Starting phenix.real_space_refine on Fri Jul 25 17:31:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6lo8_0935/07_2025/6lo8_0935.cif Found real_map, /net/cci-nas-00/data/ceres_data/6lo8_0935/07_2025/6lo8_0935.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.83 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6lo8_0935/07_2025/6lo8_0935.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6lo8_0935/07_2025/6lo8_0935.map" model { file = "/net/cci-nas-00/data/ceres_data/6lo8_0935/07_2025/6lo8_0935.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6lo8_0935/07_2025/6lo8_0935.cif" } resolution = 3.83 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 63 5.16 5 C 5075 2.51 5 N 1348 2.21 5 O 1486 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 31 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 7972 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 938 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 4, 'TRANS': 124} Chain breaks: 1 Chain: "B" Number of atoms: 1440 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1440 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 10, 'TRANS': 165} Chain breaks: 3 Chain: "C" Number of atoms: 859 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 859 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 107} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "D" Number of atoms: 984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 984 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 7, 'TRANS': 111} Chain: "E" Number of atoms: 661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 661 Classifications: {'peptide': 80} Link IDs: {'TRANS': 79} Chain: "F" Number of atoms: 660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 660 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 3, 'TRANS': 80} Chain: "G" Number of atoms: 618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 618 Classifications: {'peptide': 74} Link IDs: {'TRANS': 73} Chain: "H" Number of atoms: 581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 581 Classifications: {'peptide': 74} Link IDs: {'TRANS': 73} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "I" Number of atoms: 661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 661 Classifications: {'peptide': 80} Link IDs: {'TRANS': 79} Chain: "J" Number of atoms: 570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 570 Classifications: {'peptide': 73} Link IDs: {'TRANS': 72} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Time building chain proxies: 5.93, per 1000 atoms: 0.74 Number of scatterers: 7972 At special positions: 0 Unit cell: (132.93, 104.445, 106.555, 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 63 16.00 O 1486 8.00 N 1348 7.00 C 5075 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=13, symmetry=0 Simple disulfide: pdb=" SG CYS A 42 " - pdb=" SG CYS A 141 " distance=1.79 Simple disulfide: pdb=" SG CYS E 35 " - pdb=" SG CYS E 59 " distance=2.03 Simple disulfide: pdb=" SG CYS E 39 " - pdb=" SG CYS E 55 " distance=2.03 Simple disulfide: pdb=" SG CYS F 40 " - pdb=" SG CYS F 66 " distance=2.03 Simple disulfide: pdb=" SG CYS F 44 " - pdb=" SG CYS F 62 " distance=2.02 Simple disulfide: pdb=" SG CYS G 35 " - pdb=" SG CYS G 59 " distance=2.04 Simple disulfide: pdb=" SG CYS G 39 " - pdb=" SG CYS G 55 " distance=2.03 Simple disulfide: pdb=" SG CYS H 40 " - pdb=" SG CYS H 65 " distance=2.03 Simple disulfide: pdb=" SG CYS H 44 " - pdb=" SG CYS H 61 " distance=2.03 Simple disulfide: pdb=" SG CYS I 35 " - pdb=" SG CYS I 59 " distance=2.03 Simple disulfide: pdb=" SG CYS I 39 " - pdb=" SG CYS I 55 " distance=2.01 Simple disulfide: pdb=" SG CYS J 40 " - pdb=" SG CYS J 65 " distance=2.03 Simple disulfide: pdb=" SG CYS J 44 " - pdb=" SG CYS J 61 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.92 Conformation dependent library (CDL) restraints added in 1.1 seconds 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1860 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 2 sheets defined 80.3% alpha, 0.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.65 Creating SS restraints... Processing helix chain 'A' and resid 25 through 41 Processing helix chain 'A' and resid 42 through 65 removed outlier: 3.622A pdb=" N SER A 46 " --> pdb=" O CYS A 42 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N SER A 49 " --> pdb=" O LYS A 45 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLY A 50 " --> pdb=" O SER A 46 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N LEU A 62 " --> pdb=" O GLY A 58 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N PHE A 63 " --> pdb=" O VAL A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 146 Processing helix chain 'A' and resid 154 through 167 removed outlier: 3.998A pdb=" N PHE A 160 " --> pdb=" O VAL A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 195 Processing helix chain 'B' and resid 37 through 62 Processing helix chain 'B' and resid 62 through 71 Processing helix chain 'B' and resid 99 through 116 removed outlier: 4.063A pdb=" N TYR B 109 " --> pdb=" O VAL B 105 " (cutoff:3.500A) Proline residue: B 112 - end of helix Processing helix chain 'B' and resid 117 through 119 No H-bonds generated for 'chain 'B' and resid 117 through 119' Processing helix chain 'B' and resid 130 through 148 Processing helix chain 'B' and resid 244 through 261 removed outlier: 3.607A pdb=" N LEU B 260 " --> pdb=" O HIS B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 386 through 394 Processing helix chain 'B' and resid 395 through 412 Processing helix chain 'C' and resid 88 through 120 removed outlier: 4.060A pdb=" N PHE C 114 " --> pdb=" O PHE C 110 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N SER C 117 " --> pdb=" O LEU C 113 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLY C 118 " --> pdb=" O PHE C 114 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU C 119 " --> pdb=" O GLY C 115 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU C 120 " --> pdb=" O VAL C 116 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 137 removed outlier: 3.555A pdb=" N PHE C 137 " --> pdb=" O TYR C 133 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 167 removed outlier: 3.959A pdb=" N ALA C 154 " --> pdb=" O ALA C 150 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ILE C 155 " --> pdb=" O TYR C 151 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N HIS C 156 " --> pdb=" O LEU C 152 " (cutoff:3.500A) Processing helix chain 'C' and resid 174 through 198 removed outlier: 3.598A pdb=" N ARG C 179 " --> pdb=" O LYS C 175 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 93 Proline residue: D 91 - end of helix Processing helix chain 'D' and resid 93 through 103 removed outlier: 3.765A pdb=" N PHE D 97 " --> pdb=" O THR D 93 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR D 102 " --> pdb=" O TYR D 98 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLY D 103 " --> pdb=" O ALA D 99 " (cutoff:3.500A) Processing helix chain 'D' and resid 110 through 134 Processing helix chain 'D' and resid 140 through 166 removed outlier: 3.784A pdb=" N LYS D 144 " --> pdb=" O PRO D 140 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N LEU D 145 " --> pdb=" O ARG D 141 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 180 Processing helix chain 'E' and resid 8 through 40 removed outlier: 3.777A pdb=" N PHE E 12 " --> pdb=" O GLU E 8 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N CYS E 39 " --> pdb=" O CYS E 35 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL E 40 " --> pdb=" O PHE E 36 " (cutoff:3.500A) Processing helix chain 'E' and resid 49 through 81 removed outlier: 3.601A pdb=" N ALA E 80 " --> pdb=" O GLU E 76 " (cutoff:3.500A) Processing helix chain 'F' and resid 16 through 45 removed outlier: 3.544A pdb=" N THR F 32 " --> pdb=" O ALA F 28 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N CYS F 44 " --> pdb=" O CYS F 40 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE F 45 " --> pdb=" O LEU F 41 " (cutoff:3.500A) Processing helix chain 'F' and resid 