Starting phenix.real_space_refine on Mon Mar 11 11:55:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ahc_11782/03_2024/7ahc_11782.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ahc_11782/03_2024/7ahc_11782.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ahc_11782/03_2024/7ahc_11782.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ahc_11782/03_2024/7ahc_11782.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ahc_11782/03_2024/7ahc_11782.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ahc_11782/03_2024/7ahc_11782.pdb" } resolution = 3.3 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= 0.000 sd= 0.007 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 40 5.16 5 C 5288 2.51 5 N 1358 2.21 5 O 1484 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 31": "OD1" <-> "OD2" Residue "A PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 173": "NH1" <-> "NH2" Residue "A PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 31": "OD1" <-> "OD2" Residue "B PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 173": "NH1" <-> "NH2" Residue "B PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 29": "OE1" <-> "OE2" Residue "D GLU 33": "OE1" <-> "OE2" Residue "D TYR 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 121": "NH1" <-> "NH2" Residue "D GLU 125": "OE1" <-> "OE2" Residue "D TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 144": "NH1" <-> "NH2" Residue "D ASP 150": "OD1" <-> "OD2" Residue "D ASP 156": "OD1" <-> "OD2" Residue "D PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 200": "NH1" <-> "NH2" Residue "D ASP 205": "OD1" <-> "OD2" Residue "D PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 234": "NH1" <-> "NH2" Residue "D GLU 250": "OE1" <-> "OE2" Residue "D ASP 259": "OD1" <-> "OD2" Residue "D TYR 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 46": "OD1" <-> "OD2" Residue "C PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 121": "NH1" <-> "NH2" Residue "C TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 144": "NH1" <-> "NH2" Residue "C PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 182": "OD1" <-> "OD2" Residue "C ARG 200": "NH1" <-> "NH2" Residue "C PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 234": "NH1" <-> "NH2" Residue "C GLU 250": "OE1" <-> "OE2" Residue "C ASP 259": "OD1" <-> "OD2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 8170 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2016 Classifications: {'peptide': 272} Link IDs: {'PTRANS': 12, 'TRANS': 259} Chain: "B" Number of atoms: 2016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2016 Classifications: {'peptide': 272} Link IDs: {'PTRANS': 12, 'TRANS': 259} Chain: "D" Number of atoms: 2069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2069 Classifications: {'peptide': 260} Link IDs: {'PTRANS': 8, 'TRANS': 251} Chain: "C" Number of atoms: 2069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2069 Classifications: {'peptide': 260} Link IDs: {'PTRANS': 8, 'TRANS': 251} Time building chain proxies: 4.89, per 1000 atoms: 0.60 Number of scatterers: 8170 At special positions: 0 Unit cell: (94.116, 106.26, 104.236, 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 40 16.00 O 1484 8.00 N 1358 7.00 C 5288 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 3.02 Conformation dependent library (CDL) restraints added in 1.5 seconds 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1956 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 6 sheets defined 68.5% alpha, 4.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.81 Creating SS restraints... Processing helix chain 'A' and resid 10 through 26 removed outlier: 3.584A pdb=" N TRP A 14 " --> pdb=" O PRO A 10 " (cutoff:3.500A) Processing helix chain 'A' and resid 26 through 45 removed outlier: 3.860A pdb=" N VAL A 32 " --> pdb=" O SER A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 69 Processing helix chain 'A' and resid 72 through 89 removed outlier: 4.120A pdb=" N LEU A 84 " --> pdb=" O ILE A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 96 removed outlier: 3.800A pdb=" N SER A 96 " --> pdb=" O SER A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 122 Proline residue: A 114 - end of helix Processing helix chain 'A' and resid 122 through 139 removed outlier: 3.812A pdb=" N ALA A 126 " --> pdb=" O SER A 122 " (cutoff:3.500A) Proline residue: A 131 - end of helix removed outlier: 3.539A pdb=" N MET A 139 " --> pdb=" O PHE A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 144 removed outlier: 3.597A pdb=" N VAL A 143 " --> pdb=" O PRO A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 150 Processing helix chain 'A' and resid 156 through 180 Proline residue: A 169 - end of helix Processing helix chain 'A' and resid 183 through 193 removed outlier: 3.765A pdb=" N VAL A 187 " --> pdb=" O SER A 183 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N PHE A 193 " --> pdb=" O ALA A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 210 removed outlier: 3.576A pdb=" N PHE A 202 " --> pdb=" O ARG A 198 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N PHE A 206 " --> pdb=" O PHE A 202 " (cutoff:3.500A) Proline residue: A 207 - end of helix