Starting phenix.real_space_refine on Mon Jan 13 15:35:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ve3_43163/01_2025/8ve3_43163.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ve3_43163/01_2025/8ve3_43163.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ve3_43163/01_2025/8ve3_43163.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ve3_43163/01_2025/8ve3_43163.map" model { file = "/net/cci-nas-00/data/ceres_data/8ve3_43163/01_2025/8ve3_43163.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ve3_43163/01_2025/8ve3_43163.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 3 5.16 5 C 2111 2.51 5 N 557 2.21 5 O 539 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 3210 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 813 Classifications: {'peptide': 117} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 7, 'TRANS': 109} Unresolved non-hydrogen bonds: 92 Unresolved non-hydrogen angles: 115 Unresolved non-hydrogen dihedrals: 69 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLU:plan': 9, 'ARG:plan': 2, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 58 Chain: "B" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 801 Classifications: {'peptide': 117} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 7, 'TRANS': 109} Unresolved non-hydrogen bonds: 104 Unresolved non-hydrogen angles: 128 Unresolved non-hydrogen dihedrals: 80 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 10, 'ASN:plan1': 1, 'ASP:plan': 3, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 67 Chain: "C" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 801 Classifications: {'peptide': 116} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 7, 'TRANS': 108} Unresolved non-hydrogen bonds: 95 Unresolved non-hydrogen angles: 119 Unresolved non-hydrogen dihedrals: 71 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLU:plan': 9, 'ASN:plan1': 2, 'ARG:plan': 2, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 67 Chain: "D" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 795 Classifications: {'peptide': 116} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 6, 'TRANS': 109} Unresolved non-hydrogen bonds: 103 Unresolved non-hydrogen angles: 130 Unresolved non-hydrogen dihedrals: 76 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLU:plan': 10, 'ASN:plan1': 3, 'ARG:plan': 1, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 69 Time building chain proxies: 3.09, per 1000 atoms: 0.96 Number of scatterers: 3210 At special positions: 0 Unit cell: (76.432, 66.316, 65.192, 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 3 16.00 O 539 8.00 N 557 7.00 C 2111 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: 0.87 Conformation dependent library (CDL) restraints added in 417.1 milliseconds 916 Ramachandran restraints generated. 458 Oldfield, 0 Emsley, 458 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 876 Finding SS restraints... Secondary structure from input PDB file: 4 helices and 5 sheets defined 8.2% alpha, 51.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.48 Creating SS restraints... Processing helix chain 'A' and resid 74 through 83 removed outlier: 3.859A pdb=" N TYR A 78 " --> pdb=" O ASP A 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 83 Processing helix chain 'C' and resid 74 through 83 removed outlier: 3.747A pdb=" N TYR C 78 " --> pdb=" O ASP C 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 75 through 83 Processing sheet with id=AA1, first strand: chain 'A' and resid 23 through 24 removed outlier: 6.142A pdb=" N MET A 13 " --> pdb=" O ILE A 107 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N ALA A 109 " --> pdb=" O MET A 13 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N LYS A 15 " --> pdb=" O ALA A 109 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N LEU A 111 " --> pdb=" O LYS A 15 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N LEU A 17 " --> pdb=" O LEU A 111 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N MET B 13 " --> pdb=" O ILE B 107 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N ALA B 109 " --> pdb=" O MET B 13 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N LYS B 15 " --> pdb=" O ALA B 109 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N LEU B 111 " --> pdb=" O LYS B 15 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N LEU B 17 " --> pdb=" O LEU B 111 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N SER B 23 " --> pdb=" O ASP B 18 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 23 through 24 removed outlier: 6.142A pdb=" N MET A 13 " --> pdb=" O ILE A 107 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N ALA A 109 " --> pdb=" O MET A 13 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N LYS A 15 " --> pdb=" O ALA A 109 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N LEU A 111 " --> pdb=" O LYS A 15 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N LEU A 17 " --> pdb=" O LEU A 111 