56 through 84 removed outlier: 4.038A pdb=" N GLN F 82 " --> pdb=" O GLY F 78 " (cutoff:3.500A) Processing helix chain 'F' and resid 87 through 92 Processing helix chain 'F' and resid 93 through 98 removed outlier: 3.719A pdb=" N ARG F 97 " --> pdb=" O HIS F 94 " (cutoff:3.500A) Processing helix chain 'G' and resid 8 through 39 removed outlier: 4.212A pdb=" N CYS G 39 " --> pdb=" O CYS G 35 " (cutoff:3.500A) Processing helix chain 'G' and resid 49 through 80 removed outlier: 3.569A pdb=" N ALA G 80 " --> pdb=" O GLU G 76 " (cutoff:3.500A) Processing helix chain 'H' and resid 15 through 44 removed outlier: 3.767A pdb=" N LEU H 26 " --> pdb=" O ALA H 22 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N VAL H 29 " --> pdb=" O GLU H 25 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 84 removed outlier: 3.596A pdb=" N SER H 60 " --> pdb=" O LYS H 56 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ASP H 63 " --> pdb=" O SER H 59 " (cutoff:3.500A) Processing helix chain 'I' and resid 8 through 38 Processing helix chain 'I' and resid 49 through 81 removed outlier: 3.941A pdb=" N ALA I 80 " --> pdb=" O GLU I 76 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU I 81 " --> pdb=" O GLN I 77 " (cutoff:3.500A) Processing helix chain 'J' and resid 15 through 44 removed outlier: 3.758A pdb=" N GLU J 25 " --> pdb=" O ALA J 21 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N CYS J 44 " --> pdb=" O CYS J 40 " (cutoff:3.500A) Processing helix chain 'J' and resid 57 through 83 removed outlier: 4.003A pdb=" N ASP J 63 " --> pdb=" O SER J 59 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLN J 81 " --> pdb=" O GLY J 77 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N MET J 83 " --> pdb=" O ASN J 79 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 88 through 91 Processing sheet with id=AA2, first strand: chain 'B' and resid 240 through 241 removed outlier: 6.975A pdb=" N VAL B 240 " --> pdb=" O VAL B 373 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 611 hydrogen bonds defined for protein. 1827 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.15 Time building geometry restraints manager: 2.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1324 1.32 - 1.45: 2170 1.45 - 1.57: 4530 1.57 - 1.70: 0 1.70 - 1.82: 93 Bond restraints: 8117 Sorted by residual: bond pdb=" N PRO A 43 " pdb=" CD PRO A 43 " ideal model delta sigma weight residual 1.473 1.542 -0.069 1.40e-02 5.10e+03 2.43e+01 bond pdb=" C CYS I 55 " pdb=" O CYS I 55 " ideal model delta sigma weight residual 1.237 1.193 0.044 1.17e-02 7.31e+03 1.43e+01 bond pdb=" CA ASN G 41 " pdb=" C ASN G 41 " ideal model delta sigma weight residual 1.522 1.563 -0.042 1.72e-02 3.38e+03 5.85e+00 bond pdb=" CA CYS I 55 " pdb=" C CYS I 55 " ideal model delta sigma weight residual 1.523 1.494 0.029 1.30e-02 5.92e+03 5.05e+00 bond pdb=" CA ILE I 56 " pdb=" CB ILE I 56 " ideal model delta sigma weight residual 1.543 1.506 0.037 1.66e-02 3.63e+03 4.94e+00 ... (remaining 8112 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.82: 10745 2.82 - 5.64: 131 5.64 - 8.46: 21 8.46 - 11.28: 4 11.28 - 14.10: 2 Bond angle restraints: 10903 Sorted by residual: angle pdb=" N SER A 46 " pdb=" CA SER A 46 " pdb=" C SER A 46 " ideal model delta sigma weight residual 111.36 119.92 -8.56 1.09e+00 8.42e-01 6.16e+01 angle pdb=" N PRO A 43 " pdb=" CA PRO A 43 " pdb=" C PRO A 43 " ideal model delta sigma weight residual 112.47 98.37 14.10 2.06e+00 2.36e-01 4.69e+01 angle pdb=" N CYS I 39 " pdb=" CA CYS I 39 " pdb=" C CYS I 39 " ideal model delta sigma weight residual 112.94 122.20 -9.26 1.41e+00 5.03e-01 4.32e+01 angle pdb=" N ASP I 38 " pdb=" CA ASP I 38 " pdb=" C ASP I 38 " ideal model delta sigma weight residual 111.36 118.30 -6.94 1.09e+00 8.42e-01 4.06e+01 angle pdb=" N CYS A 42 " pdb=" CA CYS A 42 " pdb=" C CYS A 42 " ideal model delta sigma weight residual 109.81 122.37 -12.56 2.21e+00 2.05e-01 3.23e+01 ... (remaining 10898 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.54: 4298 16.54 - 33.09: 497 33.09 - 49.63: 95 49.63 - 66.18: 25 66.18 - 82.72: 13 Dihedral angle restraints: 4928 sinusoidal: 2038 harmonic: 2890 Sorted by residual: dihedral pdb=" CB CYS I 39 " pdb=" SG CYS I 39 " pdb=" SG CYS I 55 " pdb=" CB CYS I 55 " ideal model delta sinusoidal sigma weight residual 93.00 15.45 77.55 1 1.00e+01 1.00e-02 7.53e+01 dihedral pdb=" CB CYS H 44 " pdb=" SG CYS H 44 " pdb=" SG CYS H 61 " pdb=" CB CYS H 61 " ideal model delta sinusoidal sigma weight residual 93.00 168.96 -75.96 1 1.00e+01 1.00e-02 7.27e+01 dihedral pdb=" CB CYS J 44 " pdb=" SG CYS J 44 " pdb=" SG CYS J 61 " pdb=" CB CYS J 61 " ideal model delta sinusoidal sigma weight residual -86.00 -147.78 61.78 1 1.00e+01 1.00e-02 5.06e+01 ... (remaining 4925 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 1033 0.068 - 0.136: 130 0.136 - 0.204: 17 0.204 - 0.272: 3 0.272 - 0.340: 2 Chirality restraints: 1185 Sorted by residual: chirality pdb=" CA CYS I 39 " pdb=" N CYS I 39 " pdb=" C CYS I 39 " pdb=" CB CYS I 39 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.88e+00 chirality pdb=" CA ILE I 56 " pdb=" N ILE I 56 " pdb=" C ILE I 56 " pdb=" CB ILE I 56 " both_signs ideal model delta sigma weight residual False 2.43 2.13 0.30 2.00e-01 2.50e+01 2.24e+00 chirality pdb=" CA CYS I 35 " pdb=" N CYS I 35 " pdb=" C CYS I 35 " pdb=" CB CYS I 35 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.54e+00 ... (remaining 1182 not shown) Planarity restraints: 1392 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS A 42 " -0.096 5.00e-02 4.00e+02 1.46e-01 3.41e+01 pdb=" N PRO A 43 " 0.252 5.00e-02 4.00e+02 pdb=" CA PRO A 43 " -0.079 5.00e-02 4.00e+02 pdb=" CD PRO A 43 " -0.077 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR I 37 " -0.024 2.00e-02 2.50e+03 5.06e-02 2.56e+01 pdb=" C THR I 37 " 0.087 2.00e-02 2.50e+03 pdb=" O THR I 37 " -0.034 2.00e-02 2.50e+03 pdb=" N ASP I 38 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG B 107 " 0.016 2.00e-02 2.50e+03 3.22e-02 1.04e+01 pdb=" C ARG B 107 " -0.056 2.00e-02 2.50e+03 pdb=" O ARG B 107 " 0.021 2.00e-02 2.50e+03 pdb=" N ARG B 108 " 0.019 2.00e-02 2.50e+03 ... (remaining 1389 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1694 2.77 - 3.31: 7499 3.31 - 3.84: 13253 3.84 - 4.37: 14273 4.37 - 4.90: 25404 Nonbonded interactions: 62123 Sorted by model distance: nonbonded pdb=" OG SER D 71 " pdb=" O SER D 128 " model vdw 2.242 3.040 nonbonded pdb=" O MET A 36 " pdb=" OG1 THR A 40 " model vdw 2.297 3.040 nonbonded pdb=" O GLU I 33 " pdb=" OG1 THR I 37 " model vdw 2.309 3.040 nonbonded pdb=" OH TYR A 136 " pdb=" OG SER A 186 " model vdw 2.315 3.040 nonbonded pdb=" O ASP E 42 " pdb=" NZ LYS J 68 " model vdw 2.318 3.120 ... (remaining 62118 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 'E' and resid 7 through 80) selection = chain 'G' selection = (chain 'I' and resid 7 through 80) } ncs_group { reference = (chain 'H' and resid 14 through 86) selection = chain 'J' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.490 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: 0.400 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 22.330 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.030 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:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 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 : 0.006 0.246 8130 Z= 0.285 Angle : 0.938 29.165 10929 Z= 0.525 Chirality : 0.049 0.340 1185 Planarity : 0.007 0.146 1392 Dihedral : 14.877 82.722 3029 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.72 % Favored : 96.07 % Rotamer: Outliers : 0.46 % Allowed : 7.10 % Favored : 92.