Starting phenix.real_space_refine on Thu Jun 5 23:02:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zd4_39950/06_2025/8zd4_39950.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zd4_39950/06_2025/8zd4_39950.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8zd4_39950/06_2025/8zd4_39950.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zd4_39950/06_2025/8zd4_39950.map" model { file = "/net/cci-nas-00/data/ceres_data/8zd4_39950/06_2025/8zd4_39950.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zd4_39950/06_2025/8zd4_39950.cif" } resolution = 2.9 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= -0.002 sd= 0.106 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 26 5.16 5 C 4346 2.51 5 N 1147 2.21 5 O 1276 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 6795 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1588 Classifications: {'peptide': 202} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 192} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 1819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1819 Classifications: {'peptide': 224} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 11, 'TRANS': 210} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 1588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1588 Classifications: {'peptide': 202} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 192} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "G" Number of atoms: 1800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1800 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 11, 'TRANS': 208} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Time building chain proxies: 4.85, per 1000 atoms: 0.71 Number of scatterers: 6795 At special positions: 0 Unit cell: (93.5, 110, 113.3, 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 26 16.00 O 1276 8.00 N 1147 7.00 C 4346 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 43 " - pdb=" SG CYS A 111 " distance=2.03 Simple disulfide: pdb=" SG CYS A 157 " - pdb=" SG CYS A 208 " distance=2.04 Simple disulfide: pdb=" SG CYS B 41 " - pdb=" SG CYS B 113 " distance=2.04 Simple disulfide: pdb=" SG CYS D 43 " - pdb=" SG CYS D 111 " distance=2.04 Simple disulfide: pdb=" SG CYS D 157 " - pdb=" SG CYS D 208 " distance=2.04 Simple disulfide: pdb=" SG CYS G 41 " - pdb=" SG CYS G 113 " distance=2.05 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: 1.83 Conformation dependent library (CDL) restraints added in 970.8 milliseconds 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1612 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 24 sheets defined 7.5% alpha, 44.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.10 Creating SS restraints... Processing helix chain 'A' and resid 102 through 106 removed outlier: 4.120A pdb=" N SER A 106 " --> pdb=" O LEU A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 223 removed outlier: 3.586A pdb=" N PHE A 222 " --> pdb=" O SER A 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 108 removed outlier: 3.940A pdb=" N SER B 108 " --> pdb=" O GLU B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 165 removed outlier: 3.838A pdb=" N LEU B 163 " --> pdb=" O ALA B 159 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLN B 164 " --> pdb=" O GLU B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 221 removed outlier: 3.647A pdb=" N LEU B 221 " --> pdb=" O GLU B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 238 Processing helix chain 'D' and resid 202 through 206 removed outlier: 3.903A pdb=" N SER D 205 " --> pdb=" O ASP D 202 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N VAL D 206 " --> pdb=" O SER D 203 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 202 through 206' Processing helix chain 'D' and resid 219 through 223 removed outlier: 3.643A pdb=" N GLU D 223 " --> pdb=" O THR D 220 " (cutoff:3.500A) Processing helix chain 'G' and resid 104 through 108 removed outlier: 3.822A pdb=" N SER G 108 " --> pdb=" O GLU G 105 " (cutoff:3.500A) Processing helix chain 'G' and resid 157 through 165 removed outlier: 3.848A pdb=" N THR G 161 " --> pdb=" O SER G 157 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LYS G 162 " --> pdb=" O ILE G 158 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU G 163 " --> pdb=" O ALA G 159 " (cutoff:3.500A) Processing helix chain 'G' and resid 219 through 221 No H-bonds generated for 'chain 'G' and resid 219 through 221' Processing helix chain 'G' and resid 234 through 238 removed outlier: 3.586A pdb=" N VAL G 238 " --> pdb=" O LYS G 235 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 23 through 25 removed outlier: 3.537A pdb=" N LYS A 23 " --> pdb=" O GLU A 46 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU A 44 " --> pdb=" O THR A 25 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA A 95 " --> pdb=" O ASN A 86 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASN A 86 " --> pdb=" O ALA A 95 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 31 through 34 removed outlier: 3.552A pdb=" N GLU A 135 " --> pdb=" O MET A 33 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 64 through 70 removed outlier: 3.815A pdb=" N GLU A 64 " --> pdb=" O LEU A 60 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N TRP A 56 " --> pdb=" O LEU A 68 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ARG A 70 " --> pdb=" O ILE A 54 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ILE A 54 " --> pdb=" O ARG A 70 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N TYR A 53 " --> pdb=" O GLY A 114 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ASP A 115 " --> pdb=" O LYS A 123 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N LYS A 123 " --> pdb=" O ASP A 115 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 146 through 150 removed outlier: 3.582A pdb=" N LYS A 196 " --> pdb=" O CYS A 157 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N GLU A 161 " --> pdb=" O TYR A 192 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N TYR A 192 " --> pdb=" O GLU A 161 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 168 through 172 removed outlier: 4.131A pdb=" N ARG A 168 " --> pdb=" O GLN A 211 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N GLN A 211 " --> pdb=" O ARG A 168 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N THR A 207 " --> pdb=" O VAL A 172 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 176 through 179 removed outlier: 7.011A pdb=" N LYS A 199 " --> pdb=" O ILE A 177 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 27 through 31 removed outlier: 3.622A pdb=" N THR B 135 " --> pdb=" O LYS B 27 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 37 through 41 removed outlier: 3.746A pdb=" N CYS B 41 " --> pdb=" O TRP B 96 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N TRP B 96 " --> pdb=" O CYS B 41 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 74 through 77 removed outlier: 3.949A