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N MET B 13 " --> pdb=" O ILE B 107 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N ALA B 109 " --> pdb=" O MET B 13 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N LYS B 15 " --> pdb=" O ALA B 109 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N LEU B 111 " --> pdb=" O LYS B 15 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N LEU B 17 " --> pdb=" O LEU B 111 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N VAL B 14 " --> pdb=" O LEU B 55 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 41 through 48 removed outlier: 5.839A pdb=" N ARG A 34 " --> pdb=" O PRO A 43 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LYS A 70 " --> pdb=" O PHE A 33 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N ILE A 68 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N HIS A 88 " --> pdb=" O PHE B 95 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N PHE B 95 " --> pdb=" O HIS A 88 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N HIS A 90 " --> pdb=" O VAL B 93 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N VAL B 93 " --> pdb=" O HIS A 90 " (cutoff:3.500A) removed outlier: 8.602A pdb=" N GLU A 92 " --> pdb=" O ALA B 91 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N ALA B 91 " --> pdb=" O GLU A 92 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N VAL A 94 " --> pdb=" O GLU B 89 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N PHE B 95 " --> pdb=" O TYR B 69 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N ILE B 68 " --> pdb=" O LYS B 35 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N ALA B 29 " --> pdb=" O ASP B 74 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N ARG B 34 " --> pdb=" O PRO B 43 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 23 through 24 removed outlier: 6.452A pdb=" N LYS C 15 " --> pdb=" O ALA C 109 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N LEU C 111 " --> pdb=" O LYS C 15 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N LEU C 17 " --> pdb=" O LEU C 111 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N THR C 106 " --> pdb=" O VAL C 121 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N SER D 115 " --> pdb=" O SER D 112 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N MET D 13 " --> pdb=" O ILE D 107 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N ALA D 109 " --> pdb=" O MET D 13 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N LYS D 15 " --> pdb=" O ALA D 109 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N LEU D 111 " --> pdb=" O LYS D 15 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N LEU D 17 " --> pdb=" O LEU D 111 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 41 through 48 removed outlier: 6.240A pdb=" N ARG C 34 " --> pdb=" O PRO C 43 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N ILE C 68 " --> pdb=" O LYS C 35 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N VAL D 94 " --> pdb=" O GLU C 89 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N ALA C 91 " --> pdb=" O GLU D 92 " (cutoff:3.500A) removed outlier: 8.707A pdb=" N GLU D 92 " --> pdb=" O ALA C 91 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N PHE D 95 " --> pdb=" O TYR D 69 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N ILE D 68 " --> pdb=" O LYS D 35 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LYS D 70 " --> pdb=" O PHE D 33 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N ALA D 29 " --> pdb=" O ASP D 74 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N VAL D 30 " --> pdb=" O GLY D 47 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLY D 47 " --> pdb=" O VAL D 30 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N ARG D 34 " --> pdb=" O PRO D 43 " (cutoff:3.500A) 156 hydrogen bonds defined for protein. 423 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: 0.85 Time building geometry restraints manager: 1.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1005 1.34 - 1.46: 840 1.46 - 1.58: 1457 1.58 - 1.69: 0 1.69 - 1.81: 3 Bond restraints: 3305 Sorted by residual: bond pdb=" CG LEU C 111 " pdb=" CD1 LEU C 111 " ideal model delta sigma weight residual 1.521 1.481 0.040 3.30e-02 9.18e+02 1.45e+00 bond pdb=" CB VAL C 16 " pdb=" CG1 VAL C 16 " ideal model delta sigma weight residual 1.521 1.487 0.034 3.30e-02 9.18e+02 1.09e+00 bond pdb=" CG ARG D 34 " pdb=" CD ARG D 34 " ideal model delta sigma weight residual 1.520 1.491 0.029 3.00e-02 1.11e+03 9.13e-01 bond pdb=" N GLY C 22 " pdb=" CA GLY C 22 " ideal model delta sigma weight residual 1.454 1.441 0.013 1.45e-02 4.76e+03 8.53e-01 bond pdb=" CB VAL D 16 " pdb=" CG1 VAL D 16 " ideal model delta sigma weight residual 1.521 1.493 0.028 3.30e-02 9.18e+02 7.31e-01 ... (remaining 3300 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.17: 4267 1.17 - 2.35: 233 2.35 - 3.52: 39 3.52 - 4.69: 10 4.69 - 5.86: 4 Bond angle restraints: 4553 Sorted by residual: angle pdb=" CB ARG A 34 " pdb=" CG ARG A 34 " pdb=" CD