Starting phenix.real_space_refine on Fri Aug 22 17:17:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yzk_39696/08_2025/8yzk_39696.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yzk_39696/08_2025/8yzk_39696.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8yzk_39696/08_2025/8yzk_39696.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yzk_39696/08_2025/8yzk_39696.map" model { file = "/net/cci-nas-00/data/ceres_data/8yzk_39696/08_2025/8yzk_39696.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yzk_39696/08_2025/8yzk_39696.cif" } resolution = 3.4 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= 0.002 sd= 0.028 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 42 5.16 5 C 4204 2.51 5 N 1064 2.21 5 O 1160 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6470 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2039 Classifications: {'peptide': 264} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 254} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 10 Chain: "C" Number of atoms: 1190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1190 Classifications: {'peptide': 169} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 6, 'TRANS': 162} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 132 Unresolved non-hydrogen angles: 169 Unresolved non-hydrogen dihedrals: 117 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLU:plan': 2, 'GLN:plan1': 5, 'ASP:plan': 1, 'ARG:plan': 3, 'TYR:plan': 4, 'HIS:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 88 Chain: "D" Number of atoms: 1202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1202 Classifications: {'peptide': 169} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 6, 'TRANS': 162} Chain breaks: 4 Unresolved non-hydrogen bonds: 119 Unresolved non-hydrogen angles: 154 Unresolved non-hydrogen dihedrals: 106 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 1, 'ARG:plan': 2, 'TYR:plan': 5, 'GLU:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 77 Chain: "B" Number of atoms: 2039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2039 Classifications: {'peptide': 264} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 254} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 10 Time building chain proxies: 1.70, per 1000 atoms: 0.26 Number of scatterers: 6470 At special positions: 0 Unit cell: (73.216, 108.992, 103.168, 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 42 16.00 O 1160 8.00 N 1064 7.00 C 4204 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS C 60 " - pdb=" SG CYS C 125 " distance=2.03 Simple disulfide: pdb=" SG CYS C 191 " - pdb=" SG CYS C 265 " distance=2.03 Simple disulfide: pdb=" SG CYS D 60 " - pdb=" SG CYS D 125 " distance=2.03 Simple disulfide: pdb=" SG CYS D 191 " - pdb=" SG CYS D 265 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.50 Conformation dependent library (CDL) restraints added in 430.3 milliseconds Enol-peptide restraints added in 1.2 microseconds 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1612 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 9 sheets defined 51.7% alpha, 15.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.17 Creating SS restraints... Processing helix chain 'A' and resid 23 through 51 removed outlier: 4.787A pdb=" N LEU A 29 " --> pdb=" O ILE A 25 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N MET A 48 " --> pdb=" O PHE A 44 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ARG A 49 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N LYS A 50 " --> pdb=" O PHE A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 58 removed outlier: 3.889A pdb=" N ASN A 58 " --> pdb=" O CYS A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 79 Processing helix chain 'A' and resid 90 through 119 removed outlier: 4.552A pdb=" N PHE A 96 " --> pdb=" O ARG A 92 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N GLY A 97 " --> pdb=" O TYR A 93 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ARG A 119 " --> pdb=" O VAL A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 153 removed outlier: 3.917A pdb=" N CYS A 136 " --> pdb=" O ILE A 132 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N SER A 137 " --> pdb=" O ALA A 133 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LEU A 139 " --> pdb=" O GLY A 135 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N GLN A 140 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N THR A 149 " --> pdb=" O THR A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 161 Processing helix chain 'A' and resid 162 through 167 removed outlier: 3.615A pdb=" N ASN A 167 " --> pdb=" O PRO A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 191 removed outlier: 3.850A pdb=" N VAL A 171 " --> pdb=" O ASN A 167 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N TYR A 176 " --> pdb=" O VAL A 172 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N VAL A 177 " --> pdb=" O LEU A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 232 removed outlier: 3.992A pdb=" N TRP A 217 " --> pdb=" O SER A 213 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N VAL A 219 " --> pdb=" O ILE A 215 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N TRP A 220 " --> pdb=" O ILE A 216 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE A 221 " --> pdb=" O TRP A 217 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N SER A 222 " --> pdb=" O VAL A 218 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N ASN A 228 " --> pdb=" O LEU A 224 " (cutoff:3.500A) Proline residue: A 229 - end of helix Processing helix chain 'A' and resid 238 through 257 removed outlier: 3.770A pdb=" N VAL A 242 " --> pdb=" O ASP A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 265 Processing helix chain 'C' and resid 64 through 68 removed outlier: 3.628A pdb=" N TYR C 68 " --> pdb=" O LEU C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 201 removed outlier: 3.605A pdb=" N SER C 200 " --> pdb=" O THR C 197 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N HIS C 201 " --> pdb=" O PHE C 198 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 197 through 201' Processing helix chain 'D' and resid 197 through 201 removed outlier: 3.509A pdb=" N SER D 200 " --> pdb=" O THR D 197 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N HIS D 201 " --> pdb=" O PHE D 198 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 197 through 201' Processing helix chain 'D' and resid 256 through 260 removed outlier: 4.125A pdb=" N THR D 260 " --> pdb=" O ALA D 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 51 removed