Starting phenix.real_space_refine on Fri Jul 19 21:32:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t3s_41010/07_2024/8t3s_41010.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t3s_41010/07_2024/8t3s_41010.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.07 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t3s_41010/07_2024/8t3s_41010.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t3s_41010/07_2024/8t3s_41010.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t3s_41010/07_2024/8t3s_41010.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t3s_41010/07_2024/8t3s_41010.cif" } resolution = 3.07 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= 0.043 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 53 5.16 5 C 5600 2.51 5 N 1496 2.21 5 O 1620 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 25": "OE1" <-> "OE2" Residue "A GLU 166": "OE1" <-> "OE2" Residue "B GLU 130": "OE1" <-> "OE2" Residue "B GLU 172": "OE1" <-> "OE2" Residue "B PHE 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 58": "OE1" <-> "OE2" Residue "N GLU 6": "OE1" <-> "OE2" Residue "N GLU 235": "OE1" <-> "OE2" Residue "R PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 8769 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1797 Classifications: {'peptide': 230} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 6, 'TRANS': 223} Chain breaks: 1 Unresolved non-hydrogen bonds: 79 Unresolved non-hydrogen angles: 93 Unresolved non-hydrogen dihedrals: 67 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 3, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 49 Chain: "B" Number of atoms: 2622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2622 Classifications: {'peptide': 342} Link IDs: {'PTRANS': 5, 'TRANS': 336} Chain: "G" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "N" Number of atoms: 1781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1781 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Chain: "R" Number of atoms: 2063 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 2063 Classifications: {'peptide': 258} Link IDs: {'PTRANS': 14, 'TRANS': 243} Chain breaks: 3 Chain: "R" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 70 Unusual residues: {'BUA': 1, 'CLR': 1, 'PLM': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 5.36, per 1000 atoms: 0.61 Number of scatterers: 8769 At special positions: 0 Unit cell: (84.252, 123.9, 119.77, 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 53 16.00 O 1620 8.00 N 1496 7.00 C 5600 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 160 " - pdb=" SG CYS N 230 " distance=2.03 Simple disulfide: pdb=" SG CYS R 82 " - pdb=" SG CYS R 164 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.83 Conformation dependent library (CDL) restraints added in 1.6 seconds 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2092 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 14 sheets defined 38.5% alpha, 22.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.96 Creating SS restraints... Processing helix chain 'A' and resid 6 through 31 Processing helix chain 'A' and resid 45 through 49 Processing helix chain 'A' and resid 95 through 99 removed outlier: 3.527A pdb=" N GLN A 98 " --> pdb=" O LYS A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 130 Processing helix chain 'A' and resid 131 through 135 removed outlier: 3.895A pdb=" N ARG A 135 " --> pdb=" O ARG A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 156 removed outlier: 3.522A pdb=" N LEU A 149 " --> pdb=" O LYS A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 164 removed outlier: 4.026A pdb=" N TYR A 163 " --> pdb=" O LYS A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 168 removed outlier: 3.512A pdb=" N ALA A 168 " --> pdb=" O PRO A 165 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 165 through 168' Processing helix chain 'A' and resid 183 through 203 Processing helix chain 'A' and resid 222 through 243 Processing helix chain 'B' and resid 3 through 26 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 7 through 24 removed outlier: 3.613A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'N' and resid 28 through 32 Processing helix chain 'N' and resid 53 through 56 removed outlier: 3.757A pdb=" N GLY N 56 " --> pdb=" O SER N 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 53 through 56' Processing helix chain 'N' and resid 87 through 91 removed outlier: 4.037A pdb=" N THR N 91 " --> pdb=" O SER N 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 4 