Starting phenix.real_space_refine on Sat Aug 3 00:35:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yzk_39696/08_2024/8yzk_39696.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yzk_39696/08_2024/8yzk_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yzk_39696/08_2024/8yzk_39696.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yzk_39696/08_2024/8yzk_39696.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yzk_39696/08_2024/8yzk_39696.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yzk_39696/08_2024/8yzk_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 Residue "A PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 231": "OD1" <-> "OD2" Residue "D TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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: 5.22, per 1000 atoms: 0.81 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 - 3.50 Amino acid : False - 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: 2.09 Conformation dependent library (CDL) restraints added in 961.5 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: 0.68 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: 1.70 Time building geometry restraints manager: 2.30 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: 98.26 - 105.62: 115 105.62 - 112.98: 3542 112.98 - 120.34: 2492 120.34 - 127.70: 2819 127.70 - 135.06: 74 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: 1.050 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: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 20.330 Find NCS groups from input model: 0.200 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:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.660 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 7 poor density : 116 time to evaluate : 0.646 Fit side-chains outliers start: 7 outliers final: 3 residues processed: 119 average time/residue: 0.1946 time to fit residues: 30.1212 Evaluate side-chains 114 residues out of total 754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 111 time to evaluate : 0.658 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5949 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 fitting. rotamer outliers: 37 poor density : 125 time to evaluate : 0.677 Fit side-chains REVERT: D 228 TYR cc_start: 0.7066 (OUTLIER) cc_final: 0.6206 (m-10) REVERT: B 93 TYR cc_start: 0.6892 (m-80) cc_final: 0.6515 (m-80) outliers start: 37 outliers final: 19 residues processed: 151 average time/residue: 0.1717 time to fit residues: 34.5601 Evaluate side-chains 143 residues out of total 754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 123 time to evaluate : 0.638 ------------------------------------------------------------------------------- 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 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 42 optimal weight: 8.9990 chunk 23 optimal weight: 1.9990 chunk 63 optimal weight: 4.9990 chunk 51 optimal weight: 0.8980 chunk 21 optimal weight: 0.6980 chunk 76 optimal weight: 0.9990 chunk 82 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 chunk 75 optimal weight: 0.8980 chunk 26 optimal weight: 9.9990 chunk 61 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5926 moved from start: 0.1422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 6623 Z= 0.233 Angle : 0.649 13.849 9042 Z= 0.330 Chirality : 0.042 0.220 1059 Planarity : 0.005 0.065 1128 Dihedral : 5.198 44.344 916 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 14.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.03 % Favored : 90.97 % Rotamer: Outliers : 7.04 % Allowed : 35.99 % 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: -1.37 (0.30), residues: 842 helix: 0.12 (0.28), residues: 376 sheet: -1.16 (0.50), residues: 116 loop : -1.93 (0.34), residues: 350 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 0.020 0.002 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 fitting. rotamer outliers: 46 poor density : 118 time to evaluate : 0.706 Fit side-chains REVERT: A 44 PHE cc_start: 0.6911 (OUTLIER) cc_final: 0.6131 (t80) REVERT: D 203 MET cc_start: 0.4865 (OUTLIER) cc_final: 0.4246 (mtt) REVERT: B 44 PHE cc_start: 0.6576 (OUTLIER) cc_final: 0.5773 (t80) REVERT: B 224 LEU cc_start: 0.4762 (OUTLIER) cc_final: 0.4506 (tp) outliers start: 46 outliers final: 26 residues processed: 148 average time/residue: 0.1804 time to fit residues: 35.1868 Evaluate side-chains 148 residues out of total 754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 118 time to evaluate : 0.587 ------------------------------------------------------------------------------- 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 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 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 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 143 ILE 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 75 optimal weight: 0.7980 chunk 57 optimal weight: 4.9990 chunk 39 optimal weight: 0.6980 chunk 8 optimal weight: 0.0980 chunk 36 optimal weight: 5.9990 chunk 51 optimal weight: 0.0980 chunk 76 optimal weight: 2.9990 chunk 81 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 72 optimal weight: 0.6980 chunk 21 optimal weight: 0.0870 overall best weight: 0.3358 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5847 moved from start: 0.1493 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= 0.164 Angle : 0.607 13.381 9042 Z= 0.308 Chirality : 0.040 0.132 1059 Planarity : 0.004 0.063 1128 Dihedral : 4.972 43.898 916 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.96 % Favored : 92.04 % Rotamer: Outliers : 5.97 % Allowed : 35.53 % 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 (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: 0.47 (0.28), residues: 386 sheet: -1.38 (0.47), residues: 128 loop : -1.79 (0.36), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 220 HIS 0.001 0.001 HIS B 202 PHE 0.018 0.001 PHE A 158 TYR 0.018 0.001 TYR D 264 ARG 0.004 0.000 ARG B 204 *********************** 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 157 residues out of total 754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 118 time to evaluate : 0.755 Fit side-chains REVERT: A 44 PHE cc_start: 0.6898 (OUTLIER) cc_final: 0.6189 (t80) REVERT: A 224 LEU cc_start: 0.4650 (OUTLIER) cc_final: 0.4366 (mp) REVERT: B 44 PHE cc_start: 0.6501 (OUTLIER) cc_final: 0.5698 (t80) outliers start: 39 outliers final: 22 residues processed: 145 average time/residue: 0.1935 time to fit residues: 36.6508 Evaluate side-chains 142 residues out of total 754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 117 time to evaluate : 0.664 ------------------------------------------------------------------------------- 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 224 LEU 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 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 186 PHE 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 67 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 1 optimal weight: 0.0070 chunk 60 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 41 optimal weight: 0.0070 chunk 72 optimal weight: 0.7980 chunk 20 optimal weight: 4.9990 overall best weight: 0.5216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5866 moved from start: 0.1642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 6623 Z= 0.184 Angle : 0.626 14.142 9042 Z= 0.313 Chirality : 0.040 0.192 1059 Planarity : 0.004 0.062 1128 Dihedral : 4.885 42.796 916 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.55 % Favored : 91.45 % Rotamer: Outliers : 7.35 % Allowed : 34.00 % Favored : 58.65 % 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 (0.31), residues: 842 helix: 0.50 (0.28), residues: 386 sheet: -1.27 (0.47), residues: 128 loop : -1.81 (0.35), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 220 HIS 0.003 0.001 HIS A 202 PHE 0.017 0.001 PHE A 158 TYR 0.016 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 167 residues out of total 754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 119 time to evaluate : 0.577 Fit side-chains REVERT: A 44 PHE cc_start: 0.6826 (OUTLIER) cc_final: 0.6109 (t80) REVERT: A 224 LEU cc_start: 0.4647 (OUTLIER) cc_final: 0.4371 (mp) REVERT: D 203 MET cc_start: 0.4791 (OUTLIER) cc_final: 0.4256 (mtt) REVERT: B 44 PHE cc_start: 0.6492 (OUTLIER) cc_final: 0.5691 (t80) outliers start: 48 outliers final: 32 residues processed: 151 average time/residue: 0.1746 time to fit residues: 34.7145 Evaluate side-chains 155 residues out of total 754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 119 time to evaluate : 0.648 ------------------------------------------------------------------------------- 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 127 THR 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 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 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 8 SER 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 178 LEU Chi-restraints excluded: chain B residue 186 PHE Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 248 