ARG A 34 " ideal model delta sigma weight residual 111.30 115.69 -4.39 2.30e+00 1.89e-01 3.65e+00 angle pdb=" CG ARG A 34 " pdb=" CD ARG A 34 " pdb=" NE ARG A 34 " ideal model delta sigma weight residual 112.00 116.00 -4.00 2.20e+00 2.07e-01 3.31e+00 angle pdb=" N PHE B 87 " pdb=" CA PHE B 87 " pdb=" C PHE B 87 " ideal model delta sigma weight residual 113.12 110.92 2.20 1.25e+00 6.40e-01 3.10e+00 angle pdb=" N SER D 112 " pdb=" CA SER D 112 " pdb=" C SER D 112 " ideal model delta sigma weight residual 109.09 106.14 2.95 1.74e+00 3.30e-01 2.87e+00 angle pdb=" C ARG A 103 " pdb=" N ARG A 104 " pdb=" CA ARG A 104 " ideal model delta sigma weight residual 122.72 120.43 2.29 1.38e+00 5.25e-01 2.76e+00 ... (remaining 4548 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.77: 1685 11.77 - 23.54: 132 23.54 - 35.31: 47 35.31 - 47.08: 16 47.08 - 58.85: 3 Dihedral angle restraints: 1883 sinusoidal: 525 harmonic: 1358 Sorted by residual: dihedral pdb=" CA PRO B 86 " pdb=" C PRO B 86 " pdb=" N PHE B 87 " pdb=" CA PHE B 87 " ideal model delta harmonic sigma weight residual 180.00 162.30 17.70 0 5.00e+00 4.00e-02 1.25e+01 dihedral pdb=" CA LEU D 111 " pdb=" C LEU D 111 " pdb=" N SER D 112 " pdb=" CA SER D 112 " ideal model delta harmonic sigma weight residual 180.00 164.00 16.00 0 5.00e+00 4.00e-02 1.02e+01 dihedral pdb=" CA LEU C 111 " pdb=" C LEU C 111 " pdb=" N SER C 112 " pdb=" CA SER C 112 " ideal model delta harmonic sigma weight residual 180.00 164.15 15.85 0 5.00e+00 4.00e-02 1.01e+01 ... (remaining 1880 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 264 0.027 - 0.054: 155 0.054 - 0.081: 52 0.081 - 0.109: 49 0.109 - 0.136: 25 Chirality restraints: 545 Sorted by residual: chirality pdb=" CA VAL D 28 " pdb=" N VAL D 28 " pdb=" C VAL D 28 " pdb=" CB VAL D 28 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.60e-01 chirality pdb=" CA VAL A 93 " pdb=" N VAL A 93 " pdb=" C VAL A 93 " pdb=" CB VAL A 93 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.57e-01 chirality pdb=" CA VAL C 16 " pdb=" N VAL C 16 " pdb=" C VAL C 16 " pdb=" CB VAL C 16 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.46e-01 ... (remaining 542 not shown) Planarity restraints: 572 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER B 85 " -0.028 5.00e-02 4.00e+02 4.20e-02 2.82e+00 pdb=" N PRO B 86 " 0.073 5.00e-02 4.00e+02 pdb=" CA PRO B 86 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 86 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 112 " 0.022 5.00e-02 4.00e+02 3.35e-02 1.80e+00 pdb=" N PRO A 113 " -0.058 5.00e-02 4.00e+02 pdb=" CA PRO A 113 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 113 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS A 10 " 0.021 5.00e-02 4.00e+02 3.22e-02 1.66e+00 pdb=" N PRO A 11 " -0.056 5.00e-02 4.00e+02 pdb=" CA PRO A 11 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 11 " 0.018 5.00e-02 4.00e+02 ... (remaining 569 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 298 2.74 - 3.28: 2964 3.28 - 3.82: 5133 3.82 - 4.36: 5680 4.36 - 4.90: 10820 Nonbonded interactions: 24895 Sorted by model distance: nonbonded pdb=" O VAL C 65 " pdb=" OH TYR C 69 " model vdw 2.204 3.040 nonbonded pdb=" O VAL D 65 " pdb=" OH TYR D 69 " model vdw 2.255 3.040 nonbonded pdb=" NZ LYS A 15 " pdb=" O SER A 52 " model vdw 2.276 3.120 nonbonded pdb=" O VAL B 65 " pdb=" OH TYR B 69 " model vdw 2.354 3.040 nonbonded pdb=" N VAL D 28 " pdb=" OG1 THR D 49 " model vdw 2.398 3.120 ... (remaining 24890 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' and ((resid 10 and (name N or name CA or name C or name O or name CB \ )) or resid 11 through 14 or (resid 15 and (name N or name CA or name C or name \ O or name CB )) or resid 16 through 19 or (resid 20 and (name N or name CA or na \ me C or name O or name CB )) or resid 21 through 26 or (resid 27 and (name N or \ name CA or name C or name O or name CB )) or resid 28 through 33 or (resid 34 an \ d (name N or name CA or name C or name O or name CB )) or resid 35 through 48 or \ (resid 49 through 52 and (name N or name CA or name C or name O or name CB )) o \ r resid 53 or (resid 54 and (name N or name CA or name C or name O or name CB )) \ or resid 55 through 58 or (resid 59 through 63 and (name N or name CA or name C \ or name O or name CB )) or resid 64 through 74 or (resid 75 and (name N or name \ CA or name C or name O or name CB )) or resid 76 through 79 or (resid 80 throug \ h 81 and (name N or name CA or name C or name O or name CB )) or resid 82 throug \ h 97 or (resid 98 through 100 and (name N or name CA or name C or name O or name \ CB )) or resid 101 through 111 or (resid 112 and (name N or name CA or name C o \ r name O or name CB )) or resid 113 through 114 or (resid 115 and (name N or nam \ e CA or name C or name O or name CB )) or resid 116 or (resid 117 and (name N or \ name CA or name C or name O or name CB )) or resid 118 through 123 or (resid 12 \ 4 and (name N or name CA or name C or name O or