Starting phenix.real_space_refine on Tue Jan 14 09:25:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yzk_39696/01_2025/8yzk_39696.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yzk_39696/01_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_39696/01_2025/8yzk_39696.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yzk_39696/01_2025/8yzk_39696.map" model { file = "/net/cci-nas-00/data/ceres_data/8yzk_39696/01_2025/8yzk_39696.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yzk_39696/01_2025/8yzk_39696.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.028 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/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: {'GLN:plan1': 5, 'ASP:plan': 1, 'TYR:plan': 4, 'TRP:plan': 1, 'HIS:plan': 1, 'GLU:plan': 2, 'ARG:plan': 3} 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, 'TYR:plan': 5, 'TRP:plan': 1, 'ASP:plan': 1, 'GLU:plan': 1, 'ARG:plan': 2} 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: 4.50, per 1000 atoms: 0.70 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: 1.34 Conformation dependent library (CDL) restraints added in 934.8 milliseconds 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1612 Finding SS restraints... Secondary structure from input PDB file: 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: 0.70 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: 1.72 Time building geometry restraints manager: 1.57 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: 0.690 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: 0.220 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 18.160 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.260 ------------------------------------------------------------------------------- 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 6623 Z= 0.226 Angle : 0.762 18.757 9042 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (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 TRP 0.024 0.002 TRP A 220 HIS 0.012 0.002 HIS B 110 PHE 0.038 0.002 PHE B 78 TYR 0.018 0.001 TYR D 228 ARG 0.007 0.001 ARG B 267 *********************** 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 : 0.771 Fit side-chains outliers start: 7 outliers final: 3 residues processed: 119 average time/residue: 0.2039 time to fit residues: 31.6638 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 : 0.614 ------------------------------------------------------------------------------- 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 70 optimal weight: 3.9990 chunk 63 optimal weight: 4.9990 chunk 35 optimal weight: 0.9980 chunk 21 optimal weight: 0.3980 chunk 42 optimal weight: 10.0000 chunk 34 optimal weight: 0.8980 chunk 65 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 40 optimal weight: 4.9990 chunk 49 optimal weight: 5.9990 chunk 76 optimal weight: 3.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- 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 = 0.4473 r_free = 0.4473 target = 0.178700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.157742 restraints weight = 10114.126| |-----------------------------------------------------------------------------| r_work (start): 0.4217 rms_B_bonded: 2.54 r_work: 0.4115 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.4115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6201 moved from start: 0.1197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 6623 Z= 0.293 Angle : 0.689 12.673 9042 Z= 0.358 Chirality : 0.044 0.221 1059 Planarity : 0.005 0.061 1128 Dihedral : 5.614 44.479 919 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 14.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.03 % Favored : 90.97 % Rotamer: Outliers : 5.67 % Allowed : 37.06 % Favored : 57.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.30), residues: 842 helix: 0.02 (0.28), residues: 372 sheet: -1.66 (0.46), residues: 128 loop : -1.73 (0.35), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 220 HIS 0.004 0.001 HIS B 110 PHE 0.016 0.002 PHE D 198 TYR 0.012 0.002 TYR A 93 ARG 0.003 0.000 ARG C 241 *********************** 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 162 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 125 time to evaluate : 0.683 Fit side-chains REVERT: A 87 GLN cc_start: 0.6632 (OUTLIER) cc_final: 0.6427 (pm20) REVERT: A 168 VAL cc_start: 0.7503 (t) cc_final: 0.7293 (p) REVERT: D 228 TYR cc_start: 0.7177 (OUTLIER) cc_final: 0.6352 (m-10) REVERT: B 93 TYR cc_start: 0.7182 (m-80) cc_final: 0.6817 (m-80) REVERT: B 150 LEU cc_start: 0.7194 (tp) cc_final: 0.6989 (tt) outliers start: 37 outliers final: 19 residues processed: 151 average time/residue: 0.1803 time to fit residues: 36.0878 Evaluate side-chains 141 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 120 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 87 GLN Chi-restraints excluded: chain A residue 126 TRP Chi-restraints excluded: chain A residue 138 LEU 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 186 