through 38 Proline residue: R 23 - end of helix removed outlier: 3.607A pdb=" N GLN R 38 " --> pdb=" O GLY R 34 " (cutoff:3.500A) Processing helix chain 'R' and resid 42 through 61 removed outlier: 3.526A pdb=" N LEU R 61 " --> pdb=" O LEU R 57 " (cutoff:3.500A) Processing helix chain 'R' and resid 61 through 72 removed outlier: 3.523A pdb=" N LYS R 65 " --> pdb=" O LEU R 61 " (cutoff:3.500A) Processing helix chain 'R' and resid 78 through 113 removed outlier: 3.718A pdb=" N TYR R 90 " --> pdb=" O SER R 86 " (cutoff:3.500A) Processing helix chain 'R' and resid 113 through 121 Processing helix chain 'R' and resid 122 through 149 removed outlier: 3.908A pdb=" N GLY R 126 " --> pdb=" O ARG R 122 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE R 143 " --> pdb=" O GLY R 139 " (cutoff:3.500A) Processing helix chain 'R' and resid 172 through 187 removed outlier: 3.692A pdb=" N VAL R 176 " --> pdb=" O GLN R 172 " (cutoff:3.500A) Proline residue: R 178 - end of helix removed outlier: 3.533A pdb=" N CYS R 184 " --> pdb=" O ARG R 180 " (cutoff:3.500A) Processing helix chain 'R' and resid 188 through 209 Processing helix chain 'R' and resid 216 through 249 removed outlier: 3.596A pdb=" N VAL R 221 " --> pdb=" O ARG R 217 " (cutoff:3.500A) Proline residue: R 237 - end of helix removed outlier: 3.524A pdb=" N SER R 241 " --> pdb=" O PRO R 237 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N HIS R 242 " --> pdb=" O TYR R 238 " (cutoff:3.500A) Processing helix chain 'R' and resid 254 through 274 removed outlier: 3.869A pdb=" N VAL R 260 " --> pdb=" O SER R 256 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N PHE R 261 " --> pdb=" O ILE R 257 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ASN R 265 " --> pdb=" O PHE R 261 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N ALA R 266 " --> pdb=" O SER R 262 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N SER R 267 " --> pdb=" O SER R 263 " (cutoff:3.500A) Proline residue: R 270 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 33 through 36 Processing sheet with id=AA2, first strand: chain 'A' and resid 38 through 40 removed outlier: 6.386A pdb=" N LEU A 39 " --> pdb=" O VAL A 109 " (cutoff:3.500A) removed outlier: 8.150A pdb=" N ASP A 111 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ILE A 106 " --> pdb=" O ILE A 140 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N PHE A 142 " --> pdb=" O ILE A 106 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N PHE A 108 " --> pdb=" O PHE A 142 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ASN A 144 " --> pdb=" O PHE A 108 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N VAL A 110 " --> pdb=" O ASN A 144 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 45 through 50 removed outlier: 6.256A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.713A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.814A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.665A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.932A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.465A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N SER B 245 " --> pdb=" O THR B 249 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.410A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'N' and resid 11 through 12 removed outlier: 6.741A pdb=" N MET N 34 " --> pdb=" O TYR N 50 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N TYR N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'N' and resid 11 through 12 removed outlier: 4.378A pdb=" N PHE N 110 " --> pdb=" O ARG N 98 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'N' and resid 141 through 142 Processing sheet with id=AB5, first strand: chain 'N' and resid 147 through 149 removed outlier: 3.567A pdb=" N GLU N 247 " --> pdb=" O VAL N 148 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N LEU N 175 " --> pdb=" O TYR N 191 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N TYR N 191 " --> pdb=" O LEU N 175 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N TRP N 177 " --> pdb=" O LEU N 189 " (cutoff:3.500A) 434 hydrogen bonds defined for protein. 1218 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: 2.61 Time building geometry restraints manager: 4.