name CB )))) selection = (chain 'B' and (resid 10 through 14 or (resid 15 and (name N or name CA or name \ C or name O or name CB )) or resid 16 through 17 or (resid 18 through 20 and (na \ me N or name CA or name C or name O or name CB )) or resid 21 through 45 or (res \ id 46 and (name N or name CA or name C or name O or name CB )) or resid 47 throu \ gh 48 or (resid 49 through 52 and (name N or name CA or name C or name O or name \ CB )) or resid 53 through 76 or (resid 77 and (name N or name CA or name C or n \ ame O or name CB )) or resid 78 through 83 or (resid 84 through 85 and (name N o \ r name CA or name C or name O or name CB )) or resid 86 through 93 or (resid 94 \ and (name N or name CA or name C or name O or name CB )) or resid 95 or (resid 9 \ 6 through 100 and (name N or name CA or name C or name O or name CB )) or resid \ 101 through 122 or (resid 123 through 124 and (name N or name CA or name C or na \ me O or name CB )))) selection = (chain 'C' and ((resid 10 and (name N or name CA or name C or name O or name CB \ )) or resid 11 through 14 or (resid 15 and (name N or name CA or name C or name \ O or name CB )) or resid 16 through 19 or (resid 20 and (name N or name CA or na \ me C or name O or name CB )) or resid 21 through 33 or (resid 34 and (name N or \ name CA or name C or name O or name CB )) or resid 35 through 49 or (resid 50 th \ rough 52 and (name N or name CA or name C or name O or name CB )) or resid 53 th \ rough 58 or (resid 59 through 63 and (name N or name CA or name C or name O or n \ ame CB )) or resid 64 through 71 or (resid 72 and (name N or name CA or name C o \ r name O or name CB )) or resid 73 through 74 or (resid 75 and (name N or name C \ A or name C or name O or name CB )) or resid 76 through 83 or (resid 84 through \ 85 and (name N or name CA or name C or name O or name CB )) or resid 86 through \ 93 or (resid 94 and (name N or name CA or name C or name O or name CB )) or resi \ d 95 or (resid 96 through 100 and (name N or name CA or name C or name O or name \ CB )) or resid 101 through 111 or (resid 112 and (name N or name CA or name C o \ r name O or name CB )) or resid 113 through 116 or (resid 117 and (name N or nam \ e CA or name C or name O or name CB )) or resid 118 through 122 or (resid 123 th \ rough 124 and (name N or name CA or name C or name O or name CB )))) selection = (chain 'D' and ((resid 10 and (name N or name CA or name C or name O or name CB \ )) or resid 11 through 25 or (resid 26 through 27 and (name N or name CA or name \ C or name O or name CB )) or resid 28 through 33 or (resid 34 and (name N or na \ me CA or name C or name O or name CB )) or resid 35 through 48 or (resid 49 thro \ ugh 52 and (name N or name CA or name C or name O or name CB )) or resid 53 thro \ ugh 74 or (resid 75 and (name N or name CA or name C or name O or name CB )) or \ resid 76 or (resid 77 and (name N or name CA or name C or name O or name CB )) o \ r resid 78 through 79 or (resid 80 through 81 and (name N or name CA or name C o \ r name O or name CB )) or resid 82 through 93 or (resid 94 and (name N or name C \ A or name C or name O or name CB )) or resid 95 through 102 or (resid 103 throug \ h 104 and (name N or name CA or name C or name O or name CB )) or resid 105 thro \ ugh 111 or (resid 112 and (name N or name CA or name C or name O or name CB )) o \ r resid 113 through 116 or (resid 117 and (name N or name CA or name C or name O \ or name CB )) or resid 118 or (resid 119 through 120 and (name N or name CA or \ name C or name O or name CB )) or resid 121 through 124)) } 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: 0.690 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: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 13.290 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 3305 Z= 0.322 Angle : 0.650 5.865 4553 Z= 0.363 Chirality : 0.050 0.136 545 Planarity : 0.005 0.042 572 Dihedral : 11.271 58.852 1007 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % 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: 0.45 (0.40), residues: 458 helix: 0.74 (0.99), residues: 32 sheet: 0.57 (0.35), residues: 220 loop : 0.06 (0.44), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 79 HIS 0.003 0.001 HIS D 88 PHE 0.016 0.002 PHE A 64 TYR 0.014 0.002 TYR C 105 ARG 0.003 0.001 ARG A 34 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 916 Ramachandran restraints generated. 458 Oldfield, 0 Emsley, 458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 916 Ramachandran restraints generated. 458 Oldfield, 0 Emsley, 458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.361 Fit side-chains revert: symmetry clash REVERT: B 15 LYS cc_start: 0.8595 (ttpt) cc_final: 0.8288 (tttt) outliers start: 0 outliers final: 0 residues processed: 62 average time/residue: 0.2157 time to fit residues: 15.4597 Evaluate side-chains 55 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 37 optimal weight: 8.9990 chunk 33 optimal weight: 0.7980 chunk 18 optimal weight: 0.9980 chunk 11 optimal weight: 4.9990 chunk 22 optimal weight: 0.6980 chunk 17 optimal weight: 2.9990 chunk 34 optimal weight: 0.4980 chunk 13 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 25 optimal weight: 4.9990 chunk 39 optimal weight: 7.