Starting phenix.real_space_refine on Sun Apr 5 09:31:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ly6_63505/04_2026/9ly6_63505_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ly6_63505/04_2026/9ly6_63505.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.67 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ly6_63505/04_2026/9ly6_63505_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ly6_63505/04_2026/9ly6_63505_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ly6_63505/04_2026/9ly6_63505.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ly6_63505/04_2026/9ly6_63505.map" } resolution = 3.67 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= 0.009 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 37 5.16 5 C 5789 2.51 5 N 1552 2.21 5 O 1818 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 34 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9196 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 405, 3076 Classifications: {'peptide': 405} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 383} Chain breaks: 5 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 1602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1602 Classifications: {'peptide': 213} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 198} Chain breaks: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "C" Number of atoms: 1503 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1503 Classifications: {'peptide': 196} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 185} Chain breaks: 3 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 1546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1546 Classifications: {'peptide': 204} Link IDs: {'PTRANS': 9, 'TRANS': 194} Chain breaks: 5 Chain: "E" Number of atoms: 1469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1469 Classifications: {'peptide': 190} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 182} Chain breaks: 6 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Time building chain proxies: 2.21, per 1000 atoms: 0.24 Number of scatterers: 9196 At special positions: 0 Unit cell: (58.697, 128.539, 173.862, 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 37 16.00 O 1818 8.00 N 1552 7.00 C 5789 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 50 " - pdb=" SG CYS A 122 " distance=2.05 Simple disulfide: pdb=" SG CYS A 165 " - pdb=" SG CYS A 220 " distance=2.04 Simple disulfide: pdb=" SG CYS A 268 " - pdb=" SG CYS A 340 " distance=2.05 Simple disulfide: pdb=" SG CYS A 383 " - pdb=" SG CYS A 438 " distance=2.04 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " distance=2.03 Simple disulfide: pdb=" SG CYS B 145 " - pdb=" SG CYS B 201 " distance=2.03 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 87 " distance=2.04 Simple disulfide: pdb=" SG CYS C 133 " - pdb=" SG CYS C 193 " distance=2.04 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 145 " - pdb=" SG CYS D 201 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 87 " distance=2.04 Simple disulfide: pdb=" SG CYS E 133 " - pdb=" SG CYS E 193 " 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: 0.68 Conformation dependent library (CDL) restraints added in 274.7 milliseconds 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2256 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 32 sheets defined 7.0% alpha, 50.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'A' and resid 59 through 63 Processing helix chain 'A' and resid 96 through 101 removed outlier: 4.371A pdb=" N ALA A 101 " --> pdb=" O PRO A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 117 Processing helix chain 'A' and resid 186 through 188 No H-bonds generated for 'chain 'A' and resid 186 through 188' Processing helix chain 'A' and resid 277 through 280 Processing helix chain 'A' and resid 314 through 319 removed outlier: 4.308A pdb=" N ALA A 319 " --> pdb=" O PRO A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 335 Processing helix chain 'B' and resid 28 through 32 removed outlier: 3.598A pdb=" N TYR B 32 " --> pdb=" O PHE B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 91 removed outlier: 3.634A pdb=" N THR B 91 " --> pdb=" O SER B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 163 No H-bonds generated for 'chain 'B' and resid 161 through 163' Processing helix chain 'B' and resid 192 through 194 No H-bonds generated for 'chain 'B' and resid 192 through 194' Processing helix chain 'C' and resid 78 through 82 removed outlier: 3.565A pdb=" N PHE C 82 " --> pdb=" O PRO C 79 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 91 removed outlier: 3.634A pdb=" N THR D 91 " --> pdb=" O SER D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 161 through 163 No H-bonds generated for 'chain 'D' and resid 161 through 163' Processing helix chain 'D' and resid 192 through 194 No H-bonds generated for 'chain 'D' and resid 192 through 194' Processing helix chain 'E' and resid 78 through 82 removed outlier: 3.566A pdb=" N PHE E 82 " --> pdb=" O PRO E 79 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 125 Processing helix chain 'E' and resid 182 through 188 removed outlier: 3.875A pdb=" N HIS E 188 " --> pdb=" O ASP E 184 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 31 through 32 Processing sheet with id=AA2, first strand: chain 'A' and resid 38 through 41 removed outlier: 6.787A pdb=" N LEU A 65 " --> pdb=" O SER A 78 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N SER A 78 " --> pdb=" O LEU A 65 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N TRP A 67 " --> pdb=" O VAL A 76 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N VAL A 76 " --> pdb=" O SER A 87 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N SER A 87 " --> pdb=" O VAL A 76 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N SER A 78 " --> pdb=" O GLN A 85 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 46 through 48 Processing sheet with id=AA4, first strand: chain 'A' and resid 146 through 150 removed outlier: 5.452A pdb=" N PHE A 202 " --> pdb=" O GLN A 169 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 175 through 177 removed outlier: 3.599A pdb=" N GLN A 229 " --> pdb=" O ASN A 224 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 249 through 250 Processing sheet with id=AA7, first strand: chain 'A' and resid 256 through 259 removed outlier: 6.841A pdb=" N