PHE Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 238 THR Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain D residue 228 TYR Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain B residue 13 PHE 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 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 32 optimal weight: 4.9990 chunk 18 optimal weight: 0.6980 chunk 35 optimal weight: 5.9990 chunk 55 optimal weight: 4.9990 chunk 67 optimal weight: 0.5980 chunk 56 optimal weight: 7.9990 chunk 6 optimal weight: 0.9980 chunk 66 optimal weight: 0.5980 chunk 11 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 chunk 17 optimal weight: 0.0970 overall best weight: 0.5578 ------------------------------------------------------------------------------- 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 = 0.4509 r_free = 0.4509 target = 0.182867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.163187 restraints weight = 10195.755| |-----------------------------------------------------------------------------| r_work (start): 0.4270 rms_B_bonded: 2.27 r_work: 0.4174 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.4034 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.4034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6271 moved from start: 0.1289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6623 Z= 0.191 Angle : 0.621 12.920 9042 Z= 0.315 Chirality : 0.040 0.198 1059 Planarity : 0.005 0.065 1128 Dihedral : 5.107 44.298 916 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 12.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.55 % Favored : 91.45 % Rotamer: Outliers : 7.04 % Allowed : 34.92 % Favored : 58.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.31), residues: 842 helix: 0.30 (0.28), residues: 384 sheet: -1.54 (0.46), residues: 128 loop : -1.65 (0.36), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 220 HIS 0.003 0.001 HIS B 110 PHE 0.020 0.001 PHE A 78 TYR 0.009 0.001 TYR A 93 ARG 0.002 0.000 ARG C 241 *********************** 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 164 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 118 time to evaluate : 0.742 Fit side-chains REVERT: A 44 PHE cc_start: 0.7370 (OUTLIER) cc_final: 0.6560 (t80) REVERT: A 87 GLN cc_start: 0.6645 (OUTLIER) cc_final: 0.6443 (pm20) REVERT: A 224 LEU cc_start: 0.4828 (OUTLIER) cc_final: 0.4388 (mp) REVERT: D 133 ASN cc_start: 0.5500 (OUTLIER) cc_final: 0.5298 (m-40) REVERT: B 44 PHE cc_start: 0.6994 (OUTLIER) cc_final: 0.6154 (t80) REVERT: B 215 ILE cc_start: 0.7477 (OUTLIER) cc_final: 0.7276 (mm) REVERT: B 224 LEU cc_start: 0.4936 (OUTLIER) cc_final: 0.4360 (tp) outliers start: 46 outliers final: 24 residues processed: 150 average time/residue: 0.1833 time to fit residues: 36.3588 Evaluate side-chains 148 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 117 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 PHE Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 87 GLN Chi-restraints excluded: chain A residue 126 TRP Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 138 LEU 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 186 PHE 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 137 VAL Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain C residue 238 THR Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain D residue 133 ASN Chi-restraints excluded: chain D residue 182 HIS Chi-restraints excluded: chain D residue 238 THR 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 143 ILE 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 28 optimal weight: 5.9990 chunk 66 optimal weight: 0.2980 chunk 15 optimal weight: 0.5980 chunk 48 optimal weight: 20.0000 chunk 18 optimal weight: 0.6980 chunk 77 optimal weight: 5.9990 chunk 35 optimal weight: 4.9990 chunk 47 optimal weight: 8.9990 chunk 3 optimal weight: 0.7980 chunk 57 optimal weight: 1.9990 chunk 44 optimal weight: 6.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.4482 r_free = 0.4482 target = 0.179368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.157410 restraints weight = 10194.971| |-----------------------------------------------------------------------------| r_work (start): 0.4219 rms_B_bonded: 2.71 r_work: 0.4109 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.4109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6219 moved from start: 0.1572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 6623 Z= 0.236 Angle : 0.645 13.007 9042 Z= 0.329 Chirality : 0.042 0.213 1059 Planarity : 0.005 0.062 1128 Dihedral : 5.110 43.575 916 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 14.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.62 % Favored : 90.38 % Rotamer: Outliers : 7.20 % Allowed : 35.53 % Favored : 57.