outlier: 4.770A pdb=" N LEU B 29 " --> pdb=" O ILE B 25 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N MET B 48 " --> pdb=" O PHE B 44 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ARG B 49 " --> pdb=" O LEU B 45 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N LYS B 50 " --> pdb=" O PHE B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 58 removed outlier: 3.842A pdb=" N ASN B 58 " --> pdb=" O CYS B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 79 Processing helix chain 'B' and resid 90 through 119 removed outlier: 4.598A pdb=" N PHE B 96 " --> pdb=" O ARG B 92 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N GLY B 97 " --> pdb=" O TYR B 93 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ARG B 119 " --> pdb=" O VAL B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 153 removed outlier: 3.955A pdb=" N CYS B 136 " --> pdb=" O ILE B 132 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N SER B 137 " --> pdb=" O ALA B 133 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LEU B 139 " --> pdb=" O GLY B 135 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N GLN B 140 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N THR B 149 " --> pdb=" O THR B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 161 Processing helix chain 'B' and resid 162 through 167 removed outlier: 3.562A pdb=" N ASN B 167 " --> pdb=" O PRO B 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 191 removed outlier: 3.720A pdb=" N VAL B 171 " --> pdb=" O ASN B 167 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N TYR B 176 " --> pdb=" O VAL B 172 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N VAL B 177 " --> pdb=" O LEU B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 232 removed outlier: 4.057A pdb=" N TRP B 217 " --> pdb=" O SER B 213 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N VAL B 219 " --> pdb=" O ILE B 215 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE B 221 " --> pdb=" O TRP B 217 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N SER B 222 " --> pdb=" O VAL B 218 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N ASN B 228 " --> pdb=" O LEU B 224 " (cutoff:3.500A) Proline residue: B 229 - end of helix Processing helix chain 'B' and resid 238 through 257 removed outlier: 3.789A pdb=" N VAL B 242 " --> pdb=" O ASP B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 257 through 265 Processing sheet with id=AA1, first strand: chain 'C' and resid 71 through 74 removed outlier: 7.108A pdb=" N TRP C 72 " --> pdb=" O VAL C 84 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 127 through 128 removed outlier: 4.018A pdb=" N VAL C 137 " --> pdb=" O SER C 127 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 172 through 176 removed outlier: 3.740A pdb=" N GLN C 172 " --> pdb=" O SER C 194 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N SER C 194 " --> pdb=" O GLN C 172 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N TYR C 249 " --> pdb=" O SER C 240 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N SER C 240 " --> pdb=" O TYR C 249 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N THR C 238 " --> pdb=" O GLN C 251 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 213 through 216 removed outlier: 3.652A pdb=" N TYR C 277 " --> pdb=" O ARG C 267 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 213 through 216 removed outlier: 3.519A pdb=" N VAL C 284 " --> pdb=" O ALA C 261 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 82 through 86 removed outlier: 6.969A pdb=" N TRP D 72 " --> pdb=" O VAL D 84 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N SER D 71 " --> pdb=" O ASN D 126 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ASN D 126 " --> pdb=" O SER D 71 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N VAL D 137 " --> pdb=" O SER D 127 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 172 through 176 removed outlier: 3.820A pdb=" N GLN D 172 " --> pdb=" O SER D 194 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N SER D 194 " --> pdb=" O GLN D 172 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N TYR D 249 " --> pdb=" O SER D 240 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N SER D 240 " --> pdb=" O TYR D 249 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N THR D 238 " --> pdb=" O GLN D 251 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 213 through 216 removed outlier: 3.829A pdb=" N TYR D 277 " --> pdb=" O ARG D 267 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 213 through 216 370 hydrogen bonds defined for protein. 1056 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.84 Time building geometry restraints manager: 0.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2021 1.34 - 1.46: 1563 1.46 - 1.58: 2984 1.58 - 1.69: 1 1.69 - 1.81: 54 Bond restraints: 6623 Sorted by residual: bond pdb=" CB PRO C 134 " pdb=" CG PRO C 134 " ideal model delta sigma weight residual 1.492 1.583 -0.091 5.00e-02 4.00e+02 3.31e+00 bond pdb=" CB ILE B 216 " pdb=" CG2 ILE B 216 " ideal model delta sigma weight residual 1.521 1.477 0.044 3.30e-02 9.18e+02 1.77e+00 bond pdb=" CG PRO C 134 " pdb=" CD PRO C 134 " ideal model delta sigma weight residual 1.503 1.459 0.044 3.40e-02 8.65e+02 1.66e+00 bond pdb=" CB ILE A 141 " pdb=" CG2 ILE A 141 " ideal model delta sigma weight residual 1.521 1.486 0.035 3.30e-02 9.18e+02 1.12e+00 bond pdb=" CB ILE B 141 " pdb=" CG2 ILE B 141 " ideal model delta sigma weight residual 1.521 1.489 0.032 3.30e-02 9.18e+02 9.19e-01 ... (remaining 6618 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.75: 8995 3.75 - 7.50: 40 7.50 - 11.25: 5 11.25 - 15.01: 0 15.01 - 18.76: 2 Bond angle restraints: 9042 Sorted by residual: angle pdb=" CA PRO C 134 " pdb=" N PRO C 134 " pdb=" CD PRO C 134 " ideal model delta sigma weight residual 112.00 104.10 7.90 1.40e+00 5.10e-01 3.18e+01 angle pdb=" CA LEU B 166 " pdb=" CB LEU B 166 " pdb=" CG LEU B 166 " ideal model delta sigma weight residual 116.30 135.06 -18.76 3.50e+00 8.16e-02 2.87e+01 angle pdb=" CA LEU A 166 " pdb=" CB LEU A 166 " pdb=" CG LEU A 166 " ideal model delta sigma weight residual 116.30 134.30 -18.00 3.50e+00 8.16e-02 2.65e+01 angle pdb=" N ILE B 82 " pdb=" CA ILE B 82 " pdb=" C ILE B 82 " ideal model delta sigma weight residual 112.80 107.35 5.45 1.15e+00 7.56e-01 2.24e+01 angle pdb=" N ILE A 82 " pdb=" CA ILE A 82 " pdb=" C ILE A 82 " ideal model delta sigma weight residual 112.80 107.41 5.39 1.15e+00 7.56e-01 2.19e+01 ... (remaining 9037 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.74: 