LEU A 283 " --> pdb=" O SER A 296 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N SER A 296 " --> pdb=" O LEU A 283 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N TRP A 285 " --> pdb=" O VAL A 294 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N VAL A 294 " --> pdb=" O SER A 305 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N SER A 305 " --> pdb=" O VAL A 294 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N SER A 296 " --> pdb=" O GLN A 303 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 264 through 266 Processing sheet with id=AA9, first strand: chain 'A' and resid 364 through 368 removed outlier: 5.525A pdb=" N PHE A 420 " --> pdb=" O ARG A 387 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 393 through 395 removed outlier: 3.568A pdb=" N GLN A 447 " --> pdb=" O ASN A 442 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 3 through 6 Processing sheet with id=AB3, first strand: chain 'B' and resid 10 through 12 removed outlier: 4.023A pdb=" N ILE B 33 " --> pdb=" O ARG B 99 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N MET B 34 " --> pdb=" O GLY B 50 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N GLY B 50 " --> pdb=" O MET B 34 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N TRP B 36 " --> pdb=" O MET B 48 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 10 through 12 removed outlier: 4.060A pdb=" N VAL B 107 " --> pdb=" O ARG B 98 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 125 through 129 removed outlier: 6.039A pdb=" N TYR B 181 " --> pdb=" O ASP B 149 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 125 through 129 removed outlier: 6.039A pdb=" N TYR B 181 " --> pdb=" O ASP B 149 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 156 through 159 removed outlier: 4.355A pdb=" N TYR B 199 " --> pdb=" O VAL B 216 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 4 through 7 Processing sheet with id=AB9, first strand: chain 'C' and resid 10 through 12 removed outlier: 7.231A pdb=" N ILE C 32 " --> pdb=" O TYR C 48 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N TYR C 48 " --> pdb=" O ILE C 32 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N TRP C 34 " --> pdb=" O TRP C 46 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 10 through 12 removed outlier: 3.771A pdb=" N THR C 96 " --> pdb=" O GLN C 89 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 113 through 117 removed outlier: 6.194A pdb=" N TYR C 172 " --> pdb=" O ASN C 137 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 152 through 153 Processing sheet with id=AC4, first strand: chain 'D' and resid 3 through 6 Processing sheet with id=AC5, first strand: chain 'D' and resid 10 through 12 removed outlier: 4.024A pdb=" N ILE D 33 " --> pdb=" O ARG D 99 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N MET D 34 " --> pdb=" O GLY D 50 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N GLY D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N TRP D 36 " --> pdb=" O MET D 48 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 10 through 12 removed outlier: 4.059A pdb=" N VAL D 107 " --> pdb=" O ARG D 98 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 125 through 129 removed outlier: 6.039A pdb=" N TYR D 181 " --> pdb=" O ASP D 149 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 125 through 129 removed outlier: 6.039A pdb=" N TYR D 181 " --> pdb=" O ASP D 149 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 156 through 159 removed outlier: 4.355A pdb=" N TYR D 199 " --> pdb=" O VAL D 216 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 4 through 7 Processing sheet with id=AD2, first strand: chain 'E' and resid 10 through 12 removed outlier: 7.230A pdb=" N ILE E 32 " --> pdb=" O TYR E 48 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N TYR E 48 " --> pdb=" O ILE E 32 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N TRP E 34 " --> pdb=" O TRP E 46 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 10 through 12 removed outlier: 3.771A pdb=" N THR E 96 " --> pdb=" O GLN E 89 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 114 through 117 removed outlier: 6.194A pdb=" N TYR E 172 " --> pdb=" O ASN E 137 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 152 through 153 450 hydrogen bonds defined for protein. 1110 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: 1.64 Time building geometry restraints manager: 0.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2354 1.33 - 1.45: 1838 1.45 - 1.57: 5148 1.57 - 1.70: 0 1.70 - 1.82: 47 Bond restraints: 9387 Sorted by residual: bond pdb=" CZ ARG A 92 " pdb=" NH2 ARG A 92 " ideal model delta sigma weight residual 1.330 1.276 0.054 1.30e-02 5.92e+03 1.75e+01 bond pdb=" CZ ARG A 310 " pdb=" NH2 ARG A 310 " ideal model delta sigma weight residual 1.330 1.276 0.054 1.30e-02 5.92e+03 1.74e+01 bond pdb=" CA ALA D 142 " pdb=" C ALA D 142 " ideal model delta sigma weight residual 1.520 1.474 0.046 1.22e-02 6.72e+03 1.44e+01 bond pdb=" CA ALA B 142 " pdb=" C ALA B 142 " ideal model delta sigma weight residual 1.520 1.475 0.046 1.22e-02 6.72e+03 1.40e+01 bond pdb=" CA ALA B 141 " pdb=" C ALA B 141 " ideal model delta sigma weight residual 1.526 1.487 0.039 1.37e-02 5.33e+03 8.10e+00 ... (remaining 9382 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.58: 11159 1.58 - 3.16: 1276 3.16 - 4.74: 287 4.74 - 6.31: 33 6.31 - 7.89: 10 Bond angle restraints: 12765 Sorted by residual: angle pdb=" OE1 GLN A 286 " pdb=" CD GLN A 286 " pdb=" NE2 GLN A 286 " ideal model delta sigma weight residual 122.60 115.82 6.78 1.00e+00 1.00e+00 4.59e+01 angle pdb=" CA ASP A 334 " pdb=" CB ASP A 334 " pdb=" CG ASP A 334 " ideal model delta sigma weight residual 112.60 118.35 -5.75 1.00e+00 1.00e+00 3.31e+01 angle pdb=" N THR C 68 " pdb=" CA THR C 68 " pdb=" C THR C 68 " ideal model delta sigma weight residual 112.89 119.78 -6.89 1.24e+00 6.50e-01 3.09e+01 angle pdb=" N THR E 68 " pdb=" CA THR E 68 " pdb=" C THR E 68 " ideal model delta sigma weight residual 112.89 119.71 -6.82 1.24e+00 6.50e-01 3.03e+01 angle pdb=" OE1 GLN A 280 " pdb=" CD GLN A 280 " pdb=" NE2 GLN A 280 " ideal model delta sigma weight residual 122.60 117.74 4.86 1.00e+00 1.00e+00 2.36e+01 ... (remaining 12760 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 5072 17.93 - 35.85: 395 35.85 - 53.78: 92 53.78 - 71.70: 