Starting phenix.real_space_refine on Tue Dec 31 03:06:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7y3e_33592/12_2024/7y3e_33592.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y3e_33592/12_2024/7y3e_33592.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7y3e_33592/12_2024/7y3e_33592.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y3e_33592/12_2024/7y3e_33592.map" model { file = "/net/cci-nas-00/data/ceres_data/7y3e_33592/12_2024/7y3e_33592.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y3e_33592/12_2024/7y3e_33592.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.003 sd= 0.142 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 60 5.16 5 C 9522 2.51 5 N 2364 2.21 5 O 2626 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 45 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 14572 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 7254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 928, 7254 Classifications: {'peptide': 928} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 33, 'TRANS': 894} Chain breaks: 4 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 7254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 928, 7254 Classifications: {'peptide': 928} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 33, 'TRANS': 894} Chain breaks: 4 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {'R16': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {'R16': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 9.04, per 1000 atoms: 0.62 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: 4.17 Conformation dependent library (CDL) restraints added in 2.0 seconds 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3456 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 8 sheets defined 69.9% alpha, 4.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.58 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: 5.16 Time building geometry restraints manager: 4.73 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.590 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 35.800 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.080 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:13.240 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.090 ------------------------------------------------------------------------------- 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= 0.285 Angle : 0.709 6.858 20146 Z= 0.392 Chirality : 0.042 0.169 2372 Planarity : 0.004 0.042 2472 Dihedral : 14.073 89.359 5402 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 0.00 % Allowed : 0.50 % Favored : 99.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.20), residues: 1836 helix: 1.04 (0.15), residues: 1210 sheet: 1.67 (0.62), residues: 76 loop : -1.36 (0.26), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 493 HIS 0.006 0.001 HIS A 120 PHE 0.026 0.002 PHE A 834 TYR 0.012 0.002 TYR A 590 ARG 0.008 0.001 ARG A 966 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 275 time to evaluate : 1.692 Fit side-chains REVERT: A 99 GLU cc_start: 0.7119 (tt0) cc_final: 0.6888 (mm-30) REVERT: A 234 LEU cc_start: 0.8220 (mp) cc_final: 0.7905 (mp) REVERT: A 375 LEU cc_start: 0.8641 (mp) cc_final: 0.8416 (mp) REVERT: A 445 GLN cc_start: 0.7672 (tp-100) cc_final: 0.7176 (mp-120) REVERT: A 449 ARG cc_start: 0.6648 (mtm110) cc_final: 0.6353 (ttp-110) REVERT: A 562 GLN cc_start: 0.7540 (tt0) cc_final: 0.7336 (tt0) REVERT: A 579 ARG cc_start: 0.7380 (ttm170) cc_final: 0.7161 (ttp80) REVERT: A 652 LYS cc_start: 0.7869 (mmtm) cc_final: 0.7613 (pttm) REVERT: A 771 GLU cc_start: 0.7561 (tt0) cc_final: 0.6874 (tt0) REVERT: B 234 LEU cc_start: 0.8243 (mp) cc_final: 0.7963 (mp) REVERT: B 375 LEU cc_start: 0.8553 (mp) cc_final: 0.8320 (mp) REVERT: B 445 GLN cc_start: 0.7682 (tp-100) cc_final: 0.7171 (mp-120) REVERT: B 449 ARG cc_start: 0.6622 (mtm110) cc_final: 0.6334 (ttp-110) REVERT: B 562 GLN cc_start: 0.7548 (tt0) cc_final: 0.7345 (tt0) REVERT: B 579 ARG cc_start: 0.7401 (ttm170) cc_final: 0.7172 (ttp80) REVERT: B 652 LYS cc_start: 0.7906 (mmtm) cc_final: 0.7605 (pttm) REVERT: B 771 GLU cc_start: 0.7605 (tt0) cc_final: 0.7078 (tt0) REVERT: B 822 CYS cc_start: 0.8250 (p) cc_final: 0.7925 (p) outliers start: 0 outliers final: 0 residues processed: 275 average time/residue: 1.4089 time to fit residues: 426.3271 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 : 2.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 155 optimal weight: 0.5980 chunk 139 optimal weight: 5.9990 chunk 77 optimal weight: 6.9990 chunk 47 optimal weight: 3.9990 chunk 94 optimal weight: 0.3980 chunk 74 optimal weight: 3.9990 chunk 144 optimal weight: 0.9990 chunk 55 optimal weight: 0.9990 chunk 87 optimal weight: 3.9990 chunk 107 optimal weight: 4.9990 chunk 167 optimal weight: 2.