Starting phenix.real_space_refine on Wed Mar 4 15:42:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7y3e_33592/03_2026/7y3e_33592.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y3e_33592/03_2026/7y3e_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 { model { file = "/net/cci-nas-00/data/ceres_data/7y3e_33592/03_2026/7y3e_33592.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y3e_33592/03_2026/7y3e_33592.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7y3e_33592/03_2026/7y3e_33592.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y3e_33592/03_2026/7y3e_33592.map" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: 2.86, per 1000 atoms: 0.20 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: 1.22 Conformation dependent library (CDL) restraints added in 485.8 milliseconds 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: 0.50 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: 2.48 Time building geometry restraints manager: 1.61 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: 0.02 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: 2.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.200 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 13.410 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.610 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.008 0.001 ARG A 966 TYR 0.012 0.002 TYR A 590 PHE 0.026 0.002 PHE A 834 TRP 0.016 0.002 TRP A 493 HIS 0.006 0.001 HIS A 120 Details of bonding type rmsd covalent geometry : bond 0.00436 (14874) covalent geometry : angle 0.70897 (20146) hydrogen bonds : bond 0.13597 ( 980) hydrogen bonds : angle 5.95364 ( 2856) *********************** 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 : 0.523 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: 0.8321 (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: 0.5877 time to fit residues: 177.3559 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 : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 0.4980 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 0.5980 chunk 130 optimal weight: 0.4980 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 94 ASN B 277 GLN B 347 GLN ** B 537 ASN ** 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 = 0.4129 r_free = 0.4129 target = 0.191908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.150516 restraints weight = 14834.369| |-----------------------------------------------------------------------------| r_work (start): 0.3695 rms_B_bonded: 1.59 r_work: 0.3527 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3410 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.1361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14874 Z= 0.151 Angle : 0.599 6.299 20146 Z= 0.307 Chirality : 0.040 0.159 2372 Planarity : 0.004 0.038 2472 Dihedral : 5.298 45.697 2020 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 3.31 % Allowed : 10.62 % Favored : 86.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.20), residues: 1836 helix: 1.25 (0.15), residues: 1232 sheet: 1.87 (0.59), residues: 72 loop : -1.28 (0.27), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 462 TYR 0.017 0.002 TYR A 769 PHE 0.022 0.002 PHE B 607 TRP 0.016 0.002 TRP A 493 HIS 0.005 0.001 HIS B 120 Details of bonding type rmsd covalent geometry : bond 0.00344 (14874) covalent geometry : angle 0.59944 (20146) hydrogen bonds : bond 0.04487 ( 980) hydrogen bonds : angle 4.90046 ( 2856) *********************** 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 270 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 217 time to evaluate : 0.511 Fit side-chains REVERT: A 199 MET cc_start: 0.8417 (OUTLIER) cc_final: 0.8060 (mtt) REVERT: A 234 LEU cc_start: 0.8374 (mp) cc_final: 0.8114 (mp) REVERT: A 342 ASP cc_start: 0.7940 (t0) cc_final: 0.7621 (t0) REVERT: A 445 GLN cc_start: 0.7984 (tp-100) cc_final: 0.7683 (mm110) REVERT: A 449 ARG cc_start: 0.6964 (mtm110) cc_final: 0.5921 (ttp-110) REVERT: A 579 ARG cc_start: 0.7754 (ttm170) cc_final: 0.7398 (ttp80) REVERT: A 652 LYS cc_start: 0.8059 (mmtm) cc_final: 0.7377 (pttm) REVERT: A 697 LYS cc_start: 0.8174 (OUTLIER) cc_final: 0.7308 (mtmt) REVERT: A 763 LEU cc_start: 0.8550 (OUTLIER) cc_final: 0.8157 (mt) REVERT: A 866 ARG cc_start: 0.7195 (OUTLIER) cc_final: 0.6654 (tpt-90) REVERT: A 876 GLN cc_start: 0.7615 (OUTLIER) cc_final: 0.7335 (pt0) REVERT: B 199 MET cc_start: 0.8425 (OUTLIER) cc_final: 0.8163 (mtt) REVERT: B 234 LEU cc_start: 0.8360 (mp) cc_final: 0.8108 (mp) REVERT: B 342 ASP cc_start: 0.7850 (t0) cc_final: 0.7533 (t0) REVERT: B 445 GLN cc_start: 0.7995 (tp-100) cc_final: 0.7687 (mm110) REVERT: B 449 ARG cc_start: 0.6961 (mtm110) cc_final: 0.5818 (ttp-110) REVERT: B 579 ARG cc_start: 0.7761 (ttm170) cc_final: 0.7401 (ttp80) REVERT: B 652 LYS cc_start: 0.8090 (mmtm) cc_final: 0.7450 (pttm) REVERT: B 697 LYS cc_start: 0.8139 (OUTLIER) cc_final: 0.7264 (mtmt) REVERT: B 763 LEU cc_start: 0.8520 (OUTLIER) cc_final: 0.8157 (mt) outliers start: 53 outliers final: 18 residues processed: 239 average time/residue: 0.6179 time to fit residues: 161.6600 Evaluate side-chains 221 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 195 time to evaluate : 0.434 ------------------------------------------------------------------------------- 