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.08 (0.21), residues: 967 helix: -1.56 (0.14), residues: 753 sheet: -0.91 (0.97), residues: 22 loop : -3.38 (0.34), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 106 HIS 0.009 0.002 HIS C 156 PHE 0.023 0.002 PHE D 65 TYR 0.014 0.002 TYR C 133 ARG 0.005 0.000 ARG I 73 Details of bonding type rmsd hydrogen bonds : bond 0.10768 ( 611) hydrogen bonds : angle 6.13108 ( 1827) SS BOND : bond 0.06854 ( 13) SS BOND : angle 7.51084 ( 26) covalent geometry : bond 0.00489 ( 8117) covalent geometry : angle 0.86502 (10903) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 332 time to evaluate : 0.980 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 LEU cc_start: 0.8288 (mp) cc_final: 0.8030 (pp) REVERT: A 129 PHE cc_start: 0.7855 (m-80) cc_final: 0.7170 (m-10) REVERT: A 189 ILE cc_start: 0.9155 (mm) cc_final: 0.8867 (mm) REVERT: B 39 MET cc_start: 0.4281 (mtm) cc_final: 0.3602 (tmm) REVERT: B 42 TRP cc_start: 0.7701 (m100) cc_final: 0.7003 (m-10) REVERT: B 82 LYS cc_start: 0.8166 (mmpt) cc_final: 0.7807 (tptt) REVERT: C 108 TYR cc_start: 0.8142 (m-80) cc_final: 0.7629 (m-80) REVERT: C 175 LYS cc_start: 0.8895 (mmmm) cc_final: 0.8646 (tttt) REVERT: D 82 GLU cc_start: 0.8368 (tp30) cc_final: 0.8101 (tp30) REVERT: D 123 GLN cc_start: 0.8494 (tm-30) cc_final: 0.8063 (tm-30) REVERT: D 130 ILE cc_start: 0.9328 (tt) cc_final: 0.9128 (tt) REVERT: D 165 GLU cc_start: 0.8715 (mm-30) cc_final: 0.8446 (mm-30) REVERT: G 28 TYR cc_start: 0.8880 (t80) cc_final: 0.8585 (t80) REVERT: H 19 ILE cc_start: 0.9291 (tt) cc_final: 0.8881 (tp) REVERT: H 36 LEU cc_start: 0.9542 (tp) cc_final: 0.9313 (tp) REVERT: H 39 ASN cc_start: 0.8650 (m-40) cc_final: 0.7616 (m110) REVERT: I 17 GLU cc_start: 0.8570 (tp30) cc_final: 0.8214 (tp30) REVERT: I 19 LYS cc_start: 0.9305 (mmtt) cc_final: 0.8708 (mtpp) outliers start: 4 outliers final: 2 residues processed: 336 average time/residue: 0.2528 time to fit residues: 108.0478 Evaluate side-chains 232 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 230 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 CYS Chi-restraints excluded: chain I residue 35 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 80 optimal weight: 2.9990 chunk 72 optimal weight: 0.7980 chunk 39 optimal weight: 2.9990 chunk 24 optimal weight: 4.9990 chunk 48 optimal weight: 0.9990 chunk 38 optimal weight: 6.9990 chunk 74 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 86 optimal weight: 0.8980 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 ASN ** A 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 135 ASN C 156 HIS F 34 ASN F 90 ASN F 91 GLN G 20 GLN G 30 ASN G 53 GLN G 77 GLN ** H 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 30 ASN J 20 GLN J 34 ASN ** J 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 75 GLN J 85 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.073747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.059794 restraints weight = 29797.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.061360 restraints weight = 16621.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.062458 restraints weight = 11282.116| |-----------------------------------------------------------------------------| r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.2883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.102 8130 Z= 0.183 Angle : 0.735 13.877 10929 Z= 0.391 Chirality : 0.040 0.166 1185 Planarity : 0.005 0.089 1392 Dihedral : 5.561 50.963 1075 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.83 % Favored : 96.07 % Rotamer: Outliers : 3.32 % Allowed : 16.27 % Favored : 80.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.17 % 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: -0.42 (0.25), residues: 967 helix: 0.41 (0.17), residues: 761 sheet: 0.02 (1.08), residues: 22 loop : -3.00 (0.38), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 106 HIS 0.004 0.001 HIS B 65 PHE 0.012 0.001 PHE A 182 TYR 0.019 0.001 TYR H 49 ARG 0.004 0.001 ARG E 69 Details of bonding type rmsd hydrogen bonds : bond 0.04649 ( 611) hydrogen bonds : angle 4.49226 ( 1827) SS BOND : bond 0.00394 ( 13) SS BOND : angle 2.83140 ( 26) covalent geometry : bond 0.00406 ( 8117) covalent geometry : angle 0.72246 (10903) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 268 time to evaluate : 0.968 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 GLU cc_start: 0.7754 (tm-30) cc_final: 0.7242 (tm-30) REVERT: A 56 LEU cc_start: 0.8233 (mp) cc_final: 0.7964 (pp) REVERT: A 129 PHE cc_start: 0.7961 (m-80) cc_final: 0.7320 (m-80) REVERT: B 39 MET cc_start: 0.3999 (mtm) cc_final: 0.3518 (tmm) REVERT: B 67 THR cc_start: 0.8502 (m) cc_final: 0.8108 (p) REVERT: B 82 LYS cc_start: 0.8194 (mmpt) cc_final: 0.7740 (tptt) REVERT: C 103 MET cc_start: 0.8277 (mtt) cc_final: 0.8076 (mtt) REVERT: D 111 ASP cc_start: 0.7629 (t0) cc_final: 0.7128 (t0) REVERT: D 123 GLN cc_start: 0.8560 (tm-30) cc_final: 0.8322 (tm-30) REVERT: D 144 LYS cc_start: 0.8398 (tttt) cc_final: 0.8101 (pttm) REVERT: D 155 MET cc_start: 0.7861 (mmp) cc_final: 0.7615 (mmt) REVERT: D 165 GLU cc_start: 0.8640 (mm-30) cc_final: 0.8415 (mm-30) REVERT: E 11 GLU cc_start: 0.8232 (mp0) cc_final: 0.8023 (mp0) REVERT: E 64 LEU cc_start: 0.8519 (OUTLIER) cc_final: 0.8246 (mm) REVERT: F 27 ASP cc_start: 0.8816 (m-30) cc_final: 0.8353 (m-30) REVERT: F 29 MET cc_start: 0.8160 (mtp) cc_final: 0.7928 (mtt) REVERT: F 35 ASN cc_start: 0.8899 (t0) cc_final: 0.8689 (t0) REVERT: G 22 LYS cc_start: 0.8922 (tptp) cc_final: 0.8623 (tptt) REVERT: G 28 TYR cc_start: 0.8821 (t80) cc_final: 0.8616 (t80) REVERT: I 17 GLU cc_start: 0.8714 (tp30) cc_final: 0.8425 (tp30) REVERT: J 23 GLU cc_start: 0.8242 (tp30) cc_final: 0.7989 (tp30) REVERT: J 80 MET cc_start: 0.8143 (mmp) cc_final: 0.7941 (mmp) outliers start: 29 outliers final: 15 residues processed: 284 average time/residue: 0.2221 time to fit residues: 81.7987 Evaluate side-chains 244 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 228 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 CYS Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain B residue 401 ASP Chi-restraints excluded: chain D residue 105 VAL Chi-restraints excluded: chain D residue 129 CYS Chi-restraints excluded: chain D residue 149 CYS Chi-restraints excluded: chain E residue 56 ILE Chi-restraints excluded: chain E residue 64 LEU Chi-restraints excluded: chain G residue 20 GLN Chi-restraints excluded: chain H residue 26 LEU Chi-restraints excluded: chain H residue 47 THR Chi-restraints excluded: chain I residue 41 ASN Chi-restraints excluded: chain J residue 32 MET Chi-restraints excluded: chain J residue 44 CYS Chi-restraints excluded: chain J residue 61 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 24 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 chunk 63 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 56 optimal weight: 0.6980 chunk 9 optimal weight: 9.9990 chunk 82 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 chunk 39 optimal weight: 0.6980 chunk 26 optimal weight: 6.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 168 ASN F 94 HIS G 20 GLN G 72 GLN ** H 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 30 ASN ** J 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.073893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.060088 restraints weight = 30093.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.061686 restraints weight = 17102.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.062779 restraints weight = 11504.128| |-----------------------------------------------------------------------------| r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.3445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 8130 Z= 0.164 Angle : 0.708 15.480 10929 Z= 0.373 Chirality : 0.039 0.176 1185 Planarity : 0.004 0.068 1392 Dihedral : 5.274 43.377 1074 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.03 % Favored : 95.86 % Rotamer: Outliers : 3.78 % Allowed : 19.24 % Favored : 76.