GLN B 128 " --> pdb=" O ARG B 124 " (cutoff:3.500A) Proline residue: B 135 - end of helix Processing helix chain 'B' and resid 157 through 168 Processing helix chain 'B' and resid 172 through 184 removed outlier: 3.729A pdb=" N GLU B 182 " --> pdb=" O ALA B 178 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLY B 184 " --> pdb=" O LEU B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 216 removed outlier: 3.673A pdb=" N ASP B 201 " --> pdb=" O SER B 197 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N GLY B 202 " --> pdb=" O LEU B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 253 removed outlier: 3.956A pdb=" N ALA B 236 " --> pdb=" O VAL B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 278 removed outlier: 3.597A pdb=" N THR B 265 " --> pdb=" O GLU B 261 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N TYR B 274 " --> pdb=" O TYR B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 299 Processing helix chain 'B' and resid 306 through 339 removed outlier: 4.357A pdb=" N SER B 310 " --> pdb=" O ASP B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 347 removed outlier: 3.784A pdb=" N GLN B 347 " --> pdb=" O ILE B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 348 through 377 Proline residue: B 374 - end of helix Processing helix chain 'B' and resid 384 through 394 Processing helix chain 'B' and resid 398 through 411 Processing helix chain 'B' and resid 418 through 442 removed outlier: 3.752A pdb=" N SER B 442 " --> pdb=" O ILE B 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 443 through 450 Processing helix chain 'B' and resid 451 through 453 No H-bonds generated for 'chain 'B' and resid 451 through 453' Processing helix chain 'B' and resid 457 through 482 Processing helix chain 'B' and resid 492 through 500 Processing helix chain 'B' and resid 527 through 549 Processing helix chain 'B' and resid 553 through 568 Processing helix chain 'B' and resid 581 through 585 Processing helix chain 'B' and resid 590 through 594 Processing helix chain 'B' and resid 602 through 638 removed outlier: 4.189A pdb=" N TYR B 606 " --> pdb=" O LYS B 602 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N SER B 614 " --> pdb=" O GLU B 610 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N ALA B 615 " --> pdb=" O ARG B 611 " (cutoff:3.500A) Processing helix chain 'B' and resid 640 through 654 Processing helix chain 'B' and resid 654 through 668 removed outlier: 3.756A pdb=" N LYS B 658 " --> pdb=" O GLY B 654 " (cutoff:3.500A) Processing helix chain 'B' and resid 670 through 699 Processing helix chain 'B' and resid 704 through 723 Processing helix chain 'B' and resid 731 through 738 Processing helix chain 'B' and resid 739 through 744 removed outlier: 3.814A pdb=" N VAL B 743 " --> pdb=" O PRO B 740 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 751 Processing helix chain 'B' and resid 810 through 817 Processing helix chain 'B' and resid 837 through 842 Processing helix chain 'B' and resid 846 through 866 removed outlier: 3.654A pdb=" N PHE B 852 " --> pdb=" O THR B 848 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 871 removed outlier: 3.525A pdb=" N GLU B 871 " --> pdb=" O PRO B 867 " (cutoff:3.500A) Processing helix chain 'B' and resid 876 through 884 Processing helix chain 'B' and resid 1012 through 1017 removed outlier: 3.682A pdb=" N ILE B1017 " --> pdb=" O TRP B1013 " (cutoff:3.500A) Processing helix chain 'B' and resid 1033 through 1042 Processing sheet with id=AA1, first strand: chain 'A' and resid 761 through 762 removed outlier: 6.413A pdb=" N LEU A 831 " --> pdb=" O PHE A 782 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 767 through 769 removed outlier: 6.938A pdb=" N LEU A 824 " --> pdb=" O LEU A 768 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 888 through 892 removed outlier: 6.264A pdb=" N ARG A 966 " --> pdb=" O LEU A 909 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 913 through 914 Processing sheet with id=AA5, first strand: chain 'B' and resid 761 through 762 removed outlier: 6.413A pdb=" N LEU B 831 " --> pdb=" O PHE B 782 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 767 through 769 removed outlier: 6.938A pdb=" N LEU B 824 " --> pdb=" O LEU B 768 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 888 through 892 removed outlier: 6.264A pdb=" N ARG B 966 " --> pdb=" O LEU B 909 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 913 through 914 980 hydrogen bonds defined for protein. 2856 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: 4.63 Time building geometry restraints manager: 4.47 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: 4413 1.34 - 1.45: 2051 1.45 - 1.57: 8308 1.57 - 1.69: 0 1.69 - 1.81: 102 Bond restraints: 14874 Sorted by residual: bond pdb=" CA SER A 116 " pdb=" C SER A 116 " ideal model delta sigma weight residual 1.523 1.497 0.026 1.41e-02 5.03e+03 3.39e+00 bond pdb=" CA SER B 116 " pdb=" C SER B 116 " ideal model delta sigma weight residual 1.523 1.497 0.026 1.41e-02 5.03e+03 3.35e+00 bond pdb=" C PHE B 152 " pdb=" N PRO B 153 " ideal model delta sigma weight residual 1.331 1.345 -0.014 7.90e-03 1.60e+04 2.98e+00 bond pdb=" C PHE A 152 " pdb=" N PRO A 153 " ideal model delta sigma weight residual 1.331 1.345 -0.013 7.90e-03 1.60e+04 2.87e+00 bond pdb=" CG1 ILE A 361 " pdb=" CD1 ILE A 361 " ideal model delta sigma weight residual 1.513 1.459 0.054 3.90e-02 6.57e+02 1.94e+00 ... (remaining 14869 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.37: 19075 1.37 - 2.74: 838 2.74 - 4.12: 160 4.12 - 5.49: 52 5.49 - 6.86: 21 Bond angle restraints: 20146 Sorted by residual: angle pdb=" N GLN A 876 " pdb=" CA GLN A 876 " pdb=" C GLN A 876 " ideal model delta sigma weight residual 113.55 107.83 5.72 1.26e+00 6.30e-01 2.06e+01 angle pdb=" N GLN B 876 " pdb=" CA GLN B 876 " pdb=" C GLN B 876 " ideal model delta sigma weight residual 113.55 107.83 5.72 1.26e+00 6.30e-01 2.06e+01 angle pdb=" N VAL B 119 " pdb=" CA VAL B 119 " pdb=" C VAL B 119 " ideal model delta sigma weight residual 110.72 114.10 -3.38 1.01e+00 9.80e-01 1.12e+01 angle pdb=" N VAL A 119 " pdb=" CA VAL A 119 " pdb=" C VAL A 119 " ideal model delta sigma weight residual 110.72 114.09 -3.37 1.01e+00 9.80e-01 1.12e+01 angle pdb=" C ILE B1041 " pdb=" N PHE B1042 " pdb=" CA PHE B1042 " ideal model delta sigma weight residual 122.12 127.94 -5.82 1.76e+00 3.23e-01 1.09e+01 ... (remaining 20141 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 8021 17.87 - 35.74: 709 35.74 - 53.62: 88 53.62 - 71.49: 22 71.49 - 89.36: 18 Dihedral angle restraints: 8858 sinusoidal: 3498 harmonic: 5360 Sorted by residual: dihedral pdb=" CA ARG A 449 " pdb=" C ARG A 449 " pdb=" N LEU A 450 " pdb=" CA LEU A 450 " ideal model delta harmonic sigma weight residual 180.00 161.95 18.05 0 5.00e+00 4.00e-02 1.30e+01 dihedral pdb=" CA ARG B 449 " pdb=" C ARG B 449 " pdb=" N LEU B 450 " pdb=" CA LEU B 450 " ideal model delta harmonic sigma weight residual 180.00 161.97 18.03 0 5.00e+00 4.00e-02 1.30e+01 dihedral pdb=" CA LEU A 109 " pdb=" C LEU A 109 " pdb=" N LEU A 110 " pdb=" CA LEU A 110 " ideal model delta harmonic sigma weight residual 180.00 -163.60 -16.40 0 5.00e+00 4.00e-02 1.08e+01 ... (remaining 8855 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1456 0.034 - 0.068: 654 0.068 - 0.101: 209 0.101 - 0.135: 47 0.135 - 0.169: 6 Chirality restraints: 2372 Sorted by residual: chirality pdb=" CA SER A 925 " pdb=" N SER A 925 " pdb=" C SER A 925 " pdb=" CB SER A 925 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.12e-01 