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.31), residues: 842 helix: 0.21 (0.28), residues: 384 sheet: -0.99 (0.50), residues: 116 loop : -1.82 (0.35), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 220 HIS 0.003 0.001 HIS B 110 PHE 0.018 0.002 PHE A 78 TYR 0.018 0.002 TYR D 264 ARG 0.002 0.000 ARG D 241 *********************** 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 168 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 121 time to evaluate : 0.721 Fit side-chains revert: symmetry clash REVERT: A 44 PHE cc_start: 0.7124 (OUTLIER) cc_final: 0.6251 (t80) REVERT: D 203 MET cc_start: 0.4585 (OUTLIER) cc_final: 0.4119 (mtt) REVERT: B 44 PHE cc_start: 0.6798 (OUTLIER) cc_final: 0.5860 (t80) REVERT: B 224 LEU cc_start: 0.4742 (OUTLIER) cc_final: 0.4247 (tp) outliers start: 47 outliers final: 32 residues processed: 150 average time/residue: 0.1831 time to fit residues: 36.3193 Evaluate side-chains 155 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 119 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 SER Chi-restraints excluded: chain A residue 44 PHE Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 126 TRP Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 143 ILE 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 186 PHE Chi-restraints excluded: chain A residue 204 ARG Chi-restraints excluded: chain A residue 220 TRP Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain C residue 137 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 59 optimal weight: 0.5980 chunk 42 optimal weight: 6.9990 chunk 38 optimal weight: 0.8980 chunk 60 optimal weight: 0.5980 chunk 2 optimal weight: 2.9990 chunk 57 optimal weight: 4.9990 chunk 62 optimal weight: 0.9980 chunk 78 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 37 optimal weight: 0.2980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.4494 r_free = 0.4494 target = 0.180151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.158534 restraints weight = 10116.188| |-----------------------------------------------------------------------------| r_work (start): 0.4234 rms_B_bonded: 2.69 r_work: 0.4126 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.4126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6184 moved from start: 0.1629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6623 Z= 0.208 Angle : 0.638 13.602 9042 Z= 0.322 Chirality : 0.041 0.196 1059 Planarity : 0.004 0.063 1128 Dihedral : 5.002 43.153 916 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 13.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.43 % Favored : 91.57 % Rotamer: Outliers : 7.50 % Allowed : 35.07 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.31), residues: 842 helix: 0.34 (0.28), residues: 384 sheet: -0.87 (0.51), residues: 116 loop : -1.82 (0.35), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 220 HIS 0.002 0.001 HIS B 110 PHE 0.018 0.001 PHE A 158 TYR 0.017 0.001 TYR D 264 ARG 0.004 0.000 ARG A 267 *********************** 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 174 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 125 time to evaluate : 0.652 Fit side-chains revert: symmetry clash REVERT: A 44 PHE cc_start: 0.7085 (OUTLIER) cc_final: 0.6219 (t80) REVERT: D 203 MET cc_start: 0.4509 (OUTLIER) cc_final: 0.4063 (mtt) REVERT: B 44 PHE cc_start: 0.6774 (OUTLIER) cc_final: 0.5832 (t80) REVERT: B 224 LEU cc_start: 0.4561 (OUTLIER) cc_final: 0.4205 (tp) outliers start: 49 outliers final: 30 residues processed: 159 average time/residue: 0.1891 time to fit residues: 39.2119 Evaluate side-chains 156 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 122 time to evaluate : 0.737 ------------------------------------------------------------------------------- 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 67 LEU Chi-restraints excluded: chain A residue 126 TRP Chi-restraints excluded: chain A residue 138 LEU 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 186 PHE Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain C residue 137 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 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 178 LEU Chi-restraints excluded: chain B residue 180 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 79 optimal weight: 0.0370 chunk 37 optimal weight: 0.9990 chunk 62 optimal weight: 0.3980 chunk 77 optimal weight: 0.9990 chunk 33 optimal weight: 0.1980 chunk 41 optimal weight: 5.9990 chunk 63 optimal weight: 4.9990 chunk 12 optimal weight: 0.8980 chunk 5 optimal weight: 3.9990 chunk 26 optimal weight: 9.9990 chunk 55 optimal weight: 4.9990 overall best weight: 0.5060 ------------------------------------------------------------------------------- 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 = 0.4503 r_free = 0.4503 target = 0.181014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.160180 restraints weight = 10044.206| |-----------------------------------------------------------------------------| r_work (start): 0.4255 rms_B_bonded: 2.55 r_work: 0.4151 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.4151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6148 moved from start: 0.1699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 6623 Z= 0.186 Angle : 0.655 14.266 9042 Z= 0.325 Chirality : 0.041 0.200 1059 Planarity : 0.004 0.061 1128 Dihedral : 4.936 42.398 916 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 13.