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN A 277 GLN A 347 GLN ** A 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 94 ASN B 219 ASN B 277 GLN B 347 GLN ** B 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 739 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.1399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 14874 Z= 0.331 Angle : 0.653 6.386 20146 Z= 0.336 Chirality : 0.043 0.156 2372 Planarity : 0.005 0.042 2472 Dihedral : 5.536 51.387 2020 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 3.69 % Allowed : 10.12 % Favored : 86.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.20), residues: 1836 helix: 1.10 (0.15), residues: 1222 sheet: 1.95 (0.60), residues: 72 loop : -1.18 (0.27), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 854 HIS 0.008 0.001 HIS B 120 PHE 0.018 0.002 PHE B 607 TYR 0.018 0.002 TYR A 769 ARG 0.006 0.001 ARG A 462 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 213 time to evaluate : 1.644 Fit side-chains REVERT: A 234 LEU cc_start: 0.8338 (mp) cc_final: 0.8073 (mp) REVERT: A 375 LEU cc_start: 0.8639 (mp) cc_final: 0.8416 (mp) REVERT: A 449 ARG cc_start: 0.6868 (mtm110) cc_final: 0.6313 (ttp-110) REVERT: A 579 ARG cc_start: 0.7323 (ttm170) cc_final: 0.7068 (ttp80) REVERT: A 652 LYS cc_start: 0.7862 (mmtm) cc_final: 0.7660 (pttm) REVERT: A 761 MET cc_start: 0.7892 (OUTLIER) cc_final: 0.6944 (tmm) REVERT: A 763 LEU cc_start: 0.8753 (OUTLIER) cc_final: 0.8358 (mt) REVERT: A 866 ARG cc_start: 0.7273 (OUTLIER) cc_final: 0.6778 (tpt-90) REVERT: B 234 LEU cc_start: 0.8357 (mp) cc_final: 0.8108 (mp) REVERT: B 375 LEU cc_start: 0.8549 (mp) cc_final: 0.8328 (mp) REVERT: B 449 ARG cc_start: 0.6942 (mtm110) cc_final: 0.6460 (ttp-110) REVERT: B 579 ARG cc_start: 0.7346 (ttm170) cc_final: 0.7078 (ttp80) REVERT: B 763 LEU cc_start: 0.8731 (OUTLIER) cc_final: 0.8383 (mt) outliers start: 59 outliers final: 26 residues processed: 240 average time/residue: 1.3818 time to fit residues: 364.2522 Evaluate side-chains 224 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 194 time to evaluate : 1.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 199 MET Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 480 GLN Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain A residue 697 LYS Chi-restraints excluded: chain A residue 761 MET Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 778 VAL Chi-restraints excluded: chain A residue 835 ILE Chi-restraints excluded: chain A residue 866 ARG Chi-restraints excluded: chain A residue 876 GLN Chi-restraints excluded: chain A residue 1045 MET Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 199 MET Chi-restraints excluded: chain B residue 221 ASP Chi-restraints excluded: chain B residue 223 SER Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 480 GLN Chi-restraints excluded: chain B residue 697 LYS Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 835 ILE Chi-restraints excluded: chain B residue 876 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 92 optimal weight: 0.8980 chunk 51 optimal weight: 4.9990 chunk 139 optimal weight: 5.9990 chunk 113 optimal weight: 1.9990 chunk 46 optimal weight: 0.8980 chunk 167 optimal weight: 3.9990 chunk 180 optimal weight: 0.9990 chunk 149 optimal weight: 0.5980 chunk 165 optimal weight: 1.9990 chunk 57 optimal weight: 0.5980 chunk 134 optimal weight: 0.0670 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN A 200 ASN A 347 GLN A 480 GLN A 537 ASN ** A 739 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 94 ASN B 200 ASN B 347 GLN B 480 GLN B 537 ASN ** B 739 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.1917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14874 Z= 0.214 Angle : 0.562 6.314 20146 Z= 0.288 Chirality : 0.039 0.152 2372 Planarity : 0.004 0.038 2472 Dihedral : 5.189 45.846 2020 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 3.50 % Allowed : 12.69 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.20), residues: 1836 helix: 1.30 (0.15), residues: 1226 sheet: 1.79 (0.59), residues: 72 loop : -1.05 (0.27), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 493 HIS 0.005 0.001 HIS A 626 PHE 0.016 0.002 PHE B 353 TYR 0.014 0.001 TYR A 769 ARG 0.007 0.001 ARG B 378 *********************** 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 269 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 213 time to evaluate : 1.659 Fit side-chains REVERT: A 123 LYS cc_start: 0.8217 (OUTLIER) cc_final: 0.7953 (pttt) REVERT: A 419 LYS cc_start: 0.8347 (tttm) cc_final: 0.8119 (tttp) REVERT: A 449 ARG cc_start: 0.6907 (mtm110) cc_final: 0.6373 (ttp-110) REVERT: A 763 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.8326 (mt) REVERT: A 866 ARG cc_start: 0.7249 (OUTLIER) cc_final: 0.6659 (tpt-90) REVERT: A 876 GLN cc_start: 0.7699 (OUTLIER) cc_final: 0.7396 (pt0) REVERT: B 123 LYS cc_start: 0.8197 (OUTLIER) cc_final: 0.7924 (pttt) REVERT: B 342 ASP cc_start: 0.7640 (t0) cc_final: 0.7373 (t0) REVERT: B 449 ARG cc_start: 0.6926 (mtm110) cc_final: 0.6279 (ttp-110) REVERT: B 763 LEU cc_start: 0.8743 (OUTLIER) cc_final: 0.8389 (mt) REVERT: B 866 ARG cc_start: 0.7182 (tpt90) cc_final: 0.6900 (tpp80) outliers start: 56 outliers final: 19 residues processed: 238 average time/residue: 1.3118 time to fit residues: 344.9376 Evaluate side-chains 219 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 194 time to evaluate : 1.797 ------------------------------------------------------------------------------- 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 157 ASP Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 221 ASP Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 436 THR Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 480 GLN Chi-restraints excluded: chain A residue 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 123 LYS Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 480 GLN Chi-restraints excluded: chain B residue 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 165 optimal weight: 6.9990 chunk 125 optimal weight: 0.9980 chunk 86 optimal weight: 7.9990 chunk 18 optimal weight: 0.8980 chunk 79 optimal weight: 9.9990 chunk 112 optimal weight: 0.1980 chunk 167 optimal weight: 0.0970 chunk 177 optimal weight: 0.9990 chunk 87 optimal weight: 0.9990 chunk 159 optimal weight: 0.0470 chunk 47 optimal weight: 2.9990 overall best weight: 0.4476 ------------------------------------------------------------------------------- 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** B 868 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.2160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14874 Z= 0.187 Angle : 0.542 6.438 20146 Z= 0.277 Chirality : 0.039 0.152 2372 Planarity : 0.004 0.037 2472 Dihedral : 5.006 42.823 2020 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 3.50 % Allowed : 14.75 % Favored : 81.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.20), residues: 1836 helix: 1.43 (0.15), residues: 1226 sheet: 1.75 (0.59), residues: 72 loop : -0.94 (0.28), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 493 HIS 0.004 0.001 HIS B 739 PHE 0.014 0.001 PHE B 353 TYR 0.011 0.001 TYR A 769 ARG 0.006 0.000 ARG B 378 *********************** 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 256 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 200 time to evaluate : 1.697 Fit side-chains REVERT: A 123 LYS cc_start: 0.8176 (OUTLIER) cc_final: 0.7874 (pttt) REVERT: A 176 VAL cc_start: 0.8203 (t) cc_final: 0.7986 (p) REVERT: A 419 LYS cc_start: 0.8344 (tttm) cc_final: 0.8128 (tttt) REVERT: A 449 ARG cc_start: 0.6901 (mtm110) cc_final: 0.6303 (ttp-110) REVERT: A 454 ASP cc_start: 0.7218 (p0) cc_final: 0.6956 (p0) REVERT: A 611 ARG cc_start: 0.6981 (ttp-170) cc_final: 0.6645 (tmm160) REVERT: A 697 LYS cc_start: 0.8294 (OUTLIER) cc_final: 0.7647 (mtmt) REVERT: A 703 GLU cc_start: 0.7450 (OUTLIER) cc_final: 0.6974 (mt-10) REVERT: A 763 LEU cc_start: 0.8710 (OUTLIER) cc_final: 0.8297 (mt) REVERT: A 866 ARG cc_start: 0.7151 (OUTLIER) cc_final: 0.6514 (tpt-90) REVERT: A 876 GLN cc_start: 0.7765 (pt0) cc_final: 0.7556 (pt0) REVERT: B 123 LYS cc_start: 0.8138 (OUTLIER) cc_final: 0.7850 (pttt) REVERT: B 342 ASP cc_start: 0.7716 (t0) cc_final: 0.7398 (t0) REVERT: B 419 LYS cc_start: 0.8325 (tttm) cc_final: 0.8120 (tttt) REVERT: B 449 ARG cc_start: 0.6839 (mtm110) cc_final: 0.6257 (ttp-110) REVERT: B 611 ARG cc_start: 0.6996 (ttp-170) cc_final: 0.6612 (tmm160) REVERT: B 697 LYS cc_start: 0.8275 (OUTLIER) cc_final: 0.7618 (mtmt) REVERT: B 703 GLU cc_start: 0.7419 (OUTLIER) cc_final: 0.6984 (mt-10) REVERT: B 763 LEU cc_start: 0.8728 (OUTLIER) cc_final: 0.8367 (mt) outliers start: 56 outliers final: 24 residues processed: 231 average time/residue: 1.2766 time to fit residues: 327.0456 Evaluate side-chains 225 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 192 time to evaluate : 1.