chirality pdb=" CA SER B 925 " pdb=" N SER B 925 " pdb=" C SER B 925 " pdb=" CB SER B 925 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.08e-01 chirality pdb=" CG LEU A 700 " pdb=" CB LEU A 700 " pdb=" CD1 LEU A 700 " pdb=" CD2 LEU A 700 " both_signs ideal model delta sigma weight residual False -2.59 -2.75 0.16 2.00e-01 2.50e+01 6.57e-01 ... (remaining 2369 not shown) Planarity restraints: 2472 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER B1044 " 0.009 2.00e-02 2.50e+03 1.84e-02 3.37e+00 pdb=" C SER B1044 " -0.032 2.00e-02 2.50e+03 pdb=" O SER B1044 " 0.012 2.00e-02 2.50e+03 pdb=" N MET B1045 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A1044 " -0.009 2.00e-02 2.50e+03 1.82e-02 3.29e+00 pdb=" C SER A1044 " 0.031 2.00e-02 2.50e+03 pdb=" O SER A1044 " -0.012 2.00e-02 2.50e+03 pdb=" N MET A1045 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS B 774 " -0.028 5.00e-02 4.00e+02 4.24e-02 2.88e+00 pdb=" N PRO B 775 " 0.073 5.00e-02 4.00e+02 pdb=" CA PRO B 775 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 775 " -0.024 5.00e-02 4.00e+02 ... (remaining 2469 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1210 2.74 - 3.28: 15269 3.28 - 3.82: 25266 3.82 - 4.36: 31008 4.36 - 4.90: 53542 Nonbonded interactions: 126295 Sorted by model distance: nonbonded pdb=" O VAL B 439 " pdb=" OG1 THR B 443 " model vdw 2.197 3.040 nonbonded pdb=" O VAL A 439 " pdb=" OG1 THR A 443 " model vdw 2.197 3.040 nonbonded pdb=" OE1 GLU A 470 " pdb=" OH TYR B 691 " model vdw 2.198 3.040 nonbonded pdb=" OG SER A 140 " pdb=" OG SER A 169 " model vdw 2.203 3.040 nonbonded pdb=" OG SER B 140 " pdb=" OG SER B 169 " model vdw 2.203 3.040 ... (remaining 126290 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: 0.07 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: 2.350 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: 0.650 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 35.110 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.060 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:11.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 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 : 0.004 0.054 14874 Z= 0.196 Angle : 0.709 6.858 20146 Z= 0.392 Chirality : 0.042 0.169 2372 Planarity : 0.004 0.042 2472 Dihedral : 14.073 89.359 5402 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 0.00 % Allowed : 0.50 % Favored : 99.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.20), residues: 1836 helix: 1.04 (0.15), residues: 1210 sheet: 1.67 (0.62), residues: 76 loop : -1.36 (0.26), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 493 HIS 0.006 0.001 HIS A 120 PHE 0.026 0.002 PHE A 834 TYR 0.012 0.002 TYR A 590 ARG 0.008 0.001 ARG A 966 Details of bonding type rmsd hydrogen bonds : bond 0.13597 ( 980) hydrogen bonds : angle 5.95364 ( 2856) covalent geometry : bond 0.00436 (14874) covalent geometry : angle 0.70897 (20146) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 275 time to evaluate : 1.675 Fit side-chains REVERT: A 99 GLU cc_start: 0.7119 (tt0) cc_final: 0.6888 (mm-30) REVERT: A 234 LEU cc_start: 0.8220 (mp) cc_final: 0.7905 (mp) REVERT: A 375 LEU cc_start: 0.8641 (mp) cc_final: 0.8416 (mp) REVERT: A 445 GLN cc_start: 0.7672 (tp-100) cc_final: 0.7176 (mp-120) REVERT: A 449 ARG cc_start: 0.6648 (mtm110) cc_final: 0.6353 (ttp-110) REVERT: A 562 GLN cc_start: 0.7540 (tt0) cc_final: 0.7336 (tt0) REVERT: A 579 ARG cc_start: 0.7380 (ttm170) cc_final: 0.7161 (ttp80) REVERT: A 652 LYS cc_start: 0.7869 (mmtm) cc_final: 0.7613 (pttm) REVERT: A 771 GLU cc_start: 0.7561 (tt0) cc_final: 0.6874 (tt0) REVERT: B 234 LEU cc_start: 0.8243 (mp) cc_final: 0.7963 (mp) REVERT: B 375 LEU cc_start: 0.8553 (mp) cc_final: 0.8320 (mp) REVERT: B 445 GLN cc_start: 0.7682 (tp-100) cc_final: 0.7171 (mp-120) REVERT: B 449 ARG cc_start: 0.6622 (mtm110) cc_final: 0.6334 (ttp-110) REVERT: B 562 GLN cc_start: 0.7548 (tt0) cc_final: 0.7345 (tt0) REVERT: B 579 ARG cc_start: 0.7401 (ttm170) cc_final: 0.7172 (ttp80) REVERT: B 652 LYS cc_start: 0.7906 (mmtm) cc_final: 0.7605 (pttm) REVERT: B 771 GLU cc_start: 0.7605 (tt0) cc_final: 0.7078 (tt0) REVERT: B 822 CYS cc_start: 0.8250 (p) cc_final: 0.7925 (p) outliers start: 0 outliers final: 0 residues processed: 275 average time/residue: 1.2911 time to fit residues: 391.4980 Evaluate side-chains 196 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 196 time to evaluate : 1.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 155 optimal weight: 0.5980 chunk 139 optimal weight: 5.9990 chunk 77 optimal weight: 6.9990 chunk 47 optimal weight: 3.9990 chunk 94 optimal weight: 0.3980 chunk 74 optimal weight: 3.9990 chunk 144 optimal weight: 0.9990 chunk 55 optimal weight: 0.9990 chunk 87 optimal weight: 3.9990 chunk 107 optimal weight: 4.9990 chunk 167 optimal weight: 2.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN A 277 GLN A 347 GLN ** A 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 94 ASN B 219 ASN B 277 GLN B 347 GLN ** B 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 739 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.188760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.145210 restraints weight = 14820.112| |-----------------------------------------------------------------------------| r_work (start): 0.3629 rms_B_bonded: 1.46 r_work: 0.3485 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3372 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.1399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 14874 Z= 0.214 Angle : 0.653 6.386 20146 Z= 0.336 Chirality : 0.043 0.156 2372 Planarity : 0.005 0.042 2472 Dihedral : 5.536 51.387 2020 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 3.69 % Allowed : 10.12 % Favored : 86.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.20), residues: 1836 helix: 1.10 (0.15), residues: 1222 sheet: 1.95 (0.60), residues: 72 loop : -1.18 (0.27), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 854 HIS 0.008 0.001 HIS B 120 PHE 0.018 0.002 PHE B 607 TYR 0.018 0.002 TYR A 769 ARG 0.006 0.001 ARG A 462 Details of bonding type rmsd hydrogen bonds : bond 0.04863 ( 980) hydrogen bonds : angle 5.07516 ( 2856) covalent geometry : bond 0.00508 (14874) covalent geometry : angle 0.65271 (20146) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 213 time to evaluate : 1.578 Fit side-chains REVERT: A 234 LEU cc_start: 0.8424 (mp) cc_final: 0.8155 (mp) REVERT: A 342 ASP cc_start: 0.7882 (t0) cc_final: 0.7622 (t0) REVERT: A 375 LEU cc_start: 0.8572 (mp) cc_final: 0.8337 (mp) REVERT: A 445 GLN cc_start: 0.7913 (tp-100) cc_final: 0.7690 (mm110) REVERT: A 449 ARG cc_start: 0.6873 (mtm110) cc_final: 0.5820 (ttp-110) REVERT: A 579 ARG cc_start: 0.7816 (ttm170) cc_final: 0.7454 (ttp80) REVERT: A 652 LYS cc_start: 0.8077 (mmtm) cc_final: 0.7436 (pttm) REVERT: A 761 MET cc_start: 0.8037 (OUTLIER) cc_final: 0.7212 (tmm) REVERT: A 763 LEU cc_start: 0.8575 (OUTLIER) cc_final: 0.8191 (mt) REVERT: A 866 ARG cc_start: 0.7358 (OUTLIER) cc_final: 0.6839 (tpt-90) REVERT: B 234 LEU cc_start: 0.8421 (mp) cc_final: 0.8166 (mp) REVERT: B 342 ASP cc_start: 0.7818 (t0) cc_final: 0.7512 (t0) REVERT: B 375 LEU cc_start: 0.8482 (mp) cc_final: 0.8244 (mp) REVERT: B 445 GLN cc_start: 0.7890 (tp-100) cc_final: 0.7655 (mm110) REVERT: B 449 ARG cc_start: 0.6943 (mtm110) cc_final: 0.5982 (ttp-110) REVERT: B 579 ARG cc_start: 0.7825 (ttm170) cc_final: 0.7447 (ttp80) REVERT: B 652 LYS cc_start: 0.8120 (mmtm) cc_final: 0.7482 (pttm) REVERT: B 763 LEU cc_start: 0.8532 (OUTLIER) cc_final: 0.8186 (mt) outliers start: 59 outliers final: 26 residues processed: 240 average time/residue: 1.2708 time to fit residues: 334.8275 Evaluate side-chains 229 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 199 time to evaluate : 1.