Processing helix chain 'A' and resid 212 through 232 removed outlier: 3.948A pdb=" N MET A 222 " --> pdb=" O ASN A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 250 removed outlier: 4.177A pdb=" N GLY A 242 " --> pdb=" O GLY A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 276 Processing helix chain 'B' and resid 10 through 26 removed outlier: 3.584A pdb=" N TRP B 14 " --> pdb=" O PRO B 10 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 45 removed outlier: 3.861A pdb=" N VAL B 32 " --> pdb=" O SER B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 69 Processing helix chain 'B' and resid 72 through 89 removed outlier: 4.120A pdb=" N LEU B 84 " --> pdb=" O ILE B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 96 removed outlier: 3.800A pdb=" N SER B 96 " --> pdb=" O SER B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 122 Proline residue: B 114 - end of helix Processing helix chain 'B' and resid 122 through 139 removed outlier: 3.812A pdb=" N ALA B 126 " --> pdb=" O SER B 122 " (cutoff:3.500A) Proline residue: B 131 - end of helix removed outlier: 3.538A pdb=" N MET B 139 " --> pdb=" O PHE B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 144 removed outlier: 3.597A pdb=" N VAL B 143 " --> pdb=" O PRO B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 150 Processing helix chain 'B' and resid 156 through 180 Proline residue: B 169 - end of helix Processing helix chain 'B' and resid 183 through 193 removed outlier: 3.765A pdb=" N VAL B 187 " --> pdb=" O SER B 183 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N PHE B 193 " --> pdb=" O ALA B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 210 removed outlier: 3.576A pdb=" N PHE B 202 " --> pdb=" O ARG B 198 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N PHE B 206 " --> pdb=" O PHE B 202 " (cutoff:3.500A) Proline residue: B 207 - end of helix Processing helix chain 'B' and resid 212 through 232 removed outlier: 3.949A pdb=" N MET B 222 " --> pdb=" O ASN B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 250 removed outlier: 4.177A pdb=" N GLY B 242 " --> pdb=" O GLY B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 276 Processing helix chain 'D' and resid 17 through 27 removed outlier: 3.571A pdb=" N LYS D 27 " --> pdb=" O THR D 23 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 38 removed outlier: 4.094A pdb=" N ILE D 34 " --> pdb=" O PRO D 30 " (cutoff:3.500A) Processing helix chain 'D' and resid 66 through 75 removed outlier: 3.849A pdb=" N LEU D 70 " --> pdb=" O GLY D 66 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N LEU D 71 " --> pdb=" O LYS D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 95 removed outlier: 3.557A pdb=" N THR D 94 " --> pdb=" O ASP D 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 96 through 107 Processing helix chain 'D' and resid 122 through 127 Processing helix chain 'D' and resid 128 through 133 Processing helix chain 'D' and resid 137 through 153 Processing helix chain 'D' and resid 154 through 158 Processing helix chain 'D' and resid 161 through 165 Processing helix chain 'D' and resid 166 through 181 removed outlier: 4.270A pdb=" N ASN D 181 " --> pdb=" O ARG D 177 " (cutoff:3.500A) Processing helix chain 'D' and resid 196 through 214 Processing helix chain 'D' and resid 224 through 232 removed outlier: 3.595A pdb=" N ALA D 228 " --> pdb=" O ASP D 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 27 removed outlier: 3.566A pdb=" N LYS C 27 " --> pdb=" O THR C 23 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 37 removed outlier: 4.088A pdb=" N ILE C 34 " --> pdb=" O PRO C 30 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 75 removed outlier: 4.305A pdb=" N LEU C 71 " --> pdb=" O LYS C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 107 Processing helix chain 'C' and resid 122 through 127 Processing helix chain 'C' and resid 128 through 133 Processing helix chain 'C' and resid 137 through 151 Processing helix chain 'C' and resid 154 through 158 Processing helix chain 'C' and resid 161 through 165 Processing helix chain 'C' and resid 166 through 181 removed outlier: 4.210A pdb=" N ASN C 181 " --> pdb=" O ARG C 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 196 through 214 Processing helix chain 'C' and resid 224 through 232 Processing sheet with id=AA1, first strand: chain 'D' and resid 50 through 51 removed outlier: 3.544A pdb=" N ILE D 51 " --> pdb=" O ILE D 5 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N LEU D 10 " --> pdb=" O SER D 82 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N SER D 82 " --> pdb=" O LEU D 10 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 110 through 111 removed outlier: 6.232A pdb=" N LEU D 186 " --> pdb=" O ILE D 219 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 238 through 239 Processing sheet with id=AA4, first strand: chain 'C' and resid 50 through 51 removed outlier: 4.364A pdb=" N LEU C 10 " --> pdb=" O SER C 82 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N SER C 82 " --> pdb=" O LEU C 10 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 56 through 59 removed outlier: 3.892A pdb=" N PHE C 220 " --> pdb=" O PHE C 57 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N LEU C 186 " --> pdb=" O ILE C 219 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N VAL C 221 " --> pdb=" O LEU C 186 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N MET C 188 " --> pdb=" O VAL C 221 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 238 through 239 475 hydrogen bonds defined for protein. 