20 71.70 - 89.63: 16 Dihedral angle restraints: 5595 sinusoidal: 2113 harmonic: 3482 Sorted by residual: dihedral pdb=" CA SER A 305 " pdb=" C SER A 305 " pdb=" N ALA A 306 " pdb=" CA ALA A 306 " ideal model delta harmonic sigma weight residual 180.00 156.60 23.40 0 5.00e+00 4.00e-02 2.19e+01 dihedral pdb=" CD ARG C 18 " pdb=" NE ARG C 18 " pdb=" CZ ARG C 18 " pdb=" NH1 ARG C 18 " ideal model delta sinusoidal sigma weight residual 0.00 36.39 -36.39 1 1.00e+01 1.00e-02 1.87e+01 dihedral pdb=" CA ALA A 174 " pdb=" C ALA A 174 " pdb=" N GLU A 175 " pdb=" CA GLU A 175 " ideal model delta harmonic sigma weight residual 180.00 158.73 21.27 0 5.00e+00 4.00e-02 1.81e+01 ... (remaining 5592 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 1086 0.064 - 0.128: 298 0.128 - 0.191: 84 0.191 - 0.255: 7 0.255 - 0.319: 5 Chirality restraints: 1480 Sorted by residual: chirality pdb=" CA VAL B 2 " pdb=" N VAL B 2 " pdb=" C VAL B 2 " pdb=" CB VAL B 2 " both_signs ideal model delta sigma weight residual False 2.44 2.12 0.32 2.00e-01 2.50e+01 2.55e+00 chirality pdb=" CA VAL D 2 " pdb=" N VAL D 2 " pdb=" C VAL D 2 " pdb=" CB VAL D 2 " both_signs ideal model delta sigma weight residual False 2.44 2.13 0.32 2.00e-01 2.50e+01 2.49e+00 chirality pdb=" CA ASP A 154 " pdb=" N ASP A 154 " pdb=" C ASP A 154 " pdb=" CB ASP A 154 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.89e+00 ... (remaining 1477 not shown) Planarity restraints: 1619 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 178 " -0.100 2.00e-02 2.50e+03 5.72e-02 8.17e+01 pdb=" CG TRP A 178 " -0.008 2.00e-02 2.50e+03 pdb=" CD1 TRP A 178 " 0.030 2.00e-02 2.50e+03 pdb=" CD2 TRP A 178 " 0.048 2.00e-02 2.50e+03 pdb=" NE1 TRP A 178 " 0.044 2.00e-02 2.50e+03 pdb=" CE2 TRP A 178 " 0.009 2.00e-02 2.50e+03 pdb=" CE3 TRP A 178 " 0.088 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 178 " -0.068 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 178 " 0.023 2.00e-02 2.50e+03 pdb=" CH2 TRP A 178 " -0.067 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 396 " -0.099 2.00e-02 2.50e+03 5.59e-02 7.82e+01 pdb=" CG TRP A 396 " -0.009 2.00e-02 2.50e+03 pdb=" CD1 TRP A 396 " 0.039 2.00e-02 2.50e+03 pdb=" CD2 TRP A 396 " 0.041 2.00e-02 2.50e+03 pdb=" NE1 TRP A 396 " 0.042 2.00e-02 2.50e+03 pdb=" CE2 TRP A 396 " 0.007 2.00e-02 2.50e+03 pdb=" CE3 TRP A 396 " 0.083 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 396 " -0.069 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 396 " 0.029 2.00e-02 2.50e+03 pdb=" CH2 TRP A 396 " -0.063 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 285 " -0.082 2.00e-02 2.50e+03 5.49e-02 7.53e+01 pdb=" CG TRP A 285 " -0.025 2.00e-02 2.50e+03 pdb=" CD1 TRP A 285 " 0.028 2.00e-02 2.50e+03 pdb=" CD2 TRP A 285 " 0.028 2.00e-02 2.50e+03 pdb=" NE1 TRP A 285 " 0.062 2.00e-02 2.50e+03 pdb=" CE2 TRP A 285 " 0.009 2.00e-02 2.50e+03 pdb=" CE3 TRP A 285 " 0.078 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 285 " -0.076 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 285 " 0.040 2.00e-02 2.50e+03 pdb=" CH2 TRP A 285 " -0.062 2.00e-02 2.50e+03 ... (remaining 1616 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 45 2.59 - 3.17: 7064 3.17 - 3.74: 12783 3.74 - 4.32: 19148 4.32 - 4.90: 32928 Nonbonded interactions: 71968 Sorted by model distance: nonbonded pdb=" OE2 GLU C 194 " pdb=" OG1 THR C 205 " model vdw 2.011 3.040 nonbonded pdb=" OD1 ASN B 204 " pdb=" NZ LYS B 211 " model vdw 2.176 3.120 nonbonded pdb=" OD1 ASN D 204 " pdb=" NZ LYS D 211 " model vdw 2.177 3.120 nonbonded pdb=" NZ LYS D 214 " pdb=" OE2 GLU E 122 " model vdw 2.184 3.120 nonbonded pdb=" NH2 ARG D 87 " pdb=" OE2 GLU D 89 " model vdw 2.188 3.120 ... (remaining 71963 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 'B' and (resid 1 through 29 or resid 32 through 51 or resid 58 through 10 \ 0 or resid 103 through 138 or resid 140 through 151 or resid 155 through 218)) selection = (chain 'D' and (resid 1 through 12 or (resid 13 and (name N or name CA or name C \ or name O or name CB )) or resid 14 through 121 or (resid 122 and (name N or na \ me CA or name C or name O or name CB )) or resid 123 through 218)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.160 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3058 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 : 0.008 0.054 9399 Z= 0.447 Angle : 1.101 7.892 12789 Z= 0.713 Chirality : 0.066 0.319 1480 Planarity : 0.010 0.300 1619 Dihedral : 15.033 89.627 3303 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.51 % Allowed : 16.51 % Favored : 80.98 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 11.86 % Cis-general : 0.00 % 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: 1.03 (0.25), residues: 1157 helix: 0.44 (1.41), residues: 13 sheet: 0.98 (0.21), residues: 614 loop : 0.47 (0.27), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 18 TYR 0.061 0.004 TYR A 360 PHE 0.053 0.004 PHE A 129 TRP 0.100 0.010 TRP A 178 HIS 0.022 0.003 HIS A 295 Details of bonding type rmsd covalent geometry : bond 0.00773 ( 9387) covalent geometry : angle 1.10028 (12765) SS BOND : bond 0.00906 ( 12) SS BOND : angle 1.28407 ( 24) hydrogen bonds : bond 0.10763 ( 398) hydrogen bonds : angle 7.19941 ( 1110) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 247 time to evaluate : 0.281 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 VAL cc_start: 0.8568 (t) cc_final: 0.7935 (p) REVERT: A 338 PHE cc_start: 0.5190 (m-80) cc_final: 0.4470 (m-80) REVERT: B 187 VAL cc_start: 0.4698 (OUTLIER) cc_final: 0.4252 (m) outliers start: 26 outliers final: 1 residues processed: 270 average time/residue: 0.1100 time to fit residues: 39.8163 Evaluate side-chains 125 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 123 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 187 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 108 optimal weight: 0.5980 chunk 49 optimal weight: 0.2980 chunk 97 optimal weight: 1.9990 chunk 113 optimal weight: 5.9990 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 20.0000 chunk 117 optimal weight: 0.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 39 GLN ** C 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 37 GLN D 39 GLN D 205 HIS E 37 GLN ** E 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5034 r_free = 0.5034 target = 0.226779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4816 r_free = 0.4816 target = 0.206022 restraints weight = 22069.