3144 16.74 - 33.47: 475 33.47 - 50.21: 147 50.21 - 66.94: 20 66.94 - 83.68: 12 Dihedral angle restraints: 3798 sinusoidal: 1301 harmonic: 2497 Sorted by residual: dihedral pdb=" CA ASN C 204 " pdb=" C ASN C 204 " pdb=" N TRP C 205 " pdb=" CA TRP C 205 " ideal model delta harmonic sigma weight residual 180.00 160.79 19.21 0 5.00e+00 4.00e-02 1.48e+01 dihedral pdb=" CA ASN D 133 " pdb=" C ASN D 133 " pdb=" N PRO D 134 " pdb=" CA PRO D 134 " ideal model delta harmonic sigma weight residual -180.00 -161.77 -18.23 0 5.00e+00 4.00e-02 1.33e+01 dihedral pdb=" CA SER D 218 " pdb=" C SER D 218 " pdb=" N SER D 219 " pdb=" CA SER D 219 " ideal model delta harmonic sigma weight residual -180.00 -163.14 -16.86 0 5.00e+00 4.00e-02 1.14e+01 ... (remaining 3795 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 767 0.046 - 0.091: 246 0.091 - 0.137: 39 0.137 - 0.182: 6 0.182 - 0.228: 1 Chirality restraints: 1059 Sorted by residual: chirality pdb=" CG LEU B 166 " pdb=" CB LEU B 166 " pdb=" CD1 LEU B 166 " pdb=" CD2 LEU B 166 " both_signs ideal model delta sigma weight residual False -2.59 -2.82 0.23 2.00e-01 2.50e+01 1.30e+00 chirality pdb=" CB ILE B 82 " pdb=" CA ILE B 82 " pdb=" CG1 ILE B 82 " pdb=" CG2 ILE B 82 " both_signs ideal model delta sigma weight residual False 2.64 2.82 -0.18 2.00e-01 2.50e+01 7.91e-01 chirality pdb=" CA VAL C 217 " pdb=" N VAL C 217 " pdb=" C VAL C 217 " pdb=" CB VAL C 217 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.05e-01 ... (remaining 1056 not shown) Planarity restraints: 1128 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN C 133 " 0.062 5.00e-02 4.00e+02 8.94e-02 1.28e+01 pdb=" N PRO C 134 " -0.154 5.00e-02 4.00e+02 pdb=" CA PRO C 134 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO C 134 " 0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN B 234 " 0.043 5.00e-02 4.00e+02 6.55e-02 6.87e+00 pdb=" N PRO B 235 " -0.113 5.00e-02 4.00e+02 pdb=" CA PRO B 235 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO B 235 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN A 234 " -0.040 5.00e-02 4.00e+02 6.06e-02 5.87e+00 pdb=" N PRO A 235 " 0.105 5.00e-02 4.00e+02 pdb=" CA PRO A 235 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 235 " -0.031 5.00e-02 4.00e+02 ... (remaining 1125 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 374 2.72 - 3.27: 6547 3.27 - 3.81: 11420 3.81 - 4.36: 12622 4.36 - 4.90: 21449 Nonbonded interactions: 52412 Sorted by model distance: nonbonded pdb=" OG SER D 39 " pdb=" N SER D 40 " model vdw 2.181 3.120 nonbonded pdb=" O SER C 219 " pdb=" OG SER C 219 " model vdw 2.227 3.040 nonbonded pdb=" O SER D 219 " pdb=" OG SER D 219 " model vdw 2.229 3.040 nonbonded pdb=" OG SER C 202 " pdb=" OG SER C 268 " model vdw 2.239 3.040 nonbonded pdb=" O GLY A 33 " pdb=" OG1 THR A 37 " model vdw 2.259 3.040 ... (remaining 52407 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = (chain 'C' and (resid 37 through 72 or (resid 73 through 74 and (name N or name \ CA or name C or name O or name CB )) or resid 75 through 173 or (resid 174 and ( \ name N or name CA or name C or name O or name CB )) or resid 175 through 180 or \ (resid 181 and (name N or name CA or name C or name O or name CB )) or resid 182 \ through 186 or (resid 187 and (name N or name CA or name C or name O or name CB \ )) or resid 188 through 254 or (resid 255 and (name N or name CA or name C or n \ ame O or name CB )) or resid 256 through 288)) selection = (chain 'D' and (resid 37 through 40 or (resid 41 through 42 and (name N or name \ CA or name C or name O or name CB )) or resid 60 through 64 or (resid 65 through \ 66 and (name N or name CA or name C or name O or name CB )) or resid 67 through \ 73 or (resid 74 and (name N or name CA or name C or name O or name CB )) or res \ id 75 through 82 or (resid 83 through 84 and (name N or name CA or name C or nam \ e O or name CB )) or resid 85 through 134 or (resid 135 and (name N or name CA o \ r name C or name O or name CB )) or resid 136 through 200 or (resid 201 and (nam \ e N or name CA or name C or name O or name CB )) or resid 202 through 266 or (re \ sid 267 and (name N or name CA or name C or name O or name CB )) or resid 268 th \ rough 288)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 7.710 Find NCS groups from input model: 0.070 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:1.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5806 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.091 6627 Z= 0.151 Angle : 0.762 18.757 9050 Z= 0.382 Chirality : 0.044 0.228 1059 Planarity : 0.006 0.089 1128 Dihedral : 18.280 83.680 2174 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 13.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.91 % Favored : 91.09 % Rotamer: Outliers : 1.07 % Allowed : 39.05 % Favored : 59.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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 aren not related in a simple way. whole: -1.21 (0.30), residues: 842 helix: 0.33 (0.28), residues: 366 sheet: -1.23 (0.49), residues: 116 loop : -1.82 (0.34), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 267 TYR 0.018 0.001 TYR D 228 PHE 0.038 0.002 PHE B 78 TRP 0.024 0.002 TRP A 220 HIS 0.012 0.002 HIS B 110 Details of bonding type rmsd covalent geometry : bond 0.00344 ( 6623) covalent geometry : angle 0.76238 ( 9042) SS BOND : bond 0.00042 ( 4) SS BOND : angle 0.29295 ( 8) hydrogen bonds : bond 0.17712 ( 350) hydrogen bonds : angle 7.51125 ( 1056) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 116 time to evaluate : 0.213 Fit side-chains outliers start: 7 outliers final: 3 residues processed: 119 average time/residue: 0.0780 time to fit residues: 12.2667 Evaluate side-chains 114 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 111 time to evaluate : 0.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 186 PHE Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 219 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 49 optimal weight: 5.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 0.0970 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 38 optimal weight: 0.0030 chunk 61 optimal weight: 0.5980 chunk 45 optimal weight: 6.9990 chunk 74 optimal weight: 0.0870 overall best weight: 0.5568 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 208 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 = 0.4529 r_free = 0.4529 target = 0.182899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.161509 restraints weight = 10075.738| |-----------------------------------------------------------------------------| r_work (start): 0.4278 rms_B_bonded: 2.59 r_work: 0.4171 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.4171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6112 moved from start: 0.0971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 6627 Z= 0.135 Angle : 0.633 12.842 9050 Z= 0.323 Chirality : 0.041 0.199 1059 Planarity : 0.005 0.063 1128 Dihedral : 5.360 44.817 919 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.19 % Favored : 91.81 % Rotamer: Outliers : 5.21 % Allowed : 35.83 % Favored : 58.