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 199 MET Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 480 GLN Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain A residue 697 LYS Chi-restraints excluded: chain A residue 761 MET Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 778 VAL Chi-restraints excluded: chain A residue 835 ILE Chi-restraints excluded: chain A residue 866 ARG Chi-restraints excluded: chain A residue 876 GLN Chi-restraints excluded: chain A residue 1045 MET Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 199 MET Chi-restraints excluded: chain B residue 221 ASP Chi-restraints excluded: chain B residue 223 SER Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 480 GLN Chi-restraints excluded: chain B residue 697 LYS Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 835 ILE Chi-restraints excluded: chain B residue 876 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 122 optimal weight: 0.9980 chunk 3 optimal weight: 0.7980 chunk 20 optimal weight: 0.3980 chunk 79 optimal weight: 0.6980 chunk 132 optimal weight: 0.9990 chunk 109 optimal weight: 0.9980 chunk 77 optimal weight: 0.9990 chunk 152 optimal weight: 0.8980 chunk 130 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 16 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN A 200 ASN A 347 GLN A 480 GLN A 537 ASN ** A 739 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 94 ASN B 200 ASN B 347 GLN B 480 GLN B 537 ASN ** B 739 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.189951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.148298 restraints weight = 14847.365| |-----------------------------------------------------------------------------| r_work (start): 0.3666 rms_B_bonded: 1.51 r_work: 0.3497 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3377 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.1954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 14874 Z= 0.156 Angle : 0.574 6.506 20146 Z= 0.294 Chirality : 0.040 0.149 2372 Planarity : 0.004 0.039 2472 Dihedral : 5.252 47.056 2020 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 3.88 % Allowed : 12.44 % Favored : 83.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.20), residues: 1836 helix: 1.26 (0.15), residues: 1226 sheet: 1.80 (0.59), residues: 72 loop : -1.05 (0.27), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 493 HIS 0.006 0.001 HIS A 120 PHE 0.016 0.002 PHE B 353 TYR 0.014 0.001 TYR A 769 ARG 0.008 0.001 ARG A 378 Details of bonding type rmsd hydrogen bonds : bond 0.04311 ( 980) hydrogen bonds : angle 4.82299 ( 2856) covalent geometry : bond 0.00358 (14874) covalent geometry : angle 0.57387 (20146) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 213 time to evaluate : 1.574 Fit side-chains REVERT: A 123 LYS cc_start: 0.8191 (OUTLIER) cc_final: 0.7951 (pttt) REVERT: A 342 ASP cc_start: 0.7898 (t0) cc_final: 0.7519 (t0) REVERT: A 419 LYS cc_start: 0.8385 (tttm) cc_final: 0.8075 (tttp) REVERT: A 449 ARG cc_start: 0.6883 (mtm110) cc_final: 0.5787 (ttp-110) REVERT: A 454 ASP cc_start: 0.7087 (p0) cc_final: 0.6795 (p0) REVERT: A 652 LYS cc_start: 0.8062 (mmtm) cc_final: 0.7385 (pttm) REVERT: A 697 LYS cc_start: 0.8310 (OUTLIER) cc_final: 0.7440 (mtmt) REVERT: A 763 LEU cc_start: 0.8505 (OUTLIER) cc_final: 0.8115 (mt) REVERT: A 866 ARG cc_start: 0.7287 (OUTLIER) cc_final: 0.6688 (tpt-90) REVERT: A 876 GLN cc_start: 0.7556 (OUTLIER) cc_final: 0.7227 (pt0) REVERT: A 1042 PHE cc_start: 0.7429 (m-80) cc_final: 0.7220 (m-80) REVERT: B 123 LYS cc_start: 0.8173 (OUTLIER) cc_final: 0.7929 (pttt) REVERT: B 226 ILE cc_start: 0.7793 (OUTLIER) cc_final: 0.7589 (tt) REVERT: B 342 ASP cc_start: 0.7821 (t0) cc_final: 0.7485 (t0) REVERT: B 449 ARG cc_start: 0.6915 (mtm110) cc_final: 0.5730 (ttp-110) REVERT: B 652 LYS cc_start: 0.8051 (mmtm) cc_final: 0.7359 (pttm) REVERT: B 697 LYS cc_start: 0.8306 (OUTLIER) cc_final: 0.7433 (mtmt) REVERT: B 763 LEU cc_start: 0.8501 (OUTLIER) cc_final: 0.8136 (mt) REVERT: B 876 GLN cc_start: 0.7610 (OUTLIER) cc_final: 0.7396 (pt0) REVERT: B 966 ARG cc_start: 0.5584 (OUTLIER) cc_final: 0.5308 (ttp-170) REVERT: B 1042 PHE cc_start: 0.7349 (m-80) cc_final: 0.7123 (m-80) outliers start: 62 outliers final: 24 residues processed: 242 average time/residue: 1.2218 time to fit residues: 326.8982 Evaluate side-chains 231 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 196 time to evaluate : 1.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 123 LYS Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 221 ASP Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 436 THR Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 480 GLN Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain A residue 614 SER Chi-restraints excluded: chain A residue 656 GLU Chi-restraints excluded: chain A residue 697 LYS Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 778 VAL Chi-restraints excluded: chain A residue 835 ILE Chi-restraints excluded: chain A residue 866 ARG Chi-restraints excluded: chain A residue 876 GLN Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 123 LYS Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 480 GLN Chi-restraints excluded: chain B residue 697 LYS Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 778 VAL Chi-restraints excluded: chain B residue 835 ILE Chi-restraints excluded: chain B residue 876 GLN Chi-restraints excluded: chain B residue 966 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 108 optimal weight: 0.5980 chunk 169 optimal weight: 3.9990 chunk 76 optimal weight: 0.9990 chunk 87 optimal weight: 5.9990 chunk 141 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 115 optimal weight: 0.5980 chunk 1 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN A 347 GLN A 480 GLN ** A 739 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 94 ASN B 347 GLN B 480 GLN ** B 739 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.188377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.146775 restraints weight = 14859.872| |-----------------------------------------------------------------------------| r_work (start): 0.3652 rms_B_bonded: 1.55 r_work: 0.3466 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3343 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.2225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14874 Z= 0.180 Angle : 0.589 6.845 20146 Z= 0.299 Chirality : 0.041 0.147 2372 Planarity : 0.004 0.039 2472 Dihedral : 5.265 47.871 2020 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 3.88 % Allowed : 14.44 % Favored : 81.