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 258 THR Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 480 GLN 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 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 258 THR Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 480 GLN Chi-restraints excluded: chain B residue 498 SER 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 4 optimal weight: 4.9990 chunk 79 optimal weight: 0.7980 chunk 58 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 chunk 158 optimal weight: 0.8980 chunk 143 optimal weight: 0.0010 chunk 37 optimal weight: 0.6980 chunk 45 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 124 optimal weight: 0.5980 chunk 132 optimal weight: 0.6980 overall best weight: 0.5586 ------------------------------------------------------------------------------- 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 537 ASN B 94 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.191324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.148912 restraints weight = 14886.240| |-----------------------------------------------------------------------------| r_work (start): 0.3681 rms_B_bonded: 1.64 r_work: 0.3523 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3403 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.1865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14874 Z= 0.138 Angle : 0.557 6.269 20146 Z= 0.285 Chirality : 0.039 0.149 2372 Planarity : 0.004 0.040 2472 Dihedral : 5.036 43.086 2020 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 3.38 % Allowed : 12.81 % Favored : 83.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.12 (0.20), residues: 1836 helix: 1.44 (0.15), residues: 1236 sheet: 1.73 (0.58), residues: 72 loop : -1.03 (0.28), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 378 TYR 0.013 0.001 TYR A 769 PHE 0.015 0.001 PHE B 314 TRP 0.020 0.001 TRP A 493 HIS 0.005 0.001 HIS B 626 Details of bonding type rmsd covalent geometry : bond 0.00317 (14874) covalent geometry : angle 0.55670 (20146) hydrogen bonds : bond 0.04152 ( 980) hydrogen bonds : angle 4.69761 ( 2856) *********************** 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 261 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 207 time to evaluate : 0.493 Fit side-chains REVERT: A 123 LYS cc_start: 0.8222 (OUTLIER) cc_final: 0.7961 (pttt) REVERT: A 199 MET cc_start: 0.8414 (OUTLIER) cc_final: 0.7952 (mtt) REVERT: A 342 ASP cc_start: 0.7889 (t0) cc_final: 0.7552 (t0) REVERT: A 449 ARG cc_start: 0.6884 (mtm110) cc_final: 0.5863 (ttp-110) REVERT: A 652 LYS cc_start: 0.8052 (mmtm) cc_final: 0.7371 (pttm) REVERT: A 763 LEU cc_start: 0.8579 (OUTLIER) cc_final: 0.8162 (mt) REVERT: A 866 ARG cc_start: 0.7269 (OUTLIER) cc_final: 0.6681 (tpt-90) REVERT: A 876 GLN cc_start: 0.7509 (pt0) cc_final: 0.7264 (pt0) REVERT: A 1042 PHE cc_start: 0.7277 (m-80) cc_final: 0.7071 (m-80) REVERT: B 123 LYS cc_start: 0.8190 (OUTLIER) cc_final: 0.7930 (pttt) REVERT: B 199 MET cc_start: 0.8421 (OUTLIER) cc_final: 0.7997 (mtt) REVERT: B 342 ASP cc_start: 0.7819 (t0) cc_final: 0.7467 (t0) REVERT: B 352 ARG cc_start: 0.7919 (OUTLIER) cc_final: 0.7390 (mtt90) REVERT: B 445 GLN cc_start: 0.7950 (tp-100) cc_final: 0.7748 (mm110) REVERT: B 449 ARG cc_start: 0.6841 (mtm110) cc_final: 0.5743 (ttp-110) REVERT: B 579 ARG cc_start: 0.7754 (ttm170) cc_final: 0.7550 (ttp80) REVERT: B 611 ARG cc_start: 0.7265 (ttp-170) cc_final: 0.6926 (tmm160) REVERT: B 652 LYS cc_start: 0.8053 (mmtm) cc_final: 0.7362 (pttm) REVERT: B 763 LEU cc_start: 0.8589 (OUTLIER) cc_final: 0.8235 (mt) REVERT: B 866 ARG cc_start: 0.7376 (tpt170) cc_final: 0.6971 (tpp80) REVERT: B 1042 PHE cc_start: 0.7293 (m-80) cc_final: 0.7038 (m-80) outliers start: 54 outliers final: 15 residues processed: 231 average time/residue: 0.5691 time to fit residues: 144.9261 Evaluate side-chains 217 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 194 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 123 LYS Chi-restraints excluded: chain A residue 199 MET 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 736 ILE 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 B residue 122 ILE Chi-restraints excluded: chain B residue 123 LYS 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 448 LEU Chi-restraints excluded: chain B residue 480 GLN 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 69 optimal weight: 0.9980 chunk 23 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 114 optimal weight: 0.8980 chunk 112 optimal weight: 0.9990 chunk 167 optimal weight: 4.9990 chunk 180 optimal weight: 0.5980 chunk 107 optimal weight: 3.9990 chunk 70 optimal weight: 10.0000 chunk 182 optimal weight: 0.4980 chunk 75 optimal weight: 7.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.4110 r_free = 0.4110 target = 0.189785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.147214 restraints weight = 14781.608| |-----------------------------------------------------------------------------| r_work (start): 0.3660 rms_B_bonded: 1.58 r_work: 0.3491 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3370 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.2149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 14874 Z= 0.153 Angle : 0.565 7.078 20146 Z= 0.286 Chirality : 0.040 0.146 2372 Planarity : 0.004 0.038 2472 Dihedral : 5.015 43.351 2020 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 3.25 % Allowed : 14.94 % Favored : 81.