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4829 r_free = 0.4829 target = 0.208151 restraints weight = 16648.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4836 r_free = 0.4836 target = 0.208718 restraints weight = 13632.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4845 r_free = 0.4845 target = 0.209566 restraints weight = 11429.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4851 r_free = 0.4851 target = 0.209939 restraints weight = 11092.078| |-----------------------------------------------------------------------------| r_work (final): 0.4832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4363 moved from start: 0.3687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9399 Z= 0.151 Angle : 0.651 14.231 12789 Z= 0.338 Chirality : 0.046 0.160 1480 Planarity : 0.005 0.052 1619 Dihedral : 4.882 25.684 1272 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 3.67 % Allowed : 19.50 % Favored : 76.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.86 % Cis-general : 0.00 % 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: 1.47 (0.25), residues: 1157 helix: 0.38 (1.43), residues: 14 sheet: 1.30 (0.21), residues: 604 loop : 0.74 (0.28), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 67 TYR 0.020 0.002 TYR C 172 PHE 0.020 0.002 PHE D 64 TRP 0.016 0.002 TRP D 47 HIS 0.010 0.002 HIS E 33 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 9387) covalent geometry : angle 0.65111 (12765) SS BOND : bond 0.00568 ( 12) SS BOND : angle 0.81318 ( 24) hydrogen bonds : bond 0.03145 ( 398) hydrogen bonds : angle 5.52329 ( 1110) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 125 time to evaluate : 0.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 3 GLN cc_start: 0.3938 (tp-100) cc_final: 0.3702 (tt0) REVERT: D 113 LEU cc_start: 0.7193 (OUTLIER) cc_final: 0.6955 (mt) REVERT: D 149 ASP cc_start: 0.6153 (m-30) cc_final: 0.5296 (p0) REVERT: D 181 TYR cc_start: 0.2518 (m-80) cc_final: 0.2311 (m-80) REVERT: E 44 LYS cc_start: 0.7340 (OUTLIER) cc_final: 0.6972 (mmmt) REVERT: E 131 VAL cc_start: 0.4117 (t) cc_final: 0.3810 (p) outliers start: 38 outliers final: 20 residues processed: 153 average time/residue: 0.1090 time to fit residues: 22.6522 Evaluate side-chains 115 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 93 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 289 ASP Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 455 ILE Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain C residue 136 ASN Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 81 MET Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 44 LYS Chi-restraints excluded: chain E residue 87 CYS Chi-restraints excluded: chain E residue 179 THR Chi-restraints excluded: chain E residue 180 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 97 optimal weight: 0.9990 chunk 79 optimal weight: 6.9990 chunk 54 optimal weight: 0.9990 chunk 72 optimal weight: 0.7980 chunk 91 optimal weight: 1.9990 chunk 63 optimal weight: 7.9990 chunk 19 optimal weight: 6.9990 chunk 52 optimal weight: 8.9990 chunk 78 optimal weight: 0.9990 chunk 106 optimal weight: 7.9990 chunk 65 optimal weight: 0.6980 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 3 GLN E 33 HIS E 123 GLN ** E 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4969 r_free = 0.4969 target = 0.220300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4780 r_free = 0.4780 target = 0.201480 restraints weight = 23026.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4776 r_free = 0.4776 target = 0.202200 restraints weight = 23740.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4801 r_free = 0.4801 target = 0.204541 restraints weight = 17452.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4803 r_free = 0.4803 target = 0.204793 restraints weight = 12161.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4812 r_free = 0.4812 target = 0.205559 restraints weight = 12731.522| |-----------------------------------------------------------------------------| r_work (final): 0.4796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4528 moved from start: 0.5269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 9399 Z= 0.156 Angle : 0.639 11.809 12789 Z= 0.330 Chirality : 0.045 0.180 1480 Planarity : 0.005 0.049 1619 Dihedral : 4.871 25.088 1271 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 5.02 % Allowed : 17.86 % Favored : 77.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.86 % Cis-general : 0.00 % 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: 1.41 (0.25), residues: 1157 helix: 0.07 (1.32), residues: 14 sheet: 1.43 (0.21), residues: 581 loop : 0.53 (0.27), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 67 TYR 0.027 0.002 TYR C 172 PHE 0.027 0.002 PHE E 117 TRP 0.020 0.002 TRP C 147 HIS 0.006 0.001 HIS B 104 Details of bonding type rmsd covalent geometry : bond 0.00348 ( 9387) covalent geometry : angle 0.63898 (12765) SS BOND : bond 0.00512 ( 12) SS BOND : angle 0.77429 ( 24) hydrogen bonds : bond 0.03293 ( 398) hydrogen bonds : angle 5.43020 ( 1110) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 108 time to evaluate : 0.293 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 419 LEU cc_start: 0.6390 (OUTLIER) cc_final: 0.6051 (mt) REVERT: D 33 ILE cc_start: 0.6384 (OUTLIER) cc_final: 0.6151 (mm) REVERT: D 149 ASP cc_start: 0.6140 (m-30) cc_final: 0.5630 (p0) REVERT: D 181 TYR cc_start: 0.3574 (m-80) cc_final: 0.3322 (m-80) REVERT: E 57 VAL cc_start: 0.5557 (OUTLIER) cc_final: 0.5038 (p) outliers start: 52 outliers final: 29 residues processed: 148 average time/residue: 0.0835 time to fit residues: 17.5862 Evaluate side-chains 118 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 86 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 289 ASP Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 377 ASP Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 410 THR Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 188 HIS Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 33 ILE Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain E residue 76 SER Chi-restraints excluded: chain E residue 87 CYS Chi-restraints excluded: chain E residue 179 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 47 optimal weight: 10.0000 chunk 45 optimal weight: 0.9990 chunk 55 optimal weight: 6.9990 chunk 88 optimal weight: 0.9980 chunk 43 optimal weight: 0.6980 chunk 15 optimal weight: 0.7980 chunk 110 optimal weight: 0.9980 chunk 86 optimal weight: 3.9990 chunk 64 optimal weight: 0.9990 chunk 71 optimal weight: 5.9990 chunk 69 optimal weight: 0.5980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 43 GLN B 169 HIS C 33 HIS ** C 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 3 GLN D 169 HIS E 165 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4951 r_free = 0.4951 target = 0.218137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4758 r_free = 0.4758 target = 0.198728 restraints weight = 22969.