Starting phenix.real_space_refine on Mon Mar 11 05:47:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t4f_25675/03_2024/7t4f_25675.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t4f_25675/03_2024/7t4f_25675.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t4f_25675/03_2024/7t4f_25675.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t4f_25675/03_2024/7t4f_25675.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t4f_25675/03_2024/7t4f_25675.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t4f_25675/03_2024/7t4f_25675.pdb" } resolution = 2.7 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= 1.000 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 20 5.16 5 C 4516 2.51 5 N 1216 2.21 5 O 1472 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 25": "OD1" <-> "OD2" Residue "A GLU 49": "OE1" <-> "OE2" Residue "A ASP 56": "OD1" <-> "OD2" Residue "A TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 62": "OD1" <-> "OD2" Residue "A ASP 79": "OD1" <-> "OD2" Residue "A ASP 118": "OD1" <-> "OD2" Residue "A GLU 135": "OE1" <-> "OE2" Residue "A GLU 188": "OE1" <-> "OE2" Residue "A GLU 240": "OE1" <-> "OE2" Residue "B ASP 44": "OD1" <-> "OD2" Residue "B TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 56": "OD1" <-> "OD2" Residue "B ASP 57": "OD1" <-> "OD2" Residue "B GLU 63": "OE1" <-> "OE2" Residue "B GLU 135": "OE1" <-> "OE2" Residue "B GLU 188": "OE1" <-> "OE2" Residue "B GLU 240": "OE1" <-> "OE2" Residue "C ASP 25": "OD1" <-> "OD2" Residue "C ASP 57": "OD1" <-> "OD2" Residue "C ASP 61": "OD1" <-> "OD2" Residue "C ASP 66": "OD1" <-> "OD2" Residue "C PHE 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 135": "OE1" <-> "OE2" Residue "C ASP 154": "OD1" <-> "OD2" Residue "C GLU 188": "OE1" <-> "OE2" Residue "C GLU 240": "OE1" <-> "OE2" Residue "D GLU 53": "OE1" <-> "OE2" Residue "D TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 135": "OE1" <-> "OE2" Residue "D GLU 188": "OE1" <-> "OE2" Residue "D ARG 196": "NH1" <-> "NH2" Residue "D GLU 240": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 7224 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 1806 Classifications: {'peptide': 245} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 232} Chain: "B" Number of atoms: 1806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 1806 Classifications: {'peptide': 245} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 232} Chain: "C" Number of atoms: 1806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 1806 Classifications: {'peptide': 245} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 232} Chain: "D" Number of atoms: 1806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 1806 Classifications: {'peptide': 245} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 232} Time building chain proxies: 4.15, per 1000 atoms: 0.57 Number of scatterers: 7224 At special positions: 0 Unit cell: (108.9, 108.9, 127.6, 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 20 16.00 O 1472 8.00 N 1216 7.00 C 4516 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: 2.50 Conformation dependent library (CDL) restraints added in 1.4 seconds 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1776 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 16 sheets defined 8.2% alpha, 44.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.89 Creating SS restraints... Processing helix chain 'A' and resid 90 through 103 Processing helix chain 'A' and resid 151 through 156 Processing helix chain 'B' and resid 90 through 103 Processing helix chain 'B' and resid 151 through 156 removed outlier: 3.556A pdb=" N SER B 156 " --> pdb=" O GLU B 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 103 Processing helix chain 'C' and resid 151 through 156 removed outlier: 3.504A pdb=" N SER C 156 " --> pdb=" O GLU C 153 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 103 Processing helix chain 'D' and resid 151 through 156 Processing sheet with id=AA1, first strand: chain 'A' and resid 36 through 39 removed outlier: 4.601A pdb=" N LEU A 17 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N ALA A 107 " --> pdb=" O TYR A 20 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N LYS A 142 " --> pdb=" O SER A 125 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ILE A 127 " --> pdb=" O THR A 140 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N THR A 140 " --> pdb=" O ILE A 127 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N LYS A 129 " --> pdb=" O THR A 138 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N THR A 138 " --> pdb=" O LYS A 129 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N VAL A 131 " --> pdb=" O VAL A 136 " (cutoff:3.500A) removed outlier: 8.402A pdb=" N VAL A 136 " --> pdb=" O VAL A 131 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N SER A 81 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N LEU A 45 " --> pdb=" O SER A 81 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N THR A 83 " --> pdb=" O LYS A 43 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 36 through 39 removed outlier: 4.601A pdb=" N LEU A 17 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N