pdb=" N LYS B 74 " --> pdb=" O ASP B 69 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ASP B 69 " --> pdb=" O LYS B 74 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N TYR B 67 " --> pdb=" O VAL B 76 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N LEU B 66 " --> pdb=" O TRP B 53 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N TYR B 50 " --> pdb=" O TRP B 116 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N TRP B 116 " --> pdb=" O TYR B 50 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 150 through 154 removed outlier: 3.886A pdb=" N LEU B 170 " --> pdb=" O PHE B 154 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLY B 167 " --> pdb=" O VAL B 216 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N TYR B 208 " --> pdb=" O LYS B 175 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 150 through 154 removed outlier: 3.886A pdb=" N LEU B 170 " --> pdb=" O PHE B 154 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLY B 167 " --> pdb=" O VAL B 216 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N TYR B 208 " --> pdb=" O LYS B 175 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 183 through 186 removed outlier: 3.957A pdb=" N HIS B 225 " --> pdb=" O PHE B 244 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL B 229 " --> pdb=" O GLN B 240 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLN B 240 " --> pdb=" O VAL B 229 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 23 through 25 removed outlier: 3.727A pdb=" N LYS D 23 " --> pdb=" O GLU D 46 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL D 39 " --> pdb=" O ILE D 98 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 30 through 34 removed outlier: 3.565A pdb=" N LYS D 108 " --> pdb=" O GLN D 59 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N TYR D 53 " --> pdb=" O GLY D 114 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ILE D 69 " --> pdb=" O TRP D 56 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 30 through 34 removed outlier: 3.514A pdb=" N ASP D 115 " --> pdb=" O LYS D 123 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N LYS D 123 " --> pdb=" O ASP D 115 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 146 through 150 removed outlier: 4.206A pdb=" N GLU D 161 " --> pdb=" O TYR D 192 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N TYR D 192 " --> pdb=" O GLU D 161 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 168 through 172 removed outlier: 3.533A pdb=" N GLN D 211 " --> pdb=" O ARG D 168 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N THR D 207 " --> pdb=" O VAL D 172 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 178 through 179 removed outlier: 3.784A pdb=" N THR D 178 " --> pdb=" O LYS D 199 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 27 through 32 removed outlier: 3.577A pdb=" N TYR G 54 " --> pdb=" O TYR G 112 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N TRP G 116 " --> pdb=" O TYR G 50 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N TYR G 50 " --> pdb=" O TRP G 116 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N ILE G 51 " --> pdb=" O TYR G 67 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N TYR G 67 " --> pdb=" O ILE G 51 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N TRP G 53 " --> pdb=" O LEU G 65 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N TYR G 67 " --> pdb=" O VAL G 76 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 27 through 32 Processing sheet with id=AC3, first strand: chain 'G' and resid 37 through 40 removed outlier: 7.528A pdb=" N SER G 95 " --> pdb=" O PRO G 91 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 150 through 154 removed outlier: 3.737A pdb=" N LEU G 170 " --> pdb=" O PHE G 154 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 150 through 154 removed outlier: 3.737A pdb=" N LEU G 170 " --> pdb=" O PHE G 154 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 182 through 186 removed outlier: 4.127A pdb=" N HIS G 225 " --> pdb=" O PHE G 244 " (cutoff:3.500A) 248 hydrogen bonds defined for protein. 624 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: 1.94 Time building geometry restraints manager: 1.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 2083 1.34 - 1.46: 1454 1.46 - 1.58: 3389 1.58 - 1.70: 1 1.70 - 1.82: 36 Bond restraints: 6963 Sorted by residual: bond pdb=" CG PRO A 61 " pdb=" CD PRO A 61 " ideal model delta sigma weight residual 1.503 1.273 0.230 3.40e-02 8.65e+02 4.59e+01 bond pdb=" N PRO A 61 " pdb=" CA PRO A 61 " ideal model delta sigma weight residual 1.470 1.500 -0.030 1.22e-02 6.72e+03 6.08e+00 bond pdb=" C PRO B 149 " pdb=" N LYS B 150 " ideal model delta sigma weight residual 1.327 1.358 -0.031 1.32e-02 5.74e+03 5.54e+00 bond pdb=" CB PRO A 164 " pdb=" CG PRO A 164 " ideal model delta sigma weight residual 1.506 1.597 -0.091 3.90e-02 6.57e+02 5.39e+00 bond pdb=" N PRO A 61 " pdb=" CD PRO A 61 " ideal model delta sigma weight residual 1.473 1.503 -0.030 1.40e-02 5.10e+03 4.49e+00 ... (remaining 6958 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.40: 9400 4.40 - 8.80: 36 8.80 - 13.20: 4 13.20 - 17.59: 1 17.59 - 21.99: 2 Bond angle restraints: 9443 Sorted by residual: angle pdb=" N PRO A 61 " pdb=" CD PRO A 61 " pdb=" CG PRO A 61 " ideal model delta sigma weight residual 103.20 83.46 19.74 1.50e+00 4.44e-01 1.73e+02 angle pdb=" CA PRO A 164 " pdb=" N PRO A 164 " pdb=" CD PRO A 164 " ideal model delta sigma weight residual 111.50 95.19 16.31 1.40e+00 5.10e-01 1.36e+02 angle pdb=" CA PRO A 61 " pdb=" CB PRO A 61 " pdb=" CG PRO A 61 " ideal model delta sigma weight residual 104.50 82.51 21.99 1.90e+00 2.77e-01 1.34e+02 angle pdb=" CA PRO A 61 " pdb=" N PRO A 61 " pdb=" CD PRO A 61 " ideal model delta sigma weight residual 112.00 102.40 9.60 1.40e+00 5.10e-01 4.70e+01 angle pdb=" N PRO A 61 " pdb=" CA PRO A 61 " pdb=" CB PRO A 61 " ideal model delta sigma weight residual 103.19 97.05 6.14 1.00e+00 1.00e+00 3.77e+01 ... (remaining 9438 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 3644 17.86 - 35.72: 420 35.72 - 53.59: 103 53.59 - 71.45: 20 71.45 - 89.31: 10 Dihedral angle restraints: 4197 sinusoidal: 1697 harmonic: 2500 Sorted by residual: dihedral pdb=" CB CYS G 41 " pdb=" SG CYS G 41 " pdb=" SG CYS G 113 " pdb=" CB CYS G 113 " ideal model delta sinusoidal sigma weight residual -86.00 -149.85 63.85 1 1.00e+01 1.00e-02 5.37e+01 dihedral pdb=" CA TYR G 169 " pdb=" C TYR G 169 " pdb=" N LEU G 170 " pdb=" CA LEU G 170 " ideal model delta harmonic sigma weight residual -180.00 -149.41 -30.59 0 5.00e+00 4.00e-02 3.74e+01 dihedral pdb=" CB CYS D 157 " pdb=" SG CYS D 157 " pdb=" SG CYS D 208 " pdb=" CB CYS D 208 " ideal model delta sinusoidal sigma weight residual -86.00 -41.26 -44.74 1 1.00e+01 1.00e-02 2.78e+01 ... (remaining 4194 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 631 0.039 - 0.079: 273 0.079 - 0.118: 102 0.118 - 0.157: 33 0.157 - 0.197: 