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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 aren not related in a simple way. whole: -1.13 (0.31), residues: 842 helix: 0.37 (0.28), residues: 384 sheet: -1.60 (0.46), residues: 128 loop : -1.65 (0.36), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 154 TYR 0.013 0.001 TYR A 93 PHE 0.011 0.001 PHE A 44 TRP 0.017 0.001 TRP A 220 HIS 0.003 0.001 HIS B 110 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 6623) covalent geometry : angle 0.63347 ( 9042) SS BOND : bond 0.00151 ( 4) SS BOND : angle 0.52505 ( 8) hydrogen bonds : bond 0.04424 ( 350) hydrogen bonds : angle 5.48670 ( 1056) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 120 time to evaluate : 0.151 Fit side-chains REVERT: A 70 VAL cc_start: 0.6696 (OUTLIER) cc_final: 0.6414 (t) REVERT: A 87 GLN cc_start: 0.6551 (OUTLIER) cc_final: 0.6349 (pm20) REVERT: B 224 LEU cc_start: 0.4473 (OUTLIER) cc_final: 0.4102 (tp) outliers start: 34 outliers final: 13 residues processed: 143 average time/residue: 0.0708 time to fit residues: 13.4051 Evaluate side-chains 132 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 116 time to evaluate : 0.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 87 GLN Chi-restraints excluded: chain A residue 126 TRP Chi-restraints excluded: chain A residue 170 PHE Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 186 PHE Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain C residue 238 THR Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 126 TRP Chi-restraints excluded: chain B residue 186 PHE Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 238 ASP Chi-restraints excluded: chain B residue 247 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 35 optimal weight: 0.0030 chunk 38 optimal weight: 1.9990 chunk 67 optimal weight: 0.6980 chunk 2 optimal weight: 2.9990 chunk 48 optimal weight: 6.9990 chunk 59 optimal weight: 1.9990 chunk 78 optimal weight: 0.5980 chunk 83 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 chunk 4 optimal weight: 0.9980 chunk 1 optimal weight: 0.0020 overall best weight: 0.4598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 58 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4535 r_free = 0.4535 target = 0.183265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.161577 restraints weight = 10010.309| |-----------------------------------------------------------------------------| r_work (start): 0.4273 rms_B_bonded: 2.59 r_work: 0.4172 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.4172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6097 moved from start: 0.1248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 6627 Z= 0.122 Angle : 0.622 13.124 9050 Z= 0.309 Chirality : 0.040 0.190 1059 Planarity : 0.004 0.060 1128 Dihedral : 4.929 43.164 916 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.19 % Favored : 91.81 % Rotamer: Outliers : 5.67 % Allowed : 34.61 % Favored : 59.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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 aren not related in a simple way. whole: -1.00 (0.31), residues: 842 helix: 0.50 (0.28), residues: 384 sheet: -1.49 (0.46), residues: 128 loop : -1.65 (0.36), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 241 TYR 0.009 0.001 TYR A 93 PHE 0.021 0.001 PHE A 78 TRP 0.010 0.001 TRP C 205 HIS 0.003 0.001 HIS B 110 Details of bonding type rmsd covalent geometry : bond 0.00265 ( 6623) covalent geometry : angle 0.62188 ( 9042) SS BOND : bond 0.00102 ( 4) SS BOND : angle 0.50542 ( 8) hydrogen bonds : bond 0.03991 ( 350) hydrogen bonds : angle 5.14175 ( 1056) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 123 time to evaluate : 0.161 Fit side-chains REVERT: A 44 PHE cc_start: 0.7163 (OUTLIER) cc_final: 0.6317 (t80) REVERT: A 70 VAL cc_start: 0.6636 (OUTLIER) cc_final: 0.6359 (t) REVERT: C 268 SER cc_start: 0.7438 (p) cc_final: 0.7162 (p) REVERT: B 44 PHE cc_start: 0.6805 (OUTLIER) cc_final: 0.6020 (t80) outliers start: 37 outliers final: 17 residues processed: 147 average time/residue: 0.0608 time to fit residues: 12.1496 Evaluate side-chains 138 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 118 time to evaluate : 0.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 PHE Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 126 TRP Chi-restraints excluded: chain A residue 170 PHE Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain C residue 238 THR Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain D residue 238 THR Chi-restraints excluded: chain D residue 259 ASP Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain B residue 44 PHE Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 126 TRP Chi-restraints excluded: chain B residue 186 PHE Chi-restraints excluded: chain B residue 213 SER Chi-restraints excluded: chain B residue 238 ASP Chi-restraints excluded: chain B residue 247 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 10 optimal weight: 3.9990 chunk 52 optimal weight: 0.0570 chunk 68 optimal weight: 3.9990 chunk 11 optimal weight: 0.9990 chunk 64 optimal weight: 0.3980 chunk 82 optimal weight: 0.8980 chunk 29 optimal weight: 9.9990 chunk 32 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 chunk 17 optimal weight: 0.1980 chunk 30 optimal weight: 8.9990 overall best weight: 0.4898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4523 r_free = 0.4523 target = 0.182309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.161338 restraints weight = 10195.307| |-----------------------------------------------------------------------------| r_work (start): 0.4267 rms_B_bonded: 2.66 r_work: 0.4161 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.4161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6114 moved from start: 0.1409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 6627 Z= 0.123 Angle : 0.616 13.964 9050 Z= 0.306 Chirality : 0.040 0.187 1059 Planarity : 0.004 0.059 1128 Dihedral : 4.827 42.318 916 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.96 % Favored : 92.04 % Rotamer: Outliers : 6.28 % Allowed : 35.22 % Favored : 58.