ALA A 107 " --> pdb=" O TYR A 20 " (cutoff:3.500A) removed outlier: 17.808A pdb=" N ARG A 121 " --> pdb=" O ASP C 56 " (cutoff:3.500A) removed outlier: 14.231A pdb=" N ASP C 56 " --> pdb=" O ARG A 121 " (cutoff:3.500A) removed outlier: 12.286A pdb=" N TRP A 123 " --> pdb=" O SER C 54 " (cutoff:3.500A) removed outlier: 9.384A pdb=" N SER C 54 " --> pdb=" O TRP A 123 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N SER A 125 " --> pdb=" O ALA C 52 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N THR C 51 " --> pdb=" O LYS C 75 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N LYS C 75 " --> pdb=" O THR C 51 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N GLU C 53 " --> pdb=" O GLY C 73 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 51 through 56 removed outlier: 6.744A pdb=" N THR A 51 " --> pdb=" O LYS A 75 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N LYS A 75 " --> pdb=" O THR A 51 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N GLU A 53 " --> pdb=" O GLY A 73 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 163 through 167 Processing sheet with id=AA5, first strand: chain 'A' and resid 170 through 174 removed outlier: 6.687A pdb=" N THR A 171 " --> pdb=" O THR A 242 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N THR A 244 " --> pdb=" O THR A 171 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N VAL A 173 " --> pdb=" O THR A 244 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 36 through 38 removed outlier: 5.449A pdb=" N ALA B 107 " --> pdb=" O TYR B 20 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N LYS B 142 " --> pdb=" O SER B 125 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N ILE B 127 " --> pdb=" O THR B 140 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N THR B 140 " --> pdb=" O ILE B 127 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N LYS B 129 " --> pdb=" O THR B 138 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N THR B 138 " --> pdb=" O LYS B 129 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ASP B 44 " --> pdb=" O THR B 83 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N ALA B 85 " --> pdb=" O VAL B 42 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N VAL B 42 " --> pdb=" O ALA B 85 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 36 through 38 removed outlier: 5.449A pdb=" N ALA B 107 " --> pdb=" O TYR B 20 " (cutoff:3.500A) removed outlier: 17.775A pdb=" N ARG B 121 " --> pdb=" O ASP D 56 " (cutoff:3.500A) removed outlier: 14.331A pdb=" N ASP D 56 " --> pdb=" O ARG B 121 " (cutoff:3.500A) removed outlier: 12.231A pdb=" N TRP B 123 " --> pdb=" O SER D 54 " (cutoff:3.500A) removed outlier: 9.286A pdb=" N SER D 54 " --> pdb=" O TRP B 123 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N SER B 125 " --> pdb=" O ALA D 52 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N THR D 51 " --> pdb=" O LYS D 75 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N LYS D 75 " --> pdb=" O THR D 51 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N GLU D 53 " --> pdb=" O GLY D 73 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 51 through 56 removed outlier: 6.715A pdb=" N THR B 51 " --> pdb=" O LYS B 75 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N LYS B 75 " --> pdb=" O THR B 51 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N GLU B 53 " --> pdb=" O GLY B 73 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 163 through 167 Processing sheet with id=AB1, first strand: chain 'B' and resid 170 through 174 removed outlier: 6.688A pdb=" N THR B 171 " --> pdb=" O THR B 242 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N THR B 244 " --> pdb=" O THR B 171 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N VAL B 173 " --> pdb=" O THR B 244 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 36 through 38 removed outlier: 5.478A pdb=" N ALA C 107 " --> pdb=" O TYR C 20 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N LYS C 142 " --> pdb=" O SER C 125 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N ILE C 127 " --> pdb=" O THR C 140 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N THR C 140 " --> pdb=" O ILE C 127 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N LYS C 129 " --> pdb=" O THR C 138 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N THR C 138 " --> pdb=" O LYS C 129 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N VAL C 131 " --> pdb=" O VAL C 136 " (cutoff:3.500A) removed outlier: 8.448A pdb=" N VAL C 136 " --> pdb=" O VAL C 131 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N SER C 81 " --> pdb=" O LEU C 45 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N LEU C 45 " --> pdb=" O SER C 81 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N THR C 83 " --> pdb=" O LYS C 43 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 163 through 167 Processing sheet with id=AB4, first strand: chain 'C' and resid 170 through 174 removed outlier: 6.688A pdb=" N THR C 171 " --> pdb=" O THR C 242 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N THR C 244 " --> pdb=" O THR C 171 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N