8 Chirality restraints: 1047 Sorted by residual: chirality pdb=" CA ASP A 115 " pdb=" N ASP A 115 " pdb=" C ASP A 115 " pdb=" CB ASP A 115 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.68e-01 chirality pdb=" CA PHE G 177 " pdb=" N PHE G 177 " pdb=" C PHE G 177 " pdb=" CB PHE G 177 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 8.75e-01 chirality pdb=" CA TYR G 169 " pdb=" N TYR G 169 " pdb=" C TYR G 169 " pdb=" CB TYR G 169 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.74e-01 ... (remaining 1044 not shown) Planarity restraints: 1187 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR A 163 " 0.085 5.00e-02 4.00e+02 1.16e-01 2.16e+01 pdb=" N PRO A 164 " -0.200 5.00e-02 4.00e+02 pdb=" CA PRO A 164 " 0.067 5.00e-02 4.00e+02 pdb=" CD PRO A 164 " 0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASP A 115 " -0.014 2.00e-02 2.50e+03 2.82e-02 7.97e+00 pdb=" CG ASP A 115 " 0.049 2.00e-02 2.50e+03 pdb=" OD1 ASP A 115 " -0.018 2.00e-02 2.50e+03 pdb=" OD2 ASP A 115 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A 187 " 0.040 5.00e-02 4.00e+02 6.01e-02 5.78e+00 pdb=" N PRO A 188 " -0.104 5.00e-02 4.00e+02 pdb=" CA PRO A 188 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 188 " 0.034 5.00e-02 4.00e+02 ... (remaining 1184 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 699 2.75 - 3.29: 5766 3.29 - 3.82: 10007 3.82 - 4.36: 11552 4.36 - 4.90: 21286 Nonbonded interactions: 49310 Sorted by model distance: nonbonded pdb=" O TYR A 52 " pdb=" OG SER A 73 " model vdw 2.208 3.040 nonbonded pdb=" O THR G 204 " pdb=" OG1 THR G 204 " model vdw 2.209 3.040 nonbonded pdb=" OG1 THR G 139 " pdb=" OE1 GLN G 142 " model vdw 2.216 3.040 nonbonded pdb=" NH1 ARG B 101 " pdb=" O SER G 73 " model vdw 2.220 3.120 nonbonded pdb=" OG SER A 173 " pdb=" OD2 ASP A 202 " model vdw 2.234 3.040 ... (remaining 49305 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 22 through 150 or (resid 151 and (name N or name CA or nam \ e C or name O or name CB )) or resid 152 through 218 or (resid 219 and (name N o \ r name CA or name C or name O or name CB )) or resid 220 through 223)) selection = (chain 'D' and (resid 22 through 164 or (resid 165 and (name N or name CA or nam \ e C or name O or name CB )) or resid 166 through 223)) } ncs_group { reference = (chain 'B' and (resid 25 through 209 or (resid 210 and (name N or name CA or nam \ e C or name O or name CB )) or resid 211 through 240 or (resid 241 and (name N o \ r name CA or name C or name O or name CB )) or resid 242 through 246)) selection = (chain 'G' and (resid 25 through 63 or (resid 64 and (name N or name CA or name \ C or name O or name CB )) or resid 65 through 246)) } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 20.470 Find NCS groups from input model: 0.290 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:12.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7078 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 0.230 6969 Z= 0.272 Angle : 0.943 21.993 9455 Z= 0.542 Chirality : 0.053 0.197 1047 Planarity : 0.007 0.116 1187 Dihedral : 16.490 89.311 2567 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.84 % Favored : 92.04 % Rotamer: Outliers : 5.51 % Allowed : 23.75 % Favored : 70.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -1.14 (0.28), residues: 842 helix: None (None), residues: 0 sheet: -0.00 (0.28), residues: 379 loop : -1.44 (0.27), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP B 185 HIS 0.013 0.002 HIS B 89 PHE 0.030 0.003 PHE G 244 TYR 0.033 0.003 TYR G 169 ARG 0.007 0.001 ARG D 70 Details of bonding type rmsd hydrogen bonds : bond 0.31835 ( 207) hydrogen bonds : angle 11.50798 ( 624) SS BOND : bond 0.01176 ( 6) SS BOND : angle 1.67422 ( 12) covalent geometry : bond 0.00643 ( 6963) covalent geometry : angle 0.94159 ( 9443) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 93 time to evaluate : 0.833 Fit side-chains outliers start: 42 outliers final: 34 residues processed: 126 average time/residue: 0.7705 time to fit residues: 104.9856 Evaluate side-chains 115 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 81 time to evaluate : 0.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 52 TYR Chi-restraints excluded: chain A residue 61 PRO Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 78 GLU Chi-restraints excluded: chain B residue 79 SER Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain B residue 239 ASP Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 122 ASP Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 187 SER Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 216 THR Chi-restraints excluded: chain G residue 71 SER Chi-restraints excluded: chain G residue 77 LEU Chi-restraints excluded: chain G residue 100 LEU Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain G residue 132 SER Chi-restraints excluded: chain G residue 137 VAL Chi-restraints excluded: chain G residue 170 LEU Chi-restraints excluded: chain G residue 180 VAL Chi-restraints excluded: chain G residue 183 ILE Chi-restraints excluded: chain G residue 204 THR Chi-restraints excluded: chain G residue 221 LEU Chi-restraints excluded: chain G residue 229 VAL Chi-restraints excluded: chain G residue 238 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 70 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 35 optimal weight: 0.1980 chunk 21 optimal weight: 0.0570 chunk 42 optimal weight: 8.9990 chunk 34 optimal weight: 2.9990 chunk 65 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 49 optimal weight: 9.9990 chunk 76 optimal weight: 0.9980 overall best weight: 0.8500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 GLN A 120 ASN ** B 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 197 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4605 r_free = 0.4605 target = 0.214458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 89)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.147172 restraints weight = 6979.748| |-----------------------------------------------------------------------------| r_work (start): 0.3877 rms_B_bonded: 2.87 r_work: 0.3697 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7081 moved from start: 0.1078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6969 Z= 0.141 Angle : 0.663 7.066 9455 Z= 0.355 Chirality : 0.049 0.196 1047 Planarity : 0.005 0.061 1187 Dihedral : 7.958 58.157 965 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.82 % Favored : 94.06 % Rotamer: Outliers : 6.82 % Allowed : 21.78 % Favored : 71.