Starting phenix.real_space_refine on Sat Dec 28 15:44:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hqe_34948/12_2024/8hqe_34948.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hqe_34948/12_2024/8hqe_34948.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8hqe_34948/12_2024/8hqe_34948.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hqe_34948/12_2024/8hqe_34948.map" model { file = "/net/cci-nas-00/data/ceres_data/8hqe_34948/12_2024/8hqe_34948.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hqe_34948/12_2024/8hqe_34948.cif" } resolution = 2.97 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= 0.001 sd= 0.040 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 63 5.16 5 C 5649 2.51 5 N 1517 2.21 5 O 1674 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 8903 Number of models: 1 Model: "" Number of chains: 5 Chain: "B" Number of atoms: 2588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2588 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "C" Number of atoms: 414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 414 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 50} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "H" Number of atoms: 1774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1774 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 10, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "R" Number of atoms: 2440 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2440 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 6, 'TRANS': 300} Chain breaks: 1 Chain: "A" Number of atoms: 1687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1687 Classifications: {'peptide': 214} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 1, 'TRANS': 212} Chain breaks: 3 Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'HIS:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 Time building chain proxies: 5.23, per 1000 atoms: 0.59 Number of scatterers: 8903 At special positions: 0 Unit cell: (106.08, 121.68, 132.08, 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 63 16.00 O 1674 8.00 N 1517 7.00 C 5649 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 147 " - pdb=" SG CYS H 217 " distance=1.78 Simple disulfide: pdb=" SG CYS R 115 " - pdb=" SG CYS R 186 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.41 Conformation dependent library (CDL) restraints added in 1.1 seconds 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2148 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 12 sheets defined 38.4% alpha, 19.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.04 Creating SS restraints... Processing helix chain 'B' and resid 2 through 26 removed outlier: 3.688A pdb=" N LEU B 7 " --> pdb=" O GLU B 3 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLN B 9 " --> pdb=" O ASP B 5 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N GLU B 10 " --> pdb=" O GLN B 6 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ALA B 21 " --> pdb=" O GLN B 17 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.858A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 22 removed outlier: 4.349A pdb=" N LYS C 14 " --> pdb=" O ALA C 10 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL C 16 " --> pdb=" O ALA C 12 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLN C 18 " --> pdb=" O LYS C 14 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU C 19 " --> pdb=" O LEU C 15 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 45 removed outlier: 3.827A pdb=" N CYS C 41 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLU C 42 " --> pdb=" O MET C 38 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ALA C 43 " --> pdb=" O ALA C 39 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N HIS C 44 " --> pdb=" O TYR C 40 " (cutoff:3.500A) Processing helix chain 'R' and resid 38 through 71 Proline residue: R 58 - end of helix Processing helix chain 'R' and resid 75 through 92 removed outlier: 4.008A pdb=" N VAL R 79 " --> pdb=" O ASN R 75 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N TYR R 80 " --> pdb=" O VAL R 76 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N TYR R 91 " --> pdb=" O CYS R 87 " (cutoff:3.500A) Processing helix chain 'R' and resid 93 through 102 removed outlier: 4.066A pdb=" N LEU R 97 " --> pdb=" O GLY R 93 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N TRP R 98 " --> pdb=" O THR R 94 " (cutoff:3.500A) Processing helix chain 'R' and resid 112 through 145 Processing helix chain 'R' and resid 148 through 152 removed outlier: 3.843A pdb=" N ARG R 151 " --> pdb=" O LEU R 148 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLY R 152 " --> pdb=" O GLU R 149 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 148 through 152' Processing helix chain 'R' and resid 155 through 180 removed outlier: 4.185A pdb=" N ALA R 159 " --> pdb=" O ARG R 155 " (cutoff:3.500A) Proline residue: R 176 - end of helix Processing helix chain 'R' and resid 194 through 208 Processing helix chain 'R' and resid 208 through 228 removed outlier: 3.680A pdb=" N LEU R 212 " --> pdb=" O PHE R 208 " (cutoff:3.500A) Processing helix chain 'R' and resid 233 through 272 Proline residue: R 257 - end of helix Processing helix chain 'R' and resid 279 through 312 Proline residue: R 305 - end of helix removed outlier: 3.935A pdb=" N THR R 312 " --> pdb=" O TYR R 308 " (cutoff:3.500A) Processing helix chain 'R' and resid 312 through 331 Processing helix chain 'R' and resid 334 through 346 Processing helix chain 'A' and resid 6 through 31 Processing helix chain 