VAL C 173 " --> pdb=" O THR C 244 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 36 through 38 removed outlier: 5.322A pdb=" N ALA D 107 " --> pdb=" O TYR D 20 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N LYS D 142 " --> pdb=" O SER D 125 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N ILE D 127 " --> pdb=" O THR D 140 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N THR D 140 " --> pdb=" O ILE D 127 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N LYS D 129 " --> pdb=" O THR D 138 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N THR D 138 " --> pdb=" O LYS D 129 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ASP D 44 " --> pdb=" O THR D 83 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ALA D 85 " --> pdb=" O VAL D 42 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N VAL D 42 " --> pdb=" O ALA D 85 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 163 through 167 Processing sheet with id=AB7, first strand: chain 'D' and resid 170 through 174 removed outlier: 6.688A pdb=" N THR D 171 " --> pdb=" O THR D 242 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N THR D 244 " --> pdb=" O THR D 171 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N VAL D 173 " --> pdb=" O THR D 244 " (cutoff:3.500A) 296 hydrogen bonds defined for protein. 768 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: 2.04 Time building geometry restraints manager: 2.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1249 1.31 - 1.44: 1883 1.44 - 1.56: 4196 1.56 - 1.69: 0 1.69 - 1.81: 40 Bond restraints: 7368 Sorted by residual: bond pdb=" C PRO B 9 " pdb=" O PRO B 9 " ideal model delta sigma weight residual 1.233 1.187 0.046 1.16e-02 7.43e+03 1.55e+01 bond pdb=" C PRO D 9 " pdb=" O PRO D 9 " ideal model delta sigma weight residual 1.233 1.189 0.044 1.19e-02 7.06e+03 1.37e+01 bond pdb=" N VAL D 10 " pdb=" CA VAL D 10 " ideal model delta sigma weight residual 1.456 1.498 -0.042 1.14e-02 7.69e+03 1.35e+01 bond pdb=" N VAL C 10 " pdb=" CA VAL C 10 " ideal model delta sigma weight residual 1.459 1.502 -0.043 1.19e-02 7.06e+03 1.31e+01 bond pdb=" CA ALA A 13 " pdb=" CB ALA A 13 " ideal model delta sigma weight residual 1.527 1.477 0.050 1.44e-02 4.82e+03 1.20e+01 ... (remaining 7363 not shown) Histogram of bond angle deviations from ideal: 98.89 - 105.96: 214 105.96 - 113.02: 4136 113.02 - 120.08: 2336 120.08 - 127.14: 3288 127.14 - 134.21: 90 Bond angle restraints: 10064 Sorted by residual: angle pdb=" N GLY B 12 " pdb=" CA GLY B 12 " pdb=" C GLY B 12 " ideal model delta sigma weight residual 114.67 121.24 -6.57 1.10e+00 8.26e-01 3.57e+01 angle pdb=" N PRO D 9 " pdb=" CA PRO D 9 " pdb=" CB PRO D 9 " ideal model delta sigma weight residual 103.35 98.89 4.46 8.70e-01 1.32e+00 2.62e+01 angle pdb=" C THR C 15 " pdb=" CA THR C 15 " pdb=" CB THR C 15 " ideal model delta sigma weight residual 109.53 117.59 -8.06 1.69e+00 3.50e-01 2.27e+01 angle pdb=" C LYS C 11 " pdb=" CA LYS C 11 " pdb=" CB LYS C 11 " ideal model delta sigma weight residual 109.68 118.56 -8.88 2.05e+00 2.38e-01 1.88e+01 angle pdb=" C GLY B 147 " pdb=" N ARG B 148 " pdb=" CA ARG B 148 " ideal model delta sigma weight residual 121.83 128.46 -6.63 1.56e+00 4.11e-01 1.81e+01 ... (remaining 10059 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.68: 3958 17.68 - 35.35: 298 35.35 - 53.02: 71 53.02 - 70.70: 24 70.70 - 88.37: 9 Dihedral angle restraints: 4360 sinusoidal: 1588 harmonic: 2772 Sorted by residual: dihedral pdb=" CA ASP C 64 " pdb=" CB ASP C 64 " pdb=" CG ASP C 64 " pdb=" OD1 ASP C 64 " ideal model delta sinusoidal sigma weight residual -30.00 -87.53 57.53 1 2.00e+01 2.50e-03 1.11e+01 dihedral pdb=" CB GLU C 135 " pdb=" CG GLU C 135 " pdb=" CD GLU C 135 " pdb=" OE1 GLU C 135 " ideal model delta sinusoidal sigma weight residual 0.00 -88.37 88.37 1 3.00e+01 1.11e-03 1.04e+01 dihedral pdb=" CG ARG B 139 " pdb=" CD ARG B 139 " pdb=" NE ARG B 139 " pdb=" CZ ARG B 139 " ideal model delta sinusoidal sigma weight residual -90.00 -133.84 43.84 2 1.50e+01 4.44e-03 1.02e+01 ... (remaining 4357 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 883 0.046 - 0.092: 177 0.092 - 0.138: 110 0.138 - 0.184: 14 0.184 - 0.230: 8 Chirality restraints: 1192 Sorted by residual: chirality pdb=" CA VAL C 228 " pdb=" N VAL C 228 " pdb=" C VAL C 228 " pdb=" CB VAL C 228 " both_signs ideal model delta sigma weight residual False 2.44 2.67 -0.23 2.00e-01 2.50e+01 1.32e+00 chirality pdb=" CA VAL A 10 " pdb=" N VAL A 10 " pdb=" C VAL A 10 " pdb=" CB VAL A 10 " both_signs ideal model delta sigma weight residual False 2.44 2.67 -0.23 2.00e-01 2.50e+01 1.32e+00 chirality pdb=" CA VAL B 10 " pdb=" N VAL B 10 " pdb=" C VAL B 10 " pdb=" CB VAL B 10 " both_signs ideal model delta sigma weight residual False 2.44 2.66 -0.22 2.00e-01 2.50e+01 1.22e+00 ... (remaining 1189 not shown) Planarity restraints: 1292 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA B 13 " -0.013 2.00e-02 2.50e+03 2.74e-02 7.50e+00 pdb=" C ALA B 13 " 0.047 2.00e-02 2.50e+03 pdb=" O ALA B 13 " -0.018 2.00e-02 2.50e+03 pdb=" N GLY B 14 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY B 14 " 0.011 2.00e-02 2.50e+03 2.34e-02 5.45e+00 pdb=" C GLY B 14 " -0.040 2.00e-02 2.50e+03 pdb=" O GLY B 14 " 0.015 2.00e-02 2.50e+03 pdb=" N THR B 15 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA D 13 " -0.010 2.00e-02 2.50e+03 2.00e-02 3.99e+00 pdb=" C ALA D 13 " 0.035 2.00e-02 2.50e+03 pdb=" O ALA D 13 " -0.013 2.00e-02 2.50e+03 pdb=" N GLY D 14 " -0.012 2.00e-02 2.50e+03 ... (remaining 1289 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 901 2.76 - 3.30: 6247 3.30 - 3.83: 11438 3.83 - 4.37: 12925 4.37 - 4.90: 23496 Nonbonded interactions: 55007 Sorted by model distance: nonbonded pdb=" OH TYR B 108 " pdb=" OD1 ASN B 145 " model vdw 2.228 2.440 nonbonded pdb=" ND2 ASN A 29 " pdb=" OD1 ASP A 192 " model vdw 2.247 2.520 nonbonded pdb=" OG SER A 126 " pdb=" OE2 GLU C 49 " model vdw 2.254 2.440 nonbonded pdb=" OH TYR A 108 " pdb=" OD1 ASN A 145 " model vdw 2.273 2.440 nonbonded pdb=" OG SER B 32 " pdb=" OG SER B 194 " model vdw 2.337 2.440 ... (remaining 55002 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' selection = 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: 1.130 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: 3.810 Check model and map are aligned: 0.120 Set scattering table: 0.070 Process input model: 22.110 Find NCS groups from input model: 0.440 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: 0.010 Load rotamer database and sin/cos tables:11.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6873 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 : 0.004 0.050 7368 Z= 0.302 Angle : 0.701 8.884 10064 Z= 0.474 Chirality : 0.052 0.230 1192 Planarity : 0.004 0.043 1292 Dihedral : 14.605 88.374 2584 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Rotamer: Outliers : 2.44 % Allowed : 12.18 % Favored : 85.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 0.54 (0.25), residues: 972 helix: 2.35 (0.64), residues: 54 sheet: 1.09 (0.23), residues: 494 loop : -0.82 (0.25), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 123 PHE 0.010 0.001 PHE B 82 TYR 0.007 0.001 TYR A 108 ARG 0.004 0.000 ARG D 148 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 93 time to evaluate : 0.777 Fit side-chains REVERT: A 8 MET cc_start: 0.8167 (mtm) cc_final: 0.7897 (mtm) REVERT: A 11 LYS cc_start: 0.8864 (OUTLIER) cc_final: 0.7037 (mmmt) REVERT: B 11 LYS cc_start: 0.8706 (OUTLIER) cc_final: 0.6947 (mmpt) REVERT: C 31 LEU cc_start: 0.9214 (OUTLIER) cc_final: 0.8864 (mm) REVERT: C 148 ARG cc_start: 0.8413 (ttt180) cc_final: 0.6756 (mmp80) REVERT: D 43 LYS cc_start: 0.8722 (mtpp) cc_final: 0.7805 (mmtm) REVERT: D 151 MET cc_start: 0.9054 (mmm) cc_final: 0.8804 (mmm) outliers start: 19 outliers final: 7 residues processed: 108 average time/residue: 1.2009 time to fit residues: 136.8761 Evaluate side-chains 98 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 88 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 LYS Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain B residue 11 LYS Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 97 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 81 optimal weight: 2.9990 chunk 72 optimal weight: 5.9990 chunk 40 optimal weight: 7.9990 chunk 24 optimal weight: 7.9990 chunk 49 optimal weight: 2.9990 chunk 38 optimal weight: 0.5980 chunk 75 optimal weight: 7.9990 chunk 29 optimal weight: 0.9990 chunk 45 optimal weight: 40.0000 chunk 56 optimal weight: 3.9990 chunk 87 optimal weight: 9.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 177 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6959 moved from start: 0.1304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 7368 Z= 0.263 Angle : 0.528 5.500 10064 Z= 0.282 Chirality : 0.047 0.156 1192 Planarity : 0.004 0.033 1292 Dihedral : 5.507 56.210 1048 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 2.44 % Allowed : 12.69 % Favored : 84.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 0.41 (0.25), residues: 972 helix: 1.80 (0.70), residues: 56 sheet: 1.02 (0.23), residues: 494 loop : -0.86 (0.25), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 18 PHE 0.019 0.002 PHE A 120 TYR 0.011 0.001 TYR A 108 ARG 0.002 0.000 ARG B 148 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 80 time to evaluate : 0.766 Fit side-chains REVERT: A 8 MET cc_start: 0.8097 (mtm) cc_final: 0.7864 (mtm) REVERT: A 38 ARG cc_start: 0.8601 (OUTLIER) cc_final: 0.8067 (ttt90) REVERT: B 11 LYS cc_start: 0.8675 (OUTLIER) cc_final: 0.7001 (mmpt) REVERT: C 43 LYS cc_start: 0.8886 (mtpp) cc_final: 0.7602 (mmtt) REVERT: C 134 LYS cc_start: 0.8870 (OUTLIER) cc_final: 0.8407 (mtpm) REVERT: C 148 ARG cc_start: 0.8394 (ttt180) cc_final: 0.6714 (tpp-160) REVERT: D 43 LYS cc_start: 0.8770 (mtpp) cc_final: 0.7786 (mmtm) outliers start: 19 outliers final: 6 residues processed: 89 average time/residue: 1.3411 time to fit residues: 125.5314 Evaluate side-chains 85 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 76 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain B residue 11 LYS Chi-restraints excluded: chain C residue 44 ASP Chi-restraints excluded: chain C residue 134 