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.29), residues: 842 helix: 1.09 (2.24), residues: 6 sheet: 0.27 (0.28), residues: 384 loop : -1.42 (0.27), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 94 HIS 0.005 0.001 HIS B 89 PHE 0.016 0.002 PHE G 176 TYR 0.028 0.002 TYR G 169 ARG 0.003 0.000 ARG G 64 Details of bonding type rmsd hydrogen bonds : bond 0.05168 ( 207) hydrogen bonds : angle 7.70745 ( 624) SS BOND : bond 0.00883 ( 6) SS BOND : angle 1.41945 ( 12) covalent geometry : bond 0.00319 ( 6963) covalent geometry : angle 0.66102 ( 9443) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 95 time to evaluate : 0.817 Fit side-chains REVERT: A 50 TRP cc_start: 0.5994 (OUTLIER) cc_final: 0.5182 (t60) REVERT: A 153 THR cc_start: 0.7409 (m) cc_final: 0.7119 (t) REVERT: D 25 THR cc_start: 0.7565 (OUTLIER) cc_final: 0.7321 (m) REVERT: G 140 ASP cc_start: 0.6952 (OUTLIER) cc_final: 0.6746 (m-30) outliers start: 52 outliers final: 30 residues processed: 133 average time/residue: 0.7651 time to fit residues: 110.0176 Evaluate side-chains 118 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 85 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 50 TRP Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 181 ILE Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 122 ASP Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 187 SER Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 208 CYS Chi-restraints excluded: chain G residue 27 LYS Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 77 LEU Chi-restraints excluded: chain G residue 100 LEU Chi-restraints excluded: chain G residue 108 SER Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain G residue 137 VAL Chi-restraints excluded: chain G residue 140 ASP Chi-restraints excluded: chain G residue 155 LEU Chi-restraints excluded: chain G residue 169 TYR Chi-restraints excluded: chain G residue 170 LEU Chi-restraints excluded: chain G residue 180 VAL Chi-restraints excluded: chain G residue 207 THR Chi-restraints excluded: chain G residue 229 VAL Chi-restraints excluded: chain G residue 238 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 67 optimal weight: 4.9990 chunk 31 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 55 optimal weight: 5.9990 chunk 61 optimal weight: 5.9990 chunk 28 optimal weight: 0.9990 chunk 19 optimal weight: 20.0000 chunk 62 optimal weight: 0.6980 chunk 81 optimal weight: 0.1980 chunk 63 optimal weight: 1.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 ASN B 197 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4637 r_free = 0.4637 target = 0.217086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 92)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.149828 restraints weight = 7087.692| |-----------------------------------------------------------------------------| r_work (start): 0.3870 rms_B_bonded: 2.78 r_work: 0.3682 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7128 moved from start: 0.1378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6969 Z= 0.139 Angle : 0.635 6.430 9455 Z= 0.338 Chirality : 0.049 0.193 1047 Planarity : 0.005 0.073 1187 Dihedral : 7.108 57.549 942 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.13 % Favored : 92.76 % Rotamer: Outliers : 6.56 % Allowed : 22.31 % Favored : 71.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.29), residues: 842 helix: 1.67 (2.42), residues: 6 sheet: 0.33 (0.27), residues: 396 loop : -1.46 (0.28), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP G 116 HIS 0.006 0.001 HIS B 89 PHE 0.017 0.002 PHE G 176 TYR 0.026 0.002 TYR G 169 ARG 0.002 0.000 ARG A 168 Details of bonding type rmsd hydrogen bonds : bond 0.04448 ( 207) hydrogen bonds : angle 6.91738 ( 624) SS BOND : bond 0.00793 ( 6) SS BOND : angle 1.40831 ( 12) covalent geometry : bond 0.00318 ( 6963) covalent geometry : angle 0.63313 ( 9443) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 91 time to evaluate : 0.888 Fit side-chains REVERT: A 50 TRP cc_start: 0.5990 (OUTLIER) cc_final: 0.5180 (t60) REVERT: A 153 THR cc_start: 0.7342 (m) cc_final: 0.7066 (t) REVERT: B 225 HIS cc_start: 0.3554 (OUTLIER) cc_final: 0.2813 (m90) REVERT: B 241 GLU cc_start: 0.7405 (mm-30) cc_final: 0.7176 (mm-30) REVERT: D 25 THR cc_start: 0.7557 (OUTLIER) cc_final: 0.7227 (m) REVERT: D 120 ASN cc_start: 0.8037 (OUTLIER) cc_final: 0.7622 (t0) REVERT: G 198 GLU cc_start: 0.6782 (OUTLIER) cc_final: 0.6350 (tm-30) outliers start: 50 outliers final: 35 residues processed: 127 average time/residue: 0.8316 time to fit residues: 113.6388 Evaluate side-chains 123 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 83 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 50 TRP Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain A residue 80 SER Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain B residue 108 SER Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 181 ILE Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 120 ASN Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 122 ASP Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 208 CYS Chi-restraints excluded: chain D residue 216 THR Chi-restraints excluded: chain G residue 27 LYS Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 77 LEU Chi-restraints excluded: chain G residue 100 LEU Chi-restraints excluded: chain G residue 108 SER Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain G residue 132 SER Chi-restraints excluded: chain G residue 137 VAL Chi-restraints excluded: chain G residue 155 LEU Chi-restraints excluded: chain G residue 169 TYR Chi-restraints excluded: chain G residue 198 GLU Chi-restraints excluded: chain G residue 207 THR Chi-restraints excluded: chain G residue 221 LEU Chi-restraints excluded: chain G residue 229 VAL Chi-restraints excluded: chain G residue 238 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 24 optimal weight: 3.9990 chunk 13 optimal weight: 10.0000 chunk 51 optimal weight: 5.9990 chunk 21 optimal weight: 4.9990 chunk 77 optimal weight: 0.9990 chunk 17 optimal weight: 6.9990 chunk 20 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 36 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 66 optimal weight: 3.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 ASN A 218 HIS ** B 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 211 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4601 r_free = 0.4601 target = 0.213227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.145697 restraints weight = 7062.870| |-----------------------------------------------------------------------------| r_work (start): 0.3831 rms_B_bonded: 2.74 r_work: 0.3634 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7205 moved from start: 0.1358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 6969 Z= 0.251 Angle : 0.766 7.778 9455 Z= 0.408 Chirality : 0.053 0.201 1047 Planarity : 0.006 0.072 1187 Dihedral : 7.596 56.803 936 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.19 % Favored : 91.69 % Rotamer: Outliers : 10.24 % Allowed : 19.42 % Favored : 70.