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.11 (0.20), residues: 1836 helix: 1.42 (0.15), residues: 1226 sheet: 1.82 (0.59), residues: 72 loop : -0.97 (0.28), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 378 TYR 0.012 0.001 TYR B 769 PHE 0.015 0.002 PHE A 314 TRP 0.019 0.001 TRP B 493 HIS 0.005 0.001 HIS B 120 Details of bonding type rmsd covalent geometry : bond 0.00358 (14874) covalent geometry : angle 0.56494 (20146) hydrogen bonds : bond 0.04127 ( 980) hydrogen bonds : angle 4.68542 ( 2856) *********************** 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 257 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 205 time to evaluate : 0.449 Fit side-chains REVERT: A 123 LYS cc_start: 0.8163 (OUTLIER) cc_final: 0.7895 (pttt) REVERT: A 176 VAL cc_start: 0.7927 (t) cc_final: 0.7600 (p) REVERT: A 199 MET cc_start: 0.8443 (OUTLIER) cc_final: 0.7949 (mtt) REVERT: A 342 ASP cc_start: 0.7904 (t0) cc_final: 0.7521 (t0) REVERT: A 449 ARG cc_start: 0.6978 (mtm110) cc_final: 0.5999 (ttp-110) REVERT: A 472 LEU cc_start: 0.8352 (OUTLIER) cc_final: 0.8151 (tt) REVERT: A 611 ARG cc_start: 0.7261 (ttp-170) cc_final: 0.6973 (tmm160) REVERT: A 652 LYS cc_start: 0.8049 (mmtm) cc_final: 0.7392 (pttm) REVERT: A 697 LYS cc_start: 0.8293 (OUTLIER) cc_final: 0.7428 (mtmt) REVERT: A 703 GLU cc_start: 0.8211 (OUTLIER) cc_final: 0.7743 (mt-10) REVERT: A 763 LEU cc_start: 0.8583 (OUTLIER) cc_final: 0.8166 (mt) REVERT: A 866 ARG cc_start: 0.7156 (OUTLIER) cc_final: 0.6540 (tpt-90) REVERT: B 123 LYS cc_start: 0.8131 (OUTLIER) cc_final: 0.7869 (pttt) REVERT: B 176 VAL cc_start: 0.7793 (t) cc_final: 0.7527 (p) REVERT: B 199 MET cc_start: 0.8451 (OUTLIER) cc_final: 0.7963 (mtt) REVERT: B 342 ASP cc_start: 0.7809 (t0) cc_final: 0.7474 (t0) REVERT: B 419 LYS cc_start: 0.8390 (tttm) cc_final: 0.8083 (tttp) REVERT: B 445 GLN cc_start: 0.8030 (tp-100) cc_final: 0.7812 (mm110) REVERT: B 449 ARG cc_start: 0.6819 (mtm110) cc_final: 0.5791 (ttp-110) REVERT: B 579 ARG cc_start: 0.7808 (ttm170) cc_final: 0.7477 (ttp80) REVERT: B 611 ARG cc_start: 0.7317 (ttp-170) cc_final: 0.6398 (mtp-110) REVERT: B 652 LYS cc_start: 0.8046 (mmtm) cc_final: 0.7380 (pttm) REVERT: B 697 LYS cc_start: 0.8300 (OUTLIER) cc_final: 0.7450 (mtmt) REVERT: B 703 GLU cc_start: 0.8242 (OUTLIER) cc_final: 0.7797 (mt-10) REVERT: B 763 LEU cc_start: 0.8566 (OUTLIER) cc_final: 0.8191 (mt) REVERT: B 771 GLU cc_start: 0.7573 (tt0) cc_final: 0.6477 (tt0) REVERT: B 1042 PHE cc_start: 0.7634 (m-80) cc_final: 0.7423 (m-80) outliers start: 52 outliers final: 24 residues processed: 232 average time/residue: 0.6183 time to fit residues: 157.4657 Evaluate side-chains 233 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 197 time to evaluate : 0.519 ------------------------------------------------------------------------------- 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 198 LEU Chi-restraints excluded: chain A residue 199 MET 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 472 LEU Chi-restraints excluded: chain A residue 480 GLN Chi-restraints excluded: chain A residue 577 ASP Chi-restraints excluded: chain A residue 614 SER 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 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 198 LEU Chi-restraints excluded: chain B residue 199 MET 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 614 SER 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 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 57 optimal weight: 1.9990 chunk 123 optimal weight: 0.8980 chunk 68 optimal weight: 2.9990 chunk 157 optimal weight: 0.1980 chunk 179 optimal weight: 2.9990 chunk 8 optimal weight: 0.6980 chunk 51 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 chunk 54 optimal weight: 0.0270 chunk 1 optimal weight: 0.9980 chunk 86 optimal weight: 4.9990 overall best weight: 0.5638 ------------------------------------------------------------------------------- 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 = 0.4118 r_free = 0.4118 target = 0.190752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.149476 restraints weight = 14968.572| |-----------------------------------------------------------------------------| r_work (start): 0.3687 rms_B_bonded: 1.49 r_work: 0.3512 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3392 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.2327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14874 Z= 0.134 Angle : 0.541 6.855 20146 Z= 0.275 Chirality : 0.039 0.147 2372 Planarity : 0.004 0.037 2472 Dihedral : 4.893 40.888 2020 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 4.00 % Allowed : 15.69 % Favored : 80.