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4744 r_free = 0.4744 target = 0.198508 restraints weight = 25026.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4767 r_free = 0.4767 target = 0.200766 restraints weight = 18498.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4766 r_free = 0.4766 target = 0.200625 restraints weight = 13478.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4776 r_free = 0.4776 target = 0.201598 restraints weight = 13349.462| |-----------------------------------------------------------------------------| r_work (final): 0.4760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4697 moved from start: 0.6033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9399 Z= 0.137 Angle : 0.595 10.824 12789 Z= 0.309 Chirality : 0.044 0.158 1480 Planarity : 0.005 0.054 1619 Dihedral : 4.617 25.923 1271 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 3.47 % Allowed : 19.79 % Favored : 76.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.86 % Cis-general : 0.00 % 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: 1.38 (0.25), residues: 1157 helix: 0.15 (1.44), residues: 14 sheet: 1.46 (0.21), residues: 575 loop : 0.45 (0.28), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 98 TYR 0.023 0.002 TYR C 172 PHE 0.015 0.002 PHE D 64 TRP 0.012 0.002 TRP E 46 HIS 0.006 0.001 HIS B 104 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 9387) covalent geometry : angle 0.59476 (12765) SS BOND : bond 0.00534 ( 12) SS BOND : angle 0.73379 ( 24) hydrogen bonds : bond 0.02995 ( 398) hydrogen bonds : angle 5.23029 ( 1110) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 93 time to evaluate : 0.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 149 ASP cc_start: 0.6020 (m-30) cc_final: 0.5638 (p0) outliers start: 36 outliers final: 26 residues processed: 121 average time/residue: 0.0806 time to fit residues: 14.0577 Evaluate side-chains 105 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 79 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 289 ASP Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 188 HIS Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 38 ARG Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 76 SER Chi-restraints excluded: chain E residue 87 CYS Chi-restraints excluded: chain E residue 179 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 74 optimal weight: 1.9990 chunk 19 optimal weight: 0.0970 chunk 98 optimal weight: 4.9990 chunk 59 optimal weight: 5.9990 chunk 5 optimal weight: 3.9990 chunk 57 optimal weight: 10.0000 chunk 22 optimal weight: 9.9990 chunk 88 optimal weight: 0.6980 chunk 61 optimal weight: 7.9990 chunk 13 optimal weight: 0.9980 chunk 82 optimal weight: 3.9990 overall best weight: 1.5582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 61 ASN D 3 GLN ** D 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 169 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4915 r_free = 0.4915 target = 0.212779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4731 r_free = 0.4731 target = 0.194994 restraints weight = 22288.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4722 r_free = 0.4722 target = 0.194800 restraints weight = 23726.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4740 r_free = 0.4740 target = 0.196571 restraints weight = 19310.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4740 r_free = 0.4740 target = 0.196630 restraints weight = 14280.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4745 r_free = 0.4745 target = 0.197224 restraints weight = 13904.839| |-----------------------------------------------------------------------------| r_work (final): 0.4714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4902 moved from start: 0.7410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 9399 Z= 0.222 Angle : 0.696 9.243 12789 Z= 0.370 Chirality : 0.046 0.170 1480 Planarity : 0.006 0.054 1619 Dihedral : 5.369 30.371 1271 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 14.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 3.96 % Allowed : 20.37 % Favored : 75.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.86 % Cis-general : 0.00 % 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: 0.85 (0.25), residues: 1157 helix: -1.95 (1.07), residues: 20 sheet: 1.17 (0.21), residues: 568 loop : 0.09 (0.27), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 67 TYR 0.034 0.003 TYR C 172 PHE 0.017 0.002 PHE C 138 TRP 0.024 0.003 TRP C 90 HIS 0.009 0.002 HIS B 104 Details of bonding type rmsd covalent geometry : bond 0.00486 ( 9387) covalent geometry : angle 0.69485 (12765) SS BOND : bond 0.00693 ( 12) SS BOND : angle 0.98293 ( 24) hydrogen bonds : bond 0.03826 ( 398) hydrogen bonds : angle 6.10658 ( 1110) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 95 time to evaluate : 0.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 90 TRP cc_start: 0.3055 (t-100) cc_final: 0.2698 (p-90) REVERT: E 160 GLU cc_start: 0.5376 (tt0) cc_final: 0.5112 (tt0) outliers start: 41 outliers final: 27 residues processed: 126 average time/residue: 0.0900 time to fit residues: 16.1107 Evaluate side-chains 106 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 79 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 289 ASP Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain C residue 12 SER Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 38 ARG Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 76 SER Chi-restraints excluded: chain E residue 87 CYS Chi-restraints excluded: chain E residue 179 THR Chi-restraints excluded: chain E residue 180 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 64 optimal weight: 1.9990 chunk 95 optimal weight: 5.9990 chunk 14 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 37 optimal weight: 6.9990 chunk 31 optimal weight: 1.9990 chunk 114 optimal weight: 0.9980 chunk 118 optimal weight: 6.9990 chunk 16 optimal weight: 4.9990 chunk 43 optimal weight: 0.5980 chunk 50 optimal weight: 0.5980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4862 r_free = 0.4862 target = 0.208663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4656 r_free = 0.4656 target = 0.188936 restraints weight = 21673.