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.139304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.114894 restraints weight = 5337.588| |-----------------------------------------------------------------------------| r_work (start): 0.3617 rms_B_bonded: 3.43 r_work: 0.3468 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.1281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3305 Z= 0.177 Angle : 0.562 6.077 4553 Z= 0.289 Chirality : 0.048 0.145 545 Planarity : 0.005 0.039 572 Dihedral : 4.103 18.693 490 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.56 % Allowed : 9.38 % Favored : 89.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.43 (0.40), residues: 458 helix: 0.59 (0.90), residues: 36 sheet: 0.58 (0.36), residues: 208 loop : 0.06 (0.43), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 79 HIS 0.002 0.001 HIS B 88 PHE 0.011 0.001 PHE A 44 TYR 0.011 0.002 TYR D 116 ARG 0.003 0.001 ARG A 34 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 916 Ramachandran restraints generated. 458 Oldfield, 0 Emsley, 458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 916 Ramachandran restraints generated. 458 Oldfield, 0 Emsley, 458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 74 time to evaluate : 0.329 Fit side-chains REVERT: B 78 TYR cc_start: 0.6833 (t80) cc_final: 0.6605 (t80) REVERT: D 69 TYR cc_start: 0.8199 (m-10) cc_final: 0.7867 (m-10) outliers start: 4 outliers final: 4 residues processed: 77 average time/residue: 0.2023 time to fit residues: 18.0819 Evaluate side-chains 75 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 71 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 121 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 15 optimal weight: 0.3980 chunk 18 optimal weight: 5.9990 chunk 14 optimal weight: 0.0030 chunk 11 optimal weight: 5.9990 chunk 38 optimal weight: 5.9990 chunk 19 optimal weight: 2.9990 chunk 23 optimal weight: 10.0000 chunk 17 optimal weight: 4.9990 chunk 39 optimal weight: 6.9990 chunk 12 optimal weight: 0.0470 chunk 30 optimal weight: 7.9990 overall best weight: 1.6892 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 98 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.137887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.113027 restraints weight = 5363.319| |-----------------------------------------------------------------------------| r_work (start): 0.3596 rms_B_bonded: 3.48 r_work: 0.3448 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.1604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3305 Z= 0.217 Angle : 0.554 6.173 4553 Z= 0.284 Chirality : 0.049 0.143 545 Planarity : 0.005 0.041 572 Dihedral : 3.985 17.774 490 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 3.52 % Allowed : 13.28 % Favored : 83.20 % 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: 0.46 (0.40), residues: 458 helix: 0.64 (0.93), residues: 36 sheet: 0.61 (0.36), residues: 208 loop : 0.05 (0.43), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 79 HIS 0.002 0.001 HIS B 88 PHE 0.013 0.002 PHE A 44 TYR 0.022 0.002 TYR C 78 ARG 0.005 0.001 ARG C 21 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 916 Ramachandran restraints generated. 458 Oldfield, 0 Emsley, 458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 916 Ramachandran restraints generated. 458 Oldfield, 0 Emsley, 458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 67 time to evaluate : 0.369 Fit side-chains REVERT: B 15 LYS cc_start: 0.8620 (tttt) cc_final: 0.8357 (tttt) REVERT: B 78 TYR cc_start: 0.6896 (t80) cc_final: 0.6695 (t80) REVERT: D 69 TYR cc_start: 0.8304 (m-10) cc_final: 0.8026 (m-10) outliers start: 9 outliers final: 8 residues processed: 71 average time/residue: 0.2099 time to fit residues: 17.2676 Evaluate side-chains 72 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 64 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain D residue 30 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 30 optimal weight: 10.0000 chunk 42 optimal weight: 7.9990 chunk 37 optimal weight: 0.7980 chunk 15 optimal weight: 6.9990 chunk 20 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 23 optimal weight: 9.9990 chunk 24 optimal weight: 1.9990 chunk 3 optimal weight: 0.5980 chunk 9 optimal weight: 0.0050 overall best weight: 1.0798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.139877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.115547 restraints weight = 5432.646| |-----------------------------------------------------------------------------| r_work (start): 0.3627 rms_B_bonded: 3.47 r_work: 0.3477 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.1889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 3305 Z= 0.162 Angle : 0.525 6.150 4553 Z= 0.265 Chirality : 0.047 0.137 545 Planarity : 0.004 0.042 572 Dihedral : 3.722 16.784 490 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 3.52 % Allowed : 15.23 % Favored : 81.