1377 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: 2.13 Time building geometry restraints manager: 3.29 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: 2624 1.34 - 1.46: 1618 1.46 - 1.58: 3976 1.58 - 1.69: 0 1.69 - 1.81: 80 Bond restraints: 8298 Sorted by residual: bond pdb=" CB VAL A 228 " pdb=" CG2 VAL A 228 " ideal model delta sigma weight residual 1.521 1.473 0.048 3.30e-02 9.18e+02 2.16e+00 bond pdb=" CB VAL B 228 " pdb=" CG2 VAL B 228 " ideal model delta sigma weight residual 1.521 1.474 0.047 3.30e-02 9.18e+02 2.07e+00 bond pdb=" CB THR A 175 " pdb=" CG2 THR A 175 " ideal model delta sigma weight residual 1.521 1.477 0.044 3.30e-02 9.18e+02 1.78e+00 bond pdb=" CG LEU A 186 " pdb=" CD1 LEU A 186 " ideal model delta sigma weight residual 1.521 1.477 0.044 3.30e-02 9.18e+02 1.75e+00 bond pdb=" CB THR B 175 " pdb=" CG2 THR B 175 " ideal model delta sigma weight residual 1.521 1.477 0.044 3.30e-02 9.18e+02 1.74e+00 ... (remaining 8293 not shown) Histogram of bond angle deviations from ideal: 98.28 - 105.42: 158 105.42 - 112.55: 4487 112.55 - 119.69: 2632 119.69 - 126.83: 3867 126.83 - 133.97: 78 Bond angle restraints: 11222 Sorted by residual: angle pdb=" N VAL B 113 " pdb=" CA VAL B 113 " pdb=" C VAL B 113 " ideal model delta sigma weight residual 112.67 108.99 3.68 1.25e+00 6.40e-01 8.69e+00 angle pdb=" N VAL A 113 " pdb=" CA VAL A 113 " pdb=" C VAL A 113 " ideal model delta sigma weight residual 112.67 109.04 3.63 1.25e+00 6.40e-01 8.45e+00 angle pdb=" N LYS A 70 " pdb=" CA LYS A 70 " pdb=" C LYS A 70 " ideal model delta sigma weight residual 114.04 110.61 3.43 1.24e+00 6.50e-01 7.66e+00 angle pdb=" N LYS B 70 " pdb=" CA LYS B 70 " pdb=" C LYS B 70 " ideal model delta sigma weight residual 114.04 110.63 3.41 1.24e+00 6.50e-01 7.57e+00 angle pdb=" CA GLY D 61 " pdb=" C GLY D 61 " pdb=" N LEU D 62 " ideal model delta sigma weight residual 114.66 117.19 -2.53 1.10e+00 8.26e-01 5.28e+00 ... (remaining 11217 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.65: 4414 17.65 - 35.30: 466 35.30 - 52.96: 124 52.96 - 70.61: 22 70.61 - 88.26: 8 Dihedral angle restraints: 5034 sinusoidal: 2008 harmonic: 3026 Sorted by residual: dihedral pdb=" CA MET B 95 " pdb=" C MET B 95 " pdb=" N SER B 96 " pdb=" CA SER B 96 " ideal model delta harmonic sigma weight residual 180.00 155.17 24.83 0 5.00e+00 4.00e-02 2.47e+01 dihedral pdb=" CA MET A 95 " pdb=" C MET A 95 " pdb=" N SER A 96 " pdb=" CA SER A 96 " ideal model delta harmonic sigma weight residual 180.00 155.19 24.81 0 5.00e+00 4.00e-02 2.46e+01 dihedral pdb=" CA ILE B 128 " pdb=" C ILE B 128 " pdb=" N VAL B 129 " pdb=" CA VAL B 129 " ideal model delta harmonic sigma weight residual -180.00 -160.89 -19.11 0 5.00e+00 4.00e-02 1.46e+01 ... (remaining 5031 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 700 0.027 - 0.054: 370 0.054 - 0.081: 159 0.081 - 0.107: 92 0.107 - 0.134: 39 Chirality restraints: 1360 Sorted by residual: chirality pdb=" CB VAL B 164 " pdb=" CA VAL B 164 " pdb=" CG1 VAL B 164 " pdb=" CG2 VAL B 164 " both_signs ideal model delta sigma weight residual False -2.63 -2.49 -0.13 2.00e-01 2.50e+01 4.51e-01 chirality pdb=" CB VAL A 164 " pdb=" CA VAL A 164 " pdb=" CG1 VAL A 164 " pdb=" CG2 VAL A 164 " both_signs ideal model delta sigma weight residual False -2.63 -2.50 -0.13 2.00e-01 2.50e+01 4.36e-01 chirality pdb=" CA ILE C 87 " pdb=" N ILE C 87 " pdb=" C ILE C 87 " pdb=" CB ILE C 87 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.17e-01 ... (remaining 1357 not shown) Planarity restraints: 1406 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 74 " 0.027 5.00e-02 4.00e+02 4.14e-02 2.75e+00 pdb=" N PRO B 75 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO B 75 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 75 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 74 " -0.027 5.00e-02 4.00e+02 4.13e-02 2.73e+00 pdb=" N PRO A 75 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO A 75 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 75 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL C 136 " 0.023 5.00e-02 4.00e+02 3.47e-02 1.93e+00 pdb=" N PRO C 137 " -0.060 5.00e-02 4.00e+02 pdb=" CA PRO C 137 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO C 137 " 0.019 5.00e-02 4.00e+02 ... (remaining 1403 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 280 2.69 - 3.24: 9129 3.24 - 3.80: 12638 3.80 - 4.35: 16891 4.35 - 4.90: 28538 Nonbonded interactions: 67476 Sorted by model distance: nonbonded pdb=" NZ LYS C 242 " pdb=" O ILE C 243 " model vdw 2.141 2.520 nonbonded pdb=" NH2 ARG D 76 " pdb=" OE1 GLU D 79 " model vdw 2.195 2.520 nonbonded pdb=" NZ LYS C 6 " pdb=" O ILE C 7 " model vdw 2.225 2.520 nonbonded pdb=" OG SER B 195 " pdb=" OH TYR C 129 " model vdw 2.233 2.440 nonbonded pdb=" NZ LYS D 6 " pdb=" O ILE D 7 " model vdw 2.244 2.520 ... (remaining 67471 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } 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: 0.840 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: 4.100 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 24.780 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.053 8298 Z= 0.493 Angle : 0.609 7.129 11222 Z= 0.346 Chirality : 0.045 0.134 1360 Planarity : 0.004 0.041 1406 Dihedral : 15.793 88.260 3078 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 13.