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4645 r_free = 0.4645 target = 0.188481 restraints weight = 21698.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4664 r_free = 0.4664 target = 0.190339 restraints weight = 18571.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4664 r_free = 0.4664 target = 0.190371 restraints weight = 13820.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4670 r_free = 0.4670 target = 0.191010 restraints weight = 13987.664| |-----------------------------------------------------------------------------| r_work (final): 0.4675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5001 moved from start: 0.8040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 9399 Z= 0.172 Angle : 0.649 12.108 12789 Z= 0.340 Chirality : 0.045 0.189 1480 Planarity : 0.006 0.053 1619 Dihedral : 5.088 27.888 1271 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 3.86 % Allowed : 21.14 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.86 % Cis-general : 0.00 % 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: 0.70 (0.25), residues: 1157 helix: -2.09 (1.02), residues: 20 sheet: 1.01 (0.21), residues: 570 loop : 0.08 (0.27), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 38 TYR 0.041 0.002 TYR C 172 PHE 0.021 0.002 PHE A 341 TRP 0.029 0.002 TRP D 103 HIS 0.008 0.002 HIS C 197 Details of bonding type rmsd covalent geometry : bond 0.00382 ( 9387) covalent geometry : angle 0.64752 (12765) SS BOND : bond 0.00701 ( 12) SS BOND : angle 1.18706 ( 24) hydrogen bonds : bond 0.03479 ( 398) hydrogen bonds : angle 5.97207 ( 1110) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 88 time to evaluate : 0.364 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 95 LEU cc_start: 0.5855 (mt) cc_final: 0.5444 (mp) outliers start: 40 outliers final: 26 residues processed: 116 average time/residue: 0.0849 time to fit residues: 14.4062 Evaluate side-chains 101 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 75 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 289 ASP Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 120 SER Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 184 SER Chi-restraints excluded: chain C residue 12 SER Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain D residue 38 ARG Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 88 SER Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 76 SER Chi-restraints excluded: chain E residue 87 CYS Chi-restraints excluded: chain E residue 116 ILE Chi-restraints excluded: chain E residue 179 THR Chi-restraints excluded: chain E residue 180 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 17 optimal weight: 10.0000 chunk 4 optimal weight: 9.9990 chunk 28 optimal weight: 9.9990 chunk 108 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 chunk 114 optimal weight: 8.9990 chunk 32 optimal weight: 0.7980 chunk 59 optimal weight: 7.9990 chunk 61 optimal weight: 6.9990 chunk 49 optimal weight: 0.4980 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 61 ASN ** C 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 110 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 = 0.4873 r_free = 0.4873 target = 0.208239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4683 r_free = 0.4683 target = 0.190420 restraints weight = 22173.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4672 r_free = 0.4672 target = 0.189949 restraints weight = 25745.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4689 r_free = 0.4689 target = 0.191691 restraints weight = 21608.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4688 r_free = 0.4688 target = 0.191691 restraints weight = 16089.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4692 r_free = 0.4692 target = 0.192035 restraints weight = 17772.875| |-----------------------------------------------------------------------------| r_work (final): 0.4663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5142 moved from start: 0.9211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 9399 Z= 0.219 Angle : 0.729 12.547 12789 Z= 0.385 Chirality : 0.048 0.230 1480 Planarity : 0.006 0.092 1619 Dihedral : 5.689 31.298 1271 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 15.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 3.96 % Allowed : 21.14 % Favored : 74.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.86 % Cis-general : 0.00 % 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: 0.22 (0.25), residues: 1157 helix: -2.66 (0.90), residues: 20 sheet: 0.72 (0.22), residues: 556 loop : -0.25 (0.27), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 67 TYR 0.028 0.003 TYR C 35 PHE 0.024 0.002 PHE B 64 TRP 0.036 0.003 TRP D 103 HIS 0.010 0.002 HIS B 104 Details of bonding type rmsd covalent geometry : bond 0.00490 ( 9387) covalent geometry : angle 0.72783 (12765) SS BOND : bond 0.00721 ( 12) SS BOND : angle 1.19977 ( 24) hydrogen bonds : bond 0.03799 ( 398) hydrogen bonds : angle 6.51446 ( 1110) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 85 time to evaluate : 0.327 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 41 outliers final: 31 residues processed: 115 average time/residue: 0.0854 time to fit residues: 14.3943 Evaluate side-chains 104 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 73 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 PHE Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 202 PHE Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 289 ASP Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 413 MET Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 120 SER Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 184 SER Chi-restraints excluded: chain C residue 3 GLN Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain D residue 38 ARG Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 105 PHE Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 76 SER Chi-restraints excluded: chain E residue 87 CYS Chi-restraints excluded: chain E residue 180 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 37 optimal weight: 8.9990 chunk 5 optimal weight: 0.2980 chunk 48 optimal weight: 5.9990 chunk 27 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 67 optimal weight: 0.0670 chunk 33 optimal weight: 3.9990 chunk 78 optimal weight: 5.9990 chunk 106 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 overall best weight: 1.2724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4876 r_free = 0.4876 target = 0.210285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4649 r_free = 0.4649 target = 0.188448 restraints weight = 21594.