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.21 (0.20), residues: 1836 helix: 1.50 (0.15), residues: 1226 sheet: 1.84 (0.60), residues: 72 loop : -0.92 (0.28), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 378 TYR 0.011 0.001 TYR B 769 PHE 0.014 0.001 PHE A 636 TRP 0.017 0.001 TRP B 493 HIS 0.004 0.001 HIS B 120 Details of bonding type rmsd covalent geometry : bond 0.00308 (14874) covalent geometry : angle 0.54065 (20146) hydrogen bonds : bond 0.03987 ( 980) hydrogen bonds : angle 4.59379 ( 2856) *********************** 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 269 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 205 time to evaluate : 0.532 Fit side-chains REVERT: A 198 LEU cc_start: 0.8616 (OUTLIER) cc_final: 0.8349 (tp) REVERT: A 199 MET cc_start: 0.8444 (OUTLIER) cc_final: 0.7904 (mtt) REVERT: A 342 ASP cc_start: 0.7875 (t0) cc_final: 0.7379 (t0) REVERT: A 419 LYS cc_start: 0.8424 (tttm) cc_final: 0.8095 (tttp) REVERT: A 449 ARG cc_start: 0.6990 (mtm110) cc_final: 0.5946 (ttp-110) REVERT: A 555 VAL cc_start: 0.8357 (OUTLIER) cc_final: 0.8084 (m) REVERT: A 611 ARG cc_start: 0.7334 (ttp-170) cc_final: 0.6997 (tmm160) REVERT: A 652 LYS cc_start: 0.8007 (mmtm) cc_final: 0.7364 (pttm) REVERT: A 697 LYS cc_start: 0.8287 (OUTLIER) cc_final: 0.7441 (mtmt) REVERT: A 703 GLU cc_start: 0.8201 (OUTLIER) cc_final: 0.7741 (mt-10) REVERT: A 763 LEU cc_start: 0.8569 (OUTLIER) cc_final: 0.8148 (mt) REVERT: A 866 ARG cc_start: 0.7152 (OUTLIER) cc_final: 0.6505 (tpt-90) REVERT: B 199 MET cc_start: 0.8440 (OUTLIER) cc_final: 0.7886 (mtt) REVERT: B 342 ASP cc_start: 0.7773 (t0) cc_final: 0.7326 (t0) REVERT: B 352 ARG cc_start: 0.7790 (OUTLIER) cc_final: 0.7301 (mtt90) REVERT: B 419 LYS cc_start: 0.8374 (tttm) cc_final: 0.8071 (tttp) REVERT: B 445 GLN cc_start: 0.7985 (tp-100) cc_final: 0.7783 (mm110) REVERT: B 449 ARG cc_start: 0.6876 (mtm110) cc_final: 0.5709 (ttp-110) REVERT: B 555 VAL cc_start: 0.8416 (OUTLIER) cc_final: 0.8135 (m) REVERT: B 579 ARG cc_start: 0.7770 (ttm170) cc_final: 0.7424 (ttp80) REVERT: B 611 ARG cc_start: 0.7299 (ttp-170) cc_final: 0.6961 (tmm160) REVERT: B 652 LYS cc_start: 0.8021 (mmtm) cc_final: 0.7389 (pttm) REVERT: B 697 LYS cc_start: 0.8297 (OUTLIER) cc_final: 0.7453 (mtmt) REVERT: B 703 GLU cc_start: 0.8262 (OUTLIER) cc_final: 0.7817 (mt-10) REVERT: B 763 LEU cc_start: 0.8548 (OUTLIER) cc_final: 0.8176 (mt) REVERT: B 771 GLU cc_start: 0.7590 (tt0) cc_final: 0.6493 (tt0) outliers start: 64 outliers final: 31 residues processed: 234 average time/residue: 0.5486 time to fit residues: 141.6064 Evaluate side-chains 240 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 196 time to evaluate : 0.412 ------------------------------------------------------------------------------- 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 176 VAL Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 199 MET 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 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 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 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 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 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 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 763 LEU Chi-restraints excluded: chain B residue 778 VAL Chi-restraints excluded: chain B residue 808 THR Chi-restraints excluded: chain B residue 835 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 26 optimal weight: 0.8980 chunk 93 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 67 optimal weight: 0.0040 chunk 11 optimal weight: 0.6980 chunk 61 optimal weight: 0.9990 chunk 162 optimal weight: 6.9990 chunk 72 optimal weight: 5.9990 chunk 120 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 127 optimal weight: 1.9990 overall best weight: 0.9196 ------------------------------------------------------------------------------- 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 = 0.4101 r_free = 0.4101 target = 0.188849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.146089 restraints weight = 14698.338| |-----------------------------------------------------------------------------| r_work (start): 0.3650 rms_B_bonded: 1.64 r_work: 0.3470 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3347 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.2470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 14874 Z= 0.164 Angle : 0.566 7.268 20146 Z= 0.284 Chirality : 0.040 0.154 2372 Planarity : 0.004 0.038 2472 Dihedral : 4.963 43.203 2020 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 4.19 % Allowed : 16.31 % Favored : 79.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.15 (0.20), residues: 1836 helix: 1.43 (0.15), residues: 1226 sheet: 1.95 (0.62), residues: 72 loop : -0.92 (0.28), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 378 TYR 0.012 0.001 TYR B 769 PHE 0.015 0.002 PHE A 636 TRP 0.017 0.001 TRP B 493 HIS 0.006 0.001 HIS B 120 Details of bonding type rmsd covalent geometry : bond 0.00389 (14874) covalent geometry : angle 0.56586 (20146) hydrogen bonds : bond 0.04152 ( 980) hydrogen bonds : angle 4.66299 ( 2856) *********************** 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 271 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 204 time to evaluate : 0.540 Fit side-chains REVERT: A 199 MET cc_start: 0.8461 (OUTLIER) cc_final: 0.7888 (mtt) REVERT: A 342 ASP cc_start: 0.7840 (t0) cc_final: 0.7342 (t0) REVERT: A 419 LYS cc_start: 0.8452 (tttm) cc_final: 0.8113 (tttp) REVERT: A 449 ARG cc_start: 0.6916 (mtm110) cc_final: 0.5759 (ttp-110) REVERT: A 555 VAL cc_start: 0.8415 (OUTLIER) cc_final: 0.8138 (m) REVERT: A 652 LYS cc_start: 0.8063 (mmtm) cc_final: 