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.52 % Favored : 91.48 % Rotamer: Outliers : 0.11 % Allowed : 19.98 % Favored : 79.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -4.17 (0.21), residues: 1056 helix: -2.12 (0.17), residues: 654 sheet: -4.79 (0.34), residues: 74 loop : -3.24 (0.27), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP A 91 HIS 0.003 0.001 HIS D 223 PHE 0.019 0.001 PHE B 135 TYR 0.009 0.001 TYR D 45 ARG 0.002 0.000 ARG C 17 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 166 time to evaluate : 0.988 Fit side-chains revert: symmetry clash REVERT: A 44 ILE cc_start: 0.8378 (pt) cc_final: 0.7796 (pt) REVERT: B 44 ILE cc_start: 0.8327 (pt) cc_final: 0.7793 (pt) REVERT: C 62 LEU cc_start: 0.8267 (mp) cc_final: 0.7968 (mp) outliers start: 1 outliers final: 1 residues processed: 167 average time/residue: 0.2137 time to fit residues: 47.8309 Evaluate side-chains 104 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 103 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 67 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 89 optimal weight: 0.9980 chunk 80 optimal weight: 9.9990 chunk 44 optimal weight: 0.8980 chunk 27 optimal weight: 0.9980 chunk 54 optimal weight: 8.9990 chunk 42 optimal weight: 0.9990 chunk 83 optimal weight: 0.5980 chunk 32 optimal weight: 0.7980 chunk 50 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 chunk 96 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 134 GLN D 135 ASN D 171 GLN D 215 GLN D 255 ASN C 52 ASN C 164 GLN C 170 GLN C 171 GLN C 181 ASN C 255 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.1946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8298 Z= 0.223 Angle : 0.635 7.660 11222 Z= 0.328 Chirality : 0.044 0.186 1360 Planarity : 0.004 0.045 1406 Dihedral : 5.104 48.423 1114 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 3.24 % Allowed : 17.63 % Favored : 79.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.75 (0.26), residues: 1056 helix: -0.29 (0.20), residues: 650 sheet: -3.65 (0.47), residues: 80 loop : -2.06 (0.34), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 54 HIS 0.001 0.000 HIS C 223 PHE 0.010 0.001 PHE B 77 TYR 0.008 0.001 TYR D 45 ARG 0.005 0.000 ARG D 201 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 137 time to evaluate : 0.928 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 177 LEU cc_start: 0.8332 (OUTLIER) cc_final: 0.7883 (mp) REVERT: B 48 LEU cc_start: 0.3279 (OUTLIER) cc_final: 0.2924 (tt) REVERT: B 177 LEU cc_start: 0.8352 (OUTLIER) cc_final: 0.7950 (mp) REVERT: D 71 LEU cc_start: 0.8267 (OUTLIER) cc_final: 0.7985 (mp) outliers start: 29 outliers final: 10 residues processed: 162 average time/residue: 0.1819 time to fit residues: 41.0915 Evaluate side-chains 124 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 110 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 212 THR Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain C residue 60 MET Chi-restraints excluded: chain C residue 67 LYS Chi-restraints excluded: chain C residue 156 ASP Chi-restraints excluded: chain C residue 198 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 53 optimal weight: 2.9990 chunk 29 optimal weight: 0.8980 chunk 80 optimal weight: 9.9990 chunk 65 optimal weight: 3.9990 chunk 26 optimal weight: 0.8980 chunk 96 optimal weight: 0.9990 chunk 104 optimal weight: 5.9990 chunk 85 optimal weight: 6.9990 chunk 95 optimal weight: 0.9990 chunk 32 optimal weight: 0.7980 chunk 77 optimal weight: 8.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 ASN ** B 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 75 ASN D 181 ASN D 255 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.2625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8298 Z= 0.219 Angle : 0.590 7.626 11222 Z= 0.307 Chirality : 0.044 0.149 1360 Planarity : 0.004 0.047 1406 Dihedral : 4.991 46.359 1114 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 4.02 % Allowed : 17.86 % Favored : 78.