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 27 optimal weight: 0.1980 chunk 73 optimal weight: 0.6980 chunk 16 optimal weight: 0.4980 chunk 47 optimal weight: 10.0000 chunk 20 optimal weight: 2.9990 chunk 81 optimal weight: 0.9980 chunk 67 optimal weight: 0.7980 chunk 37 optimal weight: 0.0570 chunk 6 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 42 optimal weight: 7.9990 overall best weight: 0.4498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5847 moved from start: 0.1724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 6623 Z= 0.183 Angle : 0.640 14.449 9042 Z= 0.317 Chirality : 0.041 0.187 1059 Planarity : 0.004 0.062 1128 Dihedral : 4.807 41.888 916 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 13.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.96 % Favored : 92.04 % Rotamer: Outliers : 7.66 % Allowed : 34.00 % Favored : 58.35 % 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: -0.92 (0.31), residues: 842 helix: 0.56 (0.28), residues: 386 sheet: -0.78 (0.50), residues: 116 loop : -1.91 (0.35), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 220 HIS 0.003 0.001 HIS A 202 PHE 0.023 0.001 PHE B 78 TYR 0.018 0.001 TYR D 264 ARG 0.003 0.000 ARG A 204 *********************** 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 172 residues out of total 754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 122 time to evaluate : 0.706 Fit side-chains REVERT: A 44 PHE cc_start: 0.6832 (OUTLIER) cc_final: 0.6109 (t80) REVERT: A 267 ARG cc_start: 0.6708 (tmm160) cc_final: 0.6401 (tmm160) REVERT: B 44 PHE cc_start: 0.6474 (OUTLIER) cc_final: 0.5591 (t80) outliers start: 50 outliers final: 32 residues processed: 154 average time/residue: 0.1785 time to fit residues: 36.3558 Evaluate side-chains 155 residues out of total 754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 121 time to evaluate : 0.697 ------------------------------------------------------------------------------- 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 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 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 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 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 126 TRP Chi-restraints excluded: chain B residue 143 ILE 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 247 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 78 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 46 optimal weight: 0.8980 chunk 59 optimal weight: 0.1980 chunk 45 optimal weight: 0.0870 chunk 68 optimal weight: 2.9990 chunk 80 optimal weight: 4.9990 chunk 50 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5882 moved from start: 0.1883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 6623 Z= 0.205 Angle : 0.651 14.505 9042 Z= 0.322 Chirality : 0.041 0.191 1059 Planarity : 0.004 0.060 1128 Dihedral : 4.812 40.772 916 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 14.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.55 % Favored : 91.45 % Rotamer: Outliers : 6.89 % Allowed : 35.53 % 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: -0.97 (0.31), residues: 842 helix: 0.47 (0.28), residues: 388 sheet: -0.80 (0.50), residues: 116 loop : -1.89 (0.35), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 220 HIS 0.003 0.001 HIS A 202 PHE 0.022 0.001 PHE B 78 TYR 0.016 0.001 TYR D 264 ARG 0.002 0.000 ARG B 267 *********************** 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 172 residues out of total 754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 127 time to evaluate : 0.665 Fit side-chains REVERT: A 44 PHE cc_start: 0.6758 (OUTLIER) cc_final: 0.5966 (t80) REVERT: D 203 MET cc_start: 0.4795 (OUTLIER) cc_final: 0.4288 (mtt) REVERT: B 44 PHE cc_start: 0.6487 (OUTLIER) cc_final: 0.5675 (t80) outliers start: 45 outliers final: 31 residues processed: 153 average time/residue: 0.1773 time to fit residues: 35.8476 Evaluate side-chains 160 residues out of total 754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 126 time to evaluate : 0.659 ------------------------------------------------------------------------------- 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 8 SER 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 178 LEU Chi-restraints excluded: chain B residue 213 SER 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 48 optimal weight: 9.9990 chunk 24 optimal weight: 0.5980 chunk 15 optimal weight: 0.0370 chunk 51 optimal weight: 5.9990 chunk 55 optimal weight: 5.9990 chunk 40 optimal weight: 8.9990 chunk 7 optimal weight: 0.9980 chunk 63 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 77 optimal weight: 6.9990 chunk 70 optimal weight: 0.5980 overall best weight: 0.8460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5918 moved from start: 0.1972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 6623 Z= 0.233 Angle : 0.673 15.258 9042 Z= 0.335 Chirality : 0.042 0.216 1059 Planarity : 0.004 0.060 1128 Dihedral : 4.692 21.801 914 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 15.