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.20), residues: 1836 helix: 1.23 (0.15), residues: 1226 sheet: 1.85 (0.60), residues: 72 loop : -0.96 (0.28), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 493 HIS 0.007 0.001 HIS B 120 PHE 0.016 0.002 PHE B 314 TYR 0.013 0.002 TYR B 769 ARG 0.007 0.000 ARG A 378 Details of bonding type rmsd hydrogen bonds : bond 0.04355 ( 980) hydrogen bonds : angle 4.83151 ( 2856) covalent geometry : bond 0.00427 (14874) covalent geometry : angle 0.58884 (20146) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 211 time to evaluate : 1.713 Fit side-chains REVERT: A 123 LYS cc_start: 0.8136 (OUTLIER) cc_final: 0.7896 (pttt) REVERT: A 342 ASP cc_start: 0.7874 (t0) cc_final: 0.7475 (t0) REVERT: A 419 LYS cc_start: 0.8388 (tttm) cc_final: 0.8096 (tttp) REVERT: A 449 ARG cc_start: 0.6980 (mtm110) cc_final: 0.5838 (ttp-110) REVERT: A 611 ARG cc_start: 0.7300 (ttp-170) cc_final: 0.6380 (mtp-110) REVERT: A 652 LYS cc_start: 0.8080 (mmtm) cc_final: 0.7416 (pttm) REVERT: A 697 LYS cc_start: 0.8328 (OUTLIER) cc_final: 0.7474 (mtmt) REVERT: A 703 GLU cc_start: 0.8226 (OUTLIER) cc_final: 0.7760 (mt-10) REVERT: A 708 HIS cc_start: 0.7936 (t-170) cc_final: 0.7729 (t70) REVERT: A 763 LEU cc_start: 0.8543 (OUTLIER) cc_final: 0.8160 (mt) REVERT: A 866 ARG cc_start: 0.7269 (OUTLIER) cc_final: 0.6581 (tpt-90) REVERT: A 876 GLN cc_start: 0.7667 (OUTLIER) cc_final: 0.7442 (pt0) REVERT: B 123 LYS cc_start: 0.8123 (OUTLIER) cc_final: 0.7872 (pttt) REVERT: B 176 VAL cc_start: 0.7904 (t) cc_final: 0.7619 (p) REVERT: B 342 ASP cc_start: 0.7814 (t0) cc_final: 0.7415 (t0) REVERT: B 419 LYS cc_start: 0.8399 (tttm) cc_final: 0.8097 (tttp) REVERT: B 449 ARG cc_start: 0.6888 (mtm110) cc_final: 0.5779 (ttp-110) REVERT: B 611 ARG cc_start: 0.7392 (ttp-170) cc_final: 0.6503 (mtp-110) REVERT: B 652 LYS cc_start: 0.8026 (mmtm) cc_final: 0.7366 (pttm) REVERT: B 697 LYS cc_start: 0.8324 (OUTLIER) cc_final: 0.7471 (mtmt) REVERT: B 703 GLU cc_start: 0.8238 (OUTLIER) cc_final: 0.7780 (mt-10) REVERT: B 708 HIS cc_start: 0.7917 (t-170) cc_final: 0.7696 (t-90) REVERT: B 761 MET cc_start: 0.8082 (OUTLIER) cc_final: 0.7133 (tmm) REVERT: B 763 LEU cc_start: 0.8577 (OUTLIER) cc_final: 0.8235 (mt) REVERT: B 771 GLU cc_start: 0.7612 (tt0) cc_final: 0.6547 (tt0) outliers start: 62 outliers final: 30 residues processed: 242 average time/residue: 1.1971 time to fit residues: 320.7988 Evaluate side-chains 245 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 204 time to evaluate : 1.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 123 LYS Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 436 THR Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 480 GLN Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain A residue 614 SER Chi-restraints excluded: chain A residue 656 GLU Chi-restraints excluded: chain A residue 697 LYS Chi-restraints excluded: chain A residue 703 GLU Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 778 VAL Chi-restraints excluded: chain A residue 835 ILE Chi-restraints excluded: chain A residue 866 ARG Chi-restraints excluded: chain A residue 876 GLN Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 123 LYS Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 223 SER Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 480 GLN Chi-restraints excluded: chain B residue 498 SER Chi-restraints excluded: chain B residue 604 VAL Chi-restraints excluded: chain B residue 614 SER Chi-restraints excluded: chain B residue 656 GLU Chi-restraints excluded: chain B residue 697 LYS Chi-restraints excluded: chain B residue 703 GLU Chi-restraints excluded: chain B residue 761 MET Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 778 VAL Chi-restraints excluded: chain B residue 835 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 155 optimal weight: 0.6980 chunk 70 optimal weight: 20.0000 chunk 5 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 164 optimal weight: 8.9990 chunk 40 optimal weight: 0.9990 chunk 36 optimal weight: 0.7980 chunk 7 optimal weight: 0.6980 chunk 176 optimal weight: 4.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN A 480 GLN ** A 739 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 94 ASN B 480 GLN ** B 739 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 868 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.187631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.145804 restraints weight = 14761.729| |-----------------------------------------------------------------------------| r_work (start): 0.3651 rms_B_bonded: 1.57 r_work: 0.3451 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3328 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.2419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14874 Z= 0.179 Angle : 0.590 6.515 20146 Z= 0.299 Chirality : 0.041 0.145 2372 Planarity : 0.004 0.038 2472 Dihedral : 5.238 47.556 2020 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 4.25 % Allowed : 15.88 % Favored : 79.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.20), residues: 1836 helix: 1.23 (0.15), residues: 1226 sheet: 1.85 (0.61), residues: 72 loop : -0.93 (0.28), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 493 HIS 0.006 0.001 HIS B 120 PHE 0.017 0.002 PHE B 636 TYR 0.012 0.002 TYR B 769 ARG 0.007 0.000 ARG A 378 Details of bonding type rmsd hydrogen bonds : bond 0.04343 ( 980) hydrogen bonds : angle 4.80748 ( 2856) covalent geometry : bond 0.00426 (14874) covalent geometry : angle 0.58971 (20146) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 205 time to evaluate : 1.707 Fit side-chains REVERT: A 123 LYS cc_start: 0.8194 (OUTLIER) cc_final: 0.7949 (ptmt) REVERT: A 176 VAL cc_start: 0.7852 (t) cc_final: 0.7569 (p) REVERT: A 342 ASP cc_start: 0.7906 (t0) cc_final: 0.7439 (t0) REVERT: A 419 LYS cc_start: 0.8380 (tttm) cc_final: 0.8090 (tttp) REVERT: A 445 GLN cc_start: 0.7509 (OUTLIER) cc_final: 0.7003 (mm-40) REVERT: A 449 ARG cc_start: 0.7002 (mtm110) cc_final: 0.5830 (ttp-110) REVERT: A 555 VAL cc_start: 0.8437 (OUTLIER) cc_final: 0.8156 (m) REVERT: A 611 ARG cc_start: 0.7479 (ttp-170) cc_final: 0.6768 (tmm160) REVERT: A 652 LYS cc_start: 0.8097 (mmtm) cc_final: 0.7439 (pttm) REVERT: A 697 LYS cc_start: 0.8335 (OUTLIER) cc_final: 0.7490 (mtmt) REVERT: A 703 GLU cc_start: 0.8214 (OUTLIER) cc_final: 0.7730 (mt-10) REVERT: A 763 LEU cc_start: 0.8535 (OUTLIER) cc_final: 0.8148 (mt) REVERT: A 866 ARG cc_start: 0.7283 (OUTLIER) cc_final: 0.6569 (tpt-90) REVERT: A 876 GLN cc_start: 0.7491 (pt0) cc_final: 0.7189 (pt0) REVERT: B 123 LYS cc_start: 0.8123 (OUTLIER) cc_final: 0.7884 (ptmt) REVERT: B 176 VAL cc_start: 0.7837 (t) cc_final: 0.7553 (p) REVERT: B 342 ASP cc_start: 0.7859 (t0) cc_final: 0.7374 (t0) REVERT: B 352 ARG cc_start: 0.7922 (OUTLIER) cc_final: 0.7632 (mmt-90) REVERT: B 419 LYS cc_start: 0.8392 (tttm) cc_final: 0.8105 (tttp) REVERT: B 449 ARG cc_start: 0.6982 (mtm110) cc_final: 0.5963 (ttp-110) REVERT: B 555 VAL cc_start: 0.8441 (OUTLIER) cc_final: 0.8159 (m) REVERT: B 652 LYS cc_start: 0.8044 (mmtm) cc_final: 0.7367 (pttm) REVERT: B 703 GLU cc_start: 0.8251 (OUTLIER) cc_final: 0.7787 (mt-10) REVERT: B 708 HIS cc_start: 0.7913 (t-170) cc_final: 0.7695 (t-90) REVERT: B 771 GLU cc_start: 0.7636 (tt0) cc_final: 0.6543 (tt0) outliers start: 68 outliers final: 39 residues processed: 240 average time/residue: 1.1547 time to fit residues: 308.3949 Evaluate side-chains 249 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 199 time to evaluate : 1.