LYS Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain D residue 97 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 48 optimal weight: 0.0030 chunk 27 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 24 optimal weight: 8.9990 chunk 87 optimal weight: 3.9990 chunk 94 optimal weight: 50.0000 chunk 77 optimal weight: 5.9990 chunk 86 optimal weight: 0.5980 chunk 29 optimal weight: 0.9980 chunk 70 optimal weight: 30.0000 overall best weight: 1.3194 ------------------------------------------------------------------------------- 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: 0.6940 moved from start: 0.1374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 7368 Z= 0.164 Angle : 0.451 4.926 10064 Z= 0.241 Chirality : 0.045 0.151 1192 Planarity : 0.004 0.037 1292 Dihedral : 4.391 53.915 1034 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Rotamer: Outliers : 2.44 % Allowed : 13.21 % Favored : 84.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 0.39 (0.25), residues: 972 helix: 1.94 (0.69), residues: 56 sheet: 0.95 (0.23), residues: 492 loop : -0.81 (0.25), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 18 PHE 0.013 0.002 PHE D 82 TYR 0.009 0.001 TYR A 108 ARG 0.002 0.000 ARG A 139 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 82 time to evaluate : 0.803 Fit side-chains REVERT: A 38 ARG cc_start: 0.8644 (OUTLIER) cc_final: 0.8143 (ttt90) REVERT: A 212 MET cc_start: 0.6123 (OUTLIER) cc_final: 0.5326 (tpt) REVERT: B 11 LYS cc_start: 0.8689 (OUTLIER) cc_final: 0.7094 (mmpt) REVERT: B 41 LYS cc_start: 0.8926 (OUTLIER) cc_final: 0.8558 (mttp) REVERT: C 31 LEU cc_start: 0.9266 (OUTLIER) cc_final: 0.8896 (mm) REVERT: C 43 LYS cc_start: 0.8847 (mtpp) cc_final: 0.7535 (mmtt) REVERT: C 134 LYS cc_start: 0.8865 (OUTLIER) cc_final: 0.8428 (mtpm) REVERT: C 148 ARG cc_start: 0.8379 (ttt180) cc_final: 0.6683 (tpp-160) REVERT: D 43 LYS cc_start: 0.8662 (mtpp) cc_final: 0.7652 (mmtm) outliers start: 19 outliers final: 7 residues processed: 89 average time/residue: 1.3660 time to fit residues: 127.7582 Evaluate side-chains 90 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 77 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 212 MET Chi-restraints excluded: chain B residue 11 LYS Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 87 MET Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 44 ASP Chi-restraints excluded: chain C residue 134 LYS Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 97 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 0.9980 chunk 65 optimal weight: 10.0000 chunk 45 optimal weight: 6.9990 chunk 9 optimal weight: 5.9990 chunk 41 optimal weight: 20.0000 chunk 58 optimal weight: 5.9990 chunk 87 optimal weight: 5.9990 chunk 92 optimal weight: 40.0000 chunk 83 optimal weight: 4.9990 chunk 25 optimal weight: 5.9990 chunk 77 optimal weight: 1.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- 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: 0.6997 moved from start: 0.1816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.041 7368 Z= 0.424 Angle : 0.599 7.623 10064 Z= 0.318 Chirality : 0.050 0.170 1192 Planarity : 0.005 0.040 1292 Dihedral : 4.983 56.500 1034 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 2.82 % Allowed : 13.72 % Favored : 83.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 0.15 (0.25), residues: 972 helix: 1.41 (0.71), residues: 56 sheet: 0.71 (0.22), residues: 512 loop : -0.87 (0.26), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP D 18 PHE 0.025 0.002 PHE A 120 TYR 0.011 0.002 TYR B 108 ARG 0.004 0.001 ARG A 139 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 75 time to evaluate : 0.786 Fit side-chains REVERT: A 31 LEU cc_start: 0.8412 (OUTLIER) cc_final: 0.8176 (mm) REVERT: A 38 ARG cc_start: 0.8611 (OUTLIER) cc_final: 0.8103 (ttt90) REVERT: A 212 MET cc_start: 0.5944 (OUTLIER) cc_final: 0.5337 (tpt) REVERT: B 11 LYS cc_start: 0.8721 (OUTLIER) cc_final: 0.7126 (mmpt) REVERT: B 41 LYS cc_start: 0.8972 (OUTLIER) cc_final: 0.8643 (mttp) REVERT: C 31 LEU cc_start: 0.9250 (OUTLIER) cc_final: 0.8845 (mm) REVERT: C 43 LYS cc_start: 0.8879 (mtpp) cc_final: 0.7727 (mmtt) REVERT: C 134 LYS cc_start: 0.8869 (OUTLIER) cc_final: 0.8412 (mtpm) REVERT: C 148 ARG cc_start: 0.8334 (ttt180) cc_final: 0.6681 (tpp-160) REVERT: C 151 MET cc_start: 0.8984 (mmp) cc_final: 0.8724 (mmp) REVERT: D 43 LYS cc_start: 0.8726 (mtpp) cc_final: 0.7724 (mmtm) REVERT: D 53 GLU cc_start: 0.8204 (OUTLIER) cc_final: 0.7974 (pt0) outliers start: 22 outliers final: 13 residues processed: 88 average time/residue: 1.4352 time to fit residues: 132.4028 Evaluate side-chains 93 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 72 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 135 GLU Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 212 MET Chi-restraints excluded: chain B residue 11 LYS Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 44 ASP Chi-restraints excluded: chain C residue 134 LYS Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 53 GLU Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 97 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 52 