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.91 % Favored : 91.09 % Rotamer: Outliers : 6.43 % Allowed : 36.75 % 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 (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: -1.08 (0.30), residues: 842 helix: 0.39 (0.28), residues: 388 sheet: -0.87 (0.50), residues: 116 loop : -1.96 (0.34), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A 220 HIS 0.002 0.000 HIS A 202 PHE 0.022 0.001 PHE B 78 TYR 0.009 0.001 TYR D 274 ARG 0.002 0.000 ARG B 226 *********************** 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 174 residues out of total 754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 132 time to evaluate : 0.664 Fit side-chains REVERT: A 44 PHE cc_start: 0.6790 (OUTLIER) cc_final: 0.5959 (t80) REVERT: A 95 LEU cc_start: 0.7609 (mt) cc_final: 0.7316 (mp) REVERT: A 267 ARG cc_start: 0.6717 (tmm160) cc_final: 0.6340 (tmm160) REVERT: D 203 MET cc_start: 0.4814 (OUTLIER) cc_final: 0.4285 (mtt) REVERT: B 44 PHE cc_start: 0.6537 (OUTLIER) cc_final: 0.5823 (t80) REVERT: B 93 TYR cc_start: 0.6935 (m-80) cc_final: 0.6447 (m-80) outliers start: 42 outliers final: 34 residues processed: 155 average time/residue: 0.1744 time to fit residues: 35.7758 Evaluate side-chains 167 residues out of total 754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 130 time to evaluate : 0.698 ------------------------------------------------------------------------------- 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 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 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 8 SER 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 178 LEU Chi-restraints excluded: chain B residue 186 PHE Chi-restraints excluded: chain B residue 213 SER 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 75 optimal weight: 1.9990 chunk 77 optimal weight: 0.7980 chunk 45 optimal weight: 4.9990 chunk 32 optimal weight: 9.9990 chunk 59 optimal weight: 0.0270 chunk 23 optimal weight: 0.4980 chunk 68 optimal weight: 2.9990 chunk 71 optimal weight: 0.3980 chunk 49 optimal weight: 1.9990 chunk 79 optimal weight: 0.5980 chunk 48 optimal weight: 0.9980 overall best weight: 0.4638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5865 moved from start: 0.2051 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= 0.194 Angle : 0.678 15.881 9042 Z= 0.331 Chirality : 0.043 0.378 1059 Planarity : 0.004 0.061 1128 Dihedral : 4.613 21.283 914 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 14.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.19 % Favored : 91.81 % Rotamer: Outliers : 5.97 % Allowed : 36.45 % 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: -0.94 (0.31), residues: 842 helix: 0.58 (0.29), residues: 386 sheet: -0.90 (0.49), residues: 116 loop : -1.93 (0.35), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP B 220 HIS 0.003 0.001 HIS A 202 PHE 0.025 0.001 PHE B 78 TYR 0.012 0.001 TYR A 147 ARG 0.002 0.000 ARG A 226 *********************** 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 164 residues out of total 754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 125 time to evaluate : 0.652 Fit side-chains REVERT: A 44 PHE cc_start: 0.6753 (OUTLIER) cc_final: 0.5917 (t80) REVERT: A 95 LEU cc_start: 0.7601 (mt) cc_final: 0.7317 (mp) REVERT: D 203 MET cc_start: 0.4799 (OUTLIER) cc_final: 0.4312 (mtt) REVERT: B 44 PHE cc_start: 0.6507 (OUTLIER) cc_final: 0.5777 (t80) REVERT: B 93 TYR cc_start: 0.6938 (m-80) cc_final: 0.6465 (m-80) outliers start: 39 outliers final: 33 residues processed: 146 average time/residue: 0.1837 time to fit residues: 35.3446 Evaluate side-chains 161 residues out of total 754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 125 time to evaluate : 0.692 ------------------------------------------------------------------------------- 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 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 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 