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.40), residues: 458 helix: 0.77 (0.93), residues: 36 sheet: 0.71 (0.37), residues: 208 loop : 0.06 (0.43), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 79 HIS 0.002 0.001 HIS B 88 PHE 0.006 0.001 PHE C 33 TYR 0.023 0.002 TYR C 78 ARG 0.006 0.001 ARG C 21 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 916 Ramachandran restraints generated. 458 Oldfield, 0 Emsley, 458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 916 Ramachandran restraints generated. 458 Oldfield, 0 Emsley, 458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 66 time to evaluate : 0.356 Fit side-chains REVERT: B 15 LYS cc_start: 0.8564 (tttt) cc_final: 0.8361 (tttt) REVERT: D 69 TYR cc_start: 0.8287 (m-10) cc_final: 0.8054 (m-10) outliers start: 9 outliers final: 9 residues processed: 71 average time/residue: 0.2031 time to fit residues: 16.9358 Evaluate side-chains 72 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 63 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain D residue 30 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 22 optimal weight: 4.9990 chunk 13 optimal weight: 5.9990 chunk 1 optimal weight: 0.9990 chunk 17 optimal weight: 6.9990 chunk 18 optimal weight: 1.9990 chunk 40 optimal weight: 6.9990 chunk 34 optimal weight: 9.9990 chunk 10 optimal weight: 3.9990 chunk 15 optimal weight: 10.0000 chunk 21 optimal weight: 4.9990 chunk 14 optimal weight: 0.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.135155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.110237 restraints weight = 5446.239| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 3.49 r_work: 0.3411 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.1876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 3305 Z= 0.300 Angle : 0.574 6.159 4553 Z= 0.297 Chirality : 0.050 0.144 545 Planarity : 0.005 0.042 572 Dihedral : 4.068 17.608 490 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 5.08 % Allowed : 13.67 % Favored : 81.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.40), residues: 458 helix: 0.53 (0.91), residues: 36 sheet: 0.47 (0.37), residues: 208 loop : 0.01 (0.44), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP D 79 HIS 0.003 0.001 HIS B 88 PHE 0.013 0.002 PHE A 44 TYR 0.018 0.002 TYR A 116 ARG 0.005 0.001 ARG C 21 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 916 Ramachandran restraints generated. 458 Oldfield, 0 Emsley, 458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 916 Ramachandran restraints generated. 458 Oldfield, 0 Emsley, 458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 62 time to evaluate : 0.350 Fit side-chains REVERT: D 69 TYR cc_start: 0.8353 (m-10) cc_final: 0.8145 (m-10) outliers start: 13 outliers final: 10 residues processed: 69 average time/residue: 0.2053 time to fit residues: 16.4905 Evaluate side-chains 71 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 61 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain D residue 30 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 29 optimal weight: 8.9990 chunk 18 optimal weight: 4.9990 chunk 34 optimal weight: 0.9990 chunk 10 optimal weight: 5.9990 chunk 7 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 38 optimal weight: 20.0000 chunk 25 optimal weight: 6.9990 chunk 26 optimal weight: 5.9990 chunk 1 optimal weight: 6.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 98 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.134124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.109359 restraints weight = 5629.040| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 3.52 r_work: 0.3377 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.1906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 3305 Z= 0.333 Angle : 0.596 6.157 4553 Z= 0.309 Chirality : 0.050 0.147 545 Planarity : 0.005 0.048 572 Dihedral : 4.303 18.425 490 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 4.30 % Allowed : 15.62 % Favored : 80.08 % 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: 0.13 (0.41), residues: 458 helix: 0.37 (0.91), residues: 36 sheet: 0.44 (0.38), residues: 201 loop : -0.18 (0.44), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 41 HIS 0.003 0.001 HIS A 31 PHE 0.012 0.002 PHE A 33 TYR 0.019 0.002 TYR A 116 ARG 0.005 0.001 ARG C 21 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 916 Ramachandran restraints generated. 458 Oldfield, 0 Emsley, 458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 916 Ramachandran restraints generated. 