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.19 % Favored : 91.81 % Rotamer: Outliers : 7.66 % Allowed : 35.07 % Favored : 57.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.31), residues: 842 helix: 0.46 (0.28), residues: 382 sheet: -0.80 (0.51), residues: 116 loop : -1.82 (0.35), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 220 HIS 0.002 0.001 HIS B 202 PHE 0.018 0.001 PHE A 158 TYR 0.019 0.001 TYR D 264 ARG 0.003 0.000 ARG B 119 *********************** 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 175 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 125 time to evaluate : 0.699 Fit side-chains REVERT: A 44 PHE cc_start: 0.7061 (OUTLIER) cc_final: 0.6179 (t80) REVERT: A 95 LEU cc_start: 0.7662 (mt) cc_final: 0.7333 (mp) REVERT: D 203 MET cc_start: 0.4457 (OUTLIER) cc_final: 0.4058 (mtt) REVERT: B 44 PHE cc_start: 0.6770 (OUTLIER) cc_final: 0.5830 (t80) REVERT: B 224 LEU cc_start: 0.4473 (OUTLIER) cc_final: 0.4189 (tp) outliers start: 50 outliers final: 34 residues processed: 155 average time/residue: 0.1897 time to fit residues: 38.4321 Evaluate side-chains 164 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 126 time to evaluate : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 PHE Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 126 TRP Chi-restraints excluded: chain A residue 138 LEU 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 186 PHE Chi-restraints excluded: chain A residue 220 TRP 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 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 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 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 238 ASP Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 248 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 30 optimal weight: 7.9990 chunk 54 optimal weight: 0.5980 chunk 3 optimal weight: 4.9990 chunk 78 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 45 optimal weight: 6.9990 chunk 59 optimal weight: 0.8980 chunk 38 optimal weight: 0.8980 chunk 1 optimal weight: 0.1980 chunk 75 optimal weight: 0.9990 chunk 17 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.4497 r_free = 0.4497 target = 0.180266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.159383 restraints weight = 9997.587| |-----------------------------------------------------------------------------| r_work (start): 0.4246 rms_B_bonded: 2.53 r_work: 0.4142 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.4142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6162 moved from start: 0.1827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 6623 Z= 0.219 Angle : 0.669 15.171 9042 Z= 0.333 Chirality : 0.042 0.208 1059 Planarity : 0.004 0.061 1128 Dihedral : 4.901 41.640 916 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 15.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.79 % Favored : 91.21 % Rotamer: Outliers : 7.66 % Allowed : 35.38 % Favored : 56.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.31), residues: 842 helix: 0.45 (0.28), residues: 382 sheet: -0.78 (0.50), residues: 116 loop : -1.82 (0.35), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 220 HIS 0.003 0.001 HIS A 202 PHE 0.023 0.001 PHE B 78 TYR 0.017 0.001 TYR D 264 ARG 0.007 0.000 ARG A 204 *********************** 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 174 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 124 time to evaluate : 0.627 Fit side-chains REVERT: A 44 PHE cc_start: 0.7028 (OUTLIER) cc_final: 0.6156 (t80) REVERT: A 95 LEU cc_start: 0.7670 (mt) cc_final: 0.7331 (mp) REVERT: A 267 ARG cc_start: 0.7292 (ttp80) cc_final: 0.6853 (tmm160) REVERT: D 203 MET cc_start: 0.4493 (OUTLIER) cc_final: 0.4060 (mtt) REVERT: D 207 ARG cc_start: 0.6621 (ptp-170) cc_final: 0.6409 (ttm170) REVERT: B 44 PHE cc_start: 0.6779 (OUTLIER) cc_final: 0.5837 (t80) REVERT: B 93 TYR cc_start: 0.7243 (m-80) cc_final: 0.6695 (m-80) REVERT: B 224 LEU cc_start: 0.4482 (OUTLIER) cc_final: 0.4205 (tp) outliers start: 50 outliers final: 36 residues processed: 154 average time/residue: 0.1913 time to fit residues: 38.2975 Evaluate side-chains 162 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 122 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 PHE Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 126 TRP Chi-restraints excluded: chain A residue 138 LEU 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 186 PHE 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 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 Chi-restraints excluded: chain B residue 248 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 8 optimal weight: 0.0010 chunk 0 optimal weight: 5.9990 chunk 14 optimal weight: 1.9990 chunk 41 optimal weight: 5.9990 chunk 2 optimal weight: 2.9990 chunk 26 optimal weight: 9.9990 chunk 60 optimal weight: 2.9990 chunk 