Starting phenix.real_space_refine on Wed Mar 4 02:56:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ird_60811/03_2026/9ird_60811.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ird_60811/03_2026/9ird_60811.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ird_60811/03_2026/9ird_60811.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ird_60811/03_2026/9ird_60811.map" model { file = "/net/cci-nas-00/data/ceres_data/9ird_60811/03_2026/9ird_60811.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ird_60811/03_2026/9ird_60811.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.001 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 52 5.16 5 C 6336 2.51 5 N 1708 2.21 5 O 1914 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10010 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1685 Classifications: {'peptide': 214} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 201} Chain: "B" Number of atoms: 1685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1685 Classifications: {'peptide': 214} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 201} Chain: "D" Number of atoms: 1597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1597 Classifications: {'peptide': 204} Link IDs: {'CIS': 8, 'PCIS': 2, 'PTRANS': 9, 'TRANS': 184} Chain: "E" Number of atoms: 1608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1608 Classifications: {'peptide': 213} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 202} Chain: "F" Number of atoms: 1612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1612 Classifications: {'peptide': 214} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 203} Chain: "G" Number of atoms: 1823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1823 Classifications: {'peptide': 229} Link IDs: {'CIS': 2, 'PTRANS': 12, 'TRANS': 214} Time building chain proxies: 2.39, per 1000 atoms: 0.24 Number of scatterers: 10010 At special positions: 0 Unit cell: (136.817, 149.745, 130.353, 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 52 16.00 O 1914 8.00 N 1708 7.00 C 6336 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 51 " - pdb=" SG CYS A 125 " distance=2.03 Simple disulfide: pdb=" SG CYS A 165 " - pdb=" SG CYS A 219 " distance=2.03 Simple disulfide: pdb=" SG CYS B 51 " - pdb=" SG CYS B 125 " distance=2.03 Simple disulfide: pdb=" SG CYS B 165 " - pdb=" SG CYS B 219 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 92 " distance=2.03 Simple disulfide: pdb=" SG CYS D 140 " - pdb=" SG CYS D 191 " distance=2.03 Simple disulfide: pdb=" SG CYS E 52 " - pdb=" SG CYS E 126 " distance=2.03 Simple disulfide: pdb=" SG CYS E 166 " - pdb=" SG CYS E 220 " distance=2.03 Simple disulfide: pdb=" SG CYS F 52 " - pdb=" SG CYS F 126 " distance=2.03 Simple disulfide: pdb=" SG CYS F 166 " - pdb=" SG CYS F 220 " distance=2.04 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 97 " distance=2.03 Simple disulfide: pdb=" SG CYS G 154 " - pdb=" SG CYS G 210 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.80 Conformation dependent library (CDL) restraints added in 530.9 milliseconds 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2360 Finding SS restraints... Secondary structure from input PDB file: 10 helices and 27 sheets defined 3.4% alpha, 44.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'B' and resid 102 through 105 Processing helix chain 'D' and resid 29 through 31 No H-bonds generated for 'chain 'D' and resid 29 through 31' Processing helix chain 'E' and resid 90 through 94 Processing helix chain 'E' and resid 103 through 106 Processing helix chain 'E' and resid 239 through 242 Processing helix chain 'F' and resid 90 through 94 Processing helix chain 'F' and resid 117 through 121 Processing helix chain 'F' and resid 239 through 242 Processing helix chain 'G' and resid 88 through 92 removed outlier: 3.523A pdb=" N ILE G 92 " --> pdb=" O LYS G 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 217 through 221 removed outlier: 3.570A pdb=" N VAL G 221 " --> pdb=" O LYS G 218 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 31 through 33 removed outlier: 4.576A pdb=" N ALA A 109 " --> pdb=" O VAL A 99 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL A 99 " --> pdb=" O ALA A 109 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 39 through 41 removed outlier: 5.965A pdb=" N ILE A 39 " --> pdb=" O VAL A 141 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N VAL A 64 " --> pdb=" O TYR A 78 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 150 through 152 Processing sheet with id=AA4, first strand: chain 'A' and resid 150 through 152 removed outlier: 5.016A pdb=" N PHE A 201 " --> pdb=" O GLY A 169 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 185 through 186 removed outlier: 4.322A pdb=" N TRP A 178 " --> pdb=" O ALA A 186 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N SER A 218 " --> pdb=" O ARG A 179 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 31 through 33 removed outlier: 3.880A pdb=" N ALA B 109 " --> pdb=" O VAL B 99 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 39 through 42 removed outlier: 3.624A pdb=" N LYS B 79 " --> pdb=" O ARG B 82 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ARG B 82 " --> pdb=" O LYS B 79 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 153 through 156 removed outlier: 4.040A pdb=" N GLY B 155 " --> pdb=" O ARG B 162 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 165 through 170 removed outlier: 5.429A pdb=" N ILE B 166 " --> pdb=" O THR B 205 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N THR B 205 " --> pdb=" O ILE B 166 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N ARG B 168 " --> pdb=" O VAL B 203 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N VAL B 203 " --> pdb=" O ARG B 168 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ALA B 206 " --> pdb=" O LYS B 190 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 175 through 179 Processing sheet with id=AB2, first strand: chain 'D' and resid 5 through 6 Processing sheet with id=AB3, first strand: chain 'D' and resid 10 through 13 removed outlier: 3.690A pdb=" N THR D 116 " --> pdb=" O VAL D 11 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 55 through 56 removed outlier: 6.523A pdb=" N TRP D 37 " --> pdb=" O ILE D 49 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N ARG D 51 " --> pdb=" O ILE D 35 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ILE D 35 " --> pdb=" O ARG D 51 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 128 through 134 removed outlier: 6.145A pdb=" N TYR D 175 " --> pdb=" O GLU D 144 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 128 through 134 removed outlier: 6.145A pdb=" N TYR D 175 " --> pdb=" O GLU D 144 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 150 through 155 removed outlier: 3.618A pdb=" N THR D 190 " --> pdb=" O VAL D 155 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 32 through 34 Processing sheet with id=AB9, first strand: chain 'E' and resid 40 through 43 removed outlier: 5.861A pdb=" N SER E 69 " --> pdb=" O VAL E 75 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N VAL E 75 " --> pdb=" O SER E 69 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 190 through 191 removed outlier: 6.776A