458 Oldfield, 0 Emsley, 458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 65 time to evaluate : 0.286 Fit side-chains outliers start: 11 outliers final: 10 residues processed: 71 average time/residue: 0.2107 time to fit residues: 17.5874 Evaluate side-chains 71 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 61 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain D residue 30 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 39 optimal weight: 7.9990 chunk 36 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 14 optimal weight: 9.9990 chunk 25 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 18 optimal weight: 4.9990 chunk 10 optimal weight: 0.9980 chunk 1 optimal weight: 7.9990 chunk 30 optimal weight: 5.9990 chunk 42 optimal weight: 5.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 124 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.133642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.108694 restraints weight = 5504.926| |-----------------------------------------------------------------------------| r_work (start): 0.3533 rms_B_bonded: 3.50 r_work: 0.3383 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.2021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 3305 Z= 0.316 Angle : 0.590 6.154 4553 Z= 0.306 Chirality : 0.050 0.146 545 Planarity : 0.005 0.043 572 Dihedral : 4.266 14.782 490 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 4.69 % Allowed : 16.80 % Favored : 78.52 % 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: -0.03 (0.40), residues: 458 helix: 0.34 (0.90), residues: 36 sheet: 0.29 (0.38), residues: 201 loop : -0.26 (0.43), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 79 HIS 0.003 0.001 HIS B 88 PHE 0.014 0.002 PHE A 44 TYR 0.020 0.002 TYR A 116 ARG 0.006 0.001 ARG C 21 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 916 Ramachandran restraints generated. 458 Oldfield, 0 Emsley, 458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 916 Ramachandran restraints generated. 458 Oldfield, 0 Emsley, 458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 60 time to evaluate : 0.366 Fit side-chains REVERT: D 34 ARG cc_start: 0.8058 (tpt-90) cc_final: 0.7783 (ttt-90) outliers start: 12 outliers final: 11 residues processed: 68 average time/residue: 0.2132 time to fit residues: 16.7568 Evaluate side-chains 71 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 60 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 75 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 1 optimal weight: 4.9990 chunk 4 optimal weight: 3.9990 chunk 15 optimal weight: 10.0000 chunk 36 optimal weight: 10.0000 chunk 32 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 chunk 28 optimal weight: 5.9990 chunk 39 optimal weight: 7.9990 chunk 42 optimal weight: 0.4980 chunk 20 optimal weight: 5.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.136172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.111408 restraints weight = 5452.807| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 3.46 r_work: 0.3426 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.2123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3305 Z= 0.216 Angle : 0.545 6.168 4553 Z= 0.280 Chirality : 0.048 0.140 545 Planarity : 0.005 0.060 572 Dihedral : 4.010 17.767 490 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 3.91 % Allowed : 17.97 % Favored : 78.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.40), residues: 458 helix: 0.44 (0.91), residues: 36 sheet: 0.32 (0.38), residues: 201 loop : -0.21 (0.43), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 79 HIS 0.002 0.001 HIS B 88 PHE 0.007 0.001 PHE A 33 TYR 0.020 0.002 TYR A 116 ARG 0.006 0.001 ARG C 21 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 916 Ramachandran restraints generated. 458 Oldfield, 0 Emsley, 458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 916 Ramachandran restraints generated. 458 Oldfield, 0 Emsley, 458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 66 time to evaluate : 0.384 Fit side-chains REVERT: A 14 VAL cc_start: 0.8784 (t) cc_final: 0.8566 (m) REVERT: D 34 ARG cc_start: 0.8061 (tpt-90) cc_final: 0.7762 (ttt-90) outliers start: 10 outliers final: 10 residues processed: 72 average time/residue: 0.2063 time to fit residues: 17.3234 Evaluate side-chains 73 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 63 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain D residue 30 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 7 optimal weight: 0.6980 chunk 0 optimal weight: 8.9990 chunk 33 optimal weight: 0.9980 chunk 2 optimal weight: 2.9990 chunk 31 optimal weight: 7.9990 chunk 28 optimal weight: 8.9990 chunk 37 optimal weight: 10.0000 chunk 11 optimal weight: 3.9990 chunk 12 optimal weight: 0.8980 chunk 22 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.137407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.112814 restraints weight = 5501.268| |-----------------------------------------------------------------------------| r_work (start): 0.3594 rms_B_bonded: 3.49 r_work: 0.3443 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.2241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3305 Z= 0.181 Angle : 0.536 6.166 4553 Z= 0.274 Chirality : 0.048 0.140 545 Planarity : 0.005 0.044 572 Dihedral : 3.800 13.341 490 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 4.30 % Allowed : 17.58 % Favored : 78.