0.7427 (pttm) REVERT: A 697 LYS cc_start: 0.8285 (OUTLIER) cc_final: 0.7457 (mtmt) REVERT: A 703 GLU cc_start: 0.8279 (OUTLIER) cc_final: 0.7813 (mt-10) REVERT: A 708 HIS cc_start: 0.7900 (t-170) cc_final: 0.7692 (t70) REVERT: A 763 LEU cc_start: 0.8585 (OUTLIER) cc_final: 0.8178 (mt) REVERT: A 866 ARG cc_start: 0.7203 (OUTLIER) cc_final: 0.6553 (tpt-90) REVERT: B 199 MET cc_start: 0.8467 (OUTLIER) cc_final: 0.7899 (mtt) REVERT: B 342 ASP cc_start: 0.7819 (t0) cc_final: 0.7365 (t0) REVERT: B 352 ARG cc_start: 0.7894 (OUTLIER) cc_final: 0.7377 (mtt90) REVERT: B 419 LYS cc_start: 0.8384 (tttm) cc_final: 0.8084 (tttp) REVERT: B 449 ARG cc_start: 0.6804 (mtm110) cc_final: 0.5903 (ttp-110) REVERT: B 454 ASP cc_start: 0.7096 (p0) cc_final: 0.6839 (p0) REVERT: B 555 VAL cc_start: 0.8427 (OUTLIER) cc_final: 0.8145 (m) REVERT: B 579 ARG cc_start: 0.7838 (ttm170) cc_final: 0.7571 (ttp80) REVERT: B 652 LYS cc_start: 0.8002 (mmtm) cc_final: 0.7357 (pttm) REVERT: B 697 LYS cc_start: 0.8319 (OUTLIER) cc_final: 0.7489 (mtmt) REVERT: B 703 GLU cc_start: 0.8297 (OUTLIER) cc_final: 0.7844 (mt-10) REVERT: B 708 HIS cc_start: 0.7908 (t-170) cc_final: 0.7704 (t70) REVERT: B 763 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8214 (mt) REVERT: B 875 MET cc_start: 0.7911 (tpp) cc_final: 0.7504 (tpt) outliers start: 67 outliers final: 36 residues processed: 239 average time/residue: 0.5366 time to fit residues: 141.9072 Evaluate side-chains 243 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 195 time to evaluate : 0.492 ------------------------------------------------------------------------------- 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 176 VAL 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 436 THR Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 480 GLN 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 835 ILE Chi-restraints excluded: chain A residue 866 ARG Chi-restraints excluded: chain A residue 890 THR 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 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 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 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 778 VAL Chi-restraints excluded: chain B residue 835 ILE 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 38 optimal weight: 1.9990 chunk 40 optimal weight: 0.2980 chunk 55 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 2.9990 chunk 168 optimal weight: 0.9980 chunk 87 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 82 optimal weight: 5.9990 chunk 120 optimal weight: 0.5980 chunk 175 optimal weight: 7.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 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** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.188356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.145911 restraints weight = 14634.838| |-----------------------------------------------------------------------------| r_work (start): 0.3646 rms_B_bonded: 1.64 r_work: 0.3464 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3341 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.2601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 14874 Z= 0.164 Angle : 0.571 8.771 20146 Z= 0.287 Chirality : 0.040 0.149 2372 Planarity : 0.004 0.039 2472 Dihedral : 4.996 44.791 2020 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 3.69 % Allowed : 16.81 % Favored : 79.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.13 (0.20), residues: 1836 helix: 1.41 (0.15), residues: 1226 sheet: 1.93 (0.62), residues: 72 loop : -0.91 (0.28), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 378 TYR 0.012 0.001 TYR B 769 PHE 0.017 0.002 PHE A 636 TRP 0.018 0.001 TRP A 493 HIS 0.006 0.001 HIS A 120 Details of bonding type rmsd covalent geometry : bond 0.00391 (14874) covalent geometry : angle 0.57091 (20146) hydrogen bonds : bond 0.04151 ( 980) hydrogen bonds : angle 4.67253 ( 2856) *********************** 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 265 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 206 time to evaluate : 0.487 Fit side-chains REVERT: A 99 GLU cc_start: 0.7877 (tt0) cc_final: 0.7584 (tt0) REVERT: A 129 MET cc_start: 0.7619 (mmp) cc_final: 0.7361 (mmp) REVERT: A 199 MET cc_start: 0.8461 (OUTLIER) cc_final: 0.7934 (mtt) REVERT: A 342 ASP cc_start: 0.7816 (t0) cc_final: 0.7304 (t0) REVERT: A 419 LYS cc_start: 0.8416 (tttm) cc_final: 0.8103 (tttp) REVERT: A 449 ARG cc_start: 0.6891 (mtm110) cc_final: 0.6003 (ttp-110) REVERT: A 555 VAL cc_start: 0.8416 (OUTLIER) cc_final: 0.8140 (m) REVERT: A 652 LYS cc_start: 0.8060 (mmtm) cc_final: 0.7431 (pttm) REVERT: A 697 LYS cc_start: 0.8298 (OUTLIER) cc_final: 0.7468 (mtmt) REVERT: A 703 GLU cc_start: 0.8237 (OUTLIER) cc_final: 0.7768 (mt-10) REVERT: A 763 LEU cc_start: 0.8579 (OUTLIER) cc_final: 0.8169 (mt) REVERT: A 866 ARG cc_start: 0.7186 (OUTLIER) cc_final: 0.6503 (tpt-90) REVERT: A 1011 MET cc_start: 0.8800 (ttm) cc_final: 0.8532 (mtt) REVERT: B 129 MET cc_start: 0.7605 (mmp) cc_final: 0.7311 (mmp) REVERT: B 342 ASP cc_start: 0.7850 (t0) cc_final: 0.7320 (t0) REVERT: B 352 ARG cc_start: 0.7882 (OUTLIER) cc_final: 0.7597 (mmt-90) REVERT: B 419 LYS cc_start: 0.8372 (tttm) cc_final: 0.8079 (tttp) REVERT: B 449 ARG cc_start: 0.6944 (mtm110) cc_final: 