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4648 r_free = 0.4648 target = 0.189497 restraints weight = 21191.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4670 r_free = 0.4670 target = 0.191448 restraints weight = 16215.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4674 r_free = 0.4674 target = 0.191927 restraints weight = 12136.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4682 r_free = 0.4682 target = 0.192641 restraints weight = 11469.590| |-----------------------------------------------------------------------------| r_work (final): 0.4664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5180 moved from start: 0.9489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9399 Z= 0.175 Angle : 0.661 13.781 12789 Z= 0.349 Chirality : 0.046 0.196 1480 Planarity : 0.006 0.076 1619 Dihedral : 5.319 28.534 1271 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 13.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 3.57 % Allowed : 22.97 % Favored : 73.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.86 % Cis-general : 0.00 % 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: 0.18 (0.25), residues: 1157 helix: -2.79 (0.88), residues: 20 sheet: 0.68 (0.22), residues: 552 loop : -0.24 (0.27), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 67 TYR 0.027 0.002 TYR C 172 PHE 0.026 0.002 PHE B 64 TRP 0.029 0.002 TRP E 46 HIS 0.008 0.002 HIS C 197 Details of bonding type rmsd covalent geometry : bond 0.00392 ( 9387) covalent geometry : angle 0.66020 (12765) SS BOND : bond 0.00667 ( 12) SS BOND : angle 1.03807 ( 24) hydrogen bonds : bond 0.03390 ( 398) hydrogen bonds : angle 6.27065 ( 1110) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 82 time to evaluate : 0.302 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 37 outliers final: 31 residues processed: 108 average time/residue: 0.0824 time to fit residues: 13.0599 Evaluate side-chains 108 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 77 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 PHE Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 202 PHE Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 289 ASP Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 120 SER Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 38 ARG Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 105 PHE Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 112 THR Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 184 SER Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 76 SER Chi-restraints excluded: chain E residue 180 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 32 optimal weight: 0.9990 chunk 87 optimal weight: 1.9990 chunk 118 optimal weight: 9.9990 chunk 108 optimal weight: 0.8980 chunk 113 optimal weight: 0.2980 chunk 28 optimal weight: 7.9990 chunk 12 optimal weight: 7.9990 chunk 1 optimal weight: 8.9990 chunk 80 optimal weight: 3.9990 chunk 100 optimal weight: 3.9990 chunk 23 optimal weight: 0.0060 overall best weight: 0.8400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 165 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4886 r_free = 0.4886 target = 0.210936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4648 r_free = 0.4648 target = 0.188189 restraints weight = 21197.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.4644 r_free = 0.4644 target = 0.189368 restraints weight = 21165.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4661 r_free = 0.4661 target = 0.190720 restraints weight = 18951.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4668 r_free = 0.4668 target = 0.191471 restraints weight = 13184.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4672 r_free = 0.4672 target = 0.191909 restraints weight = 12463.588| |-----------------------------------------------------------------------------| r_work (final): 0.4668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5180 moved from start: 0.9622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9399 Z= 0.139 Angle : 0.627 14.000 12789 Z= 0.326 Chirality : 0.045 0.174 1480 Planarity : 0.005 0.066 1619 Dihedral : 4.971 26.261 1271 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 3.28 % Allowed : 23.46 % Favored : 73.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.86 % Cis-general : 0.00 % 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: 0.24 (0.25), residues: 1157 helix: -2.77 (0.91), residues: 20 sheet: 0.62 (0.22), residues: 564 loop : -0.11 (0.28), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 67 TYR 0.018 0.002 TYR C 172 PHE 0.036 0.002 PHE E 70 TRP 0.033 0.002 TRP E 46 HIS 0.006 0.001 HIS C 197 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 9387) covalent geometry : angle 0.62598 (12765) SS BOND : bond 0.00588 ( 12) SS BOND : angle 0.90308 ( 24) hydrogen bonds : bond 0.03074 ( 398) hydrogen bonds : angle 5.91179 ( 1110) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 98 time to evaluate : 0.