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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 aren not related in a simple way. whole: -0.85 (0.31), residues: 842 helix: 0.62 (0.29), residues: 382 sheet: -0.85 (0.50), residues: 116 loop : -1.80 (0.35), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 241 TYR 0.009 0.001 TYR A 93 PHE 0.015 0.001 PHE A 78 TRP 0.022 0.001 TRP A 220 HIS 0.002 0.001 HIS B 110 Details of bonding type rmsd covalent geometry : bond 0.00271 ( 6623) covalent geometry : angle 0.61596 ( 9042) SS BOND : bond 0.00145 ( 4) SS BOND : angle 0.44096 ( 8) hydrogen bonds : bond 0.03814 ( 350) hydrogen bonds : angle 4.97287 ( 1056) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 125 time to evaluate : 0.154 Fit side-chains REVERT: A 44 PHE cc_start: 0.7168 (OUTLIER) cc_final: 0.6355 (t80) REVERT: A 70 VAL cc_start: 0.6672 (OUTLIER) cc_final: 0.6390 (t) REVERT: A 224 LEU cc_start: 0.4723 (OUTLIER) cc_final: 0.4371 (mp) REVERT: C 268 SER cc_start: 0.7378 (p) cc_final: 0.7111 (p) REVERT: B 44 PHE cc_start: 0.6811 (OUTLIER) cc_final: 0.5977 (t80) REVERT: B 224 LEU cc_start: 0.4328 (OUTLIER) cc_final: 0.4078 (tp) outliers start: 41 outliers final: 23 residues processed: 152 average time/residue: 0.0687 time to fit residues: 14.0593 Evaluate side-chains 148 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 120 time to evaluate : 0.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 PHE Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 126 TRP Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 165 GLN Chi-restraints excluded: chain A residue 170 PHE Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 238 THR Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 238 THR Chi-restraints excluded: chain D residue 259 ASP Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain B residue 44 PHE Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 126 TRP Chi-restraints excluded: chain B residue 186 PHE Chi-restraints excluded: chain B residue 213 SER Chi-restraints excluded: chain B residue 216 ILE Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 238 ASP Chi-restraints excluded: chain B residue 247 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 35 optimal weight: 2.9990 chunk 83 optimal weight: 0.7980 chunk 29 optimal weight: 9.9990 chunk 0 optimal weight: 5.9990 chunk 39 optimal weight: 6.9990 chunk 24 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 43 optimal weight: 6.9990 chunk 63 optimal weight: 0.9990 chunk 32 optimal weight: 10.0000 chunk 73 optimal weight: 0.4980 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4472 r_free = 0.4472 target = 0.178621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.157303 restraints weight = 10237.092| |-----------------------------------------------------------------------------| r_work (start): 0.4210 rms_B_bonded: 2.57 r_work: 0.4104 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.4104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6219 moved from start: 0.1717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 6627 Z= 0.185 Angle : 0.672 13.881 9050 Z= 0.339 Chirality : 0.043 0.214 1059 Planarity : 0.004 0.057 1128 Dihedral : 5.004 41.939 916 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 14.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.86 % Favored : 90.14 % Rotamer: Outliers : 7.35 % Allowed : 35.83 % Favored : 56.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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 aren not related in a simple way. whole: -1.11 (0.30), residues: 842 helix: 0.29 (0.28), residues: 384 sheet: -0.76 (0.50), residues: 116 loop : -1.88 (0.35), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG D 207 TYR 0.019 0.002 TYR D 264 PHE 0.019 0.002 PHE B 78 TRP 0.025 0.002 TRP A 220 HIS 0.002 0.000 HIS B 110 Details of bonding type rmsd covalent geometry : bond 0.00419 ( 6623) covalent geometry : angle 0.67189 ( 9042) SS BOND : bond 0.00099 ( 4) SS BOND : angle 0.49567 ( 8) hydrogen bonds : bond 0.04400 ( 350) hydrogen bonds : angle 5.11784 ( 1056) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 128 time to evaluate : 0.217 Fit side-chains revert: symmetry clash REVERT: A 44 PHE cc_start: 0.7069 (OUTLIER) cc_final: 0.6092 (t80) REVERT: D 203 MET cc_start: 0.4573 (OUTLIER) cc_final: 0.4053 (mtt) REVERT: B 44 PHE cc_start: 0.6816 (OUTLIER) cc_final: 0.5858 (t80) REVERT: B 150 LEU cc_start: 0.7207 (tp) cc_final: 0.6983 (tt) REVERT: B 224 LEU cc_start: 0.4588 (OUTLIER) cc_final: 0.4203 (tp) outliers start: 48 outliers final: 29 residues processed: 155 average time/residue: 0.0682 time to fit residues: 14.0540 Evaluate side-chains 159 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 126 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 44 PHE Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 126 TRP Chi-restraints excluded: chain A residue 165 GLN Chi-restraints excluded: chain A residue 170 PHE Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 204 ARG Chi-restraints excluded: chain A residue 220 TRP Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 238 THR Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain D residue 182 HIS Chi-restraints excluded: chain D residue 203 MET Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 238 THR Chi-restraints excluded: chain D residue 259 ASP Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain B residue 13 PHE Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 44 PHE Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 126 TRP Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 181 MET Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 238 ASP Chi-restraints excluded: chain B residue 247 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 10 optimal weight: 0.9980 chunk 75 optimal weight: 0.5980 chunk 46 optimal weight: 1.9990 chunk 45 optimal weight: 4.9990 chunk 44 optimal weight: 5.9990 chunk 28 optimal weight: 6.9990 chunk 63 optimal weight: 4.9990 chunk 30 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4476 r_free = 0.4476 target = 0.178624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.156994 restraints weight = 10267.328| |-----------------------------------------------------------------------------| r_work (start): 0.4212 rms_B_bonded: 2.68 r_work: 0.4101 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.4101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6223 moved from start: 0.1803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 6627 Z= 0.167 Angle : 0.669 13.693 9050 Z= 0.336 Chirality : 0.042 0.221 1059 Planarity : 0.004 0.057 1128 Dihedral : 4.743 22.030 914 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 14.