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1425 1.32 - 1.44: 2464 1.44 - 1.57: 4991 1.57 - 1.69: 0 1.69 - 1.81: 76 Bond restraints: 8956 Sorted by residual: bond pdb=" CA SER B 74 " pdb=" CB SER B 74 " ideal model delta sigma weight residual 1.535 1.456 0.079 1.71e-02 3.42e+03 2.15e+01 bond pdb=" N GLN R 40 " pdb=" CA GLN R 40 " ideal model delta sigma weight residual 1.458 1.488 -0.030 7.40e-03 1.83e+04 1.66e+01 bond pdb=" CA SER B 72 " pdb=" CB SER B 72 " ideal model delta sigma weight residual 1.534 1.445 0.090 2.47e-02 1.64e+03 1.32e+01 bond pdb=" CA SER A 44 " pdb=" CB SER A 44 " ideal model delta sigma weight residual 1.528 1.475 0.053 1.59e-02 3.96e+03 1.11e+01 bond pdb=" CA SER R 92 " pdb=" CB SER R 92 " ideal model delta sigma weight residual 1.529 1.477 0.052 1.55e-02 4.16e+03 1.10e+01 ... (remaining 8951 not shown) Histogram of bond angle deviations from ideal: 98.74 - 105.83: 174 105.83 - 112.92: 4814 112.92 - 120.01: 3146 120.01 - 127.09: 3918 127.09 - 134.18: 96 Bond angle restraints: 12148 Sorted by residual: angle pdb=" N ASP B 76 " pdb=" CA ASP B 76 " pdb=" C ASP B 76 " ideal model delta sigma weight residual 112.89 104.61 8.28 1.24e+00 6.50e-01 4.46e+01 angle pdb=" N ASP B 312 " pdb=" CA ASP B 312 " pdb=" CB ASP B 312 " ideal model delta sigma weight residual 114.17 107.50 6.67 1.14e+00 7.69e-01 3.42e+01 angle pdb=" N GLN B 75 " pdb=" CA GLN B 75 " pdb=" C GLN B 75 " ideal model delta sigma weight residual 113.21 106.62 6.59 1.15e+00 7.56e-01 3.28e+01 angle pdb=" N GLY B 77 " pdb=" CA GLY B 77 " pdb=" C GLY B 77 " ideal model delta sigma weight residual 115.72 108.97 6.75 1.51e+00 4.39e-01 2.00e+01 angle pdb=" N ALA R 13 " pdb=" CA ALA R 13 " pdb=" C ALA R 13 " ideal model delta sigma weight residual 111.07 106.29 4.78 1.07e+00 8.73e-01 1.99e+01 ... (remaining 12143 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 4701 17.98 - 35.95: 528 35.95 - 53.93: 117 53.93 - 71.90: 13 71.90 - 89.88: 3 Dihedral angle restraints: 5362 sinusoidal: 2120 harmonic: 3242 Sorted by residual: dihedral pdb=" C PRO R 252 " pdb=" N PRO R 252 " pdb=" CA PRO R 252 " pdb=" CB PRO R 252 " ideal model delta harmonic sigma weight residual -120.70 -110.61 -10.09 0 2.50e+00 1.60e-01 1.63e+01 dihedral pdb=" CA HIS B 311 " pdb=" C HIS B 311 " pdb=" N ASP B 312 " pdb=" CA ASP B 312 " ideal model delta harmonic sigma weight residual 180.00 163.62 16.38 0 5.00e+00 4.00e-02 1.07e+01 dihedral pdb=" N LEU B 79 " pdb=" C LEU B 79 " pdb=" CA LEU B 79 " pdb=" CB LEU B 79 " ideal model delta harmonic sigma weight residual 122.80 114.64 8.16 0 2.50e+00 1.60e-01 1.07e+01 ... (remaining 5359 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 1183 0.067 - 0.135: 168 0.135 - 0.202: 22 0.202 - 0.270: 4 0.270 - 0.337: 1 Chirality restraints: 1378 Sorted by residual: chirality pdb=" CA LEU B 79 " pdb=" N LEU B 79 " pdb=" C LEU B 79 " pdb=" CB LEU B 79 " both_signs ideal model delta sigma weight residual False 2.51 2.85 -0.34 2.00e-01 2.50e+01 2.85e+00 chirality pdb=" CA VAL B 71 " pdb=" N VAL B 71 " pdb=" C VAL B 71 " pdb=" CB VAL B 71 " both_signs ideal model delta sigma weight residual False 2.44 2.70 -0.26 2.00e-01 2.50e+01 1.64e+00 chirality pdb=" CA LEU R 9 " pdb=" N LEU R 9 " pdb=" C LEU R 9 " pdb=" CB LEU R 9 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.55e+00 ... (remaining 1375 not shown) Planarity restraints: 1536 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER R 86 " -0.017 2.00e-02 2.50e+03 3.39e-02 1.15e+01 pdb=" C SER R 86 " 0.059 2.00e-02 2.50e+03 pdb=" O SER R 86 " -0.022 2.00e-02 2.50e+03 pdb=" N PHE R 87 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU R 62 " 0.043 5.00e-02 4.00e+02 6.50e-02 6.77e+00 pdb=" N PRO R 63 " -0.113 5.00e-02 4.00e+02 pdb=" CA PRO R 63 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO R 63 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA R 13 " -0.012 2.00e-02 2.50e+03 2.54e-02 6.46e+00 pdb=" C ALA R 13 " 0.044 2.00e-02 2.50e+03 pdb=" O ALA R 13 " -0.016 2.00e-02 2.50e+03 pdb=" N TYR R 14 " -0.015 2.00e-02 2.50e+03 ... (remaining 1533 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 516 2.73 - 3.27: 8733 3.27 - 3.81: 14843 3.81 - 4.36: 17894 4.36 - 4.90: 31450 Nonbonded interactions: 73436 Sorted by model distance: nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.185 2.440 nonbonded pdb=" O ALA R 133 " pdb=" OG SER R 137 " model vdw 2.196 2.440 nonbonded pdb=" O TYR R 238 " pdb=" OG SER R 241 " model vdw 2.227 2.440 nonbonded pdb=" O SER B 67 " pdb=" OG SER B 67 " model vdw 2.242 2.440 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.253 2.440 ... (remaining 73431 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 1.