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 123 LYS Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 436 THR Chi-restraints excluded: chain A residue 445 GLN Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 480 GLN Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 577 ASP Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 614 SER Chi-restraints excluded: chain A residue 656 GLU Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 697 LYS Chi-restraints excluded: chain A residue 703 GLU Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 778 VAL Chi-restraints excluded: chain A residue 808 THR Chi-restraints excluded: chain A residue 835 ILE Chi-restraints excluded: chain A residue 866 ARG Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 123 LYS Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 223 SER Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 352 ARG Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 480 GLN Chi-restraints excluded: chain B residue 498 SER Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain B residue 577 ASP Chi-restraints excluded: chain B residue 604 VAL Chi-restraints excluded: chain B residue 614 SER Chi-restraints excluded: chain B residue 656 GLU Chi-restraints excluded: chain B residue 675 VAL Chi-restraints excluded: chain B residue 703 GLU Chi-restraints excluded: chain B residue 778 VAL Chi-restraints excluded: chain B residue 808 THR Chi-restraints excluded: chain B residue 835 ILE Chi-restraints excluded: chain B residue 866 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 47 optimal weight: 0.3980 chunk 137 optimal weight: 0.9980 chunk 15 optimal weight: 6.9990 chunk 107 optimal weight: 6.9990 chunk 135 optimal weight: 0.5980 chunk 38 optimal weight: 0.0030 chunk 7 optimal weight: 0.9980 chunk 114 optimal weight: 0.9980 chunk 33 optimal weight: 0.8980 chunk 136 optimal weight: 0.6980 chunk 73 optimal weight: 0.9990 overall best weight: 0.5190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN A 480 GLN ** A 739 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 94 ASN B 347 GLN B 480 GLN ** B 739 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.189501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.147302 restraints weight = 14838.615| |-----------------------------------------------------------------------------| r_work (start): 0.3660 rms_B_bonded: 1.60 r_work: 0.3495 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3372 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.2530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14874 Z= 0.133 Angle : 0.549 8.218 20146 Z= 0.279 Chirality : 0.039 0.148 2372 Planarity : 0.004 0.039 2472 Dihedral : 5.022 44.514 2020 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 3.94 % Allowed : 17.19 % Favored : 78.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.20), residues: 1836 helix: 1.39 (0.15), residues: 1226 sheet: 1.87 (0.61), residues: 72 loop : -0.89 (0.28), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 493 HIS 0.004 0.001 HIS B 120 PHE 0.017 0.001 PHE A 636 TYR 0.011 0.001 TYR A 634 ARG 0.004 0.000 ARG A 378 Details of bonding type rmsd hydrogen bonds : bond 0.04029 ( 980) hydrogen bonds : angle 4.66585 ( 2856) covalent geometry : bond 0.00306 (14874) covalent geometry : angle 0.54916 (20146) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 211 time to evaluate : 1.593 Fit side-chains REVERT: A 123 LYS cc_start: 0.8171 (OUTLIER) cc_final: 0.7917 (ptmt) REVERT: A 342 ASP cc_start: 0.7826 (t0) cc_final: 0.7303 (t0) REVERT: A 419 LYS cc_start: 0.8302 (tttm) cc_final: 0.8008 (tttp) REVERT: A 449 ARG cc_start: 0.6823 (mtm110) cc_final: 0.5964 (ttp-110) REVERT: A 503 LEU cc_start: 0.8147 (OUTLIER) cc_final: 0.7735 (tp) REVERT: A 555 VAL cc_start: 0.8375 (OUTLIER) cc_final: 0.8105 (m) REVERT: A 652 LYS cc_start: 0.8083 (mmtm) cc_final: 0.7408 (pttm) REVERT: A 703 GLU cc_start: 0.8231 (OUTLIER) cc_final: 0.7762 (mt-10) REVERT: A 763 LEU cc_start: 0.8512 (OUTLIER) cc_final: 0.8126 (mt) REVERT: A 866 ARG cc_start: 0.7248 (OUTLIER) cc_final: 0.6533 (tpt-90) REVERT: A 875 MET cc_start: 0.7364 (tpp) cc_final: 0.7047 (tpt) REVERT: A 876 GLN cc_start: 0.7570 (pt0) cc_final: 0.7343 (pt0) REVERT: B 121 GLN cc_start: 0.7819 (mt0) cc_final: 0.7558 (mp10) REVERT: B 123 LYS cc_start: 0.8128 (OUTLIER) cc_final: 0.7859 (ptmt) REVERT: B 199 MET cc_start: 0.8480 (OUTLIER) cc_final: 0.7976 (mtt) REVERT: B 342 ASP cc_start: 0.7781 (t0) cc_final: 0.7350 (t0) REVERT: B 352 ARG cc_start: 0.7893 (OUTLIER) cc_final: 0.7608 (mmt-90) REVERT: B 419 LYS cc_start: 0.8360 (tttm) cc_final: 0.8073 (tttp) REVERT: B 449 ARG cc_start: 0.6894 (mtm110) cc_final: 0.5932 (ttp-110) REVERT: B 555 VAL cc_start: 0.8373 (OUTLIER) cc_final: 0.8104 (m) REVERT: B 652 LYS cc_start: 0.8043 (mmtm) cc_final: 0.7360 (pttm) REVERT: B 697 LYS cc_start: 0.8335 (OUTLIER) cc_final: 0.7497 (mtmt) REVERT: B 703 GLU cc_start: 0.8261 (OUTLIER) cc_final: 0.7800 (mt-10) REVERT: B 708 HIS cc_start: 0.7851 (t-170) cc_final: 0.7639 (t-90) REVERT: B 763 LEU cc_start: 0.8520 (OUTLIER) cc_final: 0.8131 (mt) outliers start: 63 outliers final: 34 residues processed: 239 average time/residue: 1.1356 time to fit residues: 302.0692 Evaluate side-chains 241 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 194 time to evaluate : 1.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 123 LYS Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 436 THR Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 480 GLN Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 577 ASP Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 614 SER Chi-restraints excluded: chain A residue 703 GLU Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 778 VAL Chi-restraints excluded: chain A residue 835 ILE Chi-restraints excluded: chain A residue 866 ARG Chi-restraints excluded: chain A residue 890 THR Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 123 LYS Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 199 MET Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 352 ARG Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 480 GLN Chi-restraints excluded: chain B residue 498 SER Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain B residue 577 ASP Chi-restraints excluded: chain B residue 604 VAL Chi-restraints excluded: chain B residue 614 SER Chi-restraints excluded: chain B residue 697 LYS Chi-restraints excluded: chain B residue 703 GLU Chi-restraints excluded: chain B residue 736 ILE Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 778 VAL Chi-restraints excluded: chain B residue 835 ILE Chi-restraints excluded: chain B residue 866 ARG Chi-restraints excluded: chain B residue 890 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 143 optimal weight: 2.9990 chunk 132 optimal weight: 1.9990 chunk 85 optimal weight: 0.7980 chunk 178 optimal weight: 4.9990 chunk 152 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 127 optimal weight: 2.9990 chunk 89 optimal weight: 0.8980 chunk 179 optimal weight: 7.9990 chunk 40 optimal weight: 0.9980 chunk 31 optimal weight: 0.7980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN A 347 GLN ** A 739 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 94 ASN ** B 739 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.188282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.145835 restraints weight = 14763.870| |-----------------------------------------------------------------------------| r_work (start): 0.3645 rms_B_bonded: 1.65 r_work: 0.3464 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3340 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.2609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 14874 Z= 0.163 Angle : 0.581 8.772 20146 Z= 0.292 Chirality : 0.040 0.152 2372 Planarity : 0.004 0.041 2472 Dihedral : 5.048 45.972 2020 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 4.44 % Allowed : 17.31 % Favored : 78.