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.03 % Favored : 90.97 % Rotamer: Outliers : 7.81 % Allowed : 35.53 % Favored : 56.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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 aren not related in a simple way. whole: -1.18 (0.30), residues: 842 helix: 0.27 (0.28), residues: 386 sheet: -0.79 (0.50), residues: 116 loop : -1.99 (0.34), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 226 TYR 0.023 0.002 TYR D 264 PHE 0.022 0.002 PHE B 78 TRP 0.029 0.002 TRP B 220 HIS 0.001 0.000 HIS B 110 Details of bonding type rmsd covalent geometry : bond 0.00377 ( 6623) covalent geometry : angle 0.66887 ( 9042) SS BOND : bond 0.00107 ( 4) SS BOND : angle 0.45709 ( 8) hydrogen bonds : bond 0.04259 ( 350) hydrogen bonds : angle 5.03996 ( 1056) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 123 time to evaluate : 0.227 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 PHE cc_start: 0.7104 (OUTLIER) cc_final: 0.6154 (t80) REVERT: A 95 LEU cc_start: 0.7691 (mt) cc_final: 0.7361 (mp) REVERT: A 224 LEU cc_start: 0.4698 (OUTLIER) cc_final: 0.4451 (mp) REVERT: D 203 MET cc_start: 0.4529 (OUTLIER) cc_final: 0.4050 (mtt) REVERT: B 44 PHE cc_start: 0.6814 (OUTLIER) cc_final: 0.5880 (t80) REVERT: B 93 TYR cc_start: 0.7245 (m-80) cc_final: 0.6681 (m-80) REVERT: B 224 LEU cc_start: 0.4695 (OUTLIER) cc_final: 0.4273 (tp) outliers start: 51 outliers final: 33 residues processed: 155 average time/residue: 0.0801 time to fit residues: 16.1245 Evaluate side-chains 161 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 123 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 44 PHE Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 126 TRP Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 154 ARG Chi-restraints excluded: chain A residue 165 GLN Chi-restraints excluded: chain A residue 170 PHE Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 204 ARG Chi-restraints excluded: chain A residue 220 TRP Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 238 THR Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 182 HIS Chi-restraints excluded: chain D residue 203 MET Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 238 THR Chi-restraints excluded: chain D residue 259 ASP Chi-restraints excluded: chain D residue 262 VAL Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain B residue 44 PHE Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 126 TRP Chi-restraints excluded: chain B residue 154 ARG Chi-restraints excluded: chain B residue 186 PHE Chi-restraints excluded: chain B residue 204 ARG Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 238 ASP Chi-restraints excluded: chain B residue 247 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 17 optimal weight: 0.6980 chunk 25 optimal weight: 0.6980 chunk 7 optimal weight: 0.7980 chunk 21 optimal weight: 0.6980 chunk 24 optimal weight: 0.8980 chunk 83 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 chunk 75 optimal weight: 0.5980 chunk 45 optimal weight: 4.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4490 r_free = 0.4490 target = 0.179760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.158030 restraints weight = 10074.123| |-----------------------------------------------------------------------------| r_work (start): 0.4235 rms_B_bonded: 2.68 r_work: 0.4122 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.4122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6207 moved from start: 0.1887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6627 Z= 0.146 Angle : 0.673 14.428 9050 Z= 0.334 Chirality : 0.042 0.202 1059 Planarity : 0.004 0.057 1128 Dihedral : 4.704 21.842 914 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 14.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.26 % Favored : 90.74 % Rotamer: Outliers : 7.96 % Allowed : 34.61 % Favored : 57.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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 aren not related in a simple way. whole: -1.06 (0.31), residues: 842 helix: 0.36 (0.28), residues: 384 sheet: -0.80 (0.50), residues: 116 loop : -1.88 (0.35), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 241 TYR 0.019 0.001 TYR D 264 PHE 0.024 0.002 PHE B 78 TRP 0.027 0.002 TRP B 220 HIS 0.001 0.000 HIS B 202 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 6623) covalent geometry : angle 0.67269 ( 9042) SS BOND : bond 0.00116 ( 4) SS BOND : angle 0.41929 ( 8) hydrogen bonds : bond 0.04085 ( 350) hydrogen bonds : angle 4.96991 ( 1056) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 128 time to evaluate : 0.208 Fit side-chains REVERT: A 44 PHE cc_start: 0.7017 (OUTLIER) cc_final: 0.6001 (t80) REVERT: A 267 ARG cc_start: 0.7180 (tmm160) cc_final: 0.6564 (tmm160) REVERT: D 203 MET cc_start: 0.4459 (OUTLIER) cc_final: 0.4027 (mtt) REVERT: B 44 PHE cc_start: 0.6802 (OUTLIER) cc_final: 0.5863 (t80) REVERT: B 93 TYR cc_start: 0.7228 (m-80) cc_final: 0.6704 (m-80) REVERT: B 224 LEU cc_start: 0.4557 (OUTLIER) cc_final: 0.4208 (tp) outliers start: 52 outliers final: 36 residues processed: 160 average time/residue: 0.0656 time to fit residues: 13.6333 Evaluate side-chains 166 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 126 time to evaluate : 0.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 PHE Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 126 TRP Chi-restraints excluded: chain A residue 154 ARG Chi-restraints excluded: chain A residue 165 GLN Chi-restraints excluded: chain A residue 170 PHE Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 220 TRP Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain C residue 127 SER Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 238 THR Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 182 HIS Chi-restraints excluded: chain D residue 203 MET Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 238 THR Chi-restraints excluded: chain D residue 259 ASP Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 44 PHE Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 126 TRP Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 154 ARG Chi-restraints excluded: chain B residue 165 GLN Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 186 PHE Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 238 ASP Chi-restraints excluded: chain