pdb=" N VAL E 204 " --> pdb=" O THR E 169 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N THR E 169 " --> pdb=" O VAL E 204 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N ALA E 206 " --> pdb=" O ARG E 167 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N ARG E 167 " --> pdb=" O ALA E 206 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N VAL E 208 " --> pdb=" O GLU E 165 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N GLU E 165 " --> pdb=" O VAL E 208 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N MET E 210 " --> pdb=" O HIS E 163 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N HIS E 163 " --> pdb=" O MET E 210 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N GLY E 161 " --> pdb=" O TYR E 157 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N TYR E 157 " --> pdb=" O GLY E 161 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N HIS E 163 " --> pdb=" O LYS E 155 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N TRP F 179 " --> pdb=" O ILE F 187 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 186 through 187 removed outlier: 4.354A pdb=" N TRP E 179 " --> pdb=" O ILE E 187 " (cutoff:3.500A) removed outlier: 8.800A pdb=" N VAL F 152 " --> pdb=" O THR E 232 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N SER E 234 " --> pdb=" O VAL F 152 " (cutoff:3.500A) removed outlier: 8.177A pdb=" N VAL F 154 " --> pdb=" O SER E 234 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N SER E 236 " --> pdb=" O VAL F 154 " (cutoff:3.500A) removed outlier: 8.384A pdb=" N GLY F 156 " --> pdb=" O SER E 236 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N VAL F 152 " --> pdb=" O ARG F 167 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N ARG F 167 " --> pdb=" O VAL F 152 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N VAL F 154 " --> pdb=" O GLU F 165 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N GLU F 165 " --> pdb=" O VAL F 154 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N GLY F 156 " --> pdb=" O HIS F 163 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N TYR F 202 " --> pdb=" O GLY F 170 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 32 through 34 Processing sheet with id=AC4, first strand: chain 'F' and resid 39 through 42 removed outlier: 5.600A pdb=" N ILE F 40 " --> pdb=" O LYS F 142 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N LEU F 65 " --> pdb=" O VAL F 78 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N VAL F 78 " --> pdb=" O LEU F 65 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N TRP F 67 " --> pdb=" O VAL F 76 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N VAL F 78 " --> pdb=" O VAL F 85 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 3 through 5 Processing sheet with id=AC6, first strand: chain 'G' and resid 10 through 13 removed outlier: 3.655A pdb=" N ALA G 93 " --> pdb=" O LEU G 119 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N VAL G 35 " --> pdb=" O SER G 51 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N SER G 51 " --> pdb=" O VAL G 35 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N TRP G 37 " --> pdb=" O LEU G 49 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 10 through 13 removed outlier: 3.655A pdb=" N ALA G 93 " --> pdb=" O LEU G 119 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 133 through 137 removed outlier: 3.743A pdb=" N LEU G 153 " --> pdb=" O PHE G 137 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 165 through 169 411 hydrogen bonds defined for protein. 990 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: 1.54 Time building geometry restraints manager: 1.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3288 1.34 - 1.46: 2326 1.46 - 1.58: 4530 1.58 - 1.70: 0 1.70 - 1.82: 80 Bond restraints: 10224 Sorted by residual: bond pdb=" CG PRO E 188 " pdb=" CD PRO E 188 " ideal model delta sigma weight residual 1.503 1.458 0.045 3.40e-02 8.65e+02 1.76e+00 bond pdb=" CB PRO E 193 " pdb=" CG PRO E 193 " ideal model delta sigma weight residual 1.492 1.546 -0.054 5.00e-02 4.00e+02 1.18e+00 bond pdb=" CB GLN D 42 " pdb=" CG GLN D 42 " ideal model delta sigma weight residual 1.520 1.549 -0.029 3.00e-02 1.11e+03 9.31e-01 bond pdb=" CB CYS D 92 " pdb=" SG CYS D 92 " ideal model delta sigma weight residual 1.808 1.778 0.030 3.30e-02 9.18e+02 8.31e-01 bond pdb=" CA PRO F 39 " pdb=" C PRO F 39 " ideal model delta sigma weight residual 1.520 1.532 -0.013 1.42e-02 4.96e+03 7.98e-01 ... (remaining 10219 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.23: 13687 2.23 - 4.46: 141 4.46 - 6.69: 12 6.69 - 8.92: 7 8.92 - 11.15: 3 Bond angle restraints: 13850 Sorted by residual: angle pdb=" C MET D 25 " pdb=" N LYS D 26 " pdb=" CA LYS D 26 " ideal model delta sigma weight residual 121.70 132.85 -11.15 1.80e+00 3.09e-01 3.84e+01 angle pdb=" C GLU D 52 " pdb=" N LYS D 53 " pdb=" CA LYS D 53 " ideal model delta sigma weight residual 121.70 130.71 -9.01 1.80e+00 3.09e-01 2.50e+01 angle pdb=" C GLY D 43 " pdb=" N ASN D 44 " pdb=" CA ASN D 44 " ideal model delta sigma weight residual 121.70 130.53 -8.83 1.80e+00 3.09e-01 2.41e+01 angle pdb=" C LYS G 171 " pdb=" N LYS G 172 " pdb=" CA LYS G 172 " ideal model delta sigma weight residual 121.70 130.38 -8.68 1.80e+00 3.09e-01 2.33e+01 angle pdb=" C LYS G 172 " pdb=" N SER G 173 " pdb=" CA SER G 173 " ideal model delta sigma weight residual 121.70 129.50 -7.80 1.80e+00 3.09e-01 1.88e+01 ... (remaining 13845 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 5484 17.98 - 35.96: 566 35.96 - 53.93: 108 53.93 - 71.91: 17 71.91 - 89.89: 13 Dihedral angle restraints: 6188 sinusoidal: 2498 harmonic: 3690 Sorted by residual: dihedral pdb=" CB CYS D 23 " pdb=" SG CYS D 23 " pdb=" SG CYS D 92 " pdb=" CB CYS D 92 " ideal model delta sinusoidal sigma weight residual 93.00 -179.65 -87.35 1 1.00e+01 1.00e-02 9.16e+01 dihedral pdb=" CB CYS F 166 " pdb=" SG CYS F 166 " pdb=" SG CYS F 220 " pdb=" CB CYS F 220 " ideal model delta sinusoidal sigma weight residual 93.00 44.24 48.76 1 1.00e+01 1.00e-02 3.27e+01 dihedral pdb=" CA MET A 89 " pdb=" C MET A 89 " pdb=" N GLU A 90 " pdb=" CA GLU A 90 " ideal model delta harmonic sigma weight residual -180.00 -157.24 -22.76 0 5.00e+00 4.00e-02 2.07e+01 ... (remaining 6185 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 888 0.032 - 0.063: 423 0.063 - 0.095: 112 0.095 - 0.127: 104 0.127 - 0.159: 14 Chirality restraints: 1541 Sorted by residual: chirality pdb=" CA ILE E 221 " pdb=" N ILE E 221 " pdb=" C ILE E 221 " pdb=" CB ILE E 221 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.28e-01 chirality pdb=" CA ILE D 167 " pdb=" N ILE D 167 " pdb=" C ILE D 167 " pdb=" CB ILE D 167 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.19e-01 chirality pdb=" CA ILE G 84 " pdb=" N ILE G 84 " pdb=" C ILE G 84 " pdb=" CB ILE G 84 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.75e-01 ... (remaining 1538 not shown) Planarity restraints: 1789 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY F 38 " 0.070 5.00e-02 4.00e+02 1.08e-01 1.88e+01 pdb=" N PRO F 39 " -0.187 5.00e-02 4.00e+02 pdb=" CA PRO F 39 " 0.059 5.00e-02 4.00e+02 pdb=" CD PRO F 39 " 0.058 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA E 192 " 0.044 5.00e-02 4.00e+02 6.50e-02 6.77e+00 