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 437 SER cc_start: 0.7982 (m) cc_final: 0.7637 (t) REVERT: D 215 LYS cc_start: 0.3796 (tptm) cc_final: 0.2209 (tmtt) REVERT: E 44 LYS cc_start: 0.7611 (mttt) cc_final: 0.7069 (mmmt) outliers start: 34 outliers final: 30 residues processed: 124 average time/residue: 0.0939 time to fit residues: 16.6546 Evaluate side-chains 111 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 81 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 202 PHE Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 289 ASP Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 410 THR Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 120 SER Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 165 GLN Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 38 ARG Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 112 THR Chi-restraints excluded: chain D residue 184 SER Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 69 GLU Chi-restraints excluded: chain E residue 76 SER Chi-restraints excluded: chain E residue 180 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 16 optimal weight: 0.7980 chunk 20 optimal weight: 10.0000 chunk 76 optimal weight: 0.6980 chunk 98 optimal weight: 10.0000 chunk 26 optimal weight: 4.9990 chunk 85 optimal weight: 0.8980 chunk 108 optimal weight: 0.8980 chunk 55 optimal weight: 2.9990 chunk 117 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 87 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 ASN ** A 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 165 GLN E 159 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4877 r_free = 0.4877 target = 0.210313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4651 r_free = 0.4651 target = 0.188967 restraints weight = 21454.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.4654 r_free = 0.4654 target = 0.190377 restraints weight = 22357.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4669 r_free = 0.4669 target = 0.191714 restraints weight = 18710.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4683 r_free = 0.4683 target = 0.193155 restraints weight = 12936.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4687 r_free = 0.4687 target = 0.193563 restraints weight = 11708.603| |-----------------------------------------------------------------------------| r_work (final): 0.4680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5121 moved from start: 0.9845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9399 Z= 0.144 Angle : 0.642 14.199 12789 Z= 0.333 Chirality : 0.045 0.173 1480 Planarity : 0.006 0.065 1619 Dihedral : 4.925 26.741 1271 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 2.90 % Allowed : 24.52 % Favored : 72.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.86 % Cis-general : 0.00 % 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: 0.26 (0.25), residues: 1157 helix: -2.75 (0.93), residues: 20 sheet: 0.69 (0.22), residues: 552 loop : -0.15 (0.27), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG C 141 TYR 0.018 0.002 TYR E 35 PHE 0.030 0.002 PHE E 70 TRP 0.037 0.002 TRP E 46 HIS 0.005 0.001 HIS C 197 Details of bonding type rmsd covalent geometry : bond 0.00323 ( 9387) covalent geometry : angle 0.64110 (12765) SS BOND : bond 0.00594 ( 12) SS BOND : angle 0.85648 ( 24) hydrogen bonds : bond 0.03027 ( 398) hydrogen bonds : angle 5.89679 ( 1110) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 86 time to evaluate : 0.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 437 SER cc_start: 0.7967 (m) cc_final: 0.7620 (t) REVERT: B 165 THR cc_start: 0.7301 (p) cc_final: 0.7006 (t) REVERT: D 149 ASP cc_start: 0.5757 (p0) cc_final: 0.5045 (p0) REVERT: D 215 LYS cc_start: 0.3833 (tptm) cc_final: 0.2180 (tmtt) REVERT: E 44 LYS cc_start: 0.7597 (mttt) cc_final: 0.7083 (mmmt) outliers start: 30 outliers final: 27 residues processed: 107 average time/residue: 0.0733 time to fit residues: 11.6354 Evaluate side-chains 109 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 82 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 202 PHE Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 289 ASP Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 410 THR Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 120 SER Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 165 GLN Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 38 ARG Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 112 THR Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 76 SER Chi-restraints excluded: chain E residue 180 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 36 optimal weight: 2.9990 chunk 64 optimal weight: 0.8980 chunk 69 optimal weight: 2.9990 chunk 27 optimal weight: 0.0470 chunk 94 optimal weight: 1.9990 chunk 86 optimal weight: 8.9990 chunk 47 optimal weight: 10.0000 chunk 100 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 101 optimal weight: 10.0000 chunk 58 optimal weight: 5.9990 overall best weight: 1.1884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 165 GLN ** E 88 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 = 0.4860 r_free = 0.4860 target = 0.208919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4625 r_free = 0.4625 target = 0.186414 restraints weight = 21313.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4614 r_free = 0.4614 target = 0.186892 restraints weight = 22670.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4625 r_free = 0.4625 target = 0.187943 restraints weight = 20767.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4650 r_free = 0.4650 target = 0.190200 restraints weight = 14884.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4651 r_free = 0.4651 target = 0.190424 restraints weight = 12083.506| |-----------------------------------------------------------------------------| r_work (final): 0.4644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5259 moved from start: 1.0127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9399 Z= 0.170 Angle : 0.663 14.218 12789 Z= 0.348 Chirality : 0.046 0.177 1480 Planarity : 0.006 0.065 1619 Dihedral : 5.137 28.433 1271 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 13.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 3.09 % Allowed : 24.23 % Favored : 72.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.86 % Cis-general : 0.00 % 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: 0.20 (0.25), residues: 1157 helix: -3.44 (0.73), residues: 26 sheet: 0.70 (0.22), residues: 538 loop : -0.15 (0.27), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 141 TYR 0.025 0.002 TYR C 172 PHE 0.040 0.002 PHE E 70 TRP 0.041 0.002 TRP E 46 HIS 0.006 0.002 HIS D 104 Details of bonding type rmsd covalent geometry : bond 0.00381 ( 9387) covalent geometry : angle 0.66283 (12765) SS BOND : bond 0.00613 ( 12) SS BOND : angle 0.91271 ( 24) hydrogen bonds : bond 0.03297 ( 398) hydrogen bonds : angle 6.00999 ( 1110) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1687.23 seconds wall clock time: 30 minutes 1.50 seconds (1801.50 seconds total)