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 123 LYS Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 436 THR Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 480 GLN Chi-restraints excluded: chain A residue 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 122 ILE Chi-restraints excluded: chain B residue 123 LYS Chi-restraints excluded: chain B residue 157 ASP 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 571 VAL 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 835 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 148 optimal weight: 2.9990 chunk 100 optimal weight: 0.7980 chunk 2 optimal weight: 1.9990 chunk 132 optimal weight: 1.9990 chunk 73 optimal weight: 5.9990 chunk 151 optimal weight: 0.7980 chunk 122 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 chunk 90 optimal weight: 0.7980 chunk 159 optimal weight: 0.0970 chunk 44 optimal weight: 0.6980 overall best weight: 0.6178 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.2324 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= 0.206 Angle : 0.550 7.043 20146 Z= 0.279 Chirality : 0.039 0.147 2372 Planarity : 0.004 0.038 2472 Dihedral : 4.944 42.436 2020 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 3.69 % Allowed : 15.94 % Favored : 80.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.20), residues: 1836 helix: 1.44 (0.15), residues: 1226 sheet: 1.84 (0.60), residues: 72 loop : -0.90 (0.28), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 493 HIS 0.005 0.001 HIS B 120 PHE 0.014 0.001 PHE B 314 TYR 0.011 0.001 TYR A 769 ARG 0.005 0.000 ARG B 378 *********************** 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 265 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 206 time to evaluate : 1.640 Fit side-chains REVERT: A 123 LYS cc_start: 0.8157 (OUTLIER) cc_final: 0.7874 (pttt) REVERT: A 129 MET cc_start: 0.7253 (mmp) cc_final: 0.6911 (mmp) REVERT: A 419 LYS cc_start: 0.8319 (tttm) cc_final: 0.8102 (tttp) REVERT: A 449 ARG cc_start: 0.6975 (mtm110) cc_final: 0.6374 (ttp-110) REVERT: A 555 VAL cc_start: 0.8557 (OUTLIER) cc_final: 0.8295 (m) REVERT: A 611 ARG cc_start: 0.7027 (ttp-170) cc_final: 0.6757 (tmm160) REVERT: A 697 LYS cc_start: 0.8301 (OUTLIER) cc_final: 0.7655 (mtmt) REVERT: A 703 GLU cc_start: 0.7396 (OUTLIER) cc_final: 0.6973 (mt-10) REVERT: A 708 HIS cc_start: 0.7411 (t-170) cc_final: 0.7184 (t70) REVERT: A 763 LEU cc_start: 0.8730 (OUTLIER) cc_final: 0.8331 (mt) REVERT: A 866 ARG cc_start: 0.7112 (OUTLIER) cc_final: 0.6495 (tpt-90) REVERT: B 129 MET cc_start: 0.7260 (mmp) cc_final: 0.6922 (mmp) REVERT: B 342 ASP cc_start: 0.7638 (t0) cc_final: 0.7416 (t0) REVERT: B 419 LYS cc_start: 0.8319 (tttm) cc_final: 0.8109 (tttp) REVERT: B 449 ARG cc_start: 0.6898 (mtm110) cc_final: 0.6433 (ttp-110) REVERT: B 555 VAL cc_start: 0.8567 (OUTLIER) cc_final: 0.8294 (m) REVERT: B 611 ARG cc_start: 0.7018 (ttp-170) cc_final: 0.6093 (mtp-110) REVERT: B 697 LYS cc_start: 0.8290 (OUTLIER) cc_final: 0.7641 (mtmt) REVERT: B 703 GLU cc_start: 0.7407 (OUTLIER) cc_final: 0.6980 (mt-10) REVERT: B 763 LEU cc_start: 0.8734 (OUTLIER) cc_final: 0.8359 (mt) REVERT: B 771 GLU cc_start: 0.7498 (tt0) cc_final: 0.6580 (tt0) outliers start: 59 outliers final: 32 residues processed: 235 average time/residue: 1.2686 time to fit residues: 329.5316 Evaluate side-chains 235 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 193 time to evaluate : 1.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 123 LYS Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 436 THR Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 450 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 697 LYS Chi-restraints excluded: chain A residue 703 GLU Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 778 VAL Chi-restraints excluded: chain A residue 808 THR Chi-restraints excluded: chain A residue 835 ILE Chi-restraints excluded: chain A residue 866 ARG Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 198 LEU 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 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 652 LYS 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 59 optimal weight: 0.9990 chunk 160 optimal weight: 0.4980 chunk 35 optimal weight: 3.9990 chunk 104 optimal weight: 0.8980 chunk 43 optimal weight: 2.9990 chunk 178 optimal weight: 5.9990 chunk 147 optimal weight: 0.9990 chunk 82 optimal weight: 6.9990 chunk 14 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 chunk 93 optimal weight: 0.5980 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 347 GLN ** B 739 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.2465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14874 Z= 0.230 Angle : 0.559 7.451 20146 Z= 0.283 Chirality : 0.040 0.152 2372 Planarity : 0.004 0.039 2472 Dihedral : 4.944 42.829 2020 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 3.50 % Allowed : 17.31 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.20), residues: 1836 helix: 1.46 (0.15), residues: 1226 sheet: 1.91 (0.62), residues: 72 loop : -0.87 (0.28), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 493 HIS 0.005 0.001 HIS A 120 PHE 0.014 0.002 PHE B 636 TYR 0.011 0.001 TYR A 769 ARG 0.003 0.000 ARG B 378 *********************** 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 257 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 