25 optimal weight: 0.4980 chunk 51 optimal weight: 5.9990 chunk 6 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 overall best weight: 1.2790 ------------------------------------------------------------------------------- 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 = 0.4457 r_free = 0.4457 target = 0.177295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.155477 restraints weight = 10127.837| |-----------------------------------------------------------------------------| r_work (start): 0.4187 rms_B_bonded: 2.66 r_work: 0.4077 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.4077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6266 moved from start: 0.2121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 6623 Z= 0.317 Angle : 0.732 15.853 9042 Z= 0.369 Chirality : 0.045 0.192 1059 Planarity : 0.005 0.058 1128 Dihedral : 5.171 41.318 916 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 17.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.21 % Favored : 89.79 % Rotamer: Outliers : 7.81 % Allowed : 34.76 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.30), residues: 842 helix: 0.16 (0.28), residues: 380 sheet: -0.88 (0.50), residues: 116 loop : -1.89 (0.35), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 220 HIS 0.002 0.000 HIS B 110 PHE 0.031 0.002 PHE A 158 TYR 0.012 0.002 TYR D 274 ARG 0.006 0.001 ARG A 204 *********************** 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 177 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 126 time to evaluate : 0.629 Fit side-chains REVERT: A 44 PHE cc_start: 0.7071 (OUTLIER) cc_final: 0.6091 (t80) REVERT: A 95 LEU cc_start: 0.7698 (mt) cc_final: 0.7362 (mp) REVERT: D 203 MET cc_start: 0.4614 (OUTLIER) cc_final: 0.4125 (mtt) REVERT: B 44 PHE cc_start: 0.6838 (OUTLIER) cc_final: 0.6027 (t80) REVERT: B 224 LEU cc_start: 0.4691 (OUTLIER) cc_final: 0.4212 (tp) outliers start: 51 outliers final: 35 residues processed: 158 average time/residue: 0.1933 time to fit residues: 40.0669 Evaluate side-chains 166 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 127 time to evaluate : 0.810 ------------------------------------------------------------------------------- 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 67 LEU Chi-restraints excluded: chain A residue 126 TRP Chi-restraints excluded: chain A residue 138 LEU 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 186 PHE Chi-restraints excluded: chain A residue 220 TRP 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 217 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 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 154 ARG Chi-restraints excluded: chain B residue 165 GLN Chi-restraints excluded: chain B residue 178 LEU 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 11 optimal weight: 0.8980 chunk 55 optimal weight: 0.0980 chunk 74 optimal weight: 0.9990 chunk 82 optimal weight: 0.6980 chunk 31 optimal weight: 5.9990 chunk 28 optimal weight: 5.9990 chunk 56 optimal weight: 0.7980 chunk 6 optimal weight: 0.5980 chunk 43 optimal weight: 4.9990 chunk 60 optimal weight: 0.6980 chunk 40 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.179888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.158377 restraints weight = 10148.049| |-----------------------------------------------------------------------------| r_work (start): 0.4228 rms_B_bonded: 2.70 r_work: 0.4120 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.4120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6188 moved from start: 0.2103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6623 Z= 0.218 Angle : 0.716 15.928 9042 Z= 0.347 Chirality : 0.042 0.185 1059 Planarity : 0.004 0.062 1128 Dihedral : 4.775 21.537 914 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 15.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.55 % Favored : 91.45 % Rotamer: Outliers : 6.13 % Allowed : 35.83 % Favored : 58.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.30), residues: 842 helix: 0.33 (0.28), residues: 382 sheet: -0.87 (0.50), residues: 116 loop : -1.88 (0.35), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP B 220 HIS 0.003 0.001 HIS A 202 PHE 0.026 0.001 PHE B 78 TYR 0.011 0.001 TYR B 93 ARG 0.004 0.000 ARG C 128 *********************** 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 161 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 121 time to evaluate : 0.622 Fit side-chains REVERT: A 44 PHE cc_start: 0.7026 (OUTLIER) cc_final: 0.6114 (t80) REVERT: A 95 LEU cc_start: 0.7650 (mt) cc_final: 0.7323 (mp) REVERT: A 267 ARG cc_start: 0.7146 (tmm160) cc_final: 0.6929 (tmm160) REVERT: D 203 MET cc_start: 0.4443 (OUTLIER) cc_final: 0.4049 (mtt) REVERT: B 44 PHE cc_start: 0.6835 (OUTLIER) cc_final: 0.6009 (t80) REVERT: B 93 TYR cc_start: 0.7205 (m-80) cc_final: 0.6665 (m-80) outliers start: 40 outliers final: 32 residues processed: 149 average time/residue: 0.1821 time to fit residues: 35.5909 Evaluate side-chains 155 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 