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.98 (0.26), residues: 1056 helix: 0.28 (0.21), residues: 650 sheet: -2.78 (0.55), residues: 82 loop : -1.82 (0.35), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 118 HIS 0.002 0.000 HIS D 223 PHE 0.015 0.001 PHE B 77 TYR 0.007 0.001 TYR C 260 ARG 0.002 0.000 ARG D 76 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 135 time to evaluate : 0.882 Fit side-chains revert: symmetry clash REVERT: A 107 LEU cc_start: 0.8750 (OUTLIER) cc_final: 0.8408 (mp) REVERT: A 177 LEU cc_start: 0.8413 (OUTLIER) cc_final: 0.8025 (mp) REVERT: B 48 LEU cc_start: 0.3381 (OUTLIER) cc_final: 0.3159 (tt) REVERT: B 107 LEU cc_start: 0.8770 (OUTLIER) cc_final: 0.8416 (mp) REVERT: B 177 LEU cc_start: 0.8376 (OUTLIER) cc_final: 0.7991 (mp) REVERT: D 71 LEU cc_start: 0.8153 (OUTLIER) cc_final: 0.7791 (mp) REVERT: D 231 ILE cc_start: 0.5635 (OUTLIER) cc_final: 0.5111 (tp) REVERT: C 38 THR cc_start: -0.1922 (OUTLIER) cc_final: -0.2254 (m) outliers start: 36 outliers final: 16 residues processed: 162 average time/residue: 0.1905 time to fit residues: 42.6987 Evaluate side-chains 138 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 114 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 132 ILE Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 260 ILE Chi-restraints excluded: chain D residue 11 THR Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 156 ASP Chi-restraints excluded: chain D residue 231 ILE Chi-restraints excluded: chain C residue 38 THR Chi-restraints excluded: chain C residue 67 LYS Chi-restraints excluded: chain C residue 156 ASP Chi-restraints excluded: chain C residue 198 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 95 optimal weight: 0.0270 chunk 72 optimal weight: 0.9990 chunk 50 optimal weight: 0.8980 chunk 10 optimal weight: 0.8980 chunk 46 optimal weight: 0.9990 chunk 64 optimal weight: 2.9990 chunk 96 optimal weight: 7.9990 chunk 102 optimal weight: 10.0000 chunk 91 optimal weight: 0.7980 chunk 27 optimal weight: 5.9990 chunk 85 optimal weight: 7.9990 overall best weight: 0.7240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 218 ASN D 171 GLN D 255 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.2954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8298 Z= 0.187 Angle : 0.576 7.898 11222 Z= 0.297 Chirality : 0.043 0.164 1360 Planarity : 0.004 0.047 1406 Dihedral : 4.874 42.698 1114 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 3.57 % Allowed : 20.76 % Favored : 75.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.56 (0.27), residues: 1056 helix: 0.59 (0.21), residues: 652 sheet: -2.29 (0.58), residues: 82 loop : -1.71 (0.35), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 54 HIS 0.000 0.000 HIS D 120 PHE 0.014 0.001 PHE B 77 TYR 0.005 0.001 TYR D 45 ARG 0.003 0.000 ARG C 144 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 127 time to evaluate : 0.930 Fit side-chains revert: symmetry clash REVERT: A 107 LEU cc_start: 0.8736 (OUTLIER) cc_final: 0.8389 (mp) REVERT: A 177 LEU cc_start: 0.8470 (OUTLIER) cc_final: 0.8083 (mp) REVERT: A 239 LEU cc_start: 0.8313 (OUTLIER) cc_final: 0.7999 (mt) REVERT: B 177 LEU cc_start: 0.8422 (OUTLIER) cc_final: 0.8081 (mp) REVERT: D 71 LEU cc_start: 0.7984 (OUTLIER) cc_final: 0.7756 (mt) REVERT: D 231 ILE cc_start: 0.5516 (OUTLIER) cc_final: 0.5085 (tp) REVERT: C 244 MET cc_start: 0.5351 (mtt) cc_final: 0.4926 (mtt) outliers start: 32 outliers final: 17 residues processed: 153 average time/residue: 0.1936 time to fit residues: 41.0099 Evaluate side-chains 134 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 111 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain B residue 56 MET Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 132 ILE Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 212 THR Chi-restraints excluded: chain B residue 233 MET Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 78 ILE Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 156 ASP Chi-restraints excluded: chain D residue 231 ILE Chi-restraints excluded: chain C residue 67 LYS Chi-restraints excluded: chain C residue 156 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 58 optimal weight: 8.9990 chunk 1 optimal weight: 4.9990 chunk 76 optimal weight: 0.0050 chunk 42 optimal weight: 0.6980 chunk 87 optimal weight: 0.4980 chunk 70 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 91 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 overall best weight: 0.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 255 ASN C 171 GLN C 245 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.3248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8298 Z= 0.172 Angle : 0.554 7.632 11222 Z= 0.285 Chirality : 0.042 0.188 1360 Planarity : 0.004 0.048 1406 Dihedral : 4.745 37.885 1114 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 3.79 % Allowed : 20.42 % Favored : 75.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.31 (0.27), residues: 1056 helix: 0.77 (0.21), residues: 654 sheet: -1.95 (0.60), residues: 82 loop : -1.67 (0.34), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP B 118 HIS 0.001 0.000 HIS C 223 PHE 0.012 0.001 PHE B 77 TYR 0.005 0.001 TYR D 45 ARG 0.003 0.000 ARG C 172 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 131 time to evaluate : 0.961 Fit side-chains revert: symmetry clash REVERT: A 107 LEU cc_start: 0.8741 (OUTLIER) cc_final: 0.8398 (mp) REVERT: A 177 LEU cc_start: 0.8437 (OUTLIER) cc_final: 0.8092 (mp) REVERT: B 107 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8418 (mp) REVERT: B 239 LEU cc_start: 0.8394 (OUTLIER) cc_final: 0.8074 (mt) REVERT: D 60 MET cc_start: 0.7011 (OUTLIER) cc_final: 0.6753 (mmt) REVERT: C 38 THR cc_start: -0.2200 (OUTLIER) cc_final: -0.2595 (m) REVERT: C 48 ASN cc_start: 0.7013 (OUTLIER) cc_final: 0.6468 (p0) outliers start: 34 outliers final: 20 residues processed: 156 average time/residue: 