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.20), residues: 1836 helix: 1.39 (0.15), residues: 1226 sheet: 1.90 (0.62), residues: 72 loop : -0.88 (0.28), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 493 HIS 0.006 0.001 HIS A 120 PHE 0.017 0.002 PHE A 636 TYR 0.011 0.001 TYR B 769 ARG 0.004 0.000 ARG B 611 Details of bonding type rmsd hydrogen bonds : bond 0.04167 ( 980) hydrogen bonds : angle 4.70505 ( 2856) covalent geometry : bond 0.00385 (14874) covalent geometry : angle 0.58085 (20146) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 207 time to evaluate : 1.656 Fit side-chains REVERT: A 121 GLN cc_start: 0.7854 (mp10) cc_final: 0.7630 (mp10) REVERT: A 123 LYS cc_start: 0.8170 (OUTLIER) cc_final: 0.7921 (ptmt) REVERT: A 342 ASP cc_start: 0.7763 (t0) cc_final: 0.7247 (t0) REVERT: A 419 LYS cc_start: 0.8304 (tttm) cc_final: 0.8013 (tttp) REVERT: A 445 GLN cc_start: 0.7527 (OUTLIER) cc_final: 0.7006 (mm-40) REVERT: A 449 ARG cc_start: 0.6993 (mtm110) cc_final: 0.5932 (ttp-110) REVERT: A 476 LEU cc_start: 0.8560 (mp) cc_final: 0.8268 (mt) REVERT: A 503 LEU cc_start: 0.8189 (OUTLIER) cc_final: 0.7719 (tp) REVERT: A 555 VAL cc_start: 0.8421 (OUTLIER) cc_final: 0.8155 (m) REVERT: A 652 LYS cc_start: 0.8035 (mmtm) cc_final: 0.7387 (pttm) REVERT: A 703 GLU cc_start: 0.8236 (OUTLIER) cc_final: 0.7757 (mt-10) REVERT: A 763 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.8120 (mt) REVERT: A 866 ARG cc_start: 0.7245 (OUTLIER) cc_final: 0.6550 (tpt-90) REVERT: A 875 MET cc_start: 0.7295 (tpp) cc_final: 0.7011 (tpt) REVERT: B 99 GLU cc_start: 0.7896 (tt0) cc_final: 0.7579 (mp0) REVERT: B 123 LYS cc_start: 0.8166 (OUTLIER) cc_final: 0.7926 (ptmt) REVERT: B 129 MET cc_start: 0.7600 (mmp) cc_final: 0.7325 (mmp) REVERT: B 342 ASP cc_start: 0.7792 (t0) cc_final: 0.7303 (t0) REVERT: B 352 ARG cc_start: 0.7901 (OUTLIER) cc_final: 0.7615 (mmt-90) REVERT: B 419 LYS cc_start: 0.8361 (tttm) cc_final: 0.8076 (tttp) REVERT: B 445 GLN cc_start: 0.7536 (OUTLIER) cc_final: 0.7040 (mm-40) REVERT: B 449 ARG cc_start: 0.7004 (mtm110) cc_final: 0.5961 (ttp-110) REVERT: B 454 ASP cc_start: 0.7367 (p0) cc_final: 0.7137 (p0) REVERT: B 476 LEU cc_start: 0.8559 (mp) cc_final: 0.8318 (mt) REVERT: B 555 VAL cc_start: 0.8426 (OUTLIER) cc_final: 0.8151 (m) REVERT: B 652 LYS cc_start: 0.8060 (mmtm) cc_final: 0.7372 (pttm) REVERT: B 697 LYS cc_start: 0.8382 (OUTLIER) cc_final: 0.7553 (mtmt) REVERT: B 703 GLU cc_start: 0.8251 (OUTLIER) cc_final: 0.7766 (mt-10) REVERT: B 708 HIS cc_start: 0.7892 (t-170) cc_final: 0.7679 (t-90) REVERT: B 763 LEU cc_start: 0.8516 (OUTLIER) cc_final: 0.8143 (mt) outliers start: 71 outliers final: 38 residues processed: 241 average time/residue: 1.1699 time to fit residues: 314.3193 Evaluate side-chains 248 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 196 time to evaluate : 2.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 MET Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 123 LYS Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 436 THR Chi-restraints excluded: chain A residue 445 GLN Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 577 ASP Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 614 SER Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 703 GLU Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 778 VAL Chi-restraints excluded: chain A residue 835 ILE Chi-restraints excluded: chain A residue 866 ARG Chi-restraints excluded: chain A residue 890 THR Chi-restraints excluded: chain B residue 42 MET Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 123 LYS Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 223 SER Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 352 ARG Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain B residue 445 GLN Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 498 SER Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain B residue 577 ASP Chi-restraints excluded: chain B residue 604 VAL Chi-restraints excluded: chain B residue 614 SER Chi-restraints excluded: chain B residue 675 VAL Chi-restraints excluded: chain B residue 697 LYS Chi-restraints excluded: chain B residue 703 GLU Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 835 ILE Chi-restraints excluded: chain B residue 866 ARG Chi-restraints excluded: chain B residue 890 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 27 optimal weight: 2.9990 chunk 128 optimal weight: 0.6980 chunk 153 optimal weight: 0.8980 chunk 23 optimal weight: 0.5980 chunk 135 optimal weight: 0.6980 chunk 173 optimal weight: 0.4980 chunk 107 optimal weight: 6.9990 chunk 100 optimal weight: 0.6980 chunk 64 optimal weight: 0.8980 chunk 74 optimal weight: 0.0070 chunk 76 optimal weight: 0.9980 overall best weight: 0.4998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN A 347 GLN ** A 739 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 94 ASN ** B 739 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.190799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.149739 restraints weight = 14829.033| |-----------------------------------------------------------------------------| r_work (start): 0.3682 rms_B_bonded: 1.53 r_work: 0.3499 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3378 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.2743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14874 Z= 0.128 Angle : 0.547 8.260 20146 Z= 0.276 Chirality : 0.039 0.154 2372 Planarity : 0.004 0.039 2472 Dihedral : 4.856 43.359 2020 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 4.12 % Allowed : 17.44 % Favored : 78.44 % 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: 1.24 (0.20), residues: 1836 helix: 1.51 (0.15), residues: 1226 sheet: 1.86 (0.61), residues: 72 loop : -0.89 (0.28), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 493 HIS 0.005 0.001 HIS B 120 PHE 0.017 0.001 PHE A 636 TYR 0.010 0.001 TYR B 769 ARG 0.004 0.000 ARG A 378 Details of bonding type rmsd hydrogen bonds : bond 0.03896 ( 980) hydrogen bonds : angle 4.57847 ( 2856) covalent geometry : bond 0.00296 (14874) covalent geometry : angle 0.54695 (20146) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 217 time to evaluate : 1.576 Fit side-chains REVERT: A 95 GLU cc_start: 0.8230 (mm-30) cc_final: 0.7965 (mp0) REVERT: A 123 LYS cc_start: 0.8161 (OUTLIER) cc_final: 0.7907 (ptmt) REVERT: A 176 VAL cc_start: 0.7694 (OUTLIER) cc_final: 0.7370 (p) REVERT: A 342 ASP cc_start: 0.7650 (t0) cc_final: 0.7157 (t0) REVERT: A 419 LYS cc_start: 0.8289 (tttm) cc_final: 0.7988 (tttp) REVERT: A 449 ARG cc_start: 0.7074 (mtm110) cc_final: 0.5943 (ttp-110) REVERT: A 503 LEU cc_start: 0.8207 (OUTLIER) cc_final: 0.7898 (mt) REVERT: A 555 VAL cc_start: 0.8340 (OUTLIER) cc_final: 0.8071 (m) REVERT: A 570 GLN cc_start: 0.7746 (mp10) cc_final: 0.7375 (mt0) REVERT: A 652 LYS cc_start: 0.8028 (mmtm) cc_final: 0.7350 (pttm) REVERT: A 697 LYS cc_start: 0.8308 (OUTLIER) cc_final: 0.7482 (mtmt) REVERT: A 703 GLU cc_start: 0.8241 (OUTLIER) cc_final: 0.7750 (mt-10) REVERT: A 763 LEU cc_start: 0.8505 (OUTLIER) cc_final: 0.8103 (mt) REVERT: A 866 ARG cc_start: 0.7162 (OUTLIER) cc_final: 0.6471 (tpt-90) REVERT: A 907 LEU cc_start: 0.6819 (OUTLIER) cc_final: 0.6605 (tp) REVERT: B 99 GLU cc_start: 0.7906 (tt0) cc_final: 0.7562 (mp0) REVERT: B 123 LYS cc_start: 0.8125 (OUTLIER) cc_final: 0.7861 (ptmt) REVERT: B 176 VAL cc_start: 0.7685 (OUTLIER) cc_final: 0.7357 (p) REVERT: B 199 MET cc_start: 0.8354 (OUTLIER) cc_final: 0.7840 (mtt) REVERT: B 342 ASP cc_start: 0.7768 (t0) cc_final: 0.7262 (t0) REVERT: B 352 ARG cc_start: 0.7839 (OUTLIER) cc_final: 0.7583 (mmt-90) REVERT: B 419 LYS cc_start: 0.8341 (tttm) cc_final: 0.8048 (tttp) REVERT: B 449 ARG cc_start: 0.7049 (mtm110) cc_final: 0.5894 (ttp-110) REVERT: B 503 LEU cc_start: 0.8196 (OUTLIER) cc_final: 0.7854 (mt) REVERT: B 555 VAL cc_start: 0.8355 (OUTLIER) cc_final: 0.8079 (m) REVERT: B 570 GLN cc_start: 0.7760 (mp10) cc_final: 0.7386 (mt0) REVERT: B 652 LYS cc_start: 0.8055 (mmtm) cc_final: 0.7393 (pttm) REVERT: B 697 LYS cc_start: 0.8301 (OUTLIER) cc_final: 0.7489 (mtmt) REVERT: B 703 GLU cc_start: 0.8262 (OUTLIER) cc_final: 0.7794 (mt-10) REVERT: B 708 HIS cc_start: 0.7843 (t-170) cc_final: 0.7626 (t-90) REVERT: B 763 LEU cc_start: 0.8510 (OUTLIER) cc_final: 0.8142 (mt) REVERT: B 866 ARG cc_start: 0.7215 (OUTLIER) cc_final: 0.6851 (tpp80) REVERT: B 1011 MET cc_start: 0.8745 (ttm) cc_final: 0.8526 (mtt) outliers start: 66 outliers final: 34 residues processed: 253 average time/residue: 1.1446 time to fit residues: 321.9554 Evaluate side-chains 257 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 204 time to evaluate : 1.