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 69 optimal weight: 9.9990 chunk 38 optimal weight: 5.9990 chunk 79 optimal weight: 1.9990 chunk 64 optimal weight: 9.9990 chunk 0 optimal weight: 3.9990 chunk 47 optimal weight: 40.0000 chunk 83 optimal weight: 2.9990 chunk 23 optimal weight: 20.0000 chunk 31 optimal weight: 0.7980 overall best weight: 2.1588 ------------------------------------------------------------------------------- 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: 0.6975 moved from start: 0.1783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 7368 Z= 0.240 Angle : 0.493 5.237 10064 Z= 0.262 Chirality : 0.046 0.155 1192 Planarity : 0.005 0.041 1292 Dihedral : 4.627 58.046 1034 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Rotamer: Outliers : 3.08 % Allowed : 14.10 % Favored : 82.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 0.20 (0.26), residues: 972 helix: 1.55 (0.70), residues: 56 sheet: 0.76 (0.23), residues: 510 loop : -0.87 (0.26), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP D 18 PHE 0.018 0.002 PHE A 120 TYR 0.010 0.001 TYR A 108 ARG 0.002 0.000 ARG D 121 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 77 time to evaluate : 0.790 Fit side-chains REVERT: A 31 LEU cc_start: 0.8388 (OUTLIER) cc_final: 0.8164 (mm) REVERT: A 38 ARG cc_start: 0.8601 (OUTLIER) cc_final: 0.8058 (ttt90) REVERT: B 11 LYS cc_start: 0.8718 (mmmm) cc_final: 0.7125 (mmpt) REVERT: B 41 LYS cc_start: 0.8959 (OUTLIER) cc_final: 0.8633 (mttp) REVERT: C 31 LEU cc_start: 0.9250 (OUTLIER) cc_final: 0.8858 (mm) REVERT: C 43 LYS cc_start: 0.8896 (mtpp) cc_final: 0.7716 (mmtt) REVERT: C 134 LYS cc_start: 0.8856 (OUTLIER) cc_final: 0.8398 (mtpm) REVERT: C 148 ARG cc_start: 0.8332 (ttt180) cc_final: 0.6696 (tpp-160) REVERT: D 29 ASN cc_start: 0.8789 (t0) cc_final: 0.8558 (t0) REVERT: D 43 LYS cc_start: 0.8723 (mtpp) cc_final: 0.7782 (mmtm) REVERT: D 53 GLU cc_start: 0.7992 (OUTLIER) cc_final: 0.7762 (pt0) outliers start: 24 outliers final: 13 residues processed: 93 average time/residue: 1.4466 time to fit residues: 141.2597 Evaluate side-chains 94 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 75 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 135 GLU Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 44 ASP Chi-restraints excluded: chain C residue 134 LYS Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 53 GLU Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 97 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 83 optimal weight: 2.9990 chunk 18 optimal weight: 20.0000 chunk 54 optimal weight: 8.9990 chunk 22 optimal weight: 9.9990 chunk 92 optimal weight: 8.9990 chunk 77 optimal weight: 0.8980 chunk 43 optimal weight: 30.0000 chunk 7 optimal weight: 4.9990 chunk 30 optimal weight: 4.9990 chunk 48 optimal weight: 0.0370 chunk 89 optimal weight: 0.8980 overall best weight: 1.9662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 91 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6971 moved from start: 0.1834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 7368 Z= 0.222 Angle : 0.486 5.210 10064 Z= 0.258 Chirality : 0.046 0.154 1192 Planarity : 0.004 0.042 1292 Dihedral : 4.310 59.459 1030 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 2.82 % Allowed : 15.00 % Favored : 82.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 0.28 (0.26), residues: 972 helix: 1.55 (0.69), residues: 56 sheet: 0.83 (0.23), residues: 506 loop : -0.81 (0.27), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 18 PHE 0.017 0.002 PHE A 120 TYR 0.010 0.001 TYR A 108 ARG 0.002 0.000 ARG A 139 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 77 time to evaluate : 0.793 Fit side-chains REVERT: A 38 ARG cc_start: 0.8671 (OUTLIER) cc_final: 0.8146 (ttt90) REVERT: B 11 LYS cc_start: 0.8706 (mmmm) cc_final: 0.7112 (mmpt) REVERT: B 41 LYS cc_start: 0.8944 (OUTLIER) cc_final: 0.8595 (mttp) REVERT: C 31 LEU cc_start: 0.9246 (OUTLIER) cc_final: 0.8852 (mm) REVERT: C 43 LYS cc_start: 0.8899 (mtpp) cc_final: 0.7724 (mmtt) REVERT: C 134 LYS cc_start: 0.8860 (OUTLIER) cc_final: 0.8403 (mtpm) REVERT: C 148 ARG cc_start: 0.8313 (ttt180) cc_final: 0.6670 (tpp-160) REVERT: D 29 ASN cc_start: 0.8826 (t0) cc_final: 0.8577 (t0) REVERT: D 43 LYS cc_start: 0.8706 (mtpp) cc_final: 0.7757 (mmtm) REVERT: D 53 GLU cc_start: 0.7968 (OUTLIER) cc_final: 0.7741 (pt0) outliers start: 22 outliers final: 13 residues processed: 92 average time/residue: 1.4064 time to fit residues: 135.7424 Evaluate side-chains 95 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 77 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 135 GLU Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 44 ASP Chi-restraints excluded: chain C residue 134 LYS Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 53 GLU Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 97 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 10 optimal weight: 6.9990 chunk 52 optimal weight: 1.9990 chunk 67 optimal weight: 4.9990 chunk 78 optimal weight: 0.9990 chunk 51 optimal weight: 5.9990 chunk 92 optimal weight: 4.9990 chunk 57 optimal weight: 5.9990 chunk 56 optimal weight: 0.9980 chunk 42 optimal weight: 20.0000 chunk 36 optimal weight: 2.9990 chunk 55 optimal weight: 5.