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.380 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 27.440 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 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 : 0.005 0.090 8956 Z= 0.322 Angle : 0.748 8.283 12148 Z= 0.498 Chirality : 0.051 0.337 1378 Planarity : 0.005 0.065 1536 Dihedral : 15.215 89.881 3261 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 0.53 % Allowed : 21.66 % Favored : 77.80 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 2.56 % 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: 0.78 (0.26), residues: 1099 helix: 1.51 (0.26), residues: 381 sheet: 0.16 (0.32), residues: 272 loop : 0.01 (0.30), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP R 254 HIS 0.004 0.001 HIS A 214 PHE 0.028 0.002 PHE N 240 TYR 0.043 0.002 TYR R 14 ARG 0.016 0.001 ARG R 217 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 136 time to evaluate : 0.976 Fit side-chains outliers start: 5 outliers final: 1 residues processed: 139 average time/residue: 0.2350 time to fit residues: 44.0476 Evaluate side-chains 131 residues out of total 956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 130 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 268 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 4.9990 chunk 83 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 56 optimal weight: 0.6980 chunk 44 optimal weight: 1.9990 chunk 86 optimal weight: 3.9990 chunk 33 optimal weight: 0.0050 chunk 52 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 99 optimal weight: 6.9990 overall best weight: 0.9398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 25 ASN R 148 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.0907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8956 Z= 0.204 Angle : 0.509 8.076 12148 Z= 0.271 Chirality : 0.041 0.145 1378 Planarity : 0.004 0.066 1536 Dihedral : 4.594 59.668 1314 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.56 % Allowed : 20.06 % Favored : 77.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 1.20 (0.26), residues: 1099 helix: 1.94 (0.26), residues: 373 sheet: 0.27 (0.32), residues: 270 loop : 0.30 (0.30), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 169 HIS 0.003 0.001 HIS G 44 PHE 0.024 0.001 PHE R 18 TYR 0.019 0.001 TYR R 14 ARG 0.003 0.000 ARG A 132 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 138 time to evaluate : 0.911 Fit side-chains REVERT: B 59 TYR cc_start: 0.8081 (m-80) cc_final: 0.7503 (m-80) REVERT: N 87 ARG cc_start: 0.7409 (ptp-170) cc_final: 0.7110 (ptp-170) outliers start: 24 outliers final: 17 residues processed: 151 average time/residue: 0.2288 time to fit residues: 47.8733 Evaluate side-chains 146 residues out of total 956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 129 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain N residue 63 THR Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 193 MET Chi-restraints excluded: chain N residue 198 SER Chi-restraints excluded: chain R residue 257 ILE Chi-restraints excluded: chain R residue 260 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 55 optimal weight: 0.9980 chunk 31 optimal weight: 0.9990 chunk 83 optimal weight: 1.9990 chunk 68 optimal weight: 0.5980 chunk 27 optimal weight: 3.9990 chunk 100 optimal weight: 20.0000 chunk 108 optimal weight: 0.0470 chunk 89 optimal weight: 0.0050 chunk 99 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 80 optimal weight: 6.9990 overall best weight: 0.5294 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 230 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 25 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.1350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 8956 Z= 0.148 Angle : 0.471 9.083 12148 Z= 0.244 Chirality : 0.040 0.161 1378 Planarity : 0.003 0.058 1536 Dihedral : 4.103 38.753 1312 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 2.77 % Allowed : 20.81 % Favored : 76.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.26), residues: 1099 helix: 2.21 (0.26), residues: 373 sheet: 0.24 (0.31), residues: 271 loop : 0.36 (0.31), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 169 HIS 0.002 0.001 HIS B 311 PHE 0.018 0.001 PHE R 18 TYR 0.017 0.001 TYR R 165 ARG 0.003 0.000 ARG A 194 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 141 time to evaluate : 0.960 Fit side-chains REVERT: B 59 TYR cc_start: 0.8139 (m-80) cc_final: 0.7534 (m-80) REVERT: B 338 ILE cc_start: 0.8799 (OUTLIER) cc_final: 0.8513 (mm) REVERT: N 87 ARG cc_start: 0.7338 (ptp-170) cc_final: 0.7091 (ptp-170) REVERT: R 106 GLU cc_start: 0.7855 (OUTLIER) cc_final: 0.7222 (tm-30) outliers