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.40), residues: 458 helix: 0.39 (0.91), residues: 36 sheet: 0.31 (0.37), residues: 203 loop : -0.14 (0.43), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 79 HIS 0.002 0.001 HIS B 88 PHE 0.007 0.001 PHE C 87 TYR 0.027 0.002 TYR C 78 ARG 0.003 0.001 ARG C 21 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 916 Ramachandran restraints generated. 458 Oldfield, 0 Emsley, 458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 916 Ramachandran restraints generated. 458 Oldfield, 0 Emsley, 458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 68 time to evaluate : 0.374 Fit side-chains REVERT: A 14 VAL cc_start: 0.8679 (t) cc_final: 0.8464 (m) REVERT: D 34 ARG cc_start: 0.8053 (tpt-90) cc_final: 0.7756 (ttt-90) outliers start: 11 outliers final: 10 residues processed: 75 average time/residue: 0.2185 time to fit residues: 19.1830 Evaluate side-chains 78 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 68 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 75 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 18 optimal weight: 0.9980 chunk 9 optimal weight: 10.0000 chunk 41 optimal weight: 5.9990 chunk 24 optimal weight: 4.9990 chunk 12 optimal weight: 8.9990 chunk 20 optimal weight: 7.9990 chunk 30 optimal weight: 0.9980 chunk 8 optimal weight: 6.9990 chunk 23 optimal weight: 0.6980 chunk 1 optimal weight: 0.7980 chunk 10 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN B 98 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.139820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.115376 restraints weight = 5345.990| |-----------------------------------------------------------------------------| r_work (start): 0.3631 rms_B_bonded: 3.47 r_work: 0.3484 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.2462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 3305 Z= 0.149 Angle : 0.530 7.148 4553 Z= 0.267 Chirality : 0.048 0.136 545 Planarity : 0.005 0.064 572 Dihedral : 3.637 16.737 490 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 3.91 % Allowed : 18.36 % Favored : 77.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.40), residues: 458 helix: 0.35 (0.92), residues: 36 sheet: 0.42 (0.37), residues: 203 loop : -0.08 (0.43), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 79 HIS 0.001 0.000 HIS C 56 PHE 0.016 0.001 PHE A 44 TYR 0.025 0.002 TYR C 78 ARG 0.006 0.001 ARG C 21 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 916 Ramachandran restraints generated. 458 Oldfield, 0 Emsley, 458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 916 Ramachandran restraints generated. 458 Oldfield, 0 Emsley, 458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 69 time to evaluate : 0.353 Fit side-chains REVERT: A 14 VAL cc_start: 0.8604 (t) cc_final: 0.8356 (m) REVERT: A 34 ARG cc_start: 0.7580 (ttm110) cc_final: 0.7320 (ttm110) REVERT: B 76 LYS cc_start: 0.7647 (mttt) cc_final: 0.7288 (mmtp) REVERT: D 34 ARG cc_start: 0.8039 (tpt-90) cc_final: 0.7752 (ttt-90) outliers start: 10 outliers final: 10 residues processed: 75 average time/residue: 0.2168 time to fit residues: 18.6667 Evaluate side-chains 75 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 65 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 75 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 26 optimal weight: 9.9990 chunk 19 optimal weight: 0.7980 chunk 9 optimal weight: 9.9990 chunk 42 optimal weight: 6.9990 chunk 1 optimal weight: 0.0270 chunk 15 optimal weight: 9.9990 chunk 6 optimal weight: 9.9990 chunk 22 optimal weight: 2.9990 chunk 10 optimal weight: 0.0870 chunk 33 optimal weight: 5.9990 chunk 21 optimal weight: 0.9980 overall best weight: 0.9818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.139772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.115767 restraints weight = 5411.477| |-----------------------------------------------------------------------------| r_work (start): 0.3640 rms_B_bonded: 3.46 r_work: 0.3495 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.2539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 3305 Z= 0.158 Angle : 0.564 8.234 4553 Z= 0.279 Chirality : 0.048 0.137 545 Planarity : 0.005 0.044 572 Dihedral : 3.590 12.250 490 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 4.69 % Allowed : 18.75 % Favored : 76.56 % 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: 0.23 (0.40), residues: 458 helix: 0.22 (0.91), residues: 36 sheet: 0.59 (0.37), residues: 201 loop : -0.18 (0.42), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 79 HIS 0.001 0.000 HIS B 88 PHE 0.014 0.001 PHE A 44 TYR 0.025 0.002 TYR C 78 ARG 0.003 0.001 ARG C 21 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1803.54 seconds wall clock time: 32 minutes 38.32 seconds (1958.32 seconds total)