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 91 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6980 moved from start: 0.1939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 7368 Z= 0.263 Angle : 0.513 5.641 10064 Z= 0.271 Chirality : 0.047 0.157 1192 Planarity : 0.005 0.042 1292 Dihedral : 4.425 59.895 1030 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Rotamer: Outliers : 2.95 % Allowed : 15.38 % Favored : 81.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 0.23 (0.26), residues: 972 helix: 1.47 (0.69), residues: 56 sheet: 0.80 (0.24), residues: 496 loop : -0.81 (0.26), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP D 18 PHE 0.018 0.002 PHE A 120 TYR 0.011 0.001 TYR A 108 ARG 0.002 0.000 ARG A 139 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 76 time to evaluate : 0.771 Fit side-chains REVERT: A 38 ARG cc_start: 0.8607 (OUTLIER) cc_final: 0.8055 (ttt90) REVERT: B 11 LYS cc_start: 0.8711 (mmmm) cc_final: 0.7087 (mmpt) REVERT: B 41 LYS cc_start: 0.8948 (OUTLIER) cc_final: 0.8605 (mttp) REVERT: C 31 LEU cc_start: 0.9249 (OUTLIER) cc_final: 0.8857 (mm) REVERT: C 43 LYS cc_start: 0.8902 (mtpp) cc_final: 0.7742 (mmtt) REVERT: C 134 LYS cc_start: 0.8864 (OUTLIER) cc_final: 0.8411 (mtpm) REVERT: C 148 ARG cc_start: 0.8356 (ttt180) cc_final: 0.6781 (tpp-160) REVERT: D 43 LYS cc_start: 0.8703 (mtpp) cc_final: 0.7759 (mmtm) REVERT: D 53 GLU cc_start: 0.8028 (OUTLIER) cc_final: 0.7796 (pt0) outliers start: 23 outliers final: 16 residues processed: 93 average time/residue: 1.4394 time to fit residues: 140.4421 Evaluate side-chains 96 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 75 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 135 GLU Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 87 MET Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 44 ASP Chi-restraints excluded: chain C residue 134 LYS Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 53 GLU Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 97 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 27 optimal weight: 0.9980 chunk 18 optimal weight: 9.9990 chunk 17 optimal weight: 5.9990 chunk 58 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 45 optimal weight: 10.0000 chunk 8 optimal weight: 4.9990 chunk 72 optimal weight: 3.9990 chunk 84 optimal weight: 4.9990 chunk 88 optimal weight: 20.0000 chunk 80 optimal weight: 3.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 91 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6993 moved from start: 0.2065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 7368 Z= 0.342 Angle : 0.557 6.537 10064 Z= 0.295 Chirality : 0.048 0.162 1192 Planarity : 0.005 0.044 1292 Dihedral : 4.614 59.877 1030 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 3.21 % Allowed : 15.26 % Favored : 81.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 0.11 (0.26), residues: 972 helix: 1.28 (0.70), residues: 56 sheet: 0.74 (0.23), residues: 496 loop : -0.91 (0.26), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 18 PHE 0.021 0.002 PHE A 120 TYR 0.011 0.001 TYR A 108 ARG 0.002 0.000 ARG D 121 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 76 time to evaluate : 0.858 Fit side-chains REVERT: A 38 ARG cc_start: 0.8600 (OUTLIER) cc_final: 0.8036 (ttt90) REVERT: B 11 LYS cc_start: 0.8720 (mmmm) cc_final: 0.7081 (mmpt) REVERT: B 41 LYS cc_start: 0.8961 (OUTLIER) cc_final: 0.8625 (mttp) REVERT: C 31 LEU cc_start: 0.9247 (OUTLIER) cc_final: 0.8862 (mm) REVERT: C 43 LYS cc_start: 0.8870 (mtpp) cc_final: 0.7716 (mmtt) REVERT: C 134 LYS cc_start: 0.8869 (OUTLIER) cc_final: 0.8416 (mtpm) REVERT: C 148 ARG cc_start: 0.8371 (ttt180) cc_final: 0.6772 (tpp-160) REVERT: D 43 LYS cc_start: 0.8708 (mtpp) cc_final: 0.7763 (mmtm) outliers start: 25 outliers final: 16 residues processed: 92 average time/residue: 1.4027 time to fit residues: 135.4149 Evaluate side-chains 96 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 76 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 135 GLU Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 87 MET Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 44 ASP Chi-restraints excluded: chain C residue 134 LYS Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 97 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 1.9990 chunk 88 optimal weight: 20.0000 chunk 51 optimal weight: 5.9990 chunk 37 optimal weight: 5.9990 chunk 67 optimal weight: 0.1980 chunk 26 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 chunk 81 optimal weight: 0.8980 chunk 85 optimal weight: 0.5980 chunk 56 optimal weight: 2.9990 chunk 91 optimal weight: 20.0000 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 91 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6948 moved from start: 0.1902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 7368 Z= 0.132 Angle : 0.434 5.109 10064 Z= 0.231 Chirality : 0.045 0.149 1192 Planarity : 0.004 0.044 1292 Dihedral : 4.074 58.338 1030 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Rotamer: Outliers : 2.31 % Allowed : 16.15 % Favored : 81.