start: 26 outliers final: 13 residues processed: 155 average time/residue: 0.2121 time to fit residues: 45.2508 Evaluate side-chains 149 residues out of total 956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 134 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 193 MET Chi-restraints excluded: chain R residue 106 GLU Chi-restraints excluded: chain R residue 137 SER Chi-restraints excluded: chain R residue 257 ILE Chi-restraints excluded: chain R residue 260 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 0.6980 chunk 75 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 67 optimal weight: 0.0870 chunk 100 optimal weight: 0.9980 chunk 106 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 28 optimal weight: 5.9990 overall best weight: 1.1562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 156 GLN ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 25 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.1631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8956 Z= 0.228 Angle : 0.501 8.189 12148 Z= 0.259 Chirality : 0.042 0.169 1378 Planarity : 0.003 0.053 1536 Dihedral : 4.214 32.548 1312 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 3.20 % Allowed : 20.60 % Favored : 76.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 1.41 (0.26), residues: 1099 helix: 2.23 (0.26), residues: 380 sheet: 0.29 (0.31), residues: 274 loop : 0.33 (0.31), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 169 HIS 0.006 0.001 HIS B 311 PHE 0.023 0.001 PHE R 18 TYR 0.016 0.001 TYR R 165 ARG 0.003 0.000 ARG A 194 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 134 time to evaluate : 1.041 Fit side-chains REVERT: A 122 LEU cc_start: 0.8675 (OUTLIER) cc_final: 0.8396 (mp) REVERT: B 59 TYR cc_start: 0.8316 (m-80) cc_final: 0.7723 (m-80) REVERT: N 87 ARG cc_start: 0.7409 (ptp-170) cc_final: 0.7207 (ptp-170) REVERT: N 161 ARG cc_start: 0.7641 (ttp-110) cc_final: 0.7339 (mtp85) outliers start: 30 outliers final: 20 residues processed: 150 average time/residue: 0.2150 time to fit residues: 44.4932 Evaluate side-chains 151 residues out of total 956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 130 time to evaluate : 1.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 193 MET Chi-restraints excluded: chain N residue 198 SER Chi-restraints excluded: chain R residue 137 SER Chi-restraints excluded: chain R residue 257 ILE Chi-restraints excluded: chain R residue 260 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 0.0000 chunk 60 optimal weight: 4.9990 chunk 1 optimal weight: 0.9990 chunk 79 optimal weight: 4.9990 chunk 43 optimal weight: 0.4980 chunk 90 optimal weight: 0.9990 chunk 73 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 54 optimal weight: 0.9990 chunk 95 optimal weight: 2.9990 chunk 26 optimal weight: 0.0870 overall best weight: 0.5166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.1753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 8956 Z= 0.143 Angle : 0.467 8.419 12148 Z= 0.240 Chirality : 0.040 0.182 1378 Planarity : 0.003 0.050 1536 Dihedral : 4.007 31.272 1312 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 3.09 % Allowed : 21.45 % Favored : 75.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 1.55 (0.26), residues: 1099 helix: 2.47 (0.26), residues: 374 sheet: 0.32 (0.30), residues: 284 loop : 0.37 (0.31), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 169 HIS 0.003 0.001 HIS B 311 PHE 0.020 0.001 PHE R 18 TYR 0.015 0.001 TYR R 165 ARG 0.004 0.000 ARG A 194 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 134 time to evaluate : 0.912 Fit side-chains REVERT: A 122 LEU cc_start: 0.8666 (OUTLIER) cc_final: 0.8373 (mp) REVERT: A 132 ARG cc_start: 0.8201 (mtm180) cc_final: 0.7852 (ptt180) REVERT: B 59 TYR cc_start: 0.8256 (m-80) cc_final: 0.7640 (m-80) REVERT: R 45 HIS cc_start: 0.7482 (m90) cc_final: 0.6841 (m90) REVERT: R 106 GLU cc_start: 0.7832 (OUTLIER) cc_final: 0.7304 (tm-30) outliers start: 29 outliers final: 17 residues processed: 150 average time/residue: 0.2132 time to fit residues: 44.0157 Evaluate side-chains 152 residues out of total 956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 133 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 193 MET Chi-restraints excluded: chain R residue 106 GLU Chi-restraints excluded: chain R residue 137 SER Chi-restraints excluded: chain R residue 257 ILE Chi-restraints excluded: chain R residue 260 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 2.9990 chunk 95 optimal weight: 0.6980 chunk 21 optimal weight: 0.8980 chunk 62 optimal weight: 7.9990 chunk 26 optimal weight: 4.9990 chunk 106 optimal weight: 2.9990 chunk 88 optimal weight: 0.0980 chunk 49 optimal weight: 4.9990 chunk 8 optimal weight: 0.0040 chunk 55 optimal weight: 3.9990 chunk 102 optimal weight: 0.7980 overall best weight: 0.4992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.1865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 8956 Z= 0.142 Angle : 0.464 9.154 12148 Z= 0.240 Chirality : 0.040 0.190 1378 Planarity : 0.003 0.050 1536 Dihedral : 3.924 30.335 1312 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 3.20 % Allowed : 21.24 % Favored : 75.