pdb=" N PRO E 193 " -0.112 5.00e-02 4.00e+02 pdb=" CA PRO E 193 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO E 193 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE E 187 " -0.030 5.00e-02 4.00e+02 4.36e-02 3.04e+00 pdb=" N PRO E 188 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO E 188 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO E 188 " -0.025 5.00e-02 4.00e+02 ... (remaining 1786 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 157 2.63 - 3.19: 8862 3.19 - 3.76: 13995 3.76 - 4.33: 20542 4.33 - 4.90: 34764 Nonbonded interactions: 78320 Sorted by model distance: nonbonded pdb=" N GLN E 30 " pdb=" OE1 GLN E 30 " model vdw 2.058 3.120 nonbonded pdb=" N GLN G 104 " pdb=" OE1 GLN G 104 " model vdw 2.088 3.120 nonbonded pdb=" N GLN A 228 " pdb=" OE1 GLN A 228 " model vdw 2.101 3.120 nonbonded pdb=" O GLU G 143 " pdb=" OG1 THR G 144 " model vdw 2.121 3.040 nonbonded pdb=" N GLU F 46 " pdb=" OE1 GLU F 46 " model vdw 2.139 3.120 ... (remaining 78315 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = (chain 'E' and (resid 30 through 148 or resid 150 through 152 or resid 154 throu \ gh 157 or resid 159 through 181 or resid 183 through 188 or resid 190 through 20 \ 2 or resid 204 through 212 or resid 214 through 220 or resid 222 through 223 or \ resid 225 through 242)) selection = (chain 'F' and (resid 30 through 148 or resid 150 through 152 or resid 154 throu \ gh 157 or resid 159 through 181 or resid 183 through 188 or resid 190 through 20 \ 2 or resid 204 through 212 or resid 214 through 220 or resid 222 through 223 or \ resid 225 through 242)) } 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: 2.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.510 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 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 : 0.003 0.054 10236 Z= 0.141 Angle : 0.630 11.150 13874 Z= 0.339 Chirality : 0.046 0.159 1541 Planarity : 0.005 0.108 1789 Dihedral : 15.110 89.888 3792 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.49 % Favored : 94.44 % Rotamer: Outliers : 0.09 % Allowed : 17.89 % Favored : 82.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.91 % Cis-general : 0.82 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.89 (0.23), residues: 1276 helix: -5.45 (0.28), residues: 7 sheet: -0.67 (0.21), residues: 599 loop : -1.76 (0.23), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 131 TYR 0.018 0.001 TYR G 191 PHE 0.011 0.001 PHE A 127 TRP 0.013 0.001 TRP A 66 HIS 0.004 0.001 HIS G 167 Details of bonding type rmsd covalent geometry : bond 0.00312 (10224) covalent geometry : angle 0.62844 (13850) SS BOND : bond 0.00461 ( 12) SS BOND : angle 1.20276 ( 24) hydrogen bonds : bond 0.10470 ( 386) hydrogen bonds : angle 7.34816 ( 990) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 188 time to evaluate : 0.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 ARG cc_start: 0.4656 (ttt-90) cc_final: 0.4331 (ttt-90) REVERT: A 162 ARG cc_start: 0.6915 (ttt-90) cc_final: 0.6603 (ttt-90) REVERT: B 118 GLN cc_start: 0.8267 (tm-30) cc_final: 0.8066 (tm-30) REVERT: D 99 MET cc_start: 0.5775 (mpp) cc_final: 0.5194 (mpp) REVERT: D 158 LYS cc_start: 0.7563 (mtmm) cc_final: 0.6993 (ptpp) REVERT: E 220 CYS cc_start: 0.7462 (t) cc_final: 0.7036 (t) REVERT: F 113 ILE cc_start: 0.6555 (mm) cc_final: 0.6354 (mm) REVERT: F 151 HIS cc_start: 0.5435 (t70) cc_final: 0.5209 (t70) outliers start: 1 outliers final: 0 residues processed: 188 average time/residue: 0.1080 time to fit residues: 28.1390 Evaluate side-chains 173 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 173 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 108 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 0.7980 chunk 113 optimal weight: 0.6980 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 123 optimal weight: 0.5980 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 129 GLN E 149 ASN ** F 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 216 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.138221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.115198 restraints weight = 18624.291| |-----------------------------------------------------------------------------| r_work (start): 0.3642 rms_B_bonded: 2.78 r_work: 0.3491 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.1193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10236 Z= 0.149 Angle : 0.640 8.540 13874 Z= 0.340 Chirality : 0.047 0.183 1541 Planarity : 0.004 0.040 1789 Dihedral : 4.743 22.383 1394 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 2.27 % Allowed : 18.17 % Favored : 79.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.91 % Cis-general : 0.82 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.70 (0.23), residues: 1276 helix: -4.39 (0.69), residues: 13 sheet: -0.60 (0.21), residues: 610 loop : -1.54 (0.23), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 131 TYR 0.014 0.001 TYR E 172 PHE 0.012 0.001 PHE A 127 TRP 0.017 0.001 TRP A 66 HIS 0.004 0.001 HIS B 156 Details of bonding type rmsd covalent geometry : bond 0.00342 (10224) covalent geometry : angle 0.63875 (13850) SS BOND : bond 0.00419 ( 12) SS BOND : angle 1.19400 ( 24) hydrogen bonds : bond 0.03175 ( 386) hydrogen bonds : angle 6.56897 ( 990) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 183 time to evaluate : 0.403 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 90 GLU cc_start: 0.6148 (mm-30) cc_final: 0.5719 (tp30) REVERT: A 162 ARG cc_start: 0.7459 (ttt-90) cc_final: 0.6889 (ttt-90) REVERT: A 196 ASP cc_start: 0.7936 (t70) cc_final: 0.7697 (t70) REVERT: B 196 ASP cc_start: 0.6070 (OUTLIER) cc_final: 0.5763 (p0) REVERT: D 42 GLN cc_start: 0.6972 (pp30) cc_final: 0.6680 (pp30) REVERT: D 69 ASP cc_start: 0.6910 (t0) cc_final: 0.6609 (t0) REVERT: D 158 LYS cc_start: 0.7368 (mtmm) cc_final: 0.6951 (ptpp) REVERT: E 220 CYS cc_start: 0.7524 (t) cc_final: 0.7174 (t) REVERT: E 241 PHE cc_start: 0.6949 (t80) cc_final: 0.6459 (t80) REVERT: F 34 LEU cc_start: 0.4079 (OUTLIER) cc_final: 0.3441 (tt) REVERT: F 58 MET cc_start: 0.6106 (OUTLIER) cc_final: 0.5890 (ppp) REVERT: F 151 HIS cc_start: 0.6460 (t70) cc_final: 0.6122 (t70) REVERT: G 59 ARG cc_start: 0.7402 (ttt180) cc_final: 0.7183 (ttt-90) outliers start: 25 outliers final: 12 residues processed: 198 average time/residue: 0.1134 time to fit residues: 30.6255 Evaluate side-chains 192 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 177 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain B residue 51 CYS Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain E residue 126 CYS Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 34 LEU Chi-restraints excluded: chain F residue 58 MET Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain F residue 232 THR Chi-restraints excluded: chain G residue 88 GLU Chi-restraints excluded: chain G residue 146 LEU Chi-restraints excluded: chain G residue 207 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 125 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 84 optimal weight: 3.9990 chunk 109 optimal weight: 2.9990 chunk 62 optimal weight: 0.5980 chunk 60 optimal weight: 3.9990 chunk 41 optimal weight: 0.9980 chunk 92 optimal weight: 0.9990 chunk 108 optimal weight: 0.7980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 ASN E 129 GLN ** F 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.136671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.112646 restraints weight = 18765.903| |-----------------------------------------------------------------------------| r_work (start): 0.3610 rms_B_bonded: 2.95 r_work: 0.3451 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.1497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 10236 Z= 0.184 Angle : 0.640 8.748 13874 Z= 0.340 Chirality : 0.047 0.178 1541 Planarity : 0.004 0.032 1789 Dihedral : 4.845 24.671 1394 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 3.63 % Allowed : 18.89 % Favored : 77.