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 123 LYS Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 436 THR Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 577 ASP Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 614 SER Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 697 LYS Chi-restraints excluded: chain A residue 703 GLU Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 778 VAL Chi-restraints excluded: chain A residue 835 ILE Chi-restraints excluded: chain A residue 866 ARG Chi-restraints excluded: chain A residue 890 THR Chi-restraints excluded: chain A residue 907 LEU Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 123 LYS Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 199 MET Chi-restraints excluded: chain B residue 223 SER Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 352 ARG Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain B residue 577 ASP Chi-restraints excluded: chain B residue 604 VAL Chi-restraints excluded: chain B residue 614 SER Chi-restraints excluded: chain B residue 675 VAL Chi-restraints excluded: chain B residue 697 LYS Chi-restraints excluded: chain B residue 703 GLU Chi-restraints excluded: chain B residue 736 ILE Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 835 ILE Chi-restraints excluded: chain B residue 866 ARG Chi-restraints excluded: chain B residue 890 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 126 optimal weight: 0.3980 chunk 114 optimal weight: 2.9990 chunk 124 optimal weight: 0.5980 chunk 20 optimal weight: 0.9990 chunk 140 optimal weight: 0.7980 chunk 97 optimal weight: 0.0570 chunk 171 optimal weight: 9.9990 chunk 145 optimal weight: 0.9990 chunk 70 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 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 94 ASN ** A 739 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 94 ASN ** B 739 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.190919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.149602 restraints weight = 14777.842| |-----------------------------------------------------------------------------| r_work (start): 0.3682 rms_B_bonded: 1.54 r_work: 0.3498 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3376 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.2841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14874 Z= 0.132 Angle : 0.553 8.692 20146 Z= 0.279 Chirality : 0.039 0.151 2372 Planarity : 0.004 0.041 2472 Dihedral : 4.820 43.135 2020 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 3.81 % Allowed : 17.94 % Favored : 78.25 % 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: 1.27 (0.20), residues: 1836 helix: 1.53 (0.15), residues: 1226 sheet: 1.94 (0.62), residues: 72 loop : -0.87 (0.28), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 493 HIS 0.007 0.001 HIS A 120 PHE 0.015 0.001 PHE A 636 TYR 0.011 0.001 TYR A 346 ARG 0.005 0.000 ARG B 611 Details of bonding type rmsd hydrogen bonds : bond 0.03904 ( 980) hydrogen bonds : angle 4.57947 ( 2856) covalent geometry : bond 0.00308 (14874) covalent geometry : angle 0.55313 (20146) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 216 time to evaluate : 1.597 Fit side-chains REVERT: A 95 GLU cc_start: 0.8245 (mm-30) cc_final: 0.7982 (mp0) REVERT: A 123 LYS cc_start: 0.8147 (OUTLIER) cc_final: 0.7907 (ptmt) REVERT: A 176 VAL cc_start: 0.7631 (OUTLIER) cc_final: 0.7299 (p) REVERT: A 342 ASP cc_start: 0.7714 (t0) cc_final: 0.7212 (t0) REVERT: A 419 LYS cc_start: 0.8283 (tttm) cc_final: 0.7977 (tttp) REVERT: A 503 LEU cc_start: 0.8072 (OUTLIER) cc_final: 0.7713 (mt) REVERT: A 555 VAL cc_start: 0.8329 (OUTLIER) cc_final: 0.8061 (m) REVERT: A 570 GLN cc_start: 0.7738 (mp10) cc_final: 0.7385 (mt0) REVERT: A 610 GLU cc_start: 0.8182 (mm-30) cc_final: 0.7789 (mp0) REVERT: A 652 LYS cc_start: 0.8028 (mmtm) cc_final: 0.7337 (pttm) REVERT: A 697 LYS cc_start: 0.8306 (OUTLIER) cc_final: 0.7489 (mtmt) REVERT: A 703 GLU cc_start: 0.8165 (OUTLIER) cc_final: 0.7702 (mt-10) REVERT: A 763 LEU cc_start: 0.8501 (OUTLIER) cc_final: 0.8095 (mt) REVERT: A 866 ARG cc_start: 0.7020 (OUTLIER) cc_final: 0.6683 (tpp80) REVERT: A 907 LEU cc_start: 0.6817 (OUTLIER) cc_final: 0.6609 (tp) REVERT: B 99 GLU cc_start: 0.7877 (tt0) cc_final: 0.7538 (mp0) REVERT: B 123 LYS cc_start: 0.8171 (OUTLIER) cc_final: 0.7903 (pttt) REVERT: B 176 VAL cc_start: 0.7604 (OUTLIER) cc_final: 0.7293 (p) REVERT: B 342 ASP cc_start: 0.7724 (t0) cc_final: 0.7220 (t0) REVERT: B 352 ARG cc_start: 0.7883 (OUTLIER) cc_final: 0.7620 (mmt-90) REVERT: B 419 LYS cc_start: 0.8335 (tttm) cc_final: 0.8040 (tttp) REVERT: B 449 ARG cc_start: 0.7002 (mtm110) cc_final: 0.6727 (mtm-85) REVERT: B 472 LEU cc_start: 0.8289 (OUTLIER) cc_final: 0.8035 (tt) REVERT: B 555 VAL cc_start: 0.8334 (OUTLIER) cc_final: 0.8056 (m) REVERT: B 570 GLN cc_start: 0.7733 (mp10) cc_final: 0.7375 (mt0) REVERT: B 610 GLU cc_start: 0.8242 (mm-30) cc_final: 0.7841 (mp0) REVERT: B 652 LYS cc_start: 0.8030 (mmtm) cc_final: 0.7344 (pttm) REVERT: B 697 LYS cc_start: 0.8315 (OUTLIER) cc_final: 0.7487 (mtmt) REVERT: B 703 GLU cc_start: 0.8180 (OUTLIER) cc_final: 0.7719 (mt-10) REVERT: B 708 HIS cc_start: 0.7845 (t-170) cc_final: 0.7634 (t-90) REVERT: B 763 LEU cc_start: 0.8505 (OUTLIER) cc_final: 0.8127 (mt) REVERT: B 866 ARG cc_start: 0.7192 (OUTLIER) cc_final: 0.6829 (tpp80) outliers start: 61 outliers final: 33 residues processed: 247 average time/residue: 1.1238 time to fit residues: 309.0081 Evaluate side-chains 259 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 208 time to evaluate : 1.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 123 LYS Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 436 THR Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 577 ASP Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 697 LYS Chi-restraints excluded: chain A residue 703 GLU Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 778 VAL Chi-restraints excluded: chain A residue 835 ILE Chi-restraints excluded: chain A residue 866 ARG Chi-restraints excluded: chain A residue 890 THR Chi-restraints excluded: chain A residue 907 LEU Chi-restraints excluded: chain A residue 1011 MET Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 123 LYS Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 223 SER Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 352 ARG Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain B residue 577 ASP Chi-restraints excluded: chain B residue 604 VAL Chi-restraints excluded: chain B residue 614 SER Chi-restraints excluded: chain B residue 675 VAL Chi-restraints excluded: chain B residue 697 LYS Chi-restraints excluded: chain B residue 703 GLU Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 835 ILE Chi-restraints excluded: chain B residue 866 ARG Chi-restraints excluded: chain B residue 890 THR Chi-restraints excluded: chain B residue 907 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 158 optimal weight: 0.5980 chunk 63 optimal weight: 0.5980 chunk 126 optimal weight: 2.9990 chunk 182 optimal weight: 0.5980 chunk 173 optimal weight: 1.9990 chunk 170 optimal weight: 4.9990 chunk 144 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 chunk 110 optimal weight: 0.9980 chunk 143 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN ** A 739 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 94 ASN ** B 739 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.189582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.147506 restraints weight = 14720.307| |-----------------------------------------------------------------------------| r_work (start): 0.3665 rms_B_bonded: 1.56 r_work: 0.3487 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3364 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.2894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 14874 Z= 0.149 Angle : 0.569 8.511 20146 Z= 0.287 Chirality : 0.040 0.147 2372 Planarity : 0.004 0.043 2472 Dihedral : 4.890 44.031 2020 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 3.75 % Allowed : 18.12 % Favored : 78.12 % 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: 1.25 (0.20), residues: 1836 helix: 1.49 (0.15), residues: 1228 sheet: 2.00 (0.62), residues: 72 loop : -0.85 (0.29), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 493 HIS 0.006 0.001 HIS A 120 PHE 0.017 0.001 PHE B 636 TYR 0.014 0.001 TYR A 346 ARG 0.005 0.000 ARG A 611 Details of bonding type rmsd hydrogen bonds : bond 0.04020 ( 980) hydrogen bonds : angle 4.63207 ( 2856) covalent geometry : bond 0.00355 (14874) covalent geometry : angle 0.56903 (20146) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 211 time to evaluate : 1.552 Fit side-chains REVERT: A 95 GLU cc_start: 0.8277 (mm-30) cc_final: 0.8022 (mp0) REVERT: A 123 LYS cc_start: 0.8180 (OUTLIER) cc_final: 0.7916 (pttt) REVERT: A 176 VAL cc_start: 0.7620 (OUTLIER) cc_final: 0.7305 (p) REVERT: A 342 ASP cc_start: 0.7669 (t0) cc_final: 0.7166 (t0) REVERT: A 419 LYS cc_start: 0.8286 (tttm) cc_final: 0.7986 (tttp) REVERT: A 449 ARG cc_start: 0.6957 (mtm-85) cc_final: 0.5849 (ttp-110) REVERT: A 503 LEU cc_start: 0.8047 (OUTLIER) cc_final: 0.7739 (mt) REVERT: A 555 VAL cc_start: 0.8391 (OUTLIER) cc_final: 0.8129 (m) REVERT: A 570 GLN cc_start: 0.7706 (mp10) cc_final: 0.7349 (mt0) REVERT: A 610 GLU cc_start: 0.8155 (mm-30) cc_final: 0.7750 (mp0) REVERT: A 652 LYS cc_start: 0.8048 (mmtm) cc_final: 0.7368 (pttm) REVERT: A 697 LYS cc_start: 0.8308 (OUTLIER) cc_final: 0.7512 (mtmt) REVERT: A 703 GLU cc_start: 0.8150 (OUTLIER) cc_final: 0.7703 (mt-10) REVERT: A 763 LEU cc_start: 0.8492 (OUTLIER) cc_final: 0.8082 (mt) REVERT: A 866 ARG cc_start: 0.7050 (OUTLIER) cc_final: 0.6375 (tpt-90) REVERT: B 99 GLU cc_start: 0.7899 (tt0) cc_final: 0.7622 (mp0) REVERT: B 123 LYS cc_start: 0.8186 (OUTLIER) cc_final: 0.7926 (pttt) REVERT: B 176 VAL cc_start: 0.7603 (OUTLIER) cc_final: 0.7281 (p) REVERT: B 342 ASP cc_start: 0.7681 (t0) cc_final: 0.7184 (t0) REVERT: B 352 ARG cc_start: 0.7918 (OUTLIER) cc_final: 0.7657 (mmt-90) REVERT: B 419 LYS cc_start: 0.8343 (tttm) cc_final: 0.8052 (tttp) REVERT: B 472 LEU cc_start: 0.8305 (OUTLIER) cc_final: 0.8090 (tt) REVERT: B 503 LEU cc_start: 0.8161 (OUTLIER) cc_final: 0.7798 (mt) REVERT: B 555 VAL cc_start: 0.8395 (OUTLIER) cc_final: 0.8126 (m) REVERT: B 570 GLN cc_start: 0.7704 (mp10) cc_final: 0.7357 (mt0) REVERT: B 610 GLU cc_start: 0.8259 (mm-30) cc_final: 0.7877 (mp0) REVERT: B 652 LYS cc_start: 0.8095 (mmtm) cc_final: 0.7447 (pttm) REVERT: B 697 LYS cc_start: 0.8385 (OUTLIER) cc_final: 0.7517 (mtmt) REVERT: B 703 GLU cc_start: 0.8141 (OUTLIER) cc_final: 0.7688 (mt-10) REVERT: B 708 HIS cc_start: 0.8023 (t-170) cc_final: 0.7756 (t-90) REVERT: B 763 LEU cc_start: 0.8520 (OUTLIER) cc_final: 0.8149 (mt) REVERT: B 866 ARG cc_start: 0.7195 (OUTLIER) cc_final: 0.6814 (tpp80) outliers start: 60 outliers final: 33 residues processed: 242 average time/residue: 1.1413 time to fit residues: 306.7988 Evaluate side-chains 259 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 208 time to evaluate : 1.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 123 LYS Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 436 THR Chi-restraints excluded: chain A residue 453 MET Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 577 ASP Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 697 LYS Chi-restraints excluded: chain A residue 703 GLU Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 778 VAL Chi-restraints excluded: chain A residue 835 ILE Chi-restraints excluded: chain A residue 866 ARG Chi-restraints excluded: chain A residue 890 THR Chi-restraints excluded: chain A residue 1011 MET Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 123 LYS Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 223 SER Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 352 ARG Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain B residue 453 MET Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain B residue 577 ASP Chi-restraints excluded: chain B residue 604 VAL Chi-restraints excluded: chain B residue 614 SER Chi-restraints excluded: chain B residue 675 VAL Chi-restraints excluded: chain B residue 697 LYS Chi-restraints excluded: chain B residue 703 GLU Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 835 ILE Chi-restraints excluded: chain B residue 866 ARG Chi-restraints excluded: chain B residue 890 THR Chi-restraints excluded: chain B residue 907 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 65 optimal weight: 0.9980 chunk 60 optimal weight: 2.9990 chunk 126 optimal weight: 0.0980 chunk 33 optimal weight: 0.7980 chunk 172 optimal weight: 2.9990 chunk 174 optimal weight: 4.9990 chunk 128 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 132 optimal weight: 0.7980 chunk 177 optimal weight: 0.9990 chunk 66 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN ** A 739 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 94 ASN ** B 739 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.189644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.147632 restraints weight = 14748.674| |-----------------------------------------------------------------------------| r_work (start): 0.3667 rms_B_bonded: 1.55 r_work: 0.3488 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3364 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.2946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14874 Z= 0.147 Angle : 0.565 8.460 20146 Z= 0.285 Chirality : 0.040 0.146 2372 Planarity : 0.004 0.042 2472 Dihedral : 4.899 44.373 2020 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 3.62 % Allowed : 18.38 % Favored : 78.00 % 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: 1.24 (0.20), residues: 1836 helix: 1.48 (0.15), residues: 1228 sheet: 1.98 (0.62), residues: 72 loop : -0.84 (0.29), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 493 HIS 0.006 0.001 HIS A 120 PHE 0.017 0.001 PHE A 636 TYR 0.010 0.001 TYR A 346 ARG 0.005 0.000 ARG B 611 Details of bonding type rmsd hydrogen bonds : bond 0.03992 ( 980) hydrogen bonds : angle 4.63937 ( 2856) covalent geometry : bond 0.00347 (14874) covalent geometry : angle 0.56451 (20146) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12149.67 seconds wall clock time: 210 minutes 13.41 seconds (12613.41 seconds total)