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 1.63 (0.26), residues: 1099 helix: 2.59 (0.26), residues: 374 sheet: 0.31 (0.30), residues: 284 loop : 0.40 (0.31), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 169 HIS 0.002 0.001 HIS B 311 PHE 0.023 0.001 PHE R 18 TYR 0.014 0.001 TYR R 165 ARG 0.004 0.000 ARG A 194 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 145 time to evaluate : 1.031 Fit side-chains REVERT: A 122 LEU cc_start: 0.8686 (OUTLIER) cc_final: 0.8392 (mp) REVERT: A 132 ARG cc_start: 0.8180 (mtm180) cc_final: 0.7815 (ptt180) REVERT: A 199 ASP cc_start: 0.7900 (m-30) cc_final: 0.7426 (m-30) REVERT: B 59 TYR cc_start: 0.8269 (m-80) cc_final: 0.7728 (m-80) REVERT: B 338 ILE cc_start: 0.8825 (OUTLIER) cc_final: 0.8539 (mm) REVERT: N 161 ARG cc_start: 0.7576 (ttp-110) cc_final: 0.7295 (mtp85) REVERT: R 45 HIS cc_start: 0.7448 (m90) cc_final: 0.6801 (m90) REVERT: R 106 GLU cc_start: 0.7821 (OUTLIER) cc_final: 0.7287 (tm-30) outliers start: 30 outliers final: 20 residues processed: 161 average time/residue: 0.2134 time to fit residues: 47.1459 Evaluate side-chains 163 residues out of total 956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 140 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 193 MET Chi-restraints excluded: chain N residue 198 SER Chi-restraints excluded: chain R residue 106 GLU Chi-restraints excluded: chain R residue 137 SER Chi-restraints excluded: chain R residue 257 ILE Chi-restraints excluded: chain R residue 260 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 3.9990 chunk 60 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 chunk 89 optimal weight: 0.6980 chunk 59 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 64 optimal weight: 4.9990 chunk 48 optimal weight: 0.7980 chunk 65 optimal weight: 0.7980 chunk 42 optimal weight: 0.3980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.1964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8956 Z= 0.167 Angle : 0.471 8.298 12148 Z= 0.243 Chirality : 0.040 0.166 1378 Planarity : 0.003 0.049 1536 Dihedral : 3.970 29.526 1312 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 4.16 % Allowed : 20.60 % Favored : 75.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 1.65 (0.26), residues: 1099 helix: 2.66 (0.26), residues: 374 sheet: 0.31 (0.30), residues: 279 loop : 0.36 (0.31), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 169 HIS 0.003 0.001 HIS B 311 PHE 0.022 0.001 PHE R 18 TYR 0.014 0.001 TYR R 165 ARG 0.003 0.000 ARG A 194 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 145 time to evaluate : 0.909 Fit side-chains REVERT: A 122 LEU cc_start: 0.8701 (OUTLIER) cc_final: 0.8397 (mp) REVERT: A 132 ARG cc_start: 0.8163 (mtm180) cc_final: 0.7806 (ptt180) REVERT: A 199 ASP cc_start: 0.7892 (m-30) cc_final: 0.7396 (m-30) REVERT: B 59 TYR cc_start: 0.8309 (m-80) cc_final: 0.7759 (m-80) REVERT: B 338 ILE cc_start: 0.8859 (OUTLIER) cc_final: 0.8550 (mm) REVERT: N 161 ARG cc_start: 0.7556 (ttp-110) cc_final: 0.7303 (mtp85) REVERT: R 45 HIS cc_start: 0.7451 (m90) cc_final: 0.6807 (m90) REVERT: R 106 GLU cc_start: 0.7829 (OUTLIER) cc_final: 0.7296 (tm-30) REVERT: R 187 LEU cc_start: 0.8297 (OUTLIER) cc_final: 0.7767 (mp) outliers start: 39 outliers final: 30 residues processed: 166 average time/residue: 0.2002 time to fit residues: 45.7069 Evaluate side-chains 175 residues out of total 956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 141 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain N residue 63 THR Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 193 MET Chi-restraints excluded: chain N residue 198 SER Chi-restraints excluded: chain R residue 106 GLU Chi-restraints excluded: chain R residue 137 SER Chi-restraints excluded: chain R residue 187 LEU Chi-restraints excluded: chain R residue 230 ASN Chi-restraints excluded: chain R residue 257 ILE Chi-restraints excluded: chain R residue 260 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 0.1980 chunk 31 optimal weight: 0.9990 chunk 20 optimal weight: 7.9990 chunk 67 optimal weight: 0.6980 chunk 72 optimal weight: 0.6980 chunk 52 optimal weight: 0.9990 chunk 9 optimal weight: 5.9990 chunk 83 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 101 optimal weight: 0.7980 chunk 92 optimal weight: 6.