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.17 % 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: 0.53 (0.26), residues: 967 helix: 1.12 (0.18), residues: 761 sheet: 0.17 (1.05), residues: 22 loop : -2.87 (0.40), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 106 HIS 0.004 0.001 HIS E 66 PHE 0.020 0.001 PHE C 107 TYR 0.016 0.001 TYR E 28 ARG 0.005 0.000 ARG I 26 Details of bonding type rmsd hydrogen bonds : bond 0.04465 ( 611) hydrogen bonds : angle 4.28452 ( 1827) SS BOND : bond 0.00355 ( 13) SS BOND : angle 2.63635 ( 26) covalent geometry : bond 0.00363 ( 8117) covalent geometry : angle 0.69739 (10903) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 254 time to evaluate : 0.869 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 LEU cc_start: 0.8188 (mp) cc_final: 0.7903 (pp) REVERT: A 129 PHE cc_start: 0.7928 (m-80) cc_final: 0.7223 (m-10) REVERT: A 140 GLU cc_start: 0.8360 (tm-30) cc_final: 0.8094 (tm-30) REVERT: A 194 LYS cc_start: 0.8857 (tppp) cc_final: 0.8582 (mptt) REVERT: B 39 MET cc_start: 0.3975 (mtm) cc_final: 0.3496 (tmm) REVERT: B 82 LYS cc_start: 0.8271 (mmpt) cc_final: 0.7790 (tptt) REVERT: C 107 PHE cc_start: 0.8791 (t80) cc_final: 0.8579 (t80) REVERT: C 163 HIS cc_start: 0.8812 (OUTLIER) cc_final: 0.8311 (t70) REVERT: D 78 GLN cc_start: 0.8371 (tm-30) cc_final: 0.7942 (tm-30) REVERT: D 111 ASP cc_start: 0.7821 (t0) cc_final: 0.7232 (t0) REVERT: D 123 GLN cc_start: 0.8629 (tm-30) cc_final: 0.8178 (tm-30) REVERT: D 165 GLU cc_start: 0.8625 (mm-30) cc_final: 0.8195 (mm-30) REVERT: E 18 GLN cc_start: 0.8264 (OUTLIER) cc_final: 0.8036 (mp10) REVERT: E 64 LEU cc_start: 0.8520 (OUTLIER) cc_final: 0.8316 (mm) REVERT: F 27 ASP cc_start: 0.8755 (m-30) cc_final: 0.8433 (m-30) REVERT: F 35 ASN cc_start: 0.8927 (t0) cc_final: 0.8719 (t0) REVERT: G 22 LYS cc_start: 0.8868 (tptp) cc_final: 0.8667 (tptt) REVERT: G 68 GLU cc_start: 0.7683 (tp30) cc_final: 0.7474 (tp30) REVERT: H 59 SER cc_start: 0.8914 (m) cc_final: 0.8382 (p) REVERT: H 62 LEU cc_start: 0.9047 (OUTLIER) cc_final: 0.8753 (mm) REVERT: I 10 GLN cc_start: 0.8908 (mp10) cc_final: 0.8564 (pm20) REVERT: I 11 GLU cc_start: 0.7843 (OUTLIER) cc_final: 0.7441 (mp0) REVERT: I 17 GLU cc_start: 0.8698 (tp30) cc_final: 0.8418 (tp30) outliers start: 33 outliers final: 21 residues processed: 272 average time/residue: 0.2162 time to fit residues: 76.4678 Evaluate side-chains 252 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 226 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 CYS Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 401 ASP Chi-restraints excluded: chain C residue 163 HIS Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain D residue 84 ILE Chi-restraints excluded: chain D residue 105 VAL Chi-restraints excluded: chain D residue 129 CYS Chi-restraints excluded: chain D residue 149 CYS Chi-restraints excluded: chain E residue 18 GLN Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 64 LEU Chi-restraints excluded: chain F residue 31 SER Chi-restraints excluded: chain F residue 41 LEU Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain G residue 41 ASN Chi-restraints excluded: chain H residue 26 LEU Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 62 LEU Chi-restraints excluded: chain I residue 11 GLU Chi-restraints excluded: chain I residue 41 ASN Chi-restraints excluded: chain J residue 32 MET Chi-restraints excluded: chain J residue 44 CYS Chi-restraints excluded: chain J residue 61 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 27 optimal weight: 4.9990 chunk 1 optimal weight: 10.0000 chunk 67 optimal weight: 0.7980 chunk 28 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 chunk 50 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 37 optimal weight: 6.9990 chunk 81 optimal weight: 0.6980 chunk 44 optimal weight: 4.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 20 GLN G 72 GLN H 75 GLN H 79 ASN I 30 ASN ** J 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.073826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.061301 restraints weight = 29709.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.062475 restraints weight = 15196.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.063105 restraints weight = 11442.402| |-----------------------------------------------------------------------------| r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.3720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 8130 Z= 0.168 Angle : 0.709 10.911 10929 Z= 0.371 Chirality : 0.040 0.242 1185 Planarity : 0.004 0.059 1392 Dihedral : 5.254 43.882 1074 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.76 % Favored : 95.14 % Rotamer: Outliers : 4.81 % Allowed : 19.82 % Favored : 75.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.17 % 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: 0.88 (0.26), residues: 967 helix: 1.36 (0.18), residues: 762 sheet: 0.09 (1.04), residues: 22 loop : -2.68 (0.40), residues: 183 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 106 HIS 0.004 0.001 HIS F 47 PHE 0.015 0.001 PHE C 107 TYR 0.019 0.001 TYR C 151 ARG 0.005 0.001 ARG E 26 Details of bonding type rmsd hydrogen bonds : bond 0.04471 ( 611) hydrogen bonds : angle 4.28532 ( 1827) SS BOND : bond 0.00369 ( 13) SS BOND : angle 2.40759 ( 26) covalent geometry : bond 0.00377 ( 8117) covalent geometry : angle 0.69961 (10903) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 247 time to evaluate : 0.899 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 GLU cc_start: 0.7875 (tm-30) cc_final: 0.7498 (tm-30) REVERT: A 56 LEU cc_start: 0.8242 (mp) cc_final: 0.7948 (pp) REVERT: A 140 GLU cc_start: 0.8297 (tm-30) cc_final: 0.7790 (tm-30) REVERT: A 194 LYS cc_start: 0.8874 (tppp) cc_final: 0.8601 (mptt) REVERT: B 39 MET cc_start: 0.4130 (mtm) cc_final: 0.3557 (tmm) REVERT: B 82 LYS cc_start: 0.8389 (mmpt) cc_final: 0.7947 (tptt) REVERT: D 64 MET cc_start: 0.6333 (tmm) cc_final: 0.5955 (tmm) REVERT: D 78 GLN cc_start: 0.8438 (tm-30) cc_final: 0.7887 (tm-30) REVERT: D 111 ASP cc_start: 0.7918 (t0) cc_final: 0.7308 (t0) REVERT: D 123 GLN cc_start: 0.8531 (tm-30) cc_final: 0.8136 (tm-30) REVERT: D 155 MET cc_start: 0.7632 (mmt) cc_final: 0.7413 (mmp) REVERT: D 165 GLU cc_start: 0.8610 (mm-30) cc_final: 0.8076 (mm-30) REVERT: E 23 ASP cc_start: 0.8643 (t0) cc_final: 0.8418 (t70) REVERT: E 52 GLU cc_start: 0.8654 (OUTLIER) cc_final: 0.8014 (mp0) REVERT: E 64 LEU cc_start: 0.8620 (OUTLIER) cc_final: 0.8364 (mm) REVERT: F 27 ASP cc_start: 0.8752 (m-30) cc_final: 0.8387 (m-30) REVERT: F 60 GLN cc_start: 0.8433 (mt0) cc_final: 0.7915 (mp10) REVERT: G 22 LYS cc_start: 0.8873 (tptp) cc_final: 0.8668 (tptt) REVERT: G 42 ASP cc_start: 0.7521 (t0) cc_final: 0.7136 (t0) REVERT: H 59 SER cc_start: 0.8936 (m) cc_final: 0.8456 (p) REVERT: H 62 LEU cc_start: 0.9030 (OUTLIER) cc_final: 0.8697 (mm) REVERT: I 7 LYS cc_start: 0.8853 (ptmm) cc_final: 0.8337 (tmmt) REVERT: I 10 GLN cc_start: 0.8879 (mp10) cc_final: 0.7826 (pm20) REVERT: I 11 GLU cc_start: 0.7814 (OUTLIER) cc_final: 0.7216 (mp0) REVERT: I 17 GLU cc_start: 0.8782 (tp30) cc_final: 0.8452 (tp30) REVERT: J 23 GLU cc_start: 0.8622 (tp30) cc_final: 0.8390 (tp30) outliers start: 42 outliers final: 27 residues processed: 270 average time/residue: 0.2128 time to fit residues: 75.4361 Evaluate side-chains 257 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 226 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 CYS Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 401 ASP Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain D residue 84 ILE Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 105 VAL Chi-restraints excluded: chain D residue 129 CYS Chi-restraints excluded: chain D residue 149 CYS Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 52 GLU Chi-restraints excluded: chain E residue 64 LEU Chi-restraints excluded: chain F residue 31 SER Chi-restraints excluded: chain F residue 41 LEU Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain G residue 20 GLN Chi-restraints excluded: chain G residue 41 ASN Chi-restraints excluded: chain G residue 66 HIS Chi-restraints excluded: chain H residue 26 LEU Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 29 VAL Chi-restraints excluded: chain H residue 62 LEU Chi-restraints excluded: chain I residue 11 GLU Chi-restraints excluded: chain I residue 41 ASN Chi-restraints excluded: chain J residue 32 MET Chi-restraints excluded: chain J residue 44 CYS Chi-restraints excluded: chain J residue 61 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 85 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 91 optimal weight: 0.0970 chunk 65 optimal weight: 0.0000 chunk 12 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 52 optimal weight: 0.5980 chunk 61 optimal weight: 0.2980 chunk 94 optimal weight: 4.9990 chunk 66 optimal weight: 0.7980 overall best weight: 0.