201 time to evaluate : 1.660 Fit side-chains REVERT: A 123 LYS cc_start: 0.8156 (OUTLIER) cc_final: 0.7862 (ptmt) REVERT: A 449 ARG cc_start: 0.6883 (mtm110) cc_final: 0.6369 (ttp-110) REVERT: A 555 VAL cc_start: 0.8559 (OUTLIER) cc_final: 0.8295 (m) REVERT: A 611 ARG cc_start: 0.7280 (ttp-170) cc_final: 0.6614 (tmm160) REVERT: A 697 LYS cc_start: 0.8311 (OUTLIER) cc_final: 0.7670 (mtmt) REVERT: A 703 GLU cc_start: 0.7437 (OUTLIER) cc_final: 0.7007 (mt-10) REVERT: A 708 HIS cc_start: 0.7410 (t-170) cc_final: 0.7198 (t70) REVERT: A 763 LEU cc_start: 0.8738 (OUTLIER) cc_final: 0.8327 (mt) REVERT: A 866 ARG cc_start: 0.7146 (OUTLIER) cc_final: 0.6487 (tpt-90) REVERT: A 875 MET cc_start: 0.7729 (tpp) cc_final: 0.7385 (tpt) REVERT: B 342 ASP cc_start: 0.7556 (t0) cc_final: 0.7340 (t0) REVERT: B 449 ARG cc_start: 0.6919 (mtm110) cc_final: 0.6519 (ttp-110) REVERT: B 555 VAL cc_start: 0.8562 (OUTLIER) cc_final: 0.8293 (m) REVERT: B 611 ARG cc_start: 0.7071 (ttp-170) cc_final: 0.6378 (tmm160) REVERT: B 697 LYS cc_start: 0.8309 (OUTLIER) cc_final: 0.7669 (mtmt) REVERT: B 703 GLU cc_start: 0.7448 (OUTLIER) cc_final: 0.7013 (mt-10) REVERT: B 708 HIS cc_start: 0.7399 (t-170) cc_final: 0.7198 (t70) REVERT: B 875 MET cc_start: 0.7782 (tpp) cc_final: 0.7456 (tpt) outliers start: 56 outliers final: 31 residues processed: 230 average time/residue: 1.2543 time to fit residues: 319.0530 Evaluate side-chains 231 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 191 time to evaluate : 1.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 123 LYS Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 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 652 LYS 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 157 ASP 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 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 652 LYS Chi-restraints excluded: chain B residue 697 LYS Chi-restraints excluded: chain B residue 703 GLU Chi-restraints excluded: chain B residue 778 VAL Chi-restraints excluded: chain B residue 835 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 171 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 101 optimal weight: 0.7980 chunk 130 optimal weight: 0.8980 chunk 100 optimal weight: 1.9990 chunk 149 optimal weight: 0.5980 chunk 99 optimal weight: 0.9980 chunk 177 optimal weight: 2.9990 chunk 110 optimal weight: 0.6980 chunk 108 optimal weight: 0.5980 chunk 81 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN A 480 GLN ** A 739 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 94 ASN B 347 GLN B 480 GLN ** B 739 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.2630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14874 Z= 0.217 Angle : 0.557 8.092 20146 Z= 0.280 Chirality : 0.039 0.149 2372 Planarity : 0.004 0.038 2472 Dihedral : 4.897 43.099 2020 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 4.19 % Allowed : 17.31 % Favored : 78.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.20), residues: 1836 helix: 1.50 (0.15), residues: 1226 sheet: 1.85 (0.61), residues: 72 loop : -0.86 (0.28), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 493 HIS 0.005 0.001 HIS A 120 PHE 0.015 0.001 PHE B 636 TYR 0.011 0.001 TYR B 769 ARG 0.003 0.000 ARG B 378 *********************** 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 272 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 205 time to evaluate : 1.735 Fit side-chains REVERT: A 99 GLU cc_start: 0.7123 (tt0) cc_final: 0.6776 (tt0) REVERT: A 123 LYS cc_start: 0.8094 (OUTLIER) cc_final: 0.7795 (ptmt) REVERT: A 129 MET cc_start: 0.7143 (mmp) cc_final: 0.6814 (mmp) REVERT: A 449 ARG cc_start: 0.7004 (mtm110) cc_final: 0.6534 (ttp-110) REVERT: A 555 VAL cc_start: 0.8526 (OUTLIER) cc_final: 0.8249 (m) REVERT: A 697 LYS cc_start: 0.8336 (OUTLIER) cc_final: 0.7708 (mtmt) REVERT: A 703 GLU cc_start: 0.7480 (OUTLIER) cc_final: 0.7031 (mt-10) REVERT: A 708 HIS cc_start: 0.7393 (t-170) cc_final: 0.7187 (t70) REVERT: A 763 LEU cc_start: 0.8743 (OUTLIER) cc_final: 0.8284 (mt) REVERT: A 866 ARG cc_start: 0.7103 (OUTLIER) cc_final: 0.6453 (tpt-90) REVERT: B 129 MET cc_start: 0.7187 (mmp) cc_final: 0.6820 (mmp) REVERT: B 199 MET cc_start: 0.8150 (OUTLIER) cc_final: 0.7619 (mtt) REVERT: B 342 ASP cc_start: 0.7576 (t0) cc_final: 0.7347 (t0) REVERT: B 449 ARG cc_start: 0.7006 (mtm110) cc_final: 0.6424 (ttp-110) REVERT: B 454 ASP cc_start: 0.7448 (p0) cc_final: 0.7240 (p0) REVERT: B 503 LEU cc_start: 0.8235 (OUTLIER) cc_final: 0.7869 (tp) REVERT: B 555 VAL cc_start: 0.8526 (OUTLIER) cc_final: 0.8241 (m) REVERT: B 697 LYS cc_start: 0.8318 (OUTLIER) cc_final: 0.7703 (mtmt) REVERT: B 703 GLU cc_start: 0.7463 (OUTLIER) cc_final: 0.7017 (mt-10) REVERT: B 708 HIS cc_start: 0.7405 (t-170) cc_final: 0.7196 (t-90) REVERT: B 763 LEU cc_start: 0.8773 (OUTLIER) cc_final: 0.8367 (mt) REVERT: B 866 ARG cc_start: 0.7167 (tpt170) cc_final: 0.6837 (tpp80) REVERT: B 875 MET cc_start: 0.7530 (tpp) cc_final: 0.7265 (tpt) outliers start: 67 outliers final: 34 residues processed: 242 average time/residue: 1.2130 time to fit residues: 326.1310 Evaluate side-chains 239 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 193 time to evaluate : 1.