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 178 LEU Chi-restraints excluded: chain B residue 186 PHE Chi-restraints excluded: chain B residue 188 SER Chi-restraints excluded: chain B residue 213 SER Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 248 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 37 optimal weight: 6.9990 chunk 55 optimal weight: 0.9980 chunk 83 optimal weight: 0.9980 chunk 77 optimal weight: 0.6980 chunk 66 optimal weight: 0.0770 chunk 6 optimal weight: 0.9980 chunk 51 optimal weight: 0.5980 chunk 40 optimal weight: 0.6980 chunk 52 optimal weight: 0.4980 chunk 70 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5865 moved from start: 0.2084 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= 0.194 Angle : 0.694 16.300 9042 Z= 0.336 Chirality : 0.043 0.363 1059 Planarity : 0.004 0.060 1128 Dihedral : 4.617 21.189 914 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 15.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.67 % Favored : 91.33 % Rotamer: Outliers : 5.67 % Allowed : 36.91 % 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: -0.92 (0.31), residues: 842 helix: 0.60 (0.29), residues: 386 sheet: -0.89 (0.49), residues: 116 loop : -1.92 (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 0.024 0.001 PHE B 78 TYR 0.012 0.001 TYR B 147 ARG 0.003 0.000 ARG A 226 ********************** 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 161 residues out of total 754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 124 time to evaluate : 0.667 Fit side-chains REVERT: A 44 PHE cc_start: 0.6769 (OUTLIER) cc_final: 0.5937 (t80) REVERT: A 95 LEU cc_start: 0.7599 (mt) cc_final: 0.7298 (mp) REVERT: A 264 ILE cc_start: 0.7044 (tt) cc_final: 0.6761 (pt) REVERT: A 267 ARG cc_start: 0.6640 (tmm160) cc_final: 0.6364 (tmm160) REVERT: D 203 MET cc_start: 0.4798 (OUTLIER) cc_final: 0.4319 (mtt) REVERT: D 207 ARG cc_start: 0.7555 (ttm170) cc_final: 0.7164 (ttm170) REVERT: B 44 PHE cc_start: 0.6494 (OUTLIER) cc_final: 0.5762 (t80) outliers start: 37 outliers final: 31 residues processed: 147 average time/residue: 0.1795 time to fit residues: 34.8977 Evaluate side-chains 157 residues out of total 754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 123 time to evaluate : 0.725 ------------------------------------------------------------------------------- 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 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 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 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 178 LEU Chi-restraints excluded: chain B residue 186 PHE Chi-restraints excluded: chain B residue 188 SER Chi-restraints excluded: chain B residue 213 SER Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 248 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 61 optimal weight: 0.5980 chunk 9 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 66 optimal weight: 0.5980 chunk 27 optimal weight: 9.9990 chunk 68 optimal weight: 2.9990 chunk 8 optimal weight: 0.0470 chunk 12 optimal weight: 0.6980 chunk 58 optimal weight: 0.0050 chunk 3 optimal weight: 4.9990 chunk 48 optimal weight: 10.0000 overall best weight: 0.3892 ------------------------------------------------------------------------------- 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 = 0.4527 r_free = 0.4527 target = 0.182889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.161847 restraints weight = 9906.591| |-----------------------------------------------------------------------------| r_work (start): 0.4285 rms_B_bonded: 2.53 r_work: 0.4179 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.4179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6104 moved from start: 0.2193 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= 0.179 Angle : 0.687 15.890 9042 Z= 0.330 Chirality : 0.042 0.279 1059 Planarity : 0.004 0.060 1128 Dihedral : 4.557 21.041 914 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 14.16 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.72 % Favored : 92.16 % Rotamer: Outliers : 5.51 % Allowed : 37.52 % 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: -0.85 (0.31), residues: 842 helix: 0.67 (0.29), residues: 386 sheet: -0.87 (0.48), residues: 116 loop : -1.90 (0.35), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP B 220 HIS 0.003 0.001 HIS B 202 PHE 0.024 0.001 PHE B 78 TYR 0.010 0.001 TYR B 147 ARG 0.003 0.000 ARG A 226 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1729.52 seconds wall clock time: 31 minutes 20.46 seconds (1880.46 seconds total)