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 20 GLN H 75 GLN J 39 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.075131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.061424 restraints weight = 29682.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.063018 restraints weight = 16565.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.064161 restraints weight = 11249.490| |-----------------------------------------------------------------------------| r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.3925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 8130 Z= 0.142 Angle : 0.710 11.063 10929 Z= 0.368 Chirality : 0.039 0.257 1185 Planarity : 0.004 0.059 1392 Dihedral : 5.160 43.434 1074 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.72 % Favored : 96.17 % Rotamer: Outliers : 3.44 % Allowed : 22.91 % Favored : 73.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.17 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.26), residues: 967 helix: 1.53 (0.18), residues: 758 sheet: 0.32 (1.04), residues: 22 loop : -2.52 (0.39), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 106 HIS 0.006 0.001 HIS C 163 PHE 0.033 0.001 PHE C 107 TYR 0.025 0.001 TYR C 151 ARG 0.005 0.000 ARG E 26 Details of bonding type rmsd hydrogen bonds : bond 0.04415 ( 611) hydrogen bonds : angle 4.20475 ( 1827) SS BOND : bond 0.00285 ( 13) SS BOND : angle 2.51545 ( 26) covalent geometry : bond 0.00310 ( 8117) covalent geometry : angle 0.70022 (10903) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 263 time to evaluate : 0.880 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 GLU cc_start: 0.7916 (tm-30) cc_final: 0.7470 (tm-30) REVERT: A 140 GLU cc_start: 0.8277 (tm-30) cc_final: 0.7812 (tm-30) REVERT: A 194 LYS cc_start: 0.8869 (tppp) cc_final: 0.8618 (mptt) REVERT: B 39 MET cc_start: 0.4077 (mtm) cc_final: 0.3534 (tmm) REVERT: B 82 LYS cc_start: 0.8257 (mmpt) cc_final: 0.7992 (tptt) REVERT: C 163 HIS cc_start: 0.8736 (OUTLIER) cc_final: 0.8364 (t70) REVERT: D 78 GLN cc_start: 0.8428 (tm-30) cc_final: 0.7805 (tm-30) REVERT: D 111 ASP cc_start: 0.7886 (t0) cc_final: 0.7328 (t0) REVERT: D 123 GLN cc_start: 0.8530 (tm-30) cc_final: 0.8113 (tm-30) REVERT: D 155 MET cc_start: 0.7615 (mmt) cc_final: 0.7401 (mmp) REVERT: D 165 GLU cc_start: 0.8579 (mm-30) cc_final: 0.7959 (mm-30) REVERT: E 18 GLN cc_start: 0.8438 (OUTLIER) cc_final: 0.8207 (mp10) REVERT: E 52 GLU cc_start: 0.8659 (OUTLIER) cc_final: 0.8070 (mp0) REVERT: E 64 LEU cc_start: 0.8621 (OUTLIER) cc_final: 0.8380 (mm) REVERT: E 73 ARG cc_start: 0.7903 (tpp-160) cc_final: 0.7671 (ttm-80) REVERT: F 27 ASP cc_start: 0.8727 (m-30) cc_final: 0.8373 (m-30) REVERT: F 60 GLN cc_start: 0.8425 (mt0) cc_final: 0.7798 (mp10) REVERT: G 22 LYS cc_start: 0.8854 (tptp) cc_final: 0.8552 (tptt) REVERT: G 42 ASP cc_start: 0.7620 (t0) cc_final: 0.7299 (t0) REVERT: H 59 SER cc_start: 0.8879 (m) cc_final: 0.8392 (p) REVERT: H 62 LEU cc_start: 0.9006 (OUTLIER) cc_final: 0.8694 (mm) REVERT: I 7 LYS cc_start: 0.8730 (ptmm) cc_final: 0.8213 (tmmt) REVERT: I 10 GLN cc_start: 0.8678 (mp10) cc_final: 0.7971 (pm20) REVERT: J 23 GLU cc_start: 0.8575 (tp30) cc_final: 0.8265 (tp30) outliers start: 30 outliers final: 17 residues processed: 277 average time/residue: 0.2105 time to fit residues: 76.3006 Evaluate side-chains 256 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 234 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 CYS Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 401 ASP Chi-restraints excluded: chain C residue 163 HIS Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain D residue 105 VAL Chi-restraints excluded: chain D residue 129 CYS Chi-restraints excluded: chain D residue 149 CYS Chi-restraints excluded: chain E residue 18 GLN Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 52 GLU Chi-restraints excluded: chain E residue 55 CYS Chi-restraints excluded: chain E residue 64 LEU Chi-restraints excluded: chain F residue 41 LEU Chi-restraints excluded: chain G residue 18 GLN Chi-restraints excluded: chain G residue 66 HIS Chi-restraints excluded: chain H residue 26 LEU Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 29 VAL Chi-restraints excluded: chain H residue 62 LEU Chi-restraints excluded: chain I residue 35 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 53 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 3 optimal weight: 10.0000 chunk 76 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 91 optimal weight: 7.9990 chunk 79 optimal weight: 0.8980 chunk 39 optimal weight: 0.6980 chunk 25 optimal weight: 2.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 ASN ** A 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 20 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.073194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.060819 restraints weight = 29898.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.061565 restraints weight = 16304.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.062020 restraints weight = 15119.811| |-----------------------------------------------------------------------------| r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.4121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 8130 Z= 0.199 Angle : 0.736 10.395 10929 Z= 0.384 Chirality : 0.042 0.275 1185 Planarity : 0.004 0.053 1392 Dihedral : 5.216 43.782 1074 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.38 % Favored : 94.52 % Rotamer: Outliers : 4.81 % Allowed : 23.25 % Favored : 71.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.17 % 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 (0.26), residues: 967 helix: 1.56 (0.18), residues: 759 sheet: 0.01 (1.02), residues: 22 loop : -2.50 (0.40), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 106 HIS 0.005 0.001 HIS C 163 PHE 0.034 0.002 PHE C 107 TYR 0.026 0.001 TYR C 151 ARG 0.008 0.001 ARG I 26 Details of bonding type rmsd hydrogen bonds : bond 0.04475 ( 611) hydrogen bonds : angle 4.29437 ( 1827) SS BOND : bond 0.00446 ( 13) SS BOND : angle 2.30717 ( 26) covalent geometry : bond 0.00443 ( 8117) covalent geometry : angle 0.72848 (10903) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 236 time to evaluate : 0.992 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 GLU cc_start: 0.7864 (tm-30) cc_final: 0.7356 (tm-30) REVERT: A 140 GLU cc_start: 0.8329 (tm-30) cc_final: 0.7862 (tm-30) REVERT: A 194 LYS cc_start: 0.8939 (tppp) cc_final: 0.8641 (mptt) REVERT: B 39 MET cc_start: 0.4133 (mtm) cc_final: 0.3532 (tmm) REVERT: B 82 LYS cc_start: 0.8484 (mmpt) cc_final: 0.8049 (tptt) REVERT: C 163 HIS cc_start: 0.8681 (OUTLIER) cc_final: 0.8054 (t70) REVERT: D 64 MET cc_start: 0.6243 (OUTLIER) cc_final: 0.5636 (tmm) REVERT: D 78 GLN cc_start: 0.8490 (tm-30) cc_final: 0.7909 (tm-30) REVERT: D 111 ASP cc_start: 0.8193 (t0) cc_final: 0.7732 (t0) REVERT: D 123 GLN cc_start: 0.8516 (tm-30) cc_final: 0.8146 (tm-30) REVERT: D 155 MET cc_start: 0.7668 (mmt) cc_final: 0.7445 (mmp) REVERT: D 165 GLU cc_start: 0.8573 (mm-30) cc_final: 0.8087 (mm-30) REVERT: E 18 GLN cc_start: 0.8443 (OUTLIER) cc_final: 0.8212 (mp10) REVERT: E 52 GLU cc_start: 0.8789 (OUTLIER) cc_final: 0.8181 (mp0) REVERT: E 64 LEU cc_start: 0.8514 (OUTLIER) cc_final: 0.8240 (mm) REVERT: F 27 ASP cc_start: 0.8702 (m-30) cc_final: 0.8377 (m-30) REVERT: F 60 GLN cc_start: 0.8487 (mt0) cc_final: 0.8105 (mt0) REVERT: G 22 LYS cc_start: 0.8920 (tptp) cc_final: 0.8680 (tptt) REVERT: G 42 ASP cc_start: 0.7536 (t0) cc_final: 0.7217 (t0) REVERT: H 59 SER cc_start: 0.8958 (m) cc_final: 0.8506 (p) REVERT: H 62 LEU cc_start: 0.9070 (OUTLIER) cc_final: 0.8719 (mm) REVERT: I 7 LYS cc_start: 0.8828 (ptmm) cc_final: 0.8514 (tmmt) REVERT: I 52 GLU cc_start: 0.7843 (mt-10) cc_final: 0.7603 (mm-30) outliers start: 42 outliers final: 29 residues processed: 258 average time/residue: 0.2069 time to fit residues: 70.7942 Evaluate side-chains 256 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 221 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 CYS Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 401 ASP Chi-restraints excluded: chain C residue 163 HIS Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain D residue 64 MET Chi-restraints excluded: chain D residue 84 ILE Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 105 VAL Chi-restraints excluded: chain D residue 149 CYS Chi-restraints excluded: chain E residue 14 LYS Chi-restraints excluded: chain E residue 18 GLN Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 52 GLU Chi-restraints excluded: chain E residue 64 LEU Chi-restraints excluded: chain F residue 31 SER Chi-restraints excluded: chain F residue 41 LEU Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain G residue 20 GLN Chi-restraints excluded: chain G residue 41 ASN Chi-restraints excluded: chain G residue 53 GLN Chi-restraints excluded: chain G residue 66 HIS Chi-restraints excluded: chain H residue 26 LEU Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 29 VAL Chi-restraints excluded: chain H residue 47 THR Chi-restraints excluded: chain H residue 62 LEU Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain I residue 35 CYS Chi-restraints excluded: chain I residue 41 ASN Chi-restraints excluded: chain J residue 32 MET Chi-restraints excluded: chain J residue 44 CYS Chi-restraints excluded: chain J residue 72 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 47 optimal weight: 4.9990 chunk 92 optimal weight: 0.6980 chunk 21 optimal weight: 0.6980 chunk 26 optimal weight: 0.5980 chunk 10 optimal weight: 0.9990 chunk 57 optimal weight: 0.9990 chunk 54 optimal weight: 2.9990 chunk 60 optimal weight: 0.6980 chunk 91 optimal weight: 4.9990 chunk 17 optimal weight: 1.9990 chunk 90 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 20 GLN I 30 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.074335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.060535 restraints weight = 29986.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.062169 restraints weight = 16694.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.063259 restraints weight = 11309.645| |-----------------------------------------------------------------------------| r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.4199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 8130 Z= 0.153 Angle : 0.733 11.520 10929 Z= 0.379 Chirality : 0.040 0.247 1185 Planarity : 0.004 0.056 1392 Dihedral : 5.176 43.386 1074 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.45 % Favored : 95.45 % Rotamer: Outliers : 4.01 % Allowed : 24.86 % Favored : 71.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.17 % Twisted General : 0.10 % 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 (0.26), residues: 967 helix: 1.61 (0.18), residues: 757 sheet: 0.03 (1.03), residues: 22 loop : -2.42 (0.40), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 106 HIS 0.006 0.001 HIS C 163 PHE 0.038 0.001 PHE C 107 TYR 0.031 0.001 TYR C 151 ARG 0.006 0.000 ARG E 26 Details of bonding type rmsd hydrogen bonds : bond 0.04427 ( 611) hydrogen bonds : angle 4.24042 ( 1827) SS BOND : bond 0.00311 ( 13) SS BOND : angle 2.01211 ( 26) covalent geometry : bond 0.00343 ( 8117) covalent geometry : angle 0.72728 (10903) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 244 time to evaluate : 0.878 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 GLU cc_start: 0.7648 (tm-30) cc_final: 0.7221 (tm-30) REVERT: A 45 LYS cc_start: 0.8734 (mmtt) cc_final: 0.8382 (mmtm) REVERT: A 140 GLU cc_start: 0.8287 (tm-30) cc_final: 0.7797 (tm-30) REVERT: A 194 LYS cc_start: 0.8904 (tppp) cc_final: 0.8638 (mptt) REVERT: B 39 MET cc_start: 0.4140 (mtm) cc_final: 0.3569 (tmm) REVERT: B 82 LYS cc_start: 0.8444 (mmpt) cc_final: 0.8047 (tptt) REVERT: C 163 HIS cc_start: 0.8700 (OUTLIER) cc_final: 0.8066 (t70) REVERT: D 78 GLN cc_start: 0.8450 (tm-30) cc_final: 0.7872 (tm-30) REVERT: D 111 ASP cc_start: 0.8106 (t0) cc_final: 0.7517 (t0) REVERT: D 123 GLN cc_start: 0.8527 (tm-30) cc_final: 0.8126 (tm-30) REVERT: D 155 MET cc_start: 0.7733 (mmt) cc_final: 0.7521 (mmp) REVERT: D 165 GLU cc_start: 0.8538 (mm-30) cc_final: 0.7955 (mm-30) REVERT: D 167 LYS cc_start: 0.9050 (mmmm) cc_final: 0.8819 (mmmm) REVERT: E 18 GLN cc_start: 0.8440 (OUTLIER) cc_final: 0.8179 (mp10) REVERT: E 52 GLU cc_start: 0.8694 (OUTLIER) cc_final: 0.7983 (mp0) REVERT: E 64 LEU cc_start: 0.8509 (OUTLIER) cc_final: 0.8242 (mm) REVERT: F 27 ASP cc_start: 0.8788 (m-30) cc_final: 0.8387 (m-30) REVERT: F 60 GLN cc_start: 0.8494 (mt0) cc_final: 0.7844 (mp10) REVERT: G 17 GLU cc_start: 0.8063 (tm-30) cc_final: 0.7771 (tm-30) REVERT: G 20 GLN cc_start: 0.8988 (OUTLIER) cc_final: 0.8578 (pt0) REVERT: G 22 LYS cc_start: 0.8943 (tptp) cc_final: 0.8723 (tptt) REVERT: G 42 ASP cc_start: 0.7628 (t0) cc_final: 0.7291 (t0) REVERT: H 39 ASN cc_start: 0.7985 (OUTLIER) cc_final: 0.6584 (m110) REVERT: H 59 SER cc_start: 0.8933 (m) cc_final: 0.8461 (p) REVERT: H 62 LEU cc_start: 0.9040 (OUTLIER) cc_final: 0.8709 (mm) REVERT: I 7 LYS cc_start: 0.8815 (ptmm) cc_final: 0.8246 (tptp) REVERT: I 10 GLN cc_start: 0.8408 (pm20) cc_final: 0.7548 (pm20) REVERT: I 33 GLU cc_start: 0.8154 (tm-30) cc_final: 0.7791 (tp30) outliers start: 35 outliers final: 21 residues processed: 260 average time/residue: 0.2015 time to fit residues: 69.2941 Evaluate side-chains 258 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 230 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 CYS Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 401 ASP Chi-restraints excluded: chain C residue 163 HIS Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 105 VAL Chi-restraints excluded: chain D residue 149 CYS Chi-restraints excluded: chain E residue 18 GLN Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 52 GLU Chi-restraints excluded: chain E residue 55 CYS Chi-restraints excluded: chain E residue 64 LEU Chi-restraints excluded: chain F residue 41 LEU Chi-restraints excluded: chain G residue 20 GLN Chi-restraints excluded: chain G residue 31 LEU Chi-restraints excluded: chain G residue 41 ASN Chi-restraints excluded: chain G residue 66 HIS Chi-restraints excluded: chain H residue 26 LEU Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 29 VAL Chi-restraints excluded: chain H residue 39 ASN Chi-restraints excluded: chain H residue 62 LEU Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain I residue 35 CYS Chi-restraints excluded: chain J residue 32 MET Chi-restraints excluded: chain J residue 44 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 81 optimal weight: 0.7980 chunk 34 optimal weight: 0.5980 chunk 59 optimal weight: 0.8980 chunk 44 optimal weight: 0.6980 chunk 50 optimal weight: 0.0050 chunk 78 optimal weight: 1.9990 chunk 65 optimal weight: 0.3980 chunk 35 optimal weight: 0.8980 chunk 67 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 chunk 83 optimal weight: 0.8980 overall best weight: 0.4994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 ASN D 168 ASN ** G 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 20 GLN I 30 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.075096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.061273 restraints weight = 30109.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.062912 restraints weight = 16876.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.064048 restraints weight = 11417.072| |-----------------------------------------------------------------------------| r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.4378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 8130 Z= 0.153 Angle : 0.751 12.306 10929 Z= 0.387 Chirality : 0.041 0.225 1185 Planarity : 0.004 0.054 1392 Dihedral : 5.150 43.546 1074 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.86 % Favored : 95.04 % Rotamer: Outliers : 4.01 % Allowed : 25.20 % Favored : 70.