'A' and resid 45 through 53 Processing helix chain 'A' and resid 208 through 213 removed outlier: 4.625A pdb=" N HIS A 213 " --> pdb=" O LYS A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 216 No H-bonds generated for 'chain 'A' and resid 214 through 216' Processing helix chain 'A' and resid 241 through 255 removed outlier: 3.510A pdb=" N LYS A 248 " --> pdb=" O HIS A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 278 Processing helix chain 'A' and resid 295 through 309 Processing helix chain 'A' and resid 312 through 317 removed outlier: 4.387A pdb=" N THR A 316 " --> pdb=" O LYS A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 351 removed outlier: 3.563A pdb=" N VAL A 335 " --> pdb=" O ASN A 331 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LYS A 345 " --> pdb=" O ASP A 341 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 47 through 50 removed outlier: 3.723A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL B 327 " --> pdb=" O TRP B 339 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.807A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 103 through 105 removed outlier: 4.006A pdb=" N ILE B 123 " --> pdb=" O ARG B 137 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.588A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.960A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA B 203 " --> pdb=" O SER B 207 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 229 through 234 removed outlier: 4.148A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.651A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.908A pdb=" N SER H 21 " --> pdb=" O SER H 7 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N THR H 78 " --> pdb=" O ASP H 73 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASP H 73 " --> pdb=" O THR H 78 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.626A pdb=" N TYR H 94 " --> pdb=" O THR H 115 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N MET H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N TYR H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 128 through 130 removed outlier: 3.609A pdb=" N PHE H 200 " --> pdb=" O CYS H 147 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 182 through 183 removed outlier: 6.826A pdb=" N TRP H 164 " --> pdb=" O LEU H 176 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N TYR H 178 " --> pdb=" O LEU H 162 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N LEU H 162 " --> pdb=" O TYR H 178 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N TYR H 163 " --> pdb=" O MET H 218 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 185 through 191 removed outlier: 5.845A pdb=" N VAL A 34 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N PHE A 199 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N LEU A 36 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) 434 hydrogen bonds defined for protein. 1254 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: 2.72 Time building geometry restraints manager: 2.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 2434 1.33 - 1.45: 1728 1.45 - 1.57: 4831 1.57 - 1.69: 0 1.69 - 1.81: 86 Bond restraints: 9079 Sorted by residual: bond pdb=" N LEU C 19 " pdb=" CA LEU C 19 " ideal model delta sigma weight residual 1.459 1.490 -0.030 1.23e-02 6.61e+03 6.14e+00 bond pdb=" N LEU A 310 " pdb=" CA LEU A 310 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.20e-02 6.94e+03 5.82e+00 bond pdb=" N MET C 38 " pdb=" CA MET C 38 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.26e-02 6.30e+03 5.54e+00 bond pdb=" N LYS R 239 " pdb=" CA LYS R 239 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.19e-02 7.06e+03 5.39e+00 bond pdb=" N MET A 247 " pdb=" CA MET A 247 " ideal model delta sigma weight residual 1.459 1.488 -0.030 1.28e-02 6.10e+03 5.38e+00 ... (remaining 9074 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.99: 11911 1.99 - 3.98: 317 3.98 - 5.98: 53 5.98 - 7.97: 11 7.97 - 9.96: 11 Bond angle restraints: 12303 Sorted by residual: angle pdb=" C ILE H 126 " pdb=" CA ILE H 126 " pdb=" CB ILE H 126 " ideal model delta sigma weight residual 111.23 102.28 8.95 1.08e+00 8.57e-01 6.87e+01 angle pdb=" N ILE H 126 " pdb=" CA ILE H 126 " pdb=" C ILE H 126 " ideal model delta sigma weight residual 107.98 117.84 -9.86 1.51e+00 4.39e-01 4.26e+01 angle pdb=" N ARG R 103 " pdb=" CA ARG R 103 " pdb=" C ARG R 103 " ideal model delta sigma weight residual 110.23 102.13 8.10 1.45e+00 4.76e-01 3.12e+01 angle pdb=" N VAL H 127 " pdb=" CA VAL H 127 " pdb=" C VAL H 127 " ideal model delta sigma weight residual 109.30 116.00 -6.70 1.25e+00 6.40e-01 2.87e+01 angle pdb=" C ALA B 257 " pdb=" N ASP B 258 " pdb=" CA ASP B 258 " ideal model delta sigma weight residual 121.54 130.74 -9.20 1.91e+00 2.74e-01 2.32e+01 ... (remaining 12298 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 4767 17.98 - 35.96: 474 35.96 - 53.94: 112 53.94 - 71.92: 12 71.92 - 89.90: 13 Dihedral angle restraints: 5378 sinusoidal: 2048 harmonic: 3330 Sorted by residual: dihedral pdb=" CB CYS R 115 " pdb=" SG CYS R 115 " pdb=" SG CYS R 186 " pdb=" CB CYS R 186 " ideal model delta sinusoidal sigma weight residual -86.00 -145.16 59.16 1 1.00e+01 1.00e-02 4.68e+01 dihedral pdb=" CB CYS H 147 " pdb=" SG CYS H 147 " pdb=" SG CYS H 217 " pdb=" CB CYS H 217 " ideal model delta sinusoidal sigma weight residual 93.00 136.59 -43.59 1 1.00e+01 1.00e-02 2.65e+01 dihedral pdb=" CA PHE B 278 " pdb=" C PHE B 278 " pdb=" N SER B 279 " pdb=" CA SER B 279 " ideal model delta harmonic sigma weight residual 