0.5886 (ttp-110) REVERT: B 555 VAL cc_start: 0.8421 (OUTLIER) cc_final: 0.8140 (m) REVERT: B 579 ARG cc_start: 0.7865 (ttm170) cc_final: 0.7624 (ttp80) REVERT: B 652 LYS cc_start: 0.8015 (mmtm) cc_final: 0.7379 (pttm) REVERT: B 697 LYS cc_start: 0.8313 (OUTLIER) cc_final: 0.7488 (mtmt) REVERT: B 703 GLU cc_start: 0.8266 (OUTLIER) cc_final: 0.7796 (mt-10) REVERT: B 763 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.8186 (mt) REVERT: B 875 MET cc_start: 0.7794 (tpp) cc_final: 0.7407 (tpt) REVERT: B 1011 MET cc_start: 0.8774 (ttm) cc_final: 0.8513 (mtt) outliers start: 59 outliers final: 36 residues processed: 240 average time/residue: 0.5437 time to fit residues: 144.5980 Evaluate side-chains 243 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 196 time to evaluate : 0.477 ------------------------------------------------------------------------------- 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 176 VAL 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 436 THR Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 480 GLN 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 835 ILE Chi-restraints excluded: chain A residue 866 ARG Chi-restraints excluded: chain A residue 890 THR 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 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 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 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 778 VAL Chi-restraints excluded: chain B residue 835 ILE 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 57 optimal weight: 0.7980 chunk 83 optimal weight: 8.9990 chunk 74 optimal weight: 0.0770 chunk 98 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 chunk 58 optimal weight: 0.8980 chunk 141 optimal weight: 0.6980 chunk 95 optimal weight: 0.9980 chunk 89 optimal weight: 3.9990 chunk 71 optimal weight: 0.9980 chunk 29 optimal weight: 0.6980 overall best weight: 0.6138 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.185695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.142897 restraints weight = 14726.473| |-----------------------------------------------------------------------------| r_work (start): 0.3656 rms_B_bonded: 1.61 r_work: 0.3474 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3348 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.2687 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= 0.138 Angle : 0.554 8.113 20146 Z= 0.279 Chirality : 0.039 0.153 2372 Planarity : 0.004 0.040 2472 Dihedral : 4.899 44.179 2020 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 3.50 % Allowed : 17.38 % Favored : 79.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.20 (0.20), residues: 1836 helix: 1.48 (0.15), residues: 1226 sheet: 1.93 (0.62), residues: 72 loop : -0.91 (0.28), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 611 TYR 0.011 0.001 TYR A 769 PHE 0.018 0.001 PHE A 636 TRP 0.024 0.001 TRP A 493 HIS 0.004 0.001 HIS B 120 Details of bonding type rmsd covalent geometry : bond 0.00324 (14874) covalent geometry : angle 0.55398 (20146) hydrogen bonds : bond 0.03993 ( 980) hydrogen bonds : angle 4.60833 ( 2856) *********************** 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 266 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 210 time to evaluate : 0.514 Fit side-chains REVERT: A 198 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8402 (tp) REVERT: A 342 ASP cc_start: 0.7823 (t0) cc_final: 0.7332 (t0) REVERT: A 419 LYS cc_start: 0.8412 (tttm) cc_final: 0.8100 (tttp) REVERT: A 449 ARG cc_start: 0.6992 (mtm110) cc_final: 0.5976 (ttp-110) REVERT: A 555 VAL cc_start: 0.8380 (OUTLIER) cc_final: 0.8107 (m) REVERT: A 610 GLU cc_start: 0.8250 (mm-30) cc_final: 0.7864 (mp0) REVERT: A 652 LYS cc_start: 0.8094 (mmtm) cc_final: 0.7447 (pttm) REVERT: A 703 GLU cc_start: 0.8256 (OUTLIER) cc_final: 0.7770 (mt-10) REVERT: A 763 LEU cc_start: 0.8571 (OUTLIER) cc_final: 0.8129 (mt) REVERT: A 866 ARG cc_start: 0.7161 (OUTLIER) cc_final: 0.6475 (tpt-90) REVERT: A 1011 MET cc_start: 0.8726 (ttm) cc_final: 0.8500 (mtt) REVERT: A 1045 MET cc_start: 0.5734 (tpp) cc_final: 0.5525 (tpp) REVERT: B 342 ASP cc_start: 0.7782 (t0) cc_final: 0.7271 (t0) REVERT: B 352 ARG cc_start: 0.7874 (OUTLIER) cc_final: 0.7634 (mmt-90) REVERT: B 419 LYS cc_start: 0.8363 (tttm) cc_final: 0.8070 (tttp) REVERT: B 449 ARG cc_start: 0.6962 (mtm110) cc_final: 0.5937 (ttp-110) REVERT: B 503 LEU cc_start: 0.8177 (OUTLIER) cc_final: 0.7770 (tp) REVERT: B 555 VAL cc_start: 0.8387 (OUTLIER) cc_final: 0.8110 (m) REVERT: B 579 ARG cc_start: 0.7830 (ttm170) cc_final: 0.7590 (ttp80) REVERT: B 610 GLU cc_start: 0.8236 (mm-30) cc_final: 0.7853 (mp0) REVERT: B 652 LYS cc_start: 0.8045 (mmtm) cc_final: 0.7385 (pttm) REVERT: B 703 GLU cc_start: 0.8266 (OUTLIER) cc_final: 0.7799 (mt-10) REVERT: B 763 LEU cc_start: 0.8497 (OUTLIER) cc_final: 0.8172 (mt) REVERT: B 866 ARG cc_start: 0.7156 (OUTLIER) cc_final: 0.6798 (tpp80) REVERT: B 875 MET cc_start: 0.7654 (tpp) cc_final: 0.7230 (tpt) REVERT: B 1011 MET cc_start: 0.8718 (ttm) cc_final: 0.8500 (mtt) outliers start: 56 outliers final: 34 residues processed: 238 average time/residue: 0.5350 time to fit residues: 140.9572 Evaluate side-chains 242 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 197 time to