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.17 % Twisted General : 0.10 % 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: 1.32 (0.26), residues: 967 helix: 1.67 (0.18), residues: 757 sheet: 0.20 (1.06), residues: 22 loop : -2.39 (0.41), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 106 HIS 0.005 0.001 HIS C 163 PHE 0.038 0.001 PHE C 107 TYR 0.035 0.001 TYR C 151 ARG 0.004 0.000 ARG I 26 Details of bonding type rmsd hydrogen bonds : bond 0.04391 ( 611) hydrogen bonds : angle 4.26092 ( 1827) SS BOND : bond 0.00327 ( 13) SS BOND : angle 2.05800 ( 26) covalent geometry : bond 0.00340 ( 8117) covalent geometry : angle 0.74526 (10903) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 244 time to evaluate : 1.525 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 GLU cc_start: 0.7583 (tm-30) cc_final: 0.7152 (tm-30) REVERT: A 45 LYS cc_start: 0.8778 (mmtt) cc_final: 0.8471 (mmtm) REVERT: A 140 GLU cc_start: 0.8276 (tm-30) cc_final: 0.7761 (tm-30) REVERT: A 194 LYS cc_start: 0.8899 (tppp) cc_final: 0.8638 (mptt) REVERT: B 39 MET cc_start: 0.4062 (mtm) cc_final: 0.3546 (tmm) REVERT: B 82 LYS cc_start: 0.8343 (mmpt) cc_final: 0.7984 (tptt) REVERT: C 163 HIS cc_start: 0.8711 (OUTLIER) cc_final: 0.8057 (t70) REVERT: D 64 MET cc_start: 0.6074 (OUTLIER) cc_final: 0.5456 (tmm) REVERT: D 78 GLN cc_start: 0.8455 (tm-30) cc_final: 0.7877 (tm-30) REVERT: D 111 ASP cc_start: 0.8100 (t0) cc_final: 0.7471 (t0) REVERT: D 123 GLN cc_start: 0.8509 (tm-30) cc_final: 0.8111 (tm-30) REVERT: D 155 MET cc_start: 0.7713 (mmt) cc_final: 0.7496 (mmp) REVERT: D 165 GLU cc_start: 0.8472 (mm-30) cc_final: 0.7911 (mm-30) REVERT: E 18 GLN cc_start: 0.8403 (OUTLIER) cc_final: 0.8141 (mp10) REVERT: E 52 GLU cc_start: 0.8678 (OUTLIER) cc_final: 0.7932 (mp0) REVERT: E 64 LEU cc_start: 0.8488 (OUTLIER) cc_final: 0.8238 (mm) REVERT: E 73 ARG cc_start: 0.7884 (tpp-160) cc_final: 0.7630 (ttm-80) REVERT: F 27 ASP cc_start: 0.8684 (m-30) cc_final: 0.8329 (m-30) REVERT: F 60 GLN cc_start: 0.8470 (mt0) cc_final: 0.7945 (mt0) REVERT: G 22 LYS cc_start: 0.8914 (tptp) cc_final: 0.8646 (tptt) REVERT: G 42 ASP cc_start: 0.7602 (t0) cc_final: 0.7260 (t0) REVERT: H 39 ASN cc_start: 0.7682 (m110) cc_final: 0.6444 (m110) REVERT: H 59 SER cc_start: 0.8838 (m) cc_final: 0.8399 (p) REVERT: H 62 LEU cc_start: 0.8999 (OUTLIER) cc_final: 0.8671 (mm) REVERT: I 7 LYS cc_start: 0.8782 (ptmm) cc_final: 0.8306 (tptp) REVERT: I 10 GLN cc_start: 0.8353 (pm20) cc_final: 0.7822 (pm20) REVERT: I 33 GLU cc_start: 0.8064 (tm-30) cc_final: 0.7824 (tp30) outliers start: 35 outliers final: 22 residues processed: 260 average time/residue: 0.2082 time to fit residues: 71.3445 Evaluate side-chains 254 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 226 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 CYS Chi-restraints excluded: chain A residue 129 PHE Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 401 ASP Chi-restraints excluded: chain C residue 163 HIS Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain D residue 64 MET Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 105 VAL Chi-restraints excluded: chain D residue 149 CYS Chi-restraints excluded: chain E residue 18 GLN Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 52 GLU Chi-restraints excluded: chain E residue 55 CYS Chi-restraints excluded: chain E residue 64 LEU Chi-restraints excluded: chain F residue 31 SER Chi-restraints excluded: chain F residue 41 LEU Chi-restraints excluded: chain G residue 31 LEU Chi-restraints excluded: chain G residue 41 ASN Chi-restraints excluded: chain G residue 66 HIS Chi-restraints excluded: chain H residue 26 LEU Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 29 VAL Chi-restraints excluded: chain H residue 62 LEU Chi-restraints excluded: chain I residue 35 CYS Chi-restraints excluded: chain J residue 32 MET Chi-restraints excluded: chain J residue 72 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 33 optimal weight: 0.6980 chunk 50 optimal weight: 7.9990 chunk 90 optimal weight: 0.5980 chunk 86 optimal weight: 0.7980 chunk 45 optimal weight: 3.9990 chunk 19 optimal weight: 0.7980 chunk 94 optimal weight: 0.6980 chunk 29 optimal weight: 3.9990 chunk 58 optimal weight: 4.9990 chunk 4 optimal weight: 4.9990 chunk 42 optimal weight: 0.1980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 20 GLN H 46 ASN H 79 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.074739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.062300 restraints weight = 30678.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.063436 restraints weight = 15913.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.063831 restraints weight = 13439.833| |-----------------------------------------------------------------------------| r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.4461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 8130 Z= 0.159 Angle : 0.793 12.962 10929 Z= 0.405 Chirality : 0.042 0.227 1185 Planarity : 0.004 0.055 1392 Dihedral : 5.104 43.063 1074 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.55 % Favored : 95.35 % Rotamer: Outliers : 3.55 % Allowed : 26.35 % Favored : 70.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.17 % Twisted General : 0.10 % 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: 1.36 (0.26), residues: 967 helix: 1.69 (0.18), residues: 758 sheet: 0.31 (1.06), residues: 22 loop : -2.38 (0.41), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 106 HIS 0.006 0.001 HIS C 163 PHE 0.040 0.001 PHE C 107 TYR 0.044 0.001 TYR C 151 ARG 0.007 0.000 ARG I 26 Details of bonding type rmsd hydrogen bonds : bond 0.04368 ( 611) hydrogen bonds : angle 4.26755 ( 1827) SS BOND : bond 0.00651 ( 13) SS BOND : angle 2.58064 ( 26) covalent geometry : bond 0.00361 ( 8117) covalent geometry : angle 0.78390 (10903) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 237 time to evaluate : 0.875 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 GLU cc_start: 0.7589 (tm-30) cc_final: 0.7157 (tm-30) REVERT: A 45 LYS cc_start: 0.8739 (mmtt) cc_final: 0.8436 (mmtm) REVERT: A 140 GLU cc_start: 0.8248 (tm-30) cc_final: 0.7815 (tm-30) REVERT: A 194 LYS cc_start: 0.8970 (tppp) cc_final: 0.8645 (mptt) REVERT: B 39 MET cc_start: 0.4239 (mtm) cc_final: 0.3648 (tmm) REVERT: B 82 LYS cc_start: 0.8447 (mmpt) cc_final: 0.8084 (tptt) REVERT: C 163 HIS cc_start: 0.8735 (OUTLIER) cc_final: 0.8133 (t70) REVERT: D 78 GLN cc_start: 0.8474 (tm-30) cc_final: 0.7881 (tm-30) REVERT: D 111 ASP cc_start: 0.8134 (t0) cc_final: 0.7496 (t0) REVERT: D 123 GLN cc_start: 0.8514 (tm-30) cc_final: 0.8086 (tm-30) REVERT: D 155 MET cc_start: 0.7752 (mmt) cc_final: 0.7539 (mmp) REVERT: D 165 GLU cc_start: 0.8507 (mm-30) cc_final: 0.7911 (mm-30) REVERT: E 18 GLN cc_start: 0.8470 (OUTLIER) cc_final: 0.8182 (mp10) REVERT: E 52 GLU cc_start: 0.8717 (OUTLIER) cc_final: 0.7969 (mp0) REVERT: E 64 LEU cc_start: 0.8513 (OUTLIER) cc_final: 0.8241 (mm) REVERT: F 27 ASP cc_start: 0.8785 (m-30) cc_final: 0.8479 (m-30) REVERT: F 60 GLN cc_start: 0.8448 (mt0) cc_final: 0.7984 (mt0) REVERT: G 20 GLN cc_start: 0.9094 (OUTLIER) cc_final: 0.8806 (pt0) REVERT: G 22 LYS cc_start: 0.8929 (tptp) cc_final: 0.8689 (tptt) REVERT: G 42 ASP cc_start: 0.7714 (t0) cc_final: 0.7322 (t0) REVERT: H 42 LYS cc_start: 0.8674 (mtmm) cc_final: 0.8339 (ptpp) REVERT: H 59 SER cc_start: 0.8922 (m) cc_final: 0.8492 (p) REVERT: H 62 LEU cc_start: 0.9055 (OUTLIER) cc_final: 0.8699 (mm) REVERT: I 7 LYS cc_start: 0.8897 (ptmm) cc_final: 0.8421 (tptp) REVERT: J 23 GLU cc_start: 0.8864 (tp30) cc_final: 0.8661 (tp30) outliers start: 31 outliers final: 21 residues processed: 252 average time/residue: 0.2034 time to fit residues: 68.4008 Evaluate side-chains 254 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 227 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 CYS Chi-restraints excluded: chain