B residue 247 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 26 optimal weight: 10.0000 chunk 35 optimal weight: 0.9980 chunk 59 optimal weight: 0.1980 chunk 24 optimal weight: 0.5980 chunk 52 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 chunk 39 optimal weight: 10.0000 chunk 51 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 54 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4486 r_free = 0.4486 target = 0.179444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.158517 restraints weight = 10118.709| |-----------------------------------------------------------------------------| r_work (start): 0.4232 rms_B_bonded: 2.53 r_work: 0.4128 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.4128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6184 moved from start: 0.2004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6627 Z= 0.152 Angle : 0.694 15.677 9050 Z= 0.343 Chirality : 0.045 0.473 1059 Planarity : 0.005 0.057 1128 Dihedral : 4.753 21.823 914 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 14.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.03 % Favored : 90.97 % Rotamer: Outliers : 7.35 % Allowed : 34.92 % Favored : 57.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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 aren not related in a simple way. whole: -1.11 (0.30), residues: 842 helix: 0.31 (0.28), residues: 384 sheet: -0.83 (0.50), residues: 116 loop : -1.88 (0.35), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 204 TYR 0.013 0.001 TYR A 147 PHE 0.024 0.002 PHE B 78 TRP 0.025 0.002 TRP B 220 HIS 0.001 0.000 HIS D 201 Details of bonding type rmsd covalent geometry : bond 0.00344 ( 6623) covalent geometry : angle 0.69417 ( 9042) SS BOND : bond 0.00116 ( 4) SS BOND : angle 0.39552 ( 8) hydrogen bonds : bond 0.04106 ( 350) hydrogen bonds : angle 4.96999 ( 1056) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 123 time to evaluate : 0.133 Fit side-chains REVERT: A 44 PHE cc_start: 0.7017 (OUTLIER) cc_final: 0.6012 (t80) REVERT: A 267 ARG cc_start: 0.7096 (tmm160) cc_final: 0.6550 (tmm160) REVERT: D 203 MET cc_start: 0.4464 (OUTLIER) cc_final: 0.4042 (mtt) REVERT: B 44 PHE cc_start: 0.6802 (OUTLIER) cc_final: 0.5949 (t80) REVERT: B 93 TYR cc_start: 0.7227 (m-80) cc_final: 0.6625 (m-80) REVERT: B 224 LEU cc_start: 0.4574 (OUTLIER) cc_final: 0.4248 (tp) outliers start: 48 outliers final: 35 residues processed: 154 average time/residue: 0.0704 time to fit residues: 14.2090 Evaluate side-chains 162 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 123 time to evaluate : 0.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 44 PHE Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 126 TRP Chi-restraints excluded: chain A residue 154 ARG Chi-restraints excluded: chain A residue 165 GLN Chi-restraints excluded: chain A residue 170 PHE Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 220 TRP Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain C residue 127 SER Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 238 THR Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 182 HIS Chi-restraints excluded: chain D residue 203 MET Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 238 THR Chi-restraints excluded: chain D residue 259 ASP Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain B residue 44 PHE Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 126 TRP Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 154 ARG Chi-restraints excluded: chain B residue 165 GLN Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 186 PHE Chi-restraints excluded: chain B residue 213 SER Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 247 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 53 optimal weight: 1.9990 chunk 14 optimal weight: 0.0970 chunk 57 optimal weight: 8.9990 chunk 6 optimal weight: 0.2980 chunk 15 optimal weight: 0.5980 chunk 45 optimal weight: 6.9990 chunk 8 optimal weight: 0.5980 chunk 26 optimal weight: 10.0000 chunk 63 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 85 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4486 r_free = 0.4486 target = 0.179474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.157830 restraints weight = 10319.168| |-----------------------------------------------------------------------------| r_work (start): 0.4235 rms_B_bonded: 2.71 r_work: 0.4113 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.4113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6207 moved from start: 0.2100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6627 Z= 0.150 Angle : 0.701 16.126 9050 Z= 0.342 Chirality : 0.044 0.424 1059 Planarity : 0.004 0.057 1128 Dihedral : 4.748 21.953 914 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 15.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.38 % Favored : 90.62 % Rotamer: Outliers : 7.04 % Allowed : 35.38 % Favored : 57.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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 aren not related in a simple way. whole: -1.13 (0.30), residues: 842 helix: 0.33 (0.28), residues: 386 sheet: -0.86 (0.50), residues: 116 loop : -1.96 (0.34), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 204 TYR 0.009 0.001 TYR B 147 PHE 0.024 0.001 PHE B 78 TRP 0.025 0.002 TRP B 220 HIS 0.003 0.001 HIS B 202 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 6623) covalent geometry : angle 0.70086 ( 9042) SS BOND : bond 0.00123 ( 4) SS BOND : angle 0.36449 ( 8) hydrogen bonds : bond 0.04016 ( 350) hydrogen bonds : angle 4.96745 ( 1056) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 124 time to evaluate : 0.213 Fit side-chains REVERT: A 44 PHE cc_start: 0.7058 (OUTLIER) cc_final: 0.5987 (t80) REVERT: A 267 ARG cc_start: 0.7122 (tmm160) cc_final: 0.6591 (tmm160) REVERT: D 203 MET cc_start: 0.4461 (OUTLIER) cc_final: 0.4062 (mtt) REVERT: B 44 PHE cc_start: 0.6834 (OUTLIER) cc_final: 0.5991 (t80) REVERT: B 93 TYR cc_start: 0.7291 (m-80) cc_final: 0.6696 (m-80) REVERT: B 224 LEU cc_start: 0.4587 (OUTLIER) cc_final: 0.4269 (tp) outliers start: 46 outliers final: 34 residues processed: 154 average time/residue: 0.0674 time to fit residues: 13.6449 Evaluate side-chains 161 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 123 time to evaluate : 0.