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 GLN ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.2039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 8956 Z= 0.159 Angle : 0.472 9.123 12148 Z= 0.242 Chirality : 0.040 0.195 1378 Planarity : 0.003 0.049 1536 Dihedral : 3.950 28.637 1312 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 3.95 % Allowed : 21.02 % Favored : 75.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 1.63 (0.26), residues: 1099 helix: 2.61 (0.26), residues: 381 sheet: 0.28 (0.30), residues: 279 loop : 0.37 (0.32), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 169 HIS 0.002 0.001 HIS B 311 PHE 0.022 0.001 PHE R 18 TYR 0.014 0.001 TYR R 165 ARG 0.004 0.000 ARG A 194 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 135 time to evaluate : 0.962 Fit side-chains REVERT: A 122 LEU cc_start: 0.8685 (OUTLIER) cc_final: 0.8377 (mp) REVERT: A 132 ARG cc_start: 0.8167 (mtm180) cc_final: 0.7868 (ptt180) REVERT: B 59 TYR cc_start: 0.8318 (m-80) cc_final: 0.7773 (m-80) REVERT: B 338 ILE cc_start: 0.8855 (OUTLIER) cc_final: 0.8546 (mm) REVERT: N 161 ARG cc_start: 0.7545 (ttp-110) cc_final: 0.7271 (mtp85) REVERT: R 12 MET cc_start: 0.7151 (ptm) cc_final: 0.6911 (ptm) REVERT: R 45 HIS cc_start: 0.7456 (m90) cc_final: 0.6816 (m90) REVERT: R 106 GLU cc_start: 0.7817 (OUTLIER) cc_final: 0.7295 (tm-30) REVERT: R 187 LEU cc_start: 0.8303 (OUTLIER) cc_final: 0.7772 (mp) outliers start: 37 outliers final: 29 residues processed: 157 average time/residue: 0.2106 time to fit residues: 45.5459 Evaluate side-chains 166 residues out of total 956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 133 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 193 MET Chi-restraints excluded: chain N residue 198 SER Chi-restraints excluded: chain R residue 106 GLU Chi-restraints excluded: chain R residue 137 SER Chi-restraints excluded: chain R residue 187 LEU Chi-restraints excluded: chain R residue 223 LEU Chi-restraints excluded: chain R residue 230 ASN Chi-restraints excluded: chain R residue 257 ILE Chi-restraints excluded: chain R residue 260 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 2.9990 chunk 101 optimal weight: 0.9980 chunk 59 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 chunk 77 optimal weight: 0.7980 chunk 30 optimal weight: 2.9990 chunk 89 optimal weight: 0.9990 chunk 93 optimal weight: 0.8980 chunk 64 optimal weight: 3.9990 chunk 104 optimal weight: 2.9990 chunk 63 optimal weight: 6.9990 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 32 GLN ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.2138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8956 Z= 0.190 Angle : 0.485 9.616 12148 Z= 0.250 Chirality : 0.041 0.188 1378 Planarity : 0.003 0.048 1536 Dihedral : 4.085 27.582 1312 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 3.84 % Allowed : 21.45 % Favored : 74.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 1.62 (0.26), residues: 1099 helix: 2.62 (0.26), residues: 381 sheet: 0.29 (0.30), residues: 277 loop : 0.33 (0.31), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 169 HIS 0.002 0.001 HIS B 91 PHE 0.028 0.001 PHE R 18 TYR 0.013 0.001 TYR R 165 ARG 0.004 0.000 ARG A 194 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 134 time to evaluate : 1.016 Fit side-chains REVERT: A 122 LEU cc_start: 0.8681 (OUTLIER) cc_final: 0.8376 (mp) REVERT: A 132 ARG cc_start: 0.8174 (mtm180) cc_final: 0.7897 (ptt180) REVERT: A 199 ASP cc_start: 0.7895 (m-30) cc_final: 0.7437 (m-30) REVERT: B 59 TYR cc_start: 0.8383 (m-80) cc_final: 0.7847 (m-80) REVERT: B 338 ILE cc_start: 0.8907 (OUTLIER) cc_final: 0.8582 (mm) REVERT: N 161 ARG cc_start: 0.7588 (ttp-110) cc_final: 0.7312 (mtp85) REVERT: R 45 HIS cc_start: 0.7469 (m90) cc_final: 0.6871 (m90) REVERT: R 106 GLU cc_start: 0.7836 (OUTLIER) cc_final: 0.7240 (tm-30) REVERT: R 187 LEU cc_start: 0.8281 (OUTLIER) cc_final: 0.7731 (mp) outliers start: 36 outliers final: 28 residues processed: 158 average time/residue: 0.2210 time to fit residues: 47.9233 Evaluate side-chains 163 residues out of total 956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 