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.91 % Cis-general : 0.82 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.58 (0.23), residues: 1276 helix: -5.36 (0.22), residues: 13 sheet: -0.47 (0.21), residues: 620 loop : -1.51 (0.23), residues: 643 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 131 TYR 0.019 0.002 TYR E 172 PHE 0.016 0.002 PHE A 127 TRP 0.015 0.002 TRP A 66 HIS 0.006 0.001 HIS B 156 Details of bonding type rmsd covalent geometry : bond 0.00425 (10224) covalent geometry : angle 0.63789 (13850) SS BOND : bond 0.00471 ( 12) SS BOND : angle 1.41194 ( 24) hydrogen bonds : bond 0.03323 ( 386) hydrogen bonds : angle 6.57796 ( 990) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 187 time to evaluate : 0.376 Fit side-chains revert: symmetry clash REVERT: A 46 ASN cc_start: 0.5438 (OUTLIER) cc_final: 0.4730 (p0) REVERT: A 85 THR cc_start: 0.5730 (OUTLIER) cc_final: 0.5462 (t) REVERT: A 90 GLU cc_start: 0.6276 (mm-30) cc_final: 0.5910 (tp30) REVERT: A 112 ILE cc_start: 0.4654 (tp) cc_final: 0.4437 (tp) REVERT: A 125 CYS cc_start: 0.4035 (OUTLIER) cc_final: 0.3593 (p) REVERT: A 133 TYR cc_start: 0.4259 (OUTLIER) cc_final: 0.2310 (m-80) REVERT: A 162 ARG cc_start: 0.7570 (ttt-90) cc_final: 0.6969 (ttt-90) REVERT: A 196 ASP cc_start: 0.7968 (t70) cc_final: 0.7687 (t70) REVERT: B 57 LYS cc_start: 0.9060 (ptmm) cc_final: 0.8853 (ptmm) REVERT: B 102 ASP cc_start: 0.8067 (t0) cc_final: 0.7706 (t0) REVERT: D 42 GLN cc_start: 0.7086 (pp30) cc_final: 0.6796 (pp30) REVERT: D 69 ASP cc_start: 0.6828 (t0) cc_final: 0.6297 (t0) REVERT: D 158 LYS cc_start: 0.7467 (mtmm) cc_final: 0.6988 (ptpp) REVERT: E 220 CYS cc_start: 0.7572 (t) cc_final: 0.7234 (t) REVERT: E 241 PHE cc_start: 0.7041 (t80) cc_final: 0.6514 (t80) REVERT: F 34 LEU cc_start: 0.4193 (OUTLIER) cc_final: 0.3446 (tt) REVERT: F 46 GLU cc_start: 0.6795 (mp0) cc_final: 0.6559 (mp0) REVERT: F 123 LYS cc_start: 0.5456 (tppt) cc_final: 0.5138 (tppt) REVERT: F 151 HIS cc_start: 0.6582 (t70) cc_final: 0.6283 (t70) REVERT: F 210 MET cc_start: 0.3618 (OUTLIER) cc_final: 0.3224 (tpt) outliers start: 40 outliers final: 21 residues processed: 215 average time/residue: 0.1104 time to fit residues: 32.6929 Evaluate side-chains 206 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 179 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 46 ASN Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 133 TYR Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 232 SER Chi-restraints excluded: chain B residue 51 CYS Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 34 LEU Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain F residue 210 MET Chi-restraints excluded: chain F residue 222 ILE Chi-restraints excluded: chain F residue 232 THR Chi-restraints excluded: chain G residue 88 GLU Chi-restraints excluded: chain G residue 146 LEU Chi-restraints excluded: chain G residue 197 LEU Chi-restraints excluded: chain G residue 204 LEU Chi-restraints excluded: chain G residue 205 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 93 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 chunk 64 optimal weight: 0.7980 chunk 41 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 79 optimal weight: 0.7980 chunk 113 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 chunk 117 optimal weight: 2.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 129 GLN ** F 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.136482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.112932 restraints weight = 18819.881| |-----------------------------------------------------------------------------| r_work (start): 0.3612 rms_B_bonded: 2.88 r_work: 0.3453 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.1696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10236 Z= 0.186 Angle : 0.643 8.791 13874 Z= 0.341 Chirality : 0.047 0.171 1541 Planarity : 0.004 0.032 1789 Dihedral : 4.910 24.775 1394 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 4.36 % Allowed : 19.62 % Favored : 76.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.91 % Cis-general : 0.82 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.56 (0.23), residues: 1276 helix: -4.54 (0.56), residues: 13 sheet: -0.49 (0.21), residues: 631 loop : -1.50 (0.24), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 131 TYR 0.024 0.001 TYR E 172 PHE 0.015 0.002 PHE A 127 TRP 0.014 0.001 TRP A 66 HIS 0.005 0.001 HIS B 156 Details of bonding type rmsd covalent geometry : bond 0.00432 (10224) covalent geometry : angle 0.64175 (13850) SS BOND : bond 0.00507 ( 12) SS BOND : angle 1.30077 ( 24) hydrogen bonds : bond 0.03213 ( 386) hydrogen bonds : angle 6.58142 ( 990) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 179 time to evaluate : 0.377 Fit side-chains revert: symmetry clash REVERT: A 39 ILE cc_start: 0.6755 (OUTLIER) cc_final: 0.6230 (mp) REVERT: A 85 THR cc_start: 0.5674 (OUTLIER) cc_final: 0.5368 (t) REVERT: A 90 GLU cc_start: 0.6520 (mm-30) cc_final: 0.6016 (tp30) REVERT: A 125 CYS cc_start: 0.3924 (OUTLIER) cc_final: 0.3556 (p) REVERT: A 133 TYR cc_start: 0.4274 (OUTLIER) cc_final: 0.2399 (m-80) REVERT: A 162 ARG cc_start: 0.7517 (ttt-90) cc_final: 0.6921 (ttt-90) REVERT: A 196 ASP cc_start: 0.7854 (t70) cc_final: 0.7597 (t70) REVERT: A 217 MET cc_start: 0.7226 (OUTLIER) cc_final: 0.6211 (ttt) REVERT: B 102 ASP cc_start: 0.7975 (t0) cc_final: 0.7545 (t0) REVERT: D 42 GLN cc_start: 0.7176 (pp30) cc_final: 0.6971 (pp30) REVERT: D 69 ASP cc_start: 0.6835 (t0) cc_final: 0.6085 (t0) REVERT: D 158 LYS cc_start: 0.7510 (mtmm) cc_final: 0.7046 (ptpp) REVERT: E 220 CYS cc_start: 0.7526 (t) cc_final: 0.7216 (t) REVERT: E 241 PHE cc_start: 0.7079 (t80) cc_final: 0.6552 (t80) REVERT: F 34 LEU cc_start: 0.4185 (OUTLIER) cc_final: 0.3404 (tt) REVERT: F 46 GLU cc_start: 0.6777 (mp0) cc_final: 0.6544 (mp0) REVERT: F 58 MET cc_start: 0.6242 (OUTLIER) cc_final: 0.5979 (ppp) REVERT: F 123 LYS cc_start: 0.5516 (tppt) cc_final: 0.5164 (tppt) REVERT: F 151 HIS cc_start: 0.6580 (t70) cc_final: 0.6265 (t70) REVERT: F 237 ILE cc_start: 0.6067 (OUTLIER) cc_final: 0.5478 (mp) REVERT: G 99 LEU cc_start: 0.9340 (OUTLIER) cc_final: 0.9094 (pp) outliers start: 48 outliers final: 27 residues processed: 211 average time/residue: 0.1081 time to fit residues: 31.6016 Evaluate side-chains 212 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 176 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 133 TYR Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 217 MET Chi-restraints excluded: chain A residue 232 