evaluate : 0.516 ------------------------------------------------------------------------------- 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 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 436 THR Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 480 GLN 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 736 ILE 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 63 VAL Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 198 LEU 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 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 703 GLU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 85 optimal weight: 0.9980 chunk 84 optimal weight: 6.9990 chunk 179 optimal weight: 9.9990 chunk 120 optimal weight: 0.5980 chunk 76 optimal weight: 1.9990 chunk 149 optimal weight: 0.7980 chunk 62 optimal weight: 0.6980 chunk 108 optimal weight: 0.5980 chunk 165 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 100 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.189104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.146709 restraints weight = 14780.833| |-----------------------------------------------------------------------------| r_work (start): 0.3658 rms_B_bonded: 1.60 r_work: 0.3470 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3346 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.2777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14874 Z= 0.146 Angle : 0.560 8.644 20146 Z= 0.282 Chirality : 0.040 0.149 2372 Planarity : 0.004 0.041 2472 Dihedral : 4.888 44.565 2020 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 3.62 % Allowed : 17.19 % Favored : 79.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.17 (0.20), residues: 1836 helix: 1.43 (0.15), residues: 1228 sheet: 1.96 (0.62), residues: 72 loop : -0.89 (0.28), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 378 TYR 0.011 0.001 TYR A 769 PHE 0.017 0.002 PHE A 636 TRP 0.021 0.001 TRP A 493 HIS 0.006 0.001 HIS A 120 Details of bonding type rmsd covalent geometry : bond 0.00346 (14874) covalent geometry : angle 0.56006 (20146) hydrogen bonds : bond 0.04011 ( 980) hydrogen bonds : angle 4.61257 ( 2856) *********************** 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 260 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 202 time to evaluate : 0.527 Fit side-chains REVERT: A 95 GLU cc_start: 0.8273 (mm-30) cc_final: 0.8007 (mp0) REVERT: A 121 GLN cc_start: 0.7802 (mt0) cc_final: 0.7597 (mp10) REVERT: A 198 LEU cc_start: 0.8667 (OUTLIER) cc_final: 0.8394 (tp) REVERT: A 342 ASP cc_start: 0.7804 (t0) cc_final: 0.7300 (t0) REVERT: A 419 LYS cc_start: 0.8421 (tttm) cc_final: 0.8108 (tttp) REVERT: A 449 ARG cc_start: 0.7060 (mtm110) cc_final: 0.6008 (ttp-110) REVERT: A 555 VAL cc_start: 0.8392 (OUTLIER) cc_final: 0.8117 (m) REVERT: A 652 LYS cc_start: 0.8127 (mmtm) cc_final: 0.7445 (pttm) REVERT: A 697 LYS cc_start: 0.8280 (OUTLIER) cc_final: 0.7465 (mtmt) REVERT: A 703 GLU cc_start: 0.8238 (OUTLIER) cc_final: 0.7749 (mt-10) REVERT: A 763 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.8155 (mt) REVERT: A 866 ARG cc_start: 0.7170 (OUTLIER) cc_final: 0.6481 (tpt-90) REVERT: A 907 LEU cc_start: 0.6903 (OUTLIER) cc_final: 0.6675 (tp) REVERT: B 121 GLN cc_start: 0.7795 (mt0) cc_final: 0.7591 (mp10) REVERT: B 342 ASP cc_start: 0.7789 (t0) cc_final: 0.7287 (t0) REVERT: B 352 ARG cc_start: 0.7879 (OUTLIER) cc_final: 0.7595 (mmt-90) REVERT: B 419 LYS cc_start: 0.8371 (tttm) cc_final: 0.8081 (tttp) REVERT: B 449 ARG cc_start: 0.7076 (mtm110) cc_final: 0.6069 (ttp-110) REVERT: B 503 LEU cc_start: 0.8236 (OUTLIER) cc_final: 0.7893 (mt) REVERT: B 555 VAL cc_start: 0.8401 (OUTLIER) cc_final: 0.8119 (m) REVERT: B 579 ARG cc_start: 0.7869 (ttm170) cc_final: 0.7618 (ttp80) REVERT: B 610 GLU cc_start: 0.8253 (mm-30) cc_final: 0.7859 (mp0) REVERT: B 652 LYS cc_start: 0.8017 (mmtm) cc_final: 0.7371 (pttm) REVERT: B 697 LYS cc_start: 0.8329 (OUTLIER) cc_final: 0.7507 (mtmt) REVERT: B 703 GLU cc_start: 0.8253 (OUTLIER) cc_final: 0.7769 (mt-10) REVERT: B 763 LEU cc_start: 0.8515 (OUTLIER) cc_final: 0.8184 (mt) REVERT: B 866 ARG cc_start: 0.7157 (OUTLIER) cc_final: 0.6804 (tpp80) REVERT: B 875 MET cc_start: 0.7518 (tpp) cc_final: 0.7126 (tpt) outliers start: 58 outliers final: 36 residues processed: 233 average time/residue: 0.5647 time to fit residues: 145.3778 Evaluate side-chains 246 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 196 time to evaluate : 0.484 ------------------------------------------------------------------------------- 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 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 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 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 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 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 113 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 chunk 140 optimal weight: 0.5980 chunk 115 optimal weight: 0.5980 chunk 105 optimal weight: 2.9990 chunk 181 optimal weight: 0.8980 chunk 11 optimal weight: 0.6980 chunk 142 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 71 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 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** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.189640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.147834 restraints weight = 14852.713| |-----------------------------------------------------------------------------| r_work (start): 0.3664 rms_B_bonded: 1.58 r_work: 0.3482 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3359 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.2829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 14874 Z= 0.150 Angle : 0.561 8.201 20146 Z= 0.283 Chirality : 0.040 0.148 2372 Planarity : 0.004 0.042 2472 Dihedral : 4.893 44.679 2020 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 3.31 % Allowed : 17.44 % Favored : 79.