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 123 LYS Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 436 THR Chi-restraints excluded: chain A residue 448 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 652 LYS 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 157 ASP 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 498 SER 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 652 LYS 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 109 optimal weight: 1.9990 chunk 70 optimal weight: 5.9990 chunk 105 optimal weight: 0.9980 chunk 53 optimal weight: 0.4980 chunk 34 optimal weight: 0.8980 chunk 112 optimal weight: 0.9980 chunk 120 optimal weight: 1.9990 chunk 87 optimal weight: 9.9990 chunk 16 optimal weight: 0.9990 chunk 139 optimal weight: 0.9980 chunk 161 optimal weight: 0.0020 overall best weight: 0.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN A 480 GLN ** A 739 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 94 ASN B 347 GLN B 480 GLN ** B 739 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.2741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14874 Z= 0.217 Angle : 0.553 7.535 20146 Z= 0.280 Chirality : 0.039 0.148 2372 Planarity : 0.004 0.041 2472 Dihedral : 4.853 43.437 2020 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 4.06 % Allowed : 17.94 % Favored : 78.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.20), residues: 1836 helix: 1.50 (0.15), residues: 1228 sheet: 1.86 (0.62), residues: 72 loop : -0.85 (0.28), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 493 HIS 0.006 0.001 HIS B 120 PHE 0.016 0.001 PHE A 636 TYR 0.011 0.001 TYR B 769 ARG 0.004 0.000 ARG B 378 *********************** 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 277 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 212 time to evaluate : 1.591 Fit side-chains REVERT: A 123 LYS cc_start: 0.8091 (OUTLIER) cc_final: 0.7778 (ptmt) REVERT: A 129 MET cc_start: 0.7190 (mmp) cc_final: 0.6877 (mmp) REVERT: A 449 ARG cc_start: 0.7067 (mtm110) cc_final: 0.6488 (ttp-110) REVERT: A 555 VAL cc_start: 0.8507 (OUTLIER) cc_final: 0.8245 (m) REVERT: A 697 LYS cc_start: 0.8325 (OUTLIER) cc_final: 0.7730 (mtmt) REVERT: A 703 GLU cc_start: 0.7464 (OUTLIER) cc_final: 0.7014 (mt-10) REVERT: A 708 HIS cc_start: 0.7407 (t-170) cc_final: 0.7203 (t70) REVERT: A 763 LEU cc_start: 0.8737 (OUTLIER) cc_final: 0.8275 (mt) REVERT: A 866 ARG cc_start: 0.7076 (OUTLIER) cc_final: 0.6408 (tpt-90) REVERT: B 129 MET cc_start: 0.7237 (mmp) cc_final: 0.6931 (mmp) REVERT: B 342 ASP cc_start: 0.7555 (t0) cc_final: 0.7308 (t0) REVERT: B 449 ARG cc_start: 0.7066 (mtm110) cc_final: 0.6351 (ttp-110) REVERT: B 503 LEU cc_start: 0.8293 (OUTLIER) cc_final: 0.7992 (mt) REVERT: B 555 VAL cc_start: 0.8513 (OUTLIER) cc_final: 0.8242 (m) REVERT: B 697 LYS cc_start: 0.8348 (OUTLIER) cc_final: 0.7751 (mtmt) REVERT: B 703 GLU cc_start: 0.7474 (OUTLIER) cc_final: 0.7040 (mt-10) REVERT: B 708 HIS cc_start: 0.7399 (t-170) cc_final: 0.7197 (t-90) REVERT: B 763 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8351 (mt) REVERT: B 866 ARG cc_start: 0.7154 (tpt170) cc_final: 0.6821 (tpp80) outliers start: 65 outliers final: 40 residues processed: 245 average time/residue: 1.2119 time to fit residues: 330.2452 Evaluate side-chains 245 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 194 time to evaluate : 1.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 123 LYS Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 436 THR Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 453 MET 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 652 LYS 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 A residue 1011 MET Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 223 SER Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 453 MET 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 890 THR Chi-restraints excluded: chain B residue 1011 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 169 optimal weight: 0.8980 chunk 155 optimal weight: 0.5980 chunk 165 optimal weight: 5.9990 chunk 99 optimal weight: 0.7980 chunk 71 optimal weight: 0.4980 chunk 129 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 chunk 149 optimal weight: 0.5980 chunk 156 optimal weight: 1.9990 chunk 164 optimal weight: 7.9990 chunk 108 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN A 480 GLN ** A 739 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 94 ASN B 347 GLN B 480 GLN ** B 739 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.2809 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= 0.209 Angle : 0.553 7.700 20146 Z= 0.280 Chirality : 0.039 0.149 2372 Planarity : 0.004 0.041 2472 Dihedral : 4.835 43.278 2020 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 3.81 % Allowed : 18.19 % Favored : 78.