SER Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 51 CYS Chi-restraints excluded: chain B residue 125 CYS Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 162 ILE Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 34 LEU Chi-restraints excluded: chain F residue 58 MET Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain F residue 224 SER Chi-restraints excluded: chain F residue 232 THR Chi-restraints excluded: chain F residue 237 ILE Chi-restraints excluded: chain G residue 88 GLU Chi-restraints excluded: chain G residue 99 LEU Chi-restraints excluded: chain G residue 146 LEU Chi-restraints excluded: chain G residue 197 LEU Chi-restraints excluded: chain G residue 204 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 64 optimal weight: 0.7980 chunk 42 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 101 optimal weight: 6.9990 chunk 48 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 50 optimal weight: 0.6980 chunk 31 optimal weight: 4.9990 chunk 79 optimal weight: 0.8980 chunk 16 optimal weight: 4.9990 chunk 59 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 129 GLN E 149 ASN ** F 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.135598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.111941 restraints weight = 18651.061| |-----------------------------------------------------------------------------| r_work (start): 0.3598 rms_B_bonded: 2.95 r_work: 0.3439 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.1814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 10236 Z= 0.205 Angle : 0.660 8.883 13874 Z= 0.349 Chirality : 0.047 0.169 1541 Planarity : 0.004 0.033 1789 Dihedral : 5.012 29.552 1394 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 5.00 % Allowed : 20.62 % Favored : 74.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.91 % Cis-general : 0.82 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.62 (0.23), residues: 1276 helix: -3.41 (1.09), residues: 6 sheet: -0.56 (0.20), residues: 646 loop : -1.57 (0.24), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 131 TYR 0.025 0.002 TYR E 172 PHE 0.016 0.002 PHE A 127 TRP 0.016 0.002 TRP A 66 HIS 0.006 0.001 HIS B 156 Details of bonding type rmsd covalent geometry : bond 0.00477 (10224) covalent geometry : angle 0.65804 (13850) SS BOND : bond 0.00535 ( 12) SS BOND : angle 1.26811 ( 24) hydrogen bonds : bond 0.03291 ( 386) hydrogen bonds : angle 6.68142 ( 990) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 180 time to evaluate : 0.370 Fit side-chains revert: symmetry clash REVERT: A 39 ILE cc_start: 0.6747 (OUTLIER) cc_final: 0.6240 (mp) REVERT: A 85 THR cc_start: 0.5693 (OUTLIER) cc_final: 0.5396 (t) REVERT: A 90 GLU cc_start: 0.6463 (mm-30) cc_final: 0.6000 (tp30) REVERT: A 125 CYS cc_start: 0.3847 (OUTLIER) cc_final: 0.3517 (p) REVERT: A 133 TYR cc_start: 0.4179 (OUTLIER) cc_final: 0.2531 (m-80) REVERT: A 162 ARG cc_start: 0.7516 (ttt-90) cc_final: 0.6896 (ttt-90) REVERT: A 196 ASP cc_start: 0.7857 (t70) cc_final: 0.7598 (t70) REVERT: A 217 MET cc_start: 0.7279 (OUTLIER) cc_final: 0.6295 (ttt) REVERT: B 102 ASP cc_start: 0.8002 (t0) cc_final: 0.7511 (t0) REVERT: D 69 ASP cc_start: 0.6865 (t0) cc_final: 0.6041 (t0) REVERT: D 158 LYS cc_start: 0.7490 (mtmm) cc_final: 0.7019 (ptpp) REVERT: E 220 CYS cc_start: 0.7524 (t) cc_final: 0.7114 (t) REVERT: E 241 PHE cc_start: 0.7053 (t80) cc_final: 0.6523 (t80) REVERT: F 34 LEU cc_start: 0.4215 (OUTLIER) cc_final: 0.3400 (tt) REVERT: F 58 MET cc_start: 0.6343 (OUTLIER) cc_final: 0.6051 (ppp) REVERT: F 123 LYS cc_start: 0.5461 (tppt) cc_final: 0.5089 (tppt) REVERT: F 151 HIS cc_start: 0.6581 (t70) cc_final: 0.6277 (t70) REVERT: F 221 THR cc_start: 0.8492 (OUTLIER) cc_final: 0.8269 (t) REVERT: F 237 ILE cc_start: 0.5915 (OUTLIER) cc_final: 0.5376 (mp) REVERT: G 99 LEU cc_start: 0.9307 (OUTLIER) cc_final: 0.9039 (pp) outliers start: 55 outliers final: 32 residues processed: 219 average time/residue: 0.1110 time to fit residues: 33.3313 Evaluate side-chains 217 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 175 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 133 TYR Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 217 MET Chi-restraints excluded: chain A residue 232 SER Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 51 CYS Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 125 CYS Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 30 ILE Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 162 ILE Chi-restraints excluded: chain F residue 31 PHE Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 34 LEU Chi-restraints excluded: chain F residue 58 MET Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain F residue 224 SER Chi-restraints excluded: chain F residue 232 THR Chi-restraints excluded: chain F residue 237 ILE Chi-restraints excluded: chain G residue 88 GLU Chi-restraints excluded: chain G residue 99 LEU Chi-restraints excluded: chain G residue 146 LEU Chi-restraints excluded: chain G residue 197 LEU Chi-restraints excluded: chain G residue 204 LEU Chi-restraints excluded: chain G residue 205 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 9 optimal weight: 0.7980 chunk 70 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 39 optimal weight: 4.9990 chunk 43 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 96 optimal weight: 0.9980 chunk 37 optimal weight: 3.9990 chunk 97 optimal weight: 0.0010 chunk 50 optimal weight: 0.6980 chunk 6 optimal weight: 3.9990 overall best weight: 0.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 42 GLN ** E 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 129 GLN ** F 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.137778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.114225 restraints weight = 18787.598| |-----------------------------------------------------------------------------| r_work (start): 0.3630 rms_B_bonded: 3.00 r_work: 0.3477 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.1948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 10236 Z= 0.141 Angle : 0.615 8.579 13874 Z= 0.325 Chirality : 0.046 0.187 1541 Planarity : 0.004 0.032 1789 Dihedral : 4.773 32.084 1394 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 3.36 % Allowed : 22.71 % Favored : 73.