0.1965 time to fit residues: 41.9111 Evaluate side-chains 140 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 113 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 56 MET Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 233 MET Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 260 ILE Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 60 MET Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain C residue 38 THR Chi-restraints excluded: chain C residue 48 ASN Chi-restraints excluded: chain C residue 60 MET Chi-restraints excluded: chain C residue 67 LYS Chi-restraints excluded: chain C residue 156 ASP Chi-restraints excluded: chain C residue 245 GLN Chi-restraints excluded: chain C residue 251 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 92 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 chunk 60 optimal weight: 5.9990 chunk 25 optimal weight: 0.5980 chunk 102 optimal weight: 10.0000 chunk 85 optimal weight: 5.9990 chunk 47 optimal weight: 0.9980 chunk 8 optimal weight: 0.0060 chunk 33 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 98 optimal weight: 4.9990 overall best weight: 0.6998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 GLN ** D 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.3375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8298 Z= 0.182 Angle : 0.558 7.533 11222 Z= 0.285 Chirality : 0.042 0.162 1360 Planarity : 0.004 0.047 1406 Dihedral : 4.706 34.495 1114 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 3.79 % Allowed : 21.09 % Favored : 75.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.16 (0.27), residues: 1056 helix: 0.82 (0.21), residues: 658 sheet: -1.73 (0.62), residues: 82 loop : -1.51 (0.35), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP B 54 HIS 0.001 0.000 HIS C 223 PHE 0.013 0.001 PHE B 135 TYR 0.005 0.001 TYR D 45 ARG 0.001 0.000 ARG C 142 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 126 time to evaluate : 1.005 Fit side-chains REVERT: A 107 LEU cc_start: 0.8753 (OUTLIER) cc_final: 0.8415 (mp) REVERT: B 107 LEU cc_start: 0.8760 (OUTLIER) cc_final: 0.8434 (mp) REVERT: B 139 MET cc_start: 0.7943 (ptp) cc_final: 0.7665 (ptp) REVERT: B 177 LEU cc_start: 0.8394 (OUTLIER) cc_final: 0.8114 (mp) REVERT: D 60 MET cc_start: 0.7030 (OUTLIER) cc_final: 0.6686 (mmm) REVERT: D 71 LEU cc_start: 0.7967 (OUTLIER) cc_final: 0.7704 (mt) REVERT: C 38 THR cc_start: -0.2292 (OUTLIER) cc_final: -0.2746 (m) REVERT: C 48 ASN cc_start: 0.7006 (OUTLIER) cc_final: 0.6450 (p0) outliers start: 34 outliers final: 21 residues processed: 151 average time/residue: 0.1980 time to fit residues: 41.2970 Evaluate side-chains 140 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 112 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 56 MET Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 56 MET Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 132 ILE Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 212 THR Chi-restraints excluded: chain B residue 260 ILE Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 60 MET Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain C residue 5 ILE Chi-restraints excluded: chain C residue 38 THR Chi-restraints excluded: chain C residue 48 ASN Chi-restraints excluded: chain C residue 60 MET Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 156 ASP Chi-restraints excluded: chain C residue 251 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 11 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 chunk 86 optimal weight: 3.9990 chunk 57 optimal weight: 0.9990 chunk 102 optimal weight: 2.9990 chunk 63 optimal weight: 0.4980 chunk 62 optimal weight: 0.9980 chunk 47 optimal weight: 0.7980 chunk 40 optimal weight: 0.5980 chunk 61 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 GLN D 255 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.3573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8298 Z= 0.198 Angle : 0.594 13.805 11222 Z= 0.296 Chirality : 0.044 0.358 1360 Planarity : 0.004 0.047 1406 Dihedral : 4.555 20.301 1110 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 4.35 % Allowed : 20.65 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.14 (0.27), residues: 1056 helix: 0.73 (0.20), residues: 680 sheet: -1.59 (0.64), residues: 82 loop : -1.43 (0.36), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP B 21 HIS 0.000 0.000 HIS C 120 PHE 0.026 0.001 PHE A 53 TYR 0.005 0.001 TYR D 45 ARG 0.003 0.000 ARG C 230 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 125 time to evaluate : 1.022 Fit side-chains REVERT: A 107 LEU cc_start: 0.8762 (OUTLIER) cc_final: 0.8443 (mp) REVERT: A 177 LEU cc_start: 0.8393 (OUTLIER) cc_final: 0.8108 (mp) REVERT: B 107 LEU cc_start: 0.8775 (OUTLIER) cc_final: 0.8458 (mp) REVERT: B 139 MET cc_start: 0.7986 (ptp) cc_final: 0.7703 (ptp) REVERT: B 177 LEU cc_start: 0.8356 (OUTLIER) cc_final: 0.8079 (mp) REVERT: B 239 LEU cc_start: 0.8532 (OUTLIER) cc_final: 0.8186 (mt) REVERT: D 60 MET cc_start: 0.6938 (OUTLIER) cc_final: 0.6628 (mmm) REVERT: D 71 LEU cc_start: 0.7947 (OUTLIER) cc_final: 0.7688 (mt) REVERT: C 48 ASN cc_start: 0.7028 (OUTLIER) cc_final: 0.6459 (p0) outliers start: 39 outliers final: 21 residues