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.17 (0.20), residues: 1836 helix: 1.43 (0.15), residues: 1228 sheet: 2.02 (0.63), residues: 72 loop : -0.89 (0.28), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 611 TYR 0.011 0.001 TYR A 769 PHE 0.018 0.002 PHE A 636 TRP 0.021 0.001 TRP A 493 HIS 0.005 0.001 HIS A 120 Details of bonding type rmsd covalent geometry : bond 0.00354 (14874) covalent geometry : angle 0.56117 (20146) hydrogen bonds : bond 0.04020 ( 980) hydrogen bonds : angle 4.62570 ( 2856) ********************** 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 252 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 199 time to evaluate : 0.520 Fit side-chains REVERT: A 95 GLU cc_start: 0.8237 (mm-30) cc_final: 0.7976 (mp0) REVERT: A 342 ASP cc_start: 0.7753 (t0) cc_final: 0.7263 (t0) REVERT: A 419 LYS cc_start: 0.8399 (tttm) cc_final: 0.8085 (tttp) REVERT: A 555 VAL cc_start: 0.8414 (OUTLIER) cc_final: 0.8143 (m) REVERT: A 652 LYS cc_start: 0.8112 (mmtm) cc_final: 0.7437 (pttm) REVERT: A 697 LYS cc_start: 0.8283 (OUTLIER) cc_final: 0.7463 (mtmt) REVERT: A 703 GLU cc_start: 0.8175 (OUTLIER) cc_final: 0.7725 (mt-10) REVERT: A 763 LEU cc_start: 0.8519 (OUTLIER) cc_final: 0.8156 (mt) REVERT: A 866 ARG cc_start: 0.7157 (OUTLIER) cc_final: 0.6462 (tpt-90) REVERT: A 907 LEU cc_start: 0.6878 (OUTLIER) cc_final: 0.6668 (tp) REVERT: B 342 ASP cc_start: 0.7744 (t0) cc_final: 0.7229 (t0) REVERT: B 352 ARG cc_start: 0.7882 (OUTLIER) cc_final: 0.7585 (mmt-90) REVERT: B 419 LYS cc_start: 0.8353 (tttm) cc_final: 0.8065 (tttp) REVERT: B 555 VAL cc_start: 0.8393 (OUTLIER) cc_final: 0.8119 (m) REVERT: B 579 ARG cc_start: 0.7845 (ttm170) cc_final: 0.7597 (ttp80) REVERT: B 610 GLU cc_start: 0.8225 (mm-30) cc_final: 0.7848 (mp0) REVERT: B 652 LYS cc_start: 0.8003 (mmtm) cc_final: 0.7362 (pttm) REVERT: B 697 LYS cc_start: 0.8320 (OUTLIER) cc_final: 0.7498 (mtmt) REVERT: B 703 GLU cc_start: 0.8192 (OUTLIER) cc_final: 0.7755 (mt-10) REVERT: B 763 LEU cc_start: 0.8526 (OUTLIER) cc_final: 0.8189 (mt) REVERT: B 866 ARG cc_start: 0.7120 (OUTLIER) cc_final: 0.6759 (tpp80) REVERT: B 875 MET cc_start: 0.7462 (tpp) cc_final: 0.7084 (tpt) outliers start: 53 outliers final: 35 residues processed: 229 average time/residue: 0.5648 time to fit residues: 142.9807 Evaluate side-chains 239 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 192 time to evaluate : 0.569 ------------------------------------------------------------------------------- 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 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 480 GLN Chi-restraints excluded: chain A residue 555 VAL 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 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 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 89 optimal weight: 0.0870 chunk 104 optimal weight: 0.0670 chunk 79 optimal weight: 0.6980 chunk 106 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 183 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 21 optimal weight: 0.5980 chunk 110 optimal weight: 0.7980 chunk 32 optimal weight: 0.5980 chunk 135 optimal weight: 0.8980 overall best weight: 0.4096 ------------------------------------------------------------------------------- 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 = 0.4126 r_free = 0.4126 target = 0.191331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.149942 restraints weight = 14849.889| |-----------------------------------------------------------------------------| r_work (start): 0.3688 rms_B_bonded: 1.54 r_work: 0.3511 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3391 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.2910 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= 0.124 Angle : 0.543 8.142 20146 Z= 0.274 Chirality : 0.039 0.152 2372 Planarity : 0.004 0.041 2472 Dihedral : 4.761 42.626 2020 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 2.94 % Allowed : 18.19 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.32 (0.20), residues: 1836 helix: 1.57 (0.15), residues: 1228 sheet: 2.04 (0.63), residues: 72 loop : -0.89 (0.28), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 611 TYR 0.010 0.001 TYR A 346 PHE 0.017 0.001 PHE B 636 TRP 0.021 0.001 TRP B 493 HIS 0.008 0.001 HIS A 120 Details of bonding type rmsd covalent geometry : bond 0.00282 (14874) covalent geometry : angle 0.54251 (20146) hydrogen bonds : bond 0.03816 ( 980) hydrogen bonds : angle 4.53421 ( 2856) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5258.38 seconds wall clock time: 90 minutes 12.93 seconds (5412.93 seconds total)