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.91 % Cis-general : 0.82 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.50 (0.23), residues: 1276 helix: -3.33 (1.16), residues: 6 sheet: -0.44 (0.20), residues: 639 loop : -1.53 (0.24), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 131 TYR 0.015 0.001 TYR E 172 PHE 0.012 0.001 PHE A 127 TRP 0.010 0.001 TRP A 66 HIS 0.004 0.001 HIS F 53 Details of bonding type rmsd covalent geometry : bond 0.00325 (10224) covalent geometry : angle 0.61425 (13850) SS BOND : bond 0.00365 ( 12) SS BOND : angle 1.11250 ( 24) hydrogen bonds : bond 0.03011 ( 386) hydrogen bonds : angle 6.35242 ( 990) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 177 time to evaluate : 0.397 Fit side-chains revert: symmetry clash REVERT: A 39 ILE cc_start: 0.6723 (OUTLIER) cc_final: 0.6181 (mp) REVERT: A 85 THR cc_start: 0.5772 (OUTLIER) cc_final: 0.5488 (t) REVERT: A 90 GLU cc_start: 0.6694 (mm-30) cc_final: 0.6087 (tp30) REVERT: A 125 CYS cc_start: 0.3759 (OUTLIER) cc_final: 0.3400 (p) REVERT: A 196 ASP cc_start: 0.7833 (t70) cc_final: 0.7564 (t70) REVERT: D 69 ASP cc_start: 0.6883 (t0) cc_final: 0.6016 (t0) REVERT: D 158 LYS cc_start: 0.7476 (mtmm) cc_final: 0.7018 (ptpp) REVERT: D 163 PHE cc_start: 0.8594 (m-80) cc_final: 0.8367 (m-10) REVERT: E 220 CYS cc_start: 0.7577 (t) cc_final: 0.7221 (t) REVERT: E 241 PHE cc_start: 0.7073 (t80) cc_final: 0.6514 (t80) REVERT: F 34 LEU cc_start: 0.4112 (OUTLIER) cc_final: 0.3395 (tt) REVERT: F 58 MET cc_start: 0.6268 (OUTLIER) cc_final: 0.6019 (ppp) REVERT: F 123 LYS cc_start: 0.5465 (tppt) cc_final: 0.5095 (tppt) REVERT: F 151 HIS cc_start: 0.6468 (t70) cc_final: 0.6173 (t70) REVERT: F 237 ILE cc_start: 0.6061 (OUTLIER) cc_final: 0.5520 (mp) outliers start: 37 outliers final: 24 residues processed: 201 average time/residue: 0.1079 time to fit residues: 30.0950 Evaluate side-chains 204 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 174 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 51 CYS Chi-restraints excluded: chain B residue 125 CYS Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 30 ILE Chi-restraints excluded: chain D residue 42 GLN Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 162 ILE Chi-restraints excluded: chain F residue 31 PHE Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 34 LEU Chi-restraints excluded: chain F residue 58 MET Chi-restraints excluded: chain F residue 63 MET Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain F residue 224 SER Chi-restraints excluded: chain F residue 232 THR Chi-restraints excluded: chain F residue 237 ILE Chi-restraints excluded: chain G residue 197 LEU Chi-restraints excluded: chain G residue 204 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 27 optimal weight: 0.0060 chunk 121 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 1 optimal weight: 5.9990 chunk 123 optimal weight: 0.9990 chunk 93 optimal weight: 3.9990 chunk 52 optimal weight: 0.5980 chunk 104 optimal weight: 0.5980 chunk 70 optimal weight: 0.8980 chunk 87 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 overall best weight: 0.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 42 GLN ** E 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 129 GLN ** F 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 180 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.138407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.114605 restraints weight = 18694.251| |-----------------------------------------------------------------------------| r_work (start): 0.3635 rms_B_bonded: 3.02 r_work: 0.3473 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 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 0.041 10236 Z= 0.134 Angle : 0.615 8.670 13874 Z= 0.325 Chirality : 0.046 0.182 1541 Planarity : 0.004 0.031 1789 Dihedral : 4.667 32.341 1394 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 4.81 % Allowed : 21.53 % Favored : 73.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.91 % Cis-general : 0.82 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.41 (0.23), residues: 1276 helix: -3.19 (1.29), residues: 6 sheet: -0.37 (0.20), residues: 641 loop : -1.48 (0.24), residues: 629 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 50 TYR 0.015 0.001 TYR E 172 PHE 0.011 0.001 PHE A 127 TRP 0.009 0.001 TRP A 66 HIS 0.004 0.001 HIS F 53 Details of bonding type rmsd covalent geometry : bond 0.00309 (10224) covalent geometry : angle 0.61371 (13850) SS BOND : bond 0.00363 ( 12) SS BOND : angle 1.04631 ( 24) hydrogen bonds : bond 0.02927 ( 386) hydrogen bonds : angle 6.21980 ( 990) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 181 time to evaluate : 0.378 Fit side-chains revert: symmetry clash REVERT: A 39 ILE cc_start: 0.6705 (OUTLIER) cc_final: 0.6190 (mp) REVERT: A 85 THR cc_start: 0.5799 (OUTLIER) cc_final: 0.5516 (t) REVERT: A 90 GLU cc_start: 0.6790 (mm-30) cc_final: 0.6075 (tp30) REVERT: A 126 TYR cc_start: 0.5514 (t80) cc_final: 0.4332 (m-80) REVERT: A 133 TYR cc_start: 0.4097 (OUTLIER) cc_final: 0.2378 (m-80) REVERT: A 196 ASP cc_start: 0.7813 (t70) cc_final: 0.7565 (t70) REVERT: A 217 MET cc_start: 0.7061 (mmp) cc_final: 0.6300 (ttm) REVERT: A 231 GLU cc_start: 0.7891 (pp20) cc_final: 0.7633 (pm20) REVERT: B 102 ASP cc_start: 0.7887 (t0) cc_final: 0.7449 (t0) REVERT: B 118 GLN cc_start: 0.8019 (pp30) cc_final: 0.7790 (pp30) REVERT: D 69 ASP cc_start: 0.6984 (t0) cc_final: 0.6152 (t0) REVERT: D 158 LYS cc_start: 0.7453 (mtmm) cc_final: 0.7040 (ptpp) REVERT: D 163 PHE cc_start: 0.8627 (m-80) cc_final: 0.8392 (m-10) REVERT: E 197 ASP cc_start: 0.7848 (t0) cc_final: 0.7605 (t0) REVERT: E 220 CYS cc_start: 0.7514 (t) cc_final: 0.7169 (t) REVERT: E 241 PHE cc_start: 0.7051 (t80) cc_final: 0.6519 (t80) REVERT: F 34 LEU cc_start: 0.4274 (OUTLIER) cc_final: 0.3461 (tt) REVERT: F 58 MET cc_start: 0.6227 (OUTLIER) cc_final: 0.5751 (ppp) REVERT: F 123 LYS cc_start: 0.5629 (tppt) cc_final: 0.5291 (tppt) REVERT: F 151 HIS cc_start: 0.6397 (t70) cc_final: 0.5741 (t70) REVERT: F 221 THR cc_start: 0.8400 (OUTLIER) cc_final: 0.8143 (t) REVERT: F 237 ILE cc_start: 0.6097 (OUTLIER) cc_final: 0.5511 (mp) outliers start: 53 outliers final: 35 residues processed: 219 average time/residue: 0.1107 time to fit residues: 33.2506 Evaluate side-chains 219 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 177 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 133 TYR Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 232 SER Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 51 CYS Chi-restraints excluded: chain B residue 125 CYS Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 30 ILE Chi-restraints excluded: chain D residue 41 THR Chi-restraints excluded: chain D residue 42 GLN Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 162 ILE Chi-restraints excluded: chain F residue 31 PHE Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 34 LEU Chi-restraints excluded: chain F residue 58 MET Chi-restraints excluded: chain F residue 63 MET Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain F residue 224 SER Chi-restraints excluded: chain F residue 232 THR Chi-restraints excluded: chain F residue 237 ILE Chi-restraints excluded: chain G residue 8 GLN Chi-restraints excluded: chain G residue 146 LEU Chi-restraints excluded: chain G residue 185 MET Chi-restraints excluded: chain G residue 192 MET Chi-restraints excluded: chain G residue 197 LEU Chi-restraints excluded: chain G residue 204 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 16 optimal weight: 1.9990 chunk 98 optimal weight: 3.9990 chunk 4 optimal weight: 0.4980 chunk 50 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 108 optimal weight: 0.3980 chunk 67 optimal weight: 2.9990 chunk 84 optimal weight: 6.9990 chunk 72 optimal weight: 0.7980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 129 GLN ** F 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 180 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.136668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.112849 restraints weight = 18726.334| |-----------------------------------------------------------------------------| r_work (start): 0.3608 rms_B_bonded: 3.00 r_work: 0.3447 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.2054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10236 Z= 0.191 Angle : 0.658 8.773 13874 Z= 0.348 Chirality : 0.047 0.222 1541 Planarity : 0.004 0.034 1789 Dihedral : 4.863 30.358 1394 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 4.81 % Allowed : 21.98 % Favored : 73.