processed: 154 average time/residue: 0.2304 time to fit residues: 49.4906 Evaluate side-chains 140 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 111 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 56 MET Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 56 MET Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 132 ILE Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 212 THR Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 260 ILE Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 60 MET Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 156 ASP Chi-restraints excluded: chain C residue 5 ILE Chi-restraints excluded: chain C residue 48 ASN Chi-restraints excluded: chain C residue 60 MET Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 156 ASP Chi-restraints excluded: chain C residue 251 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 30 optimal weight: 0.7980 chunk 20 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 chunk 64 optimal weight: 1.9990 chunk 69 optimal weight: 4.9990 chunk 50 optimal weight: 0.2980 chunk 9 optimal weight: 0.5980 chunk 80 optimal weight: 9.9990 chunk 92 optimal weight: 2.9990 chunk 97 optimal weight: 0.7980 chunk 89 optimal weight: 1.9990 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 199 GLN D 255 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.3704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8298 Z= 0.183 Angle : 0.586 11.578 11222 Z= 0.294 Chirality : 0.043 0.335 1360 Planarity : 0.004 0.048 1406 Dihedral : 4.551 20.069 1110 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 3.46 % Allowed : 22.21 % Favored : 74.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.03 (0.27), residues: 1056 helix: 0.80 (0.21), residues: 680 sheet: -1.50 (0.65), residues: 82 loop : -1.37 (0.36), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 54 HIS 0.001 0.000 HIS D 223 PHE 0.029 0.001 PHE A 53 TYR 0.004 0.001 TYR D 45 ARG 0.003 0.000 ARG C 172 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 116 time to evaluate : 0.892 Fit side-chains REVERT: A 45 THR cc_start: 0.8808 (OUTLIER) cc_final: 0.8573 (t) REVERT: A 107 LEU cc_start: 0.8739 (OUTLIER) cc_final: 0.8415 (mp) REVERT: A 177 LEU cc_start: 0.8338 (OUTLIER) cc_final: 0.8040 (mp) REVERT: B 107 LEU cc_start: 0.8771 (OUTLIER) cc_final: 0.8457 (mp) REVERT: B 139 MET cc_start: 0.7998 (ptp) cc_final: 0.7703 (ptp) REVERT: B 177 LEU cc_start: 0.8326 (OUTLIER) cc_final: 0.8064 (mp) REVERT: B 239 LEU cc_start: 0.8543 (OUTLIER) cc_final: 0.8177 (mt) REVERT: D 60 MET cc_start: 0.6870 (OUTLIER) cc_final: 0.6528 (mmm) REVERT: C 48 ASN cc_start: 0.7004 (OUTLIER) cc_final: 0.6477 (p0) outliers start: 31 outliers final: 20 residues processed: 140 average time/residue: 0.1900 time to fit residues: 37.0842 Evaluate side-chains 139 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 111 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 56 MET Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 199 GLN Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 56 MET Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 212 THR Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 260 ILE Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 60 MET Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain C residue 5 ILE Chi-restraints excluded: chain C residue 48 ASN Chi-restraints excluded: chain C residue 60 MET Chi-restraints excluded: chain C residue 156 ASP Chi-restraints excluded: chain C residue 251 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 95 optimal weight: 4.9990 chunk 97 optimal weight: 1.9990 chunk 57 optimal weight: 6.9990 chunk 41 optimal weight: 0.8980 chunk 74 optimal weight: 0.8980 chunk 29 optimal weight: 0.9980 chunk 86 optimal weight: 0.8980 chunk 90 optimal weight: 5.9990 chunk 94 optimal weight: 0.5980 chunk 62 optimal weight: 4.9990 chunk 100 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.3786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8298 Z= 0.203 Angle : 0.602 11.052 11222 Z= 0.300 Chirality : 0.044 0.327 1360 Planarity : 0.004 0.050 1406 Dihedral : 4.580 20.421 1110 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 3.57 % Allowed : 21.99 % Favored : 74.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.02 (0.27), residues: 1056 helix: 0.83 (0.21), residues: 680 sheet: -1.49 (0.65), residues: 82 loop : -1.32 (0.36), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 54 HIS 0.001 0.000 HIS D 223 PHE 0.025 0.001 PHE A 53 TYR 0.005 0.001 TYR B 144 ARG 0.004 0.000 ARG A 198 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 117 time to evaluate : 0.990 Fit side-chains REVERT: A 45 THR cc_start: 0.8824 (OUTLIER) cc_final: 0.8592 (t) REVERT: A 107 LEU cc_start: 0.8750 (OUTLIER) cc_final: 0.8447 (mp) REVERT: A 177 LEU cc_start: 0.8332 (OUTLIER) cc_final: 0.8074 (mp) REVERT: B 45 THR cc_start: 0.8795 (OUTLIER) cc_final: 0.8574 (t) REVERT: B 107 LEU cc_start: 0.8783 (OUTLIER) cc_final: 0.8460 (mp) REVERT: B 139 MET cc_start: 0.8034 (ptp) cc_final: 0.7719 (ptp) REVERT: B 177 LEU cc_start: 0.8320 (OUTLIER) cc_final: 0.8063 (mp) REVERT: B 214 MET cc_start: 0.7966 (mmm) cc_final: 0.7702 (mmp) REVERT: B 239 LEU cc_start: 0.8571 (OUTLIER) cc_final: 0.8192 (mt) REVERT: D 60 MET cc_start: 0.6906 (tpp) cc_final: 0.6565 (mmm) REVERT: C 48 ASN cc_start: 0.6949 (OUTLIER) cc_final: 0.6398 (p0) outliers start: 32 outliers final: 19 residues processed: 141 average time/residue: 0.2006 time to fit residues: 39.3043 Evaluate side-chains 138 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 111 time to evaluate : 1.