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 44 PHE Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 126 TRP Chi-restraints excluded: chain A residue 154 ARG Chi-restraints excluded: chain A residue 165 GLN Chi-restraints excluded: chain A residue 170 PHE Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 220 TRP Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain C residue 127 SER Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 238 THR Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 182 HIS Chi-restraints excluded: chain D residue 203 MET Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 238 THR Chi-restraints excluded: chain D residue 259 ASP Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 44 PHE Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 126 TRP Chi-restraints excluded: chain B residue 154 ARG Chi-restraints excluded: chain B residue 165 GLN Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 186 PHE Chi-restraints excluded: chain B residue 213 SER Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 247 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 65 optimal weight: 2.9990 chunk 54 optimal weight: 0.4980 chunk 24 optimal weight: 0.5980 chunk 11 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 chunk 80 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 chunk 52 optimal weight: 0.6980 chunk 8 optimal weight: 0.8980 chunk 19 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4491 r_free = 0.4491 target = 0.180016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.159033 restraints weight = 10075.222| |-----------------------------------------------------------------------------| r_work (start): 0.4255 rms_B_bonded: 2.53 r_work: 0.4136 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.4136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6198 moved from start: 0.2158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6627 Z= 0.146 Angle : 0.701 15.670 9050 Z= 0.341 Chirality : 0.043 0.341 1059 Planarity : 0.004 0.057 1128 Dihedral : 4.728 22.066 914 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 14.96 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.67 % Favored : 91.21 % Rotamer: Outliers : 6.28 % Allowed : 35.83 % Favored : 57.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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 aren not related in a simple way. whole: -1.10 (0.30), residues: 842 helix: 0.38 (0.28), residues: 386 sheet: -0.86 (0.50), residues: 116 loop : -1.96 (0.34), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 204 TYR 0.011 0.001 TYR B 147 PHE 0.024 0.001 PHE B 78 TRP 0.025 0.002 TRP B 220 HIS 0.003 0.001 HIS B 202 Details of bonding type rmsd covalent geometry : bond 0.00330 ( 6623) covalent geometry : angle 0.70131 ( 9042) SS BOND : bond 0.00125 ( 4) SS BOND : angle 0.35609 ( 8) hydrogen bonds : bond 0.03940 ( 350) hydrogen bonds : angle 4.93436 ( 1056) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 119 time to evaluate : 0.212 Fit side-chains REVERT: A 44 PHE cc_start: 0.7067 (OUTLIER) cc_final: 0.5999 (t80) REVERT: D 203 MET cc_start: 0.4485 (OUTLIER) cc_final: 0.4097 (mtt) REVERT: D 207 ARG cc_start: 0.7695 (ttm170) cc_final: 0.7096 (ttm170) REVERT: B 44 PHE cc_start: 0.6875 (OUTLIER) cc_final: 0.6105 (t80) REVERT: B 93 TYR cc_start: 0.7246 (m-80) cc_final: 0.6664 (m-80) REVERT: B 224 LEU cc_start: 0.4675 (OUTLIER) cc_final: 0.4393 (tp) outliers start: 41 outliers final: 35 residues processed: 145 average time/residue: 0.0790 time to fit residues: 14.8513 Evaluate side-chains 156 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 117 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 SER Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 44 PHE Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 126 TRP Chi-restraints excluded: chain A residue 154 ARG Chi-restraints excluded: chain A residue 165 GLN Chi-restraints excluded: chain A residue 170 PHE Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 220 TRP Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain C residue 127 SER Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 238 THR Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 182 HIS Chi-restraints excluded: chain D residue 203 MET Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 238 THR Chi-restraints excluded: chain D residue 259 ASP Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 44 PHE Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 126 TRP Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 154 ARG Chi-restraints excluded: chain B residue 165 GLN Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 186 PHE Chi-restraints excluded: chain B residue 213 SER Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 247 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 24 optimal weight: 0.5980 chunk 63 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 chunk 74 optimal weight: 0.1980 chunk 10 optimal weight: 1.9990 chunk 54 optimal weight: 0.0980 chunk 70 optimal weight: 3.9990 chunk 26 optimal weight: 9.9990 chunk 17 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 32 optimal weight: 0.0050 overall best weight: 0.3794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4520 r_free = 0.4520 target = 0.182243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.160826 restraints weight = 10150.135| |-----------------------------------------------------------------------------| r_work (start): 0.4269 rms_B_bonded: 2.70 r_work: 0.4149 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.4149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6139 moved from start: 0.2203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6627 Z= 0.123 Angle : 0.683 15.609 9050 Z= 0.330 Chirality : 0.041 0.281 1059 Planarity : 0.004 0.057 1128 Dihedral : 4.584 21.286 914 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 13.77 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.31 % Favored : 91.57 % Rotamer: Outliers : 6.58 % Allowed : 35.99 % Favored : 57.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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 aren not related in a simple way. whole: -0.91 (0.31), residues: 842 helix: 0.62 (0.28), residues: 382 sheet: -0.87 (0.49), residues: 116 loop : -1.91 (0.34), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 204 TYR 0.008 0.001 TYR C 264 PHE 0.024 0.001 PHE B 78 TRP 0.024 0.002 TRP B 220 HIS 0.003 0.001 HIS B 202 Details of bonding type rmsd covalent geometry : bond 0.00275 ( 6623) covalent geometry : angle 0.68317 ( 9042) SS BOND : bond 0.00146 ( 4) SS BOND : angle 0.33544 ( 8) hydrogen bonds : bond 0.03591 ( 350) hydrogen bonds : angle 4.80674 ( 1056) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1459.26 seconds wall clock time: 25 minutes 40.51 seconds (1540.51 seconds total)