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.28), residues: 842 helix: 2.29 (2.66), residues: 6 sheet: 0.17 (0.28), residues: 386 loop : -1.69 (0.26), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP G 94 HIS 0.012 0.002 HIS B 89 PHE 0.026 0.003 PHE G 176 TYR 0.044 0.003 TYR G 169 ARG 0.004 0.001 ARG G 31 Details of bonding type rmsd hydrogen bonds : bond 0.05429 ( 207) hydrogen bonds : angle 6.95739 ( 624) SS BOND : bond 0.01389 ( 6) SS BOND : angle 1.80968 ( 12) covalent geometry : bond 0.00594 ( 6963) covalent geometry : angle 0.76363 ( 9443) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 89 time to evaluate : 0.856 Fit side-chains REVERT: A 50 TRP cc_start: 0.5891 (OUTLIER) cc_final: 0.5077 (t60) REVERT: A 153 THR cc_start: 0.7364 (m) cc_final: 0.7094 (t) REVERT: B 225 HIS cc_start: 0.3556 (OUTLIER) cc_final: 0.2919 (m90) REVERT: B 241 GLU cc_start: 0.7270 (mm-30) cc_final: 0.7053 (mm-30) REVERT: D 120 ASN cc_start: 0.8023 (OUTLIER) cc_final: 0.7512 (t0) REVERT: D 179 GLU cc_start: 0.7417 (OUTLIER) cc_final: 0.7112 (tt0) REVERT: G 198 GLU cc_start: 0.6865 (OUTLIER) cc_final: 0.6334 (tm-30) outliers start: 78 outliers final: 49 residues processed: 147 average time/residue: 0.9212 time to fit residues: 145.7839 Evaluate side-chains 131 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 77 time to evaluate : 1.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 50 TRP Chi-restraints excluded: chain A residue 52 TYR Chi-restraints excluded: chain A residue 80 SER Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 149 MET Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 108 SER Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 181 ILE Chi-restraints excluded: chain B residue 202 MET Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 120 ASN Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 122 ASP Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 179 GLU Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 208 CYS Chi-restraints excluded: chain D residue 216 THR Chi-restraints excluded: chain G residue 27 LYS Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 77 LEU Chi-restraints excluded: chain G residue 100 LEU Chi-restraints excluded: chain G residue 108 SER Chi-restraints excluded: chain G residue 113 CYS Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain G residue 132 SER Chi-restraints excluded: chain G residue 137 VAL Chi-restraints excluded: chain G residue 153 ILE Chi-restraints excluded: chain G residue 155 LEU Chi-restraints excluded: chain G residue 169 TYR Chi-restraints excluded: chain G residue 170 LEU Chi-restraints excluded: chain G residue 180 VAL Chi-restraints excluded: chain G residue 198 GLU Chi-restraints excluded: chain G residue 202 MET Chi-restraints excluded: chain G residue 207 THR Chi-restraints excluded: chain G residue 229 VAL Chi-restraints excluded: chain G residue 238 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 1 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 chunk 72 optimal weight: 0.8980 chunk 63 optimal weight: 0.9980 chunk 69 optimal weight: 0.5980 chunk 74 optimal weight: 0.2980 chunk 60 optimal weight: 0.9980 chunk 7 optimal weight: 0.0870 chunk 75 optimal weight: 3.9990 chunk 14 optimal weight: 7.9990 chunk 54 optimal weight: 2.9990 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 ASN A 218 HIS B 197 GLN D 211 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4622 r_free = 0.4622 target = 0.216141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 95)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.153198 restraints weight = 7001.240| |-----------------------------------------------------------------------------| r_work (start): 0.3975 rms_B_bonded: 2.51 r_work: 0.3711 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7122 moved from start: 0.1704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 6969 Z= 0.121 Angle : 0.613 7.564 9455 Z= 0.325 Chirality : 0.048 0.178 1047 Planarity : 0.005 0.059 1187 Dihedral : 7.290 57.662 936 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.94 % Favored : 93.94 % Rotamer: Outliers : 6.43 % Allowed : 23.36 % Favored : 70.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.29), residues: 842 helix: 1.57 (2.55), residues: 6 sheet: 0.35 (0.27), residues: 395 loop : -1.47 (0.28), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 94 HIS 0.004 0.001 HIS B 184 PHE 0.014 0.002 PHE G 176 TYR 0.027 0.001 TYR G 169 ARG 0.004 0.000 ARG B 118 Details of bonding type rmsd hydrogen bonds : bond 0.03591 ( 207) hydrogen bonds : angle 6.45954 ( 624) SS BOND : bond 0.01039 ( 6) SS BOND : angle 2.06139 ( 12) covalent geometry : bond 0.00276 ( 6963) covalent geometry : angle 0.60891 ( 9443) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 96 time to evaluate : 0.734 Fit side-chains REVERT: A 50 TRP cc_start: 0.5852 (OUTLIER) cc_final: 0.5045 (t60) REVERT: A 153 THR cc_start: 0.7167 (m) cc_final: 0.6935 (t) REVERT: B 241 GLU cc_start: 0.7271 (mm-30) cc_final: 0.7011 (mm-30) REVERT: D 36 ARG cc_start: 0.7019 (tpp80) cc_final: 0.6785 (ttp-110) REVERT: D 120 ASN cc_start: 0.8038 (OUTLIER) cc_final: 0.7583 (t0) REVERT: G 182 LYS cc_start: 0.7804 (OUTLIER) cc_final: 0.7566 (tttm) outliers start: 49 outliers final: 31 residues processed: 137 average time/residue: 0.7896 time to fit residues: 116.6473 Evaluate side-chains 119 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 85 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 50 TRP Chi-restraints excluded: chain A residue 80 SER Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain B residue 78 GLU Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain D residue 120 ASN Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 122 ASP Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 216 THR Chi-restraints excluded: chain G residue 27 LYS Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 77 LEU Chi-restraints excluded: chain G residue 108 SER Chi-restraints excluded: chain G residue 113 CYS Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain G residue 132 SER Chi-restraints excluded: chain G residue 137 VAL Chi-restraints excluded: chain G residue 169 TYR Chi-restraints excluded: chain G residue 182 LYS Chi-restraints excluded: chain G residue 207 THR Chi-restraints excluded: chain G residue 229 VAL Chi-restraints excluded: chain G residue 238 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 63 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 chunk 1 optimal weight: 0.0980 chunk 11 optimal weight: 0.7980 chunk 48 optimal weight: 4.9990 chunk 31 optimal weight: 0.0670 chunk 53 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 chunk 14 optimal weight: 9.9990 chunk 78 optimal weight: 2.9990 chunk 18 optimal weight: 8.9990 overall best weight: 0.5720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4633 r_free = 0.4633 target = 0.216929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 93)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.149896 restraints weight = 7032.594| |-----------------------------------------------------------------------------| r_work (start): 0.3911 rms_B_bonded: 2.53 r_work: 0.3701 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7105 moved from start: 0.1896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6969 Z= 0.114 Angle : 0.594 6.821 9455 Z= 0.314 Chirality : 0.047 0.177 1047 Planarity : 0.005 0.062 1187 Dihedral : 7.046 59.601 934 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.18 % Favored : 93.71 % Rotamer: Outliers : 6.30 % Allowed : 24.15 % Favored : 69.