A residue 129 PHE Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain B residue 401 ASP Chi-restraints excluded: chain C residue 163 HIS Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 105 VAL Chi-restraints excluded: chain D residue 149 CYS Chi-restraints excluded: chain E residue 18 GLN Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 52 GLU Chi-restraints excluded: chain E residue 55 CYS Chi-restraints excluded: chain E residue 64 LEU Chi-restraints excluded: chain F residue 31 SER Chi-restraints excluded: chain F residue 41 LEU Chi-restraints excluded: chain G residue 20 GLN Chi-restraints excluded: chain G residue 31 LEU Chi-restraints excluded: chain G residue 41 ASN Chi-restraints excluded: chain G residue 53 GLN Chi-restraints excluded: chain G residue 66 HIS Chi-restraints excluded: chain H residue 26 LEU Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 29 VAL Chi-restraints excluded: chain H residue 62 LEU Chi-restraints excluded: chain J residue 32 MET Chi-restraints excluded: chain J residue 72 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 28 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 35 optimal weight: 7.9990 chunk 84 optimal weight: 1.9990 chunk 75 optimal weight: 0.5980 chunk 91 optimal weight: 0.6980 chunk 12 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 39 optimal weight: 5.9990 chunk 89 optimal weight: 0.9980 chunk 54 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 20 GLN H 39 ASN ** I 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 66 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.074545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.062356 restraints weight = 30072.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.062733 restraints weight = 16308.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.063694 restraints weight = 12461.765| |-----------------------------------------------------------------------------| r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.4565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 8130 Z= 0.168 Angle : 0.815 13.069 10929 Z= 0.416 Chirality : 0.043 0.361 1185 Planarity : 0.004 0.081 1392 Dihedral : 5.152 43.427 1074 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.96 % Favored : 94.93 % Rotamer: Outliers : 2.98 % Allowed : 27.03 % Favored : 69.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.17 % Twisted General : 0.10 % 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: 1.37 (0.26), residues: 967 helix: 1.71 (0.18), residues: 758 sheet: 0.24 (1.06), residues: 22 loop : -2.41 (0.40), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 106 HIS 0.006 0.002 HIS C 163 PHE 0.015 0.001 PHE F 86 TYR 0.039 0.001 TYR C 151 ARG 0.017 0.001 ARG I 26 Details of bonding type rmsd hydrogen bonds : bond 0.04388 ( 611) hydrogen bonds : angle 4.31399 ( 1827) SS BOND : bond 0.00449 ( 13) SS BOND : angle 2.58466 ( 26) covalent geometry : bond 0.00389 ( 8117) covalent geometry : angle 0.80647 (10903) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 232 time to evaluate : 1.159 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 GLU cc_start: 0.7554 (tm-30) cc_final: 0.7069 (tm-30) REVERT: A 45 LYS cc_start: 0.8786 (mmtt) cc_final: 0.8519 (mmtm) REVERT: A 140 GLU cc_start: 0.8254 (tm-30) cc_final: 0.8034 (tm-30) REVERT: A 194 LYS cc_start: 0.8912 (tppp) cc_final: 0.8628 (mptt) REVERT: B 39 MET cc_start: 0.4262 (mtm) cc_final: 0.3672 (tmm) REVERT: B 82 LYS cc_start: 0.8287 (mmpt) cc_final: 0.7927 (tptt) REVERT: C 163 HIS cc_start: 0.8723 (OUTLIER) cc_final: 0.8126 (t70) REVERT: D 64 MET cc_start: 0.6034 (OUTLIER) cc_final: 0.5537 (tmm) REVERT: D 78 GLN cc_start: 0.8471 (tm-30) cc_final: 0.7885 (tm-30) REVERT: D 111 ASP cc_start: 0.8159 (t0) cc_final: 0.7541 (t0) REVERT: D 123 GLN cc_start: 0.8484 (tm-30) cc_final: 0.8086 (tm-30) REVERT: D 155 MET cc_start: 0.7692 (mmt) cc_final: 0.7481 (mmp) REVERT: D 165 GLU cc_start: 0.8491 (mm-30) cc_final: 0.8025 (mm-30) REVERT: E 18 GLN cc_start: 0.8394 (OUTLIER) cc_final: 0.8107 (mp10) REVERT: E 52 GLU cc_start: 0.8701 (OUTLIER) cc_final: 0.8044 (mp0) REVERT: E 73 ARG cc_start: 0.7864 (tpp-160) cc_final: 0.7609 (ttm-80) REVERT: F 27 ASP cc_start: 0.8738 (m-30) cc_final: 0.8463 (m-30) REVERT: F 60 GLN cc_start: 0.8461 (mt0) cc_final: 0.7848 (mp10) REVERT: G 22 LYS cc_start: 0.8902 (tptp) cc_final: 0.8674 (tptt) REVERT: G 42 ASP cc_start: 0.7600 (t0) cc_final: 0.7199 (t0) REVERT: H 42 LYS cc_start: 0.8598 (mtmm) cc_final: 0.8235 (ptpp) REVERT: H 59 SER cc_start: 0.8902 (m) cc_final: 0.8454 (p) REVERT: H 62 LEU cc_start: 0.9046 (OUTLIER) cc_final: 0.8723 (mm) REVERT: I 7 LYS cc_start: 0.8836 (ptmm) cc_final: 0.8486 (tmmt) REVERT: I 22 LYS cc_start: 0.8651 (tmtt) cc_final: 0.7240 (ttmm) outliers start: 26 outliers final: 18 residues processed: 246 average time/residue: 0.2174 time to fit residues: 70.7759 Evaluate side-chains 245 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 222 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 PHE Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain B residue 401 ASP Chi-restraints excluded: chain C residue 163 HIS Chi-restraints excluded: chain C residue 165 ILE Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain D residue 64 MET Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 105 VAL Chi-restraints excluded: chain D residue 149 CYS Chi-restraints excluded: chain E residue 18 GLN Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 52 GLU Chi-restraints excluded: chain E residue 55 CYS Chi-restraints excluded: chain F residue 31 SER Chi-restraints excluded: chain F residue 41 LEU Chi-restraints excluded: chain G residue 53 GLN Chi-restraints excluded: chain G residue 66 HIS Chi-restraints excluded: chain H residue 26 LEU Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 29 VAL Chi-restraints excluded: chain H residue 62 LEU Chi-restraints excluded: chain J residue 72 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 84 optimal weight: 7.9990 chunk 25 optimal weight: 4.9990 chunk 80 optimal weight: 3.9990 chunk 42 optimal weight: 0.8980 chunk 81 optimal weight: 0.3980 chunk 61 optimal weight: 0.0010 chunk 27 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 76 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 chunk 21 optimal weight: 3.9990 overall best weight: 0.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 20 GLN H 79 ASN ** I 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 66 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.074902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.061146 restraints weight = 30367.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.062731 restraints weight = 17007.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.063879 restraints weight = 11549.927| |-----------------------------------------------------------------------------| r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.4607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 8130 Z= 0.162 Angle : 0.825 16.692 10929 Z= 0.419 Chirality : 0.043 0.306 1185 Planarity : 0.004 0.045 1392 Dihedral : 4.950 43.835 1073 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.34 % Favored : 95.55 % Rotamer: Outliers : 3.44 % Allowed : 27.49 % Favored : 69.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.17 % Twisted General : 0.10 % 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: 1.36 (0.26), residues: 967 helix: 1.70 (0.18), residues: 761 sheet: 0.29 (1.07), residues: 22 loop : -2.49 (0.41), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 106 HIS 0.006 0.001 HIS C 163 PHE 0.024 0.001 PHE C 107 TYR 0.037 0.001 TYR C 151 ARG 0.006 0.000 ARG E 26 Details of bonding type rmsd hydrogen bonds : bond 0.04386 ( 611) hydrogen bonds : angle 4.34033 ( 1827) SS BOND : bond 0.00311 ( 13) SS BOND : angle 2.04059 ( 26) covalent geometry : bond 0.00370 ( 8117) covalent geometry : angle 0.81994 (10903) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3064.02 seconds wall clock time: 53 minutes 47.12 seconds (3227.12 seconds total)