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 0.34 (0.26), residues: 972 helix: 1.61 (0.68), residues: 56 sheet: 0.90 (0.24), residues: 480 loop : -0.72 (0.26), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 36 PHE 0.011 0.001 PHE B 82 TYR 0.008 0.001 TYR A 108 ARG 0.001 0.000 ARG D 121 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 80 time to evaluate : 0.826 Fit side-chains REVERT: A 140 THR cc_start: 0.9021 (m) cc_final: 0.8814 (m) REVERT: B 11 LYS cc_start: 0.8709 (mmmm) cc_final: 0.7110 (mmpt) REVERT: B 41 LYS cc_start: 0.8912 (OUTLIER) cc_final: 0.8563 (mttp) REVERT: C 31 LEU cc_start: 0.9242 (OUTLIER) cc_final: 0.8856 (mm) REVERT: C 43 LYS cc_start: 0.8847 (mtpp) cc_final: 0.7573 (mmtt) REVERT: C 148 ARG cc_start: 0.8347 (ttt180) cc_final: 0.6788 (tpp-160) REVERT: D 29 ASN cc_start: 0.8741 (t0) cc_final: 0.8533 (t0) REVERT: D 43 LYS cc_start: 0.8667 (mtpp) cc_final: 0.7705 (mmtm) REVERT: D 94 GLN cc_start: 0.8546 (mt0) cc_final: 0.8335 (mt0) outliers start: 18 outliers final: 10 residues processed: 93 average time/residue: 1.3699 time to fit residues: 133.8654 Evaluate side-chains 92 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 80 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 87 MET Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 44 ASP Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 191 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 55 optimal weight: 8.9990 chunk 43 optimal weight: 20.0000 chunk 63 optimal weight: 8.9990 chunk 95 optimal weight: 50.0000 chunk 88 optimal weight: 20.0000 chunk 76 optimal weight: 4.9990 chunk 7 optimal weight: 8.9990 chunk 58 optimal weight: 4.9990 chunk 46 optimal weight: 0.9990 chunk 60 optimal weight: 0.0770 chunk 81 optimal weight: 0.8980 overall best weight: 2.3944 ------------------------------------------------------------------------------- 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: 0.6978 moved from start: 0.2021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 7368 Z= 0.264 Angle : 0.510 5.515 10064 Z= 0.269 Chirality : 0.047 0.156 1192 Planarity : 0.005 0.045 1292 Dihedral : 4.367 59.022 1030 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 1.92 % Allowed : 16.54 % Favored : 81.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 0.25 (0.26), residues: 972 helix: 1.44 (0.68), residues: 56 sheet: 0.83 (0.24), residues: 496 loop : -0.80 (0.26), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 18 PHE 0.019 0.002 PHE A 120 TYR 0.011 0.001 TYR A 108 ARG 0.003 0.000 ARG A 139 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 77 time to evaluate : 0.760 Fit side-chains REVERT: B 11 LYS cc_start: 0.8708 (mmmm) cc_final: 0.7076 (mmpt) REVERT: B 41 LYS cc_start: 0.8949 (OUTLIER) cc_final: 0.8582 (mttp) REVERT: C 31 LEU cc_start: 0.9246 (OUTLIER) cc_final: 0.8857 (mm) REVERT: C 43 LYS cc_start: 0.8909 (mtpp) cc_final: 0.7734 (mmtt) REVERT: C 134 LYS cc_start: 0.8865 (OUTLIER) cc_final: 0.8414 (mtpm) REVERT: C 148 ARG cc_start: 0.8366 (ttt180) cc_final: 0.6775 (tpp-160) REVERT: D 29 ASN cc_start: 0.8785 (t0) cc_final: 0.8571 (t0) REVERT: D 43 LYS cc_start: 0.8704 (mtpp) cc_final: 0.7750 (mmtm) outliers start: 15 outliers final: 11 residues processed: 87 average time/residue: 1.4832 time to fit residues: 135.2377 Evaluate side-chains 90 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 76 time to evaluate : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 87 MET Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 44 ASP Chi-restraints excluded: chain C residue 134 LYS Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 191 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 23 optimal weight: 30.0000 chunk 70 optimal weight: 8.9990 chunk 11 optimal weight: 0.9990 chunk 21 optimal weight: 20.0000 chunk 76 optimal weight: 0.3980 chunk 31 optimal weight: 4.9990 chunk 78 optimal weight: 4.9990 chunk 9 optimal weight: 5.9990 chunk 14 optimal weight: 2.9990 chunk 66 optimal weight: 5.9990 chunk 4 optimal weight: 0.0570 overall best weight: 1.8904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 91 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.194898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.109882 restraints weight = 7708.340| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 2.38 r_work: 0.3121 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.2012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7368 Z= 0.216 Angle : 0.482 5.220 10064 Z= 0.255 Chirality : 0.046 0.154 1192 Planarity : 0.005 0.045 1292 Dihedral : 4.255 58.605 1030 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 1.92 % Allowed : 16.41 % Favored : 81.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 0.30 (0.26), residues: 972 helix: 1.48 (0.68), residues: 56 sheet: 0.86 (0.24), residues: 496 loop : -0.78 (0.27), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 18 PHE 0.016 0.002 PHE A 120 TYR 0.010 0.001 TYR A 108 ARG 0.002 0.000 ARG A 139 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2999.88 seconds wall clock time: 54 minutes 6.44 seconds (3246.44 seconds total)