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.29), residues: 842 helix: 0.87 (2.58), residues: 6 sheet: 0.42 (0.26), residues: 421 loop : -1.35 (0.29), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 94 HIS 0.003 0.001 HIS B 184 PHE 0.016 0.001 PHE A 67 TYR 0.026 0.001 TYR G 169 ARG 0.006 0.000 ARG D 70 Details of bonding type rmsd hydrogen bonds : bond 0.03361 ( 207) hydrogen bonds : angle 6.10564 ( 624) SS BOND : bond 0.00581 ( 6) SS BOND : angle 1.62805 ( 12) covalent geometry : bond 0.00267 ( 6963) covalent geometry : angle 0.59165 ( 9443) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 88 time to evaluate : 0.740 Fit side-chains REVERT: A 50 TRP cc_start: 0.5893 (OUTLIER) cc_final: 0.5081 (t60) REVERT: A 67 PHE cc_start: 0.7393 (OUTLIER) cc_final: 0.6599 (t80) REVERT: A 153 THR cc_start: 0.7280 (m) cc_final: 0.7038 (t) REVERT: B 241 GLU cc_start: 0.7230 (mm-30) cc_final: 0.7018 (mm-30) REVERT: D 120 ASN cc_start: 0.7982 (OUTLIER) cc_final: 0.7526 (t0) REVERT: D 179 GLU cc_start: 0.7378 (tp30) cc_final: 0.7074 (tt0) REVERT: G 182 LYS cc_start: 0.7817 (OUTLIER) cc_final: 0.7593 (tttm) outliers start: 48 outliers final: 32 residues processed: 126 average time/residue: 0.7805 time to fit residues: 106.2788 Evaluate side-chains 120 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 84 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 50 TRP Chi-restraints excluded: chain A residue 67 PHE Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 78 GLU Chi-restraints excluded: chain B residue 108 SER Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain D residue 120 ASN Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 169 ILE Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 216 THR Chi-restraints excluded: chain G residue 27 LYS Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 77 LEU Chi-restraints excluded: chain G residue 108 SER Chi-restraints excluded: chain G residue 113 CYS Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain G residue 132 SER Chi-restraints excluded: chain G residue 137 VAL Chi-restraints excluded: chain G residue 169 TYR Chi-restraints excluded: chain G residue 180 VAL Chi-restraints excluded: chain G residue 182 LYS Chi-restraints excluded: chain G residue 207 THR Chi-restraints excluded: chain G residue 229 VAL Chi-restraints excluded: chain G residue 238 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 2 optimal weight: 0.9990 chunk 31 optimal weight: 0.7980 chunk 23 optimal weight: 0.7980 chunk 14 optimal weight: 7.9990 chunk 79 optimal weight: 2.9990 chunk 40 optimal weight: 7.9990 chunk 67 optimal weight: 0.5980 chunk 72 optimal weight: 0.0970 chunk 53 optimal weight: 0.9990 chunk 63 optimal weight: 2.9990 chunk 80 optimal weight: 0.9980 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4630 r_free = 0.4630 target = 0.216893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 88)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.151255 restraints weight = 6964.995| |-----------------------------------------------------------------------------| r_work (start): 0.3916 rms_B_bonded: 2.82 r_work: 0.3703 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7090 moved from start: 0.2029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6969 Z= 0.116 Angle : 0.594 7.040 9455 Z= 0.313 Chirality : 0.047 0.181 1047 Planarity : 0.005 0.061 1187 Dihedral : 6.701 59.044 932 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.41 % Favored : 93.47 % Rotamer: Outliers : 6.82 % Allowed : 23.88 % Favored : 69.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.29), residues: 842 helix: 0.50 (2.62), residues: 6 sheet: 0.51 (0.26), residues: 421 loop : -1.29 (0.29), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 94 HIS 0.004 0.001 HIS B 89 PHE 0.015 0.002 PHE A 67 TYR 0.025 0.001 TYR G 169 ARG 0.005 0.000 ARG D 70 Details of bonding type rmsd hydrogen bonds : bond 0.03359 ( 207) hydrogen bonds : angle 5.87682 ( 624) SS BOND : bond 0.00640 ( 6) SS BOND : angle 1.35404 ( 12) covalent geometry : bond 0.00274 ( 6963) covalent geometry : angle 0.59195 ( 9443) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 88 time to evaluate : 0.762 Fit side-chains REVERT: A 50 TRP cc_start: 0.5885 (OUTLIER) cc_final: 0.5074 (t60) REVERT: A 67 PHE cc_start: 0.7304 (OUTLIER) cc_final: 0.6468 (t80) REVERT: A 80 SER cc_start: 0.5342 (OUTLIER) cc_final: 0.4907 (m) REVERT: A 153 THR cc_start: 0.7244 (m) cc_final: 0.7015 (t) REVERT: A 178 THR cc_start: 0.6761 (m) cc_final: 0.6435 (p) REVERT: A 199 LYS cc_start: 0.6569 (OUTLIER) cc_final: 0.6322 (ptpp) REVERT: B 226 ARG cc_start: 0.5537 (OUTLIER) cc_final: 0.4994 (mmm-85) REVERT: B 241 GLU cc_start: 0.7247 (mm-30) cc_final: 0.6947 (mm-30) REVERT: D 25 THR cc_start: 0.7427 (OUTLIER) cc_final: 0.7081 (m) REVERT: D 70 ARG cc_start: 0.7257 (ttm-80) cc_final: 0.6803 (ttp-170) REVERT: D 120 ASN cc_start: 0.8056 (OUTLIER) cc_final: 0.7600 (t0) REVERT: D 179 GLU cc_start: 0.7277 (tp30) cc_final: 0.6919 (tt0) REVERT: G 172 LEU cc_start: 0.6499 (OUTLIER) cc_final: 0.6297 (tp) outliers start: 52 outliers final: 35 residues processed: 129 average time/residue: 0.8004 time to fit residues: 111.5028 Evaluate side-chains 125 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 82 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 50 TRP Chi-restraints excluded: chain A residue 67 PHE Chi-restraints excluded: chain A residue 80 SER Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 199 LYS Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 78 GLU Chi-restraints excluded: chain B residue 108 SER Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 226 ARG Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 120 ASN Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 122 ASP Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 169 ILE Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 216 THR Chi-restraints excluded: chain G residue 27 LYS Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 77 LEU Chi-restraints excluded: chain G residue 108 SER Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain G residue 132 SER Chi-restraints excluded: chain G residue 137 VAL Chi-restraints excluded: chain G residue 153 ILE Chi-restraints excluded: chain G residue 172 LEU Chi-restraints excluded: chain G residue 180 VAL Chi-restraints excluded: chain G residue 207 THR Chi-restraints excluded: chain G residue 229 VAL Chi-restraints excluded: chain G residue 238 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 12 optimal weight: 10.0000 chunk 41 optimal weight: 0.1980 chunk 38 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 9 optimal weight: 8.9990 chunk 32 optimal weight: 0.7980 chunk 6 optimal weight: 10.0000 chunk 23 optimal weight: 0.9980 chunk 50 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 chunk 19 optimal weight: 6.