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.91 % Cis-general : 0.82 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.48 (0.23), residues: 1276 helix: -3.20 (1.28), residues: 6 sheet: -0.43 (0.20), residues: 645 loop : -1.52 (0.24), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 50 TYR 0.023 0.001 TYR E 172 PHE 0.015 0.002 PHE A 127 TRP 0.009 0.001 TRP G 196 HIS 0.005 0.001 HIS B 156 Details of bonding type rmsd covalent geometry : bond 0.00445 (10224) covalent geometry : angle 0.65690 (13850) SS BOND : bond 0.00572 ( 12) SS BOND : angle 1.25125 ( 24) hydrogen bonds : bond 0.03203 ( 386) hydrogen bonds : angle 6.39299 ( 990) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 173 time to evaluate : 0.384 Fit side-chains revert: symmetry clash REVERT: A 39 ILE cc_start: 0.6602 (OUTLIER) cc_final: 0.6111 (mp) REVERT: A 85 THR cc_start: 0.5764 (OUTLIER) cc_final: 0.5469 (t) REVERT: A 90 GLU cc_start: 0.6847 (mm-30) cc_final: 0.6098 (tp30) REVERT: A 133 TYR cc_start: 0.4076 (OUTLIER) cc_final: 0.2522 (m-80) REVERT: A 196 ASP cc_start: 0.7843 (t70) cc_final: 0.7524 (t70) REVERT: A 217 MET cc_start: 0.7193 (mmp) cc_final: 0.6330 (ttm) REVERT: B 102 ASP cc_start: 0.7972 (t0) cc_final: 0.7482 (t0) REVERT: D 69 ASP cc_start: 0.6911 (t0) cc_final: 0.6003 (t0) REVERT: D 158 LYS cc_start: 0.7484 (mtmm) cc_final: 0.6992 (ptpp) REVERT: E 220 CYS cc_start: 0.7557 (t) cc_final: 0.7198 (t) REVERT: E 241 PHE cc_start: 0.7133 (t80) cc_final: 0.6574 (t80) REVERT: F 34 LEU cc_start: 0.4251 (OUTLIER) cc_final: 0.3382 (tt) REVERT: F 58 MET cc_start: 0.6185 (OUTLIER) cc_final: 0.5937 (ppp) REVERT: F 151 HIS cc_start: 0.6538 (t70) cc_final: 0.6234 (t70) REVERT: F 210 MET cc_start: 0.3393 (OUTLIER) cc_final: 0.3025 (tpp) REVERT: F 237 ILE cc_start: 0.6051 (OUTLIER) cc_final: 0.5784 (mp) REVERT: G 99 LEU cc_start: 0.9298 (OUTLIER) cc_final: 0.9040 (pp) outliers start: 53 outliers final: 36 residues processed: 210 average time/residue: 0.1053 time to fit residues: 30.7289 Evaluate side-chains 216 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 172 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 133 TYR Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 232 SER Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 51 CYS Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 125 CYS Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 30 ILE Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 162 ILE Chi-restraints excluded: chain F residue 31 PHE Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 34 LEU Chi-restraints excluded: chain F residue 58 MET Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain F residue 210 MET Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain F residue 224 SER Chi-restraints excluded: chain F residue 232 THR Chi-restraints excluded: chain F residue 237 ILE Chi-restraints excluded: chain G residue 8 GLN Chi-restraints excluded: chain G residue 99 LEU Chi-restraints excluded: chain G residue 146 LEU Chi-restraints excluded: chain G residue 185 MET Chi-restraints excluded: chain G residue 192 MET Chi-restraints excluded: chain G residue 197 LEU Chi-restraints excluded: chain G residue 204 LEU Chi-restraints excluded: chain G residue 207 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 2 optimal weight: 0.8980 chunk 22 optimal weight: 0.9990 chunk 111 optimal weight: 0.9980 chunk 9 optimal weight: 0.8980 chunk 39 optimal weight: 0.5980 chunk 80 optimal weight: 9.9990 chunk 65 optimal weight: 0.9990 chunk 120 optimal weight: 0.8980 chunk 72 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 chunk 42 optimal weight: 0.0170 overall best weight: 0.6618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 42 GLN ** E 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 129 GLN ** F 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.138369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.114779 restraints weight = 18668.173| |-----------------------------------------------------------------------------| r_work (start): 0.3639 rms_B_bonded: 3.05 r_work: 0.3477 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.2163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 10236 Z= 0.140 Angle : 0.627 8.540 13874 Z= 0.332 Chirality : 0.046 0.191 1541 Planarity : 0.004 0.038 1789 Dihedral : 4.699 30.394 1394 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 4.36 % Allowed : 22.43 % Favored : 73.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.91 % Cis-general : 0.82 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.36 (0.23), residues: 1276 helix: None (None), residues: 0 sheet: -0.34 (0.20), residues: 633 loop : -1.47 (0.24), residues: 643 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 131 TYR 0.013 0.001 TYR E 172 PHE 0.012 0.001 PHE B 240 TRP 0.008 0.001 TRP F 67 HIS 0.004 0.001 HIS F 53 Details of bonding type rmsd covalent geometry : bond 0.00324 (10224) covalent geometry : angle 0.62625 (13850) SS BOND : bond 0.00398 ( 12) SS BOND : angle 1.09758 ( 24) hydrogen bonds : bond 0.02958 ( 386) hydrogen bonds : angle 6.16968 ( 990) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 179 time to evaluate : 0.363 Fit side-chains revert: symmetry clash REVERT: A 39 ILE cc_start: 0.6661 (OUTLIER) cc_final: 0.6129 (mp) REVERT: A 85 THR cc_start: 0.5807 (OUTLIER) cc_final: 0.5525 (t) REVERT: A 89 MET cc_start: 0.6641 (ppp) cc_final: 0.6368 (ppp) REVERT: A 90 GLU cc_start: 0.6841 (mm-30) cc_final: 0.6291 (tp30) REVERT: A 133 TYR cc_start: 0.3936 (OUTLIER) cc_final: 0.2374 (m-80) REVERT: A 196 ASP cc_start: 0.7709 (t70) cc_final: 0.7411 (t70) REVERT: A 217 MET cc_start: 0.7099 (mmp) cc_final: 0.6280 (ttm) REVERT: A 231 GLU cc_start: 0.7868 (pp20) cc_final: 0.7548 (pm20) REVERT: B 102 ASP cc_start: 0.7922 (t0) cc_final: 0.7414 (t0) REVERT: D 69 ASP cc_start: 0.6857 (t0) cc_final: 0.5962 (t0) REVERT: D 158 LYS cc_start: 0.7475 (mtmm) cc_final: 0.7014 (ptpp) REVERT: E 220 CYS cc_start: 0.7566 (t) cc_final: 0.7202 (t) REVERT: E 241 PHE cc_start: 0.7077 (t80) cc_final: 0.6548 (t80) REVERT: F 34 LEU cc_start: 0.4218 (OUTLIER) cc_final: 0.3420 (tt) REVERT: F 58 MET cc_start: 0.6117 (OUTLIER) cc_final: 0.5671 (ppp) REVERT: F 151 HIS cc_start: 0.6479 (t70) cc_final: 0.5715 (t70) REVERT: F 210 MET cc_start: 0.3397 (tpt) cc_final: 0.3068 (tpp) REVERT: F 221 THR cc_start: 0.8260 (OUTLIER) cc_final: 0.8021 (t) REVERT: F 237 ILE cc_start: 0.6177 (OUTLIER) cc_final: 0.5907 (mp) outliers start: 48 outliers final: 34 residues processed: 212 average time/residue: 0.1088 time to fit residues: 31.7119 Evaluate side-chains 213 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 172 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 133 TYR Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 232 SER Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 51 CYS Chi-restraints excluded: chain B residue 125 CYS Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 30 ILE Chi-restraints excluded: chain D residue 42 