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.20), residues: 1836 helix: 1.51 (0.15), residues: 1228 sheet: 1.90 (0.62), residues: 72 loop : -0.86 (0.28), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 493 HIS 0.006 0.001 HIS B 120 PHE 0.015 0.001 PHE A 636 TYR 0.010 0.001 TYR B 769 ARG 0.004 0.000 ARG A 378 *********************** 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 268 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 207 time to evaluate : 1.558 Fit side-chains REVERT: A 123 LYS cc_start: 0.8079 (OUTLIER) cc_final: 0.7763 (ptmt) REVERT: A 129 MET cc_start: 0.7220 (mmp) cc_final: 0.6931 (mmp) REVERT: A 449 ARG cc_start: 0.7065 (mtm110) cc_final: 0.6516 (ttp-110) REVERT: A 555 VAL cc_start: 0.8511 (OUTLIER) cc_final: 0.8242 (m) REVERT: A 610 GLU cc_start: 0.7989 (mm-30) cc_final: 0.7737 (mp0) REVERT: A 697 LYS cc_start: 0.8328 (OUTLIER) cc_final: 0.7730 (mtmt) REVERT: A 703 GLU cc_start: 0.7448 (OUTLIER) cc_final: 0.7025 (mt-10) REVERT: A 708 HIS cc_start: 0.7403 (t-170) cc_final: 0.7188 (t-90) REVERT: A 763 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.8258 (mt) REVERT: A 866 ARG cc_start: 0.7012 (OUTLIER) cc_final: 0.6723 (tpp80) REVERT: B 129 MET cc_start: 0.7233 (mmp) cc_final: 0.6903 (mmp) REVERT: B 342 ASP cc_start: 0.7543 (t0) cc_final: 0.7291 (t0) REVERT: B 449 ARG cc_start: 0.6899 (mtm110) cc_final: 0.6497 (ttp-110) REVERT: B 555 VAL cc_start: 0.8510 (OUTLIER) cc_final: 0.8243 (m) REVERT: B 610 GLU cc_start: 0.7942 (mm-30) cc_final: 0.7579 (mp0) REVERT: B 697 LYS cc_start: 0.8352 (OUTLIER) cc_final: 0.7757 (mtmt) REVERT: B 703 GLU cc_start: 0.7460 (OUTLIER) cc_final: 0.7033 (mt-10) REVERT: B 708 HIS cc_start: 0.7393 (t-170) cc_final: 0.7192 (t-90) REVERT: B 763 LEU cc_start: 0.8710 (OUTLIER) cc_final: 0.8349 (mt) REVERT: B 866 ARG cc_start: 0.7104 (tpt170) cc_final: 0.6781 (tpp80) outliers start: 61 outliers final: 36 residues processed: 238 average time/residue: 1.2041 time to fit residues: 318.1259 Evaluate side-chains 243 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 197 time to evaluate : 1.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 123 LYS Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 436 THR Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 577 ASP Chi-restraints excluded: chain A residue 614 SER Chi-restraints excluded: chain A residue 652 LYS Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 697 LYS Chi-restraints excluded: chain A residue 703 GLU Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 778 VAL Chi-restraints excluded: chain A residue 835 ILE Chi-restraints excluded: chain A residue 866 ARG Chi-restraints excluded: chain A residue 890 THR Chi-restraints excluded: chain A residue 1011 MET Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 157 ASP 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 453 MET Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 480 GLN Chi-restraints excluded: chain B residue 498 SER Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain B residue 577 ASP Chi-restraints excluded: chain B residue 604 VAL Chi-restraints excluded: chain B residue 614 SER Chi-restraints excluded: chain B residue 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 Chi-restraints excluded: chain B residue 907 LEU Chi-restraints excluded: chain B residue 1011 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 174 optimal weight: 0.8980 chunk 106 optimal weight: 0.9980 chunk 82 optimal weight: 5.9990 chunk 121 optimal weight: 0.8980 chunk 183 optimal weight: 2.9990 chunk 168 optimal weight: 0.9990 chunk 145 optimal weight: 0.6980 chunk 15 optimal weight: 0.9980 chunk 112 optimal weight: 0.8980 chunk 89 optimal weight: 0.0570 chunk 115 optimal weight: 0.6980 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN A 480 GLN ** A 739 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 94 ASN B 347 GLN B 480 GLN ** B 739 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.2860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14874 Z= 0.214 Angle : 0.556 7.865 20146 Z= 0.281 Chirality : 0.040 0.148 2372 Planarity : 0.004 0.042 2472 Dihedral : 4.831 43.379 2020 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 3.25 % Allowed : 18.94 % Favored : 77.