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4633 r_free = 0.4633 target = 0.216864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 100)---------------| | r_work = 0.3963 r_free = 0.3963 target = 0.150677 restraints weight = 7052.802| |-----------------------------------------------------------------------------| r_work (start): 0.3932 rms_B_bonded: 2.35 r_work: 0.3710 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7110 moved from start: 0.2052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6969 Z= 0.124 Angle : 0.617 7.885 9455 Z= 0.323 Chirality : 0.048 0.207 1047 Planarity : 0.005 0.061 1187 Dihedral : 6.539 58.413 932 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.77 % Favored : 93.11 % Rotamer: Outliers : 6.43 % Allowed : 24.54 % Favored : 69.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.29), residues: 842 helix: -2.17 (2.05), residues: 6 sheet: 0.52 (0.26), residues: 425 loop : -1.28 (0.29), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 94 HIS 0.004 0.001 HIS B 89 PHE 0.015 0.002 PHE G 176 TYR 0.017 0.001 TYR G 169 ARG 0.006 0.000 ARG D 70 Details of bonding type rmsd hydrogen bonds : bond 0.03473 ( 207) hydrogen bonds : angle 5.85385 ( 624) SS BOND : bond 0.00733 ( 6) SS BOND : angle 1.45089 ( 12) covalent geometry : bond 0.00293 ( 6963) covalent geometry : angle 0.61515 ( 9443) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 87 time to evaluate : 0.873 Fit side-chains REVERT: A 50 TRP cc_start: 0.5926 (OUTLIER) cc_final: 0.5114 (t60) REVERT: A 67 PHE cc_start: 0.7341 (OUTLIER) cc_final: 0.6514 (t80) REVERT: A 80 SER cc_start: 0.5322 (OUTLIER) cc_final: 0.4901 (m) REVERT: A 153 THR cc_start: 0.7254 (m) cc_final: 0.7037 (t) REVERT: B 209 MET cc_start: 0.7645 (ppp) cc_final: 0.7353 (tmm) REVERT: B 226 ARG cc_start: 0.5638 (OUTLIER) cc_final: 0.5093 (mmm-85) REVERT: B 241 GLU cc_start: 0.7277 (mm-30) cc_final: 0.6943 (mm-30) REVERT: D 25 THR cc_start: 0.7435 (OUTLIER) cc_final: 0.7097 (m) REVERT: D 70 ARG cc_start: 0.7415 (ttm-80) cc_final: 0.7025 (ttp-170) REVERT: D 120 ASN cc_start: 0.8039 (OUTLIER) cc_final: 0.7575 (t0) REVERT: D 179 GLU cc_start: 0.7243 (tp30) cc_final: 0.6895 (tt0) outliers start: 49 outliers final: 35 residues processed: 125 average time/residue: 0.9205 time to fit residues: 124.7236 Evaluate side-chains 123 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 82 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 50 TRP Chi-restraints excluded: chain A residue 67 PHE Chi-restraints excluded: chain A residue 80 SER Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 78 GLU Chi-restraints excluded: chain B residue 108 SER Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 226 ARG Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 120 ASN Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 122 ASP Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 169 ILE Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 216 THR Chi-restraints excluded: chain G residue 27 LYS Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 77 LEU Chi-restraints excluded: chain G residue 108 SER Chi-restraints excluded: chain G residue 113 CYS Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain G residue 132 SER Chi-restraints excluded: chain G residue 137 VAL Chi-restraints excluded: chain G residue 153 ILE Chi-restraints excluded: chain G residue 170 LEU Chi-restraints excluded: chain G residue 180 VAL Chi-restraints excluded: chain G residue 207 THR Chi-restraints excluded: chain G residue 229 VAL Chi-restraints excluded: chain G residue 238 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 80 optimal weight: 0.9990 chunk 66 optimal weight: 4.9990 chunk 60 optimal weight: 0.9980 chunk 16 optimal weight: 8.9990 chunk 11 optimal weight: 0.7980 chunk 83 optimal weight: 3.9990 chunk 42 optimal weight: 10.0000 chunk 43 optimal weight: 2.9990 chunk 18 optimal weight: 9.9990 chunk 5 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 ASN D 211 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4595 r_free = 0.4595 target = 0.212968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.149141 restraints weight = 7064.396| |-----------------------------------------------------------------------------| r_work (start): 0.3907 rms_B_bonded: 2.65 r_work: 0.3650 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7122 moved from start: 0.1875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 6969 Z= 0.214 Angle : 0.732 7.912 9455 Z= 0.387 Chirality : 0.051 0.193 1047 Planarity : 0.006 0.066 1187 Dihedral : 6.964 58.207 932 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.19 % Favored : 91.69 % Rotamer: Outliers : 6.43 % Allowed : 24.67 % Favored : 68.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.29), residues: 842 helix: -1.75 (2.06), residues: 6 sheet: 0.41 (0.26), residues: 421 loop : -1.51 (0.28), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 185 HIS 0.009 0.002 HIS B 89 PHE 0.024 0.003 PHE G 176 TYR 0.036 0.002 TYR G 169 ARG 0.005 0.001 ARG D 70 Details of bonding type rmsd hydrogen bonds : bond 0.04672 ( 207) hydrogen bonds : angle 6.13726 ( 624) SS BOND : bond 0.01243 ( 6) SS BOND : angle 1.77517 ( 12) covalent geometry : bond 0.00505 ( 6963) covalent geometry : angle 0.72939 ( 9443) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 89 time to evaluate : 0.809 Fit side-chains REVERT: A 50 TRP cc_start: 0.5914 (OUTLIER) cc_final: 0.5091 (t60) REVERT: A 80 SER cc_start: 0.5307 (OUTLIER) cc_final: 0.4897 (m) REVERT: A 153 THR cc_start: 0.7407 (m) cc_final: 0.7152 (t) REVERT: B 209 MET cc_start: 0.7615 (ppp) cc_final: 0.7291 (tmm) REVERT: B 226 ARG cc_start: 0.5693 (OUTLIER) cc_final: 0.5068 (mmm-85) REVERT: B 241 GLU cc_start: 0.7133 (mm-30) cc_final: 0.6772 (mm-30) REVERT: D 25 THR cc_start: 0.7449 (OUTLIER) cc_final: 0.7122 (m) REVERT: D 70 ARG cc_start: 0.7585 (OUTLIER) cc_final: 0.7150 (ttp-170) REVERT: D 120 ASN cc_start: 0.8061 (OUTLIER) cc_final: 0.7583 (t0) REVERT: D 179 GLU cc_start: 0.7368 (tp30) cc_final: 0.7147 (tt0) REVERT: G 169 TYR cc_start: 0.6902 (OUTLIER) cc_final: 0.5735 (p90) outliers start: 49 outliers final: 34 residues processed: 125 average time/residue: 0.8731 time to fit residues: 118.4420 Evaluate side-chains 119 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 78 time to evaluate : 1.