120 time to evaluate : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 PHE Chi-restraints excluded: chain A residue 126 TRP Chi-restraints excluded: chain A residue 138 LEU 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 186 PHE 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 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 217 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 215 ILE 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 81 optimal weight: 0.0980 chunk 14 optimal weight: 0.3980 chunk 6 optimal weight: 0.0980 chunk 26 optimal weight: 10.0000 chunk 51 optimal weight: 0.6980 chunk 43 optimal weight: 6.9990 chunk 44 optimal weight: 0.2980 chunk 79 optimal weight: 0.9980 chunk 60 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 29 optimal weight: 6.9990 overall best weight: 0.3180 ------------------------------------------------------------------------------- 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 = 0.4519 r_free = 0.4519 target = 0.182160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.161403 restraints weight = 10210.527| |-----------------------------------------------------------------------------| r_work (start): 0.4289 rms_B_bonded: 2.58 r_work: 0.4172 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.4172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6135 moved from start: 0.2121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6623 Z= 0.189 Angle : 0.717 16.329 9042 Z= 0.344 Chirality : 0.042 0.218 1059 Planarity : 0.004 0.060 1128 Dihedral : 4.691 21.113 914 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 14.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.79 % Favored : 91.21 % Rotamer: Outliers : 5.82 % Allowed : 36.60 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.30), residues: 842 helix: 0.46 (0.28), residues: 386 sheet: -0.88 (0.49), residues: 116 loop : -1.94 (0.35), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP B 220 HIS 0.003 0.001 HIS A 202 PHE 0.027 0.001 PHE B 78 TYR 0.012 0.001 TYR B 93 ARG 0.005 0.000 ARG B 119 ********************** 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 159 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 121 time to evaluate : 0.640 Fit side-chains REVERT: A 44 PHE cc_start: 0.7023 (OUTLIER) cc_final: 0.6115 (t80) REVERT: A 95 LEU cc_start: 0.7700 (mt) cc_final: 0.7373 (mp) REVERT: A 267 ARG cc_start: 0.7067 (tmm160) cc_final: 0.6626 (tmm160) REVERT: D 203 MET cc_start: 0.4429 (OUTLIER) cc_final: 0.4093 (mtt) REVERT: B 44 PHE cc_start: 0.6781 (OUTLIER) cc_final: 0.6018 (t80) REVERT: B 110 HIS cc_start: 0.6861 (t-170) cc_final: 0.6625 (t-170) outliers start: 38 outliers final: 31 residues processed: 145 average time/residue: 0.2169 time to fit residues: 40.5237 Evaluate side-chains 155 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 121 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 PHE Chi-restraints excluded: chain A residue 126 TRP Chi-restraints excluded: chain A residue 138 LEU 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 186 PHE 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 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 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 211 LEU Chi-restraints excluded: chain B residue 215 ILE 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 62 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 3 optimal weight: 3.9990 chunk 52 optimal weight: 0.0000 chunk 15 optimal weight: 0.0670 chunk 33 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 46 optimal weight: 6.9990 overall best weight: 0.7724 ------------------------------------------------------------------------------- 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 = 0.4490 r_free = 0.4490 target = 0.179850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.158707 restraints weight = 10252.154| |-----------------------------------------------------------------------------| r_work (start): 0.4231 rms_B_bonded: 2.58 r_work: 0.4128 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.4128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6163 moved from start: 0.2223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 6623 Z= 0.243 Angle : 0.731 15.848 9042 Z= 0.355 Chirality : 0.043 0.258 1059 Planarity : 0.004 0.060 1128 Dihedral : 4.769 21.793 914 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 16.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.50 % Favored : 90.50 % Rotamer: Outliers : 5.82 % Allowed : 36.45 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.30), residues: 842 helix: 0.38 (0.28), residues: 386 sheet: -0.90 (0.49), residues: 116 loop : -1.80 (0.35), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP B 220 HIS 0.002 0.001 HIS A 202 PHE 0.025 0.002 PHE A 158 TYR 0.013 0.001 TYR A 147 ARG 0.005 0.001 ARG C 207 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3385.99 seconds wall clock time: 60 minutes 43.13 seconds (3643.13 seconds total)