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 56 MET Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 199 GLN Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 56 MET Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 132 ILE Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 212 THR Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 260 ILE Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 156 ASP Chi-restraints excluded: chain C residue 5 ILE Chi-restraints excluded: chain C residue 48 ASN Chi-restraints excluded: chain C residue 156 ASP Chi-restraints excluded: chain C residue 251 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 61 optimal weight: 2.9990 chunk 47 optimal weight: 0.5980 chunk 69 optimal weight: 4.9990 chunk 105 optimal weight: 7.9990 chunk 97 optimal weight: 0.9990 chunk 84 optimal weight: 3.9990 chunk 8 optimal weight: 0.7980 chunk 64 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 89 optimal weight: 0.9990 overall best weight: 0.8786 ------------------------------------------------------------------------------- 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: 0.7762 moved from start: 0.3871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8298 Z= 0.210 Angle : 0.618 10.523 11222 Z= 0.305 Chirality : 0.044 0.324 1360 Planarity : 0.004 0.051 1406 Dihedral : 4.579 21.168 1110 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 3.24 % Allowed : 22.43 % Favored : 74.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.04 (0.27), residues: 1056 helix: 0.84 (0.21), residues: 680 sheet: -1.50 (0.65), residues: 82 loop : -1.29 (0.37), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 54 HIS 0.001 0.000 HIS C 223 PHE 0.026 0.001 PHE A 53 TYR 0.005 0.001 TYR B 144 ARG 0.007 0.000 ARG C 172 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 116 time to evaluate : 0.921 Fit side-chains REVERT: A 45 THR cc_start: 0.8839 (OUTLIER) cc_final: 0.8617 (t) REVERT: A 107 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8443 (mp) REVERT: A 177 LEU cc_start: 0.8328 (OUTLIER) cc_final: 0.8064 (mp) REVERT: B 45 THR cc_start: 0.8817 (OUTLIER) cc_final: 0.8601 (t) REVERT: B 107 LEU cc_start: 0.8759 (OUTLIER) cc_final: 0.8454 (mp) REVERT: B 177 LEU cc_start: 0.8315 (OUTLIER) cc_final: 0.8054 (mp) REVERT: B 214 MET cc_start: 0.7946 (mmm) cc_final: 0.7702 (mmp) REVERT: D 60 MET cc_start: 0.6904 (tpp) cc_final: 0.6594 (mmm) REVERT: D 71 LEU cc_start: 0.7937 (OUTLIER) cc_final: 0.7667 (mt) REVERT: C 48 ASN cc_start: 0.6935 (OUTLIER) cc_final: 0.6376 (p0) outliers start: 29 outliers final: 19 residues processed: 141 average time/residue: 0.1872 time to fit residues: 36.8229 Evaluate side-chains 135 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 108 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 56 MET Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 56 MET Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 132 ILE Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 212 THR Chi-restraints excluded: chain B residue 260 ILE Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 156 ASP Chi-restraints excluded: chain C residue 5 ILE Chi-restraints excluded: chain C residue 48 ASN Chi-restraints excluded: chain C residue 156 ASP Chi-restraints excluded: chain C residue 251 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 25 optimal weight: 1.9990 chunk 77 optimal weight: 8.9990 chunk 12 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 84 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 86 optimal weight: 0.8980 chunk 10 optimal weight: 0.2980 chunk 15 optimal weight: 0.7980 chunk 73 optimal weight: 1.9990 chunk 4 optimal weight: 0.0570 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 255 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.178303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.144144 restraints weight = 10193.148| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 1.64 r_work: 0.3226 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3103 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.3990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8298 Z= 0.183 Angle : 0.605 10.327 11222 Z= 0.299 Chirality : 0.044 0.312 1360 Planarity : 0.004 0.051 1406 Dihedral : 4.539 21.447 1110 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.90 % Allowed : 22.66 % Favored : 74.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.15 (0.27), residues: 1056 helix: 0.92 (0.21), residues: 680 sheet: -1.41 (0.65), residues: 82 loop : -1.23 (0.37), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 54 HIS 0.001 0.000 HIS C 9 PHE 0.025 0.001 PHE A 53 TYR 0.004 0.001 TYR B 144 ARG 0.004 0.000 ARG C 172 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1975.70 seconds wall clock time: 36 minutes 24.85 seconds (2184.85 seconds total)