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 50 TRP Chi-restraints excluded: chain A residue 80 SER Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain B residue 78 GLU Chi-restraints excluded: chain B residue 108 SER Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 226 ARG Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 70 ARG Chi-restraints excluded: chain D residue 120 ASN Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 122 ASP Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 169 ILE Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 216 THR Chi-restraints excluded: chain G residue 27 LYS Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 77 LEU Chi-restraints excluded: chain G residue 108 SER Chi-restraints excluded: chain G residue 113 CYS Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain G residue 132 SER Chi-restraints excluded: chain G residue 137 VAL Chi-restraints excluded: chain G residue 153 ILE Chi-restraints excluded: chain G residue 169 TYR Chi-restraints excluded: chain G residue 170 LEU Chi-restraints excluded: chain G residue 180 VAL Chi-restraints excluded: chain G residue 207 THR Chi-restraints excluded: chain G residue 229 VAL Chi-restraints excluded: chain G residue 238 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 19 optimal weight: 10.0000 chunk 38 optimal weight: 5.9990 chunk 43 optimal weight: 0.9980 chunk 0 optimal weight: 9.9990 chunk 7 optimal weight: 10.0000 chunk 35 optimal weight: 0.1980 chunk 51 optimal weight: 4.9990 chunk 62 optimal weight: 0.7980 chunk 47 optimal weight: 10.0000 chunk 9 optimal weight: 5.9990 chunk 33 optimal weight: 5.9990 overall best weight: 2.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 ASN ** B 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 22 GLN D 211 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4578 r_free = 0.4578 target = 0.211321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.143676 restraints weight = 7152.365| |-----------------------------------------------------------------------------| r_work (start): 0.3836 rms_B_bonded: 2.85 r_work: 0.3625 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7165 moved from start: 0.1850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 6969 Z= 0.270 Angle : 0.817 8.988 9455 Z= 0.433 Chirality : 0.055 0.206 1047 Planarity : 0.006 0.070 1187 Dihedral : 7.451 59.037 932 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.03 % Favored : 90.86 % Rotamer: Outliers : 6.17 % Allowed : 24.93 % Favored : 68.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.28), residues: 842 helix: -1.16 (2.05), residues: 6 sheet: 0.22 (0.27), residues: 406 loop : -1.77 (0.27), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 94 HIS 0.012 0.002 HIS B 89 PHE 0.028 0.003 PHE G 176 TYR 0.047 0.003 TYR G 169 ARG 0.006 0.001 ARG D 70 Details of bonding type rmsd hydrogen bonds : bond 0.05318 ( 207) hydrogen bonds : angle 6.43007 ( 624) SS BOND : bond 0.01586 ( 6) SS BOND : angle 1.97454 ( 12) covalent geometry : bond 0.00637 ( 6963) covalent geometry : angle 0.81492 ( 9443) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 81 time to evaluate : 0.834 Fit side-chains REVERT: A 50 TRP cc_start: 0.5943 (OUTLIER) cc_final: 0.5112 (t60) REVERT: A 80 SER cc_start: 0.5325 (OUTLIER) cc_final: 0.4910 (m) REVERT: B 100 LEU cc_start: 0.8691 (OUTLIER) cc_final: 0.8369 (mp) REVERT: B 209 MET cc_start: 0.7683 (ppp) cc_final: 0.7360 (tmm) REVERT: B 226 ARG cc_start: 0.5377 (OUTLIER) cc_final: 0.4855 (mmm-85) REVERT: B 241 GLU cc_start: 0.7231 (mm-30) cc_final: 0.6847 (mm-30) REVERT: D 25 THR cc_start: 0.7499 (OUTLIER) cc_final: 0.7140 (m) REVERT: D 70 ARG cc_start: 0.7522 (OUTLIER) cc_final: 0.7000 (ttp-170) REVERT: D 120 ASN cc_start: 0.8064 (OUTLIER) cc_final: 0.7563 (t0) REVERT: G 169 TYR cc_start: 0.6983 (OUTLIER) cc_final: 0.5700 (p90) outliers start: 47 outliers final: 32 residues processed: 117 average time/residue: 0.7788 time to fit residues: 99.2902 Evaluate side-chains 116 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 76 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 50 TRP Chi-restraints excluded: chain A residue 80 SER Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 108 SER Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 226 ARG Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 70 ARG Chi-restraints excluded: chain D residue 120 ASN Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 122 ASP Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 216 THR Chi-restraints excluded: chain G residue 27 LYS Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 77 LEU Chi-restraints excluded: chain G residue 108 SER Chi-restraints excluded: chain G residue 113 CYS Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain G residue 132 SER Chi-restraints excluded: chain G residue 137 VAL Chi-restraints excluded: chain G residue 153 ILE Chi-restraints excluded: chain G residue 169 TYR Chi-restraints excluded: chain G residue 170 LEU Chi-restraints excluded: chain G residue 180 VAL Chi-restraints excluded: chain G residue 207 THR Chi-restraints excluded: chain G residue 229 VAL Chi-restraints excluded: chain G residue 238 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 44 optimal weight: 0.9990 chunk 55 optimal weight: 0.9980 chunk 69 optimal weight: 0.9980 chunk 7 optimal weight: 10.0000 chunk 20 optimal weight: 3.9990 chunk 61 optimal weight: 6.9990 chunk 38 optimal weight: 0.3980 chunk 27 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 50 optimal weight: 0.1980 chunk 53 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 ASN ** B 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 22 GLN D 211 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4616 r_free = 0.4616 target = 0.215375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 109)---------------| | r_work = 0.3918 r_free = 0.3918 target = 0.147602 restraints weight = 7067.386| |-----------------------------------------------------------------------------| r_work (start): 0.3881 rms_B_bonded: 2.70 r_work: 0.3688 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7122 moved from start: 0.2040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 6969 Z= 0.129 Angle : 0.648 7.650 9455 Z= 0.340 Chirality : 0.048 0.191 1047 Planarity : 0.005 0.064 1187 Dihedral : 6.898 58.498 932 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.29 % Favored : 93.59 % Rotamer: Outliers : 5.25 % Allowed : 26.12 % Favored : 68.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.29), residues: 842 helix: -2.10 (2.19), residues: 6 sheet: 0.40 (0.26), residues: 420 loop : -1.59 (0.28), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 94 HIS 0.009 0.001 HIS B 52 PHE 0.016 0.002 PHE A 67 TYR 0.018 0.001 TYR G 169 ARG 0.005 0.000 ARG D 70 Details of bonding type rmsd hydrogen bonds : bond 0.03493 ( 207) hydrogen bonds : angle 6.01799 ( 624) SS BOND : bond 0.00702 ( 6) SS BOND : angle 1.43691 ( 12) covalent geometry : bond 0.00305 ( 6963) covalent geometry : angle 0.64631 ( 9443) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11794.10 seconds wall clock time: 206 minutes 58.88 seconds (12418.88 seconds total)