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.20), residues: 1836 helix: 1.51 (0.15), residues: 1228 sheet: 1.95 (0.62), residues: 72 loop : -0.86 (0.28), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 493 HIS 0.007 0.001 HIS A 120 PHE 0.015 0.001 PHE A 636 TYR 0.010 0.001 TYR B 769 ARG 0.007 0.000 ARG A 611 ********************** 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 253 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 201 time to evaluate : 1.573 Fit side-chains REVERT: A 123 LYS cc_start: 0.8077 (OUTLIER) cc_final: 0.7774 (ptmt) REVERT: A 129 MET cc_start: 0.7227 (mmp) cc_final: 0.6953 (mmp) REVERT: A 449 ARG cc_start: 0.7059 (mtm110) cc_final: 0.6765 (mtm-85) REVERT: A 555 VAL cc_start: 0.8513 (OUTLIER) cc_final: 0.8242 (m) REVERT: A 610 GLU cc_start: 0.7975 (mm-30) cc_final: 0.7618 (mp0) REVERT: A 697 LYS cc_start: 0.8326 (OUTLIER) cc_final: 0.7732 (mtmt) REVERT: A 703 GLU cc_start: 0.7448 (OUTLIER) cc_final: 0.7032 (mt-10) REVERT: A 763 LEU cc_start: 0.8656 (OUTLIER) cc_final: 0.8275 (mt) REVERT: A 866 ARG cc_start: 0.6999 (OUTLIER) cc_final: 0.6714 (tpp80) REVERT: B 129 MET cc_start: 0.7240 (mmp) cc_final: 0.6940 (mmp) REVERT: B 342 ASP cc_start: 0.7532 (t0) cc_final: 0.7279 (t0) REVERT: B 449 ARG cc_start: 0.7001 (mtm110) cc_final: 0.6759 (mtm-85) REVERT: B 555 VAL cc_start: 0.8511 (OUTLIER) cc_final: 0.8242 (m) REVERT: B 570 GLN cc_start: 0.7859 (mp10) cc_final: 0.7532 (mt0) REVERT: B 610 GLU cc_start: 0.7932 (mm-30) cc_final: 0.7578 (mp0) REVERT: B 697 LYS cc_start: 0.8334 (OUTLIER) cc_final: 0.7738 (mtmt) REVERT: B 703 GLU cc_start: 0.7450 (OUTLIER) cc_final: 0.7028 (mt-10) REVERT: B 763 LEU cc_start: 0.8704 (OUTLIER) cc_final: 0.8339 (mt) REVERT: B 866 ARG cc_start: 0.7100 (tpt170) cc_final: 0.6774 (tpp80) outliers start: 52 outliers final: 33 residues processed: 230 average time/residue: 1.2366 time to fit residues: 314.9089 Evaluate side-chains 239 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 196 time to evaluate : 1.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 123 LYS Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 436 THR Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 577 ASP 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 1011 MET Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 157 ASP 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 453 MET Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 498 SER Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain B residue 577 ASP Chi-restraints excluded: chain B residue 604 VAL Chi-restraints excluded: chain B residue 614 SER Chi-restraints excluded: chain B residue 675 VAL Chi-restraints excluded: chain B residue 697 LYS Chi-restraints excluded: chain B residue 703 GLU Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 778 VAL Chi-restraints excluded: chain B residue 835 ILE Chi-restraints excluded: chain B residue 890 THR Chi-restraints excluded: chain B residue 907 LEU Chi-restraints excluded: chain B residue 1011 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 155 optimal weight: 0.5980 chunk 44 optimal weight: 0.6980 chunk 134 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 40 optimal weight: 0.6980 chunk 146 optimal weight: 0.6980 chunk 61 optimal weight: 0.7980 chunk 150 optimal weight: 0.0070 chunk 18 optimal weight: 0.9980 chunk 26 optimal weight: 0.6980 chunk 128 optimal weight: 0.8980 overall best weight: 0.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN A 480 GLN ** A 739 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 94 ASN B 347 GLN B 480 GLN ** B 739 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.191266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.149611 restraints weight = 14757.734| |-----------------------------------------------------------------------------| r_work (start): 0.3681 rms_B_bonded: 1.54 r_work: 0.3518 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3399 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.2930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14874 Z= 0.196 Angle : 0.545 7.883 20146 Z= 0.276 Chirality : 0.039 0.152 2372 Planarity : 0.004 0.042 2472 Dihedral : 4.760 42.471 2020 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 3.25 % Allowed : 18.88 % Favored : 77.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.20), residues: 1836 helix: 1.55 (0.15), residues: 1228 sheet: 1.93 (0.62), residues: 72 loop : -0.85 (0.28), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 493 HIS 0.005 0.001 HIS A 120 PHE 0.016 0.001 PHE A 636 TYR 0.015 0.001 TYR B 346 ARG 0.004 0.000 ARG A 611 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5534.56 seconds wall clock time: 100 minutes 33.15 seconds (6033.15 seconds total)