131 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 193 MET Chi-restraints excluded: chain N residue 198 SER Chi-restraints excluded: chain R residue 106 GLU Chi-restraints excluded: chain R residue 137 SER Chi-restraints excluded: chain R residue 187 LEU Chi-restraints excluded: chain R residue 223 LEU Chi-restraints excluded: chain R residue 230 ASN Chi-restraints excluded: chain R residue 257 ILE Chi-restraints excluded: chain R residue 260 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 49 optimal weight: 4.9990 chunk 72 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 chunk 100 optimal weight: 0.1980 chunk 87 optimal weight: 0.0570 chunk 9 optimal weight: 4.9990 chunk 67 optimal weight: 0.8980 chunk 53 optimal weight: 3.9990 chunk 69 optimal weight: 0.6980 chunk 92 optimal weight: 5.9990 chunk 26 optimal weight: 8.9990 overall best weight: 0.7700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 GLN ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.2202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8956 Z= 0.173 Angle : 0.482 9.073 12148 Z= 0.250 Chirality : 0.040 0.184 1378 Planarity : 0.003 0.048 1536 Dihedral : 4.025 26.803 1312 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 3.31 % Allowed : 22.31 % Favored : 74.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 1.62 (0.26), residues: 1099 helix: 2.63 (0.26), residues: 381 sheet: 0.28 (0.30), residues: 277 loop : 0.33 (0.31), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 169 HIS 0.002 0.001 HIS B 91 PHE 0.027 0.001 PHE R 18 TYR 0.013 0.001 TYR R 165 ARG 0.004 0.000 ARG A 194 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 132 time to evaluate : 1.026 Fit side-chains REVERT: A 122 LEU cc_start: 0.8685 (OUTLIER) cc_final: 0.8404 (mp) REVERT: A 132 ARG cc_start: 0.8164 (mtm180) cc_final: 0.7896 (ptt180) REVERT: B 59 TYR cc_start: 0.8396 (m-80) cc_final: 0.7866 (m-80) REVERT: B 338 ILE cc_start: 0.8887 (OUTLIER) cc_final: 0.8574 (mm) REVERT: N 161 ARG cc_start: 0.7570 (ttp-110) cc_final: 0.7290 (mtp85) REVERT: R 45 HIS cc_start: 0.7434 (m90) cc_final: 0.6821 (m90) REVERT: R 106 GLU cc_start: 0.7815 (OUTLIER) cc_final: 0.7261 (tm-30) REVERT: R 187 LEU cc_start: 0.8286 (OUTLIER) cc_final: 0.7765 (mp) outliers start: 31 outliers final: 27 residues processed: 152 average time/residue: 0.2144 time to fit residues: 44.6740 Evaluate side-chains 162 residues out of total 956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 131 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 193 MET Chi-restraints excluded: chain N residue 198 SER Chi-restraints excluded: chain R residue 106 GLU Chi-restraints excluded: chain R residue 137 SER Chi-restraints excluded: chain R residue 187 LEU Chi-restraints excluded: chain R residue 223 LEU Chi-restraints excluded: chain R residue 230 ASN Chi-restraints excluded: chain R residue 257 ILE Chi-restraints excluded: chain R residue 260 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 80 optimal weight: 3.9990 chunk 12 optimal weight: 4.9990 chunk 24 optimal weight: 6.9990 chunk 87 optimal weight: 0.0870 chunk 36 optimal weight: 2.9990 chunk 89 optimal weight: 0.8980 chunk 11 optimal weight: 0.3980 chunk 16 optimal weight: 3.9990 chunk 76 optimal weight: 9.9990 chunk 4 optimal weight: 4.9990 chunk 63 optimal weight: 6.9990 overall best weight: 1.6762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 131 ASN B 239 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.159367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.112121 restraints weight = 9704.057| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 2.26 r_work: 0.3031 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2883 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.2311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 8956 Z= 0.289 Angle : 0.531 9.978 12148 Z= 0.275 Chirality : 0.042 0.175 1378 Planarity : 0.004 0.048 1536 Dihedral : 4.443 33.524 1312 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 3.63 % Allowed : 21.99 % Favored : 74.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 1.45 (0.26), residues: 1099 helix: 2.50 (0.26), residues: 381 sheet: 0.08 (0.31), residues: 270 loop : 0.29 (0.31), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 133 HIS 0.004 0.001 HIS R 45 PHE 0.027 0.002 PHE R 18 TYR 0.013 0.001 TYR R 165 ARG 0.004 0.000 ARG A 194 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2256.22 seconds wall clock time: 40 minutes 52.44 seconds (2452.44 seconds total)