GLN Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 162 ILE Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 34 LEU Chi-restraints excluded: chain F residue 58 MET Chi-restraints excluded: chain F residue 63 MET Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain F residue 224 SER Chi-restraints excluded: chain F residue 232 THR Chi-restraints excluded: chain F residue 237 ILE Chi-restraints excluded: chain G residue 8 GLN Chi-restraints excluded: chain G residue 99 LEU Chi-restraints excluded: chain G residue 192 MET Chi-restraints excluded: chain G residue 197 LEU Chi-restraints excluded: chain G residue 204 LEU Chi-restraints excluded: chain G residue 207 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 104 optimal weight: 2.9990 chunk 14 optimal weight: 0.8980 chunk 73 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 111 optimal weight: 0.0870 chunk 69 optimal weight: 0.6980 chunk 11 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 52 optimal weight: 0.7980 chunk 49 optimal weight: 0.9990 overall best weight: 0.6960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 42 GLN ** E 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 129 GLN E 149 ASN ** F 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 180 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.138579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.114956 restraints weight = 18585.299| |-----------------------------------------------------------------------------| r_work (start): 0.3641 rms_B_bonded: 3.04 r_work: 0.3480 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.2305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10236 Z= 0.144 Angle : 0.638 8.840 13874 Z= 0.337 Chirality : 0.046 0.176 1541 Planarity : 0.004 0.040 1789 Dihedral : 4.697 29.787 1394 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 4.27 % Allowed : 22.71 % Favored : 73.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.91 % Cis-general : 0.82 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.39 (0.23), residues: 1276 helix: -3.24 (1.24), residues: 6 sheet: -0.32 (0.21), residues: 626 loop : -1.50 (0.24), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 131 TYR 0.015 0.001 TYR E 172 PHE 0.014 0.001 PHE B 240 TRP 0.007 0.001 TRP F 67 HIS 0.004 0.001 HIS F 53 Details of bonding type rmsd covalent geometry : bond 0.00333 (10224) covalent geometry : angle 0.63657 (13850) SS BOND : bond 0.00410 ( 12) SS BOND : angle 1.15534 ( 24) hydrogen bonds : bond 0.02996 ( 386) hydrogen bonds : angle 6.12941 ( 990) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 180 time to evaluate : 0.358 Fit side-chains revert: symmetry clash REVERT: A 39 ILE cc_start: 0.6585 (OUTLIER) cc_final: 0.6116 (mp) REVERT: A 85 THR cc_start: 0.5789 (OUTLIER) cc_final: 0.5513 (t) REVERT: A 89 MET cc_start: 0.6589 (ppp) cc_final: 0.6338 (ppp) REVERT: A 90 GLU cc_start: 0.6910 (mm-30) cc_final: 0.6408 (tp30) REVERT: A 133 TYR cc_start: 0.3889 (OUTLIER) cc_final: 0.2529 (m-80) REVERT: A 196 ASP cc_start: 0.7720 (t70) cc_final: 0.7416 (t70) REVERT: A 231 GLU cc_start: 0.7891 (pp20) cc_final: 0.7564 (pm20) REVERT: B 102 ASP cc_start: 0.7955 (t0) cc_final: 0.7481 (t0) REVERT: D 69 ASP cc_start: 0.6860 (t0) cc_final: 0.5966 (t0) REVERT: D 158 LYS cc_start: 0.7428 (mtmm) cc_final: 0.6961 (ptpp) REVERT: E 178 GLN cc_start: 0.8036 (mm-40) cc_final: 0.7649 (mm110) REVERT: E 220 CYS cc_start: 0.7585 (t) cc_final: 0.7090 (t) REVERT: E 241 PHE cc_start: 0.7078 (t80) cc_final: 0.6572 (t80) REVERT: F 34 LEU cc_start: 0.4222 (OUTLIER) cc_final: 0.3419 (tt) REVERT: F 58 MET cc_start: 0.6152 (OUTLIER) cc_final: 0.5659 (ppp) REVERT: F 142 LYS cc_start: 0.7942 (tmtt) cc_final: 0.7665 (tttm) REVERT: F 151 HIS cc_start: 0.6486 (t70) cc_final: 0.5706 (t70) REVERT: F 210 MET cc_start: 0.3417 (OUTLIER) cc_final: 0.3069 (tpp) REVERT: F 221 THR cc_start: 0.8295 (OUTLIER) cc_final: 0.8037 (t) REVERT: F 237 ILE cc_start: 0.6184 (OUTLIER) cc_final: 0.5912 (mp) REVERT: G 99 LEU cc_start: 0.9325 (OUTLIER) cc_final: 0.9114 (pp) outliers start: 47 outliers final: 34 residues processed: 210 average time/residue: 0.1069 time to fit residues: 31.0814 Evaluate side-chains 220 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 177 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 133 TYR Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 232 SER Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 51 CYS Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 125 CYS Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 30 ILE Chi-restraints excluded: chain D residue 42 GLN Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 162 ILE Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 34 LEU Chi-restraints excluded: chain F residue 58 MET Chi-restraints excluded: chain F residue 63 MET Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain F residue 210 MET Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain F residue 224 SER Chi-restraints excluded: chain F residue 232 THR Chi-restraints excluded: chain F residue 237 ILE Chi-restraints excluded: chain G residue 8 GLN Chi-restraints excluded: chain G residue 99 LEU Chi-restraints excluded: chain G residue 185 MET Chi-restraints excluded: chain G residue 192 MET Chi-restraints excluded: chain G residue 197 LEU Chi-restraints excluded: chain G residue 204 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 59 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 14 optimal weight: 0.3980 chunk 119 optimal weight: 0.9980 chunk 26 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 108 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 84 optimal weight: 4.9990 chunk 93 optimal weight: 1.9990 chunk 102 optimal weight: 0.7980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 129 GLN ** F 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 180 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.137167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.113883 restraints weight = 18802.386| |-----------------------------------------------------------------------------| r_work (start): 0.3621 rms_B_bonded: 3.21 r_work: 0.3457 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.2263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 10236 Z= 0.179 Angle : 0.654 8.699 13874 Z= 0.346 Chirality : 0.047 0.166 1541 Planarity : 0.004 0.043 1789 Dihedral : 4.832 29.217 1394 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 4.00 % Allowed : 22.98 % Favored : 73.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.91 % Cis-general : 0.82 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.42 (0.23), residues: 1276 helix: -3.26 (1.22), residues: 6 sheet: -0.38 (0.20), residues: 639 loop : -1.48 (0.24), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 50 TYR 0.019 0.001 TYR E 172 PHE 0.016 0.002 PHE B 240 TRP 0.008 0.001 TRP G 196 HIS 0.005 0.001 HIS B 156 Details of bonding type rmsd covalent geometry : bond 0.00418 (10224) covalent geometry : angle 0.65293 (13850) SS BOND : bond 0.00489 ( 12) SS BOND : angle 1.24763 ( 24) hydrogen bonds : bond 0.03169 ( 386) hydrogen bonds : angle 6.26229 ( 990) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2742.70 seconds wall clock time: 47 minutes 43.88 seconds (2863.88 seconds total)