180.00 161.82 18.18 0 5.00e+00 4.00e-02 1.32e+01 ... (remaining 5375 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1047 0.052 - 0.105: 289 0.105 - 0.157: 66 0.157 - 0.210: 6 0.210 - 0.262: 2 Chirality restraints: 1410 Sorted by residual: chirality pdb=" CB VAL R 99 " pdb=" CA VAL R 99 " pdb=" CG1 VAL R 99 " pdb=" CG2 VAL R 99 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.72e+00 chirality pdb=" CA ASP B 258 " pdb=" N ASP B 258 " pdb=" C ASP B 258 " pdb=" CB ASP B 258 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" CB VAL R 253 " pdb=" CA VAL R 253 " pdb=" CG1 VAL R 253 " pdb=" CG2 VAL R 253 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 8.05e-01 ... (remaining 1407 not shown) Planarity restraints: 1555 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR H 223 " 0.056 5.00e-02 4.00e+02 8.48e-02 1.15e+01 pdb=" N PRO H 224 " -0.147 5.00e-02 4.00e+02 pdb=" CA PRO H 224 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO H 224 " 0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA R 256 " 0.043 5.00e-02 4.00e+02 6.37e-02 6.50e+00 pdb=" N PRO R 257 " -0.110 5.00e-02 4.00e+02 pdb=" CA PRO R 257 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO R 257 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU R 95 " 0.042 5.00e-02 4.00e+02 6.30e-02 6.36e+00 pdb=" N PRO R 96 " -0.109 5.00e-02 4.00e+02 pdb=" CA PRO R 96 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO R 96 " 0.035 5.00e-02 4.00e+02 ... (remaining 1552 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 714 2.74 - 3.28: 8933 3.28 - 3.82: 15105 3.82 - 4.36: 17064 4.36 - 4.90: 29478 Nonbonded interactions: 71294 Sorted by model distance: nonbonded pdb=" O VAL H 127 " pdb=" OG SER H 150 " model vdw 2.202 3.040 nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 2.246 3.040 nonbonded pdb=" O VAL R 177 " pdb=" OG1 THR R 180 " model vdw 2.260 3.040 nonbonded pdb=" N VAL H 127 " pdb=" OG SER H 150 " model vdw 2.271 3.120 nonbonded pdb=" OG SER H 192 " pdb=" OG1 THR H 203 " model vdw 2.283 3.040 ... (remaining 71289 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 0.340 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: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 22.710 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.050 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:12.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 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 0.052 9079 Z= 0.260 Angle : 0.832 9.961 12303 Z= 0.463 Chirality : 0.051 0.262 1410 Planarity : 0.006 0.085 1555 Dihedral : 15.687 89.902 3221 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 0.31 % Allowed : 18.75 % Favored : 80.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.23), residues: 1127 helix: -0.92 (0.23), residues: 412 sheet: -0.61 (0.32), residues: 266 loop : -1.61 (0.28), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 339 HIS 0.009 0.002 HIS R 174 PHE 0.020 0.002 PHE A 323 TYR 0.017 0.002 TYR R 91 ARG 0.004 0.000 ARG A 32 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 54 time to evaluate : 0.986 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 57 average time/residue: 1.5142 time to fit residues: 91.9362 Evaluate side-chains 43 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 41 time to evaluate : 1.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 150 SER Chi-restraints excluded: chain R residue 178 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 5.9990 chunk 84 optimal weight: 9.9990 chunk 47 optimal weight: 4.9990 chunk 28 optimal weight: 8.9990 chunk 57 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 87 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 53 optimal weight: 7.9990 chunk 65 optimal weight: 2.9990 chunk 101 optimal weight: 9.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 110 ASN B 230 ASN A 244 HIS A 256 ASN A 346 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.1294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 9079 Z= 0.239 Angle : 0.591 6.760 12303 Z= 0.318 Chirality : 0.042 0.144 1410 Planarity : 0.005 0.072 1555 Dihedral : 4.834 49.776 1246 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 1.88 % Allowed : 19.69 % Favored : 78.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.25), residues: 1127 helix: 0.41 (0.25), residues: 421 sheet: -0.51 (0.33), residues: 261 loop : -1.42 (0.28), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 169 HIS 0.006 0.001 HIS H 35 PHE 0.014 0.001 PHE A 323 TYR 0.011 0.001 TYR H 178 ARG 0.003 0.000 ARG A 21 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 40 time to evaluate : 1.085 Fit side-chains revert: symmetry clash outliers start: 18 outliers final: 4 residues processed: 56 average time/residue: 1.3484 time to fit residues: 81.1658 Evaluate side-chains 42 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 38 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain R residue 178 PHE Chi-restraints excluded: chain R residue 335 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 56 optimal weight: 0.2980 chunk 31 optimal weight: 8.9990 chunk 84 optimal weight: 9.9990 chunk 69 optimal weight: 7.9990 chunk 28 optimal weight: 1.9990 chunk 101 optimal weight: 6.9990 chunk 110 optimal weight: 4.9990 chunk 90 optimal weight: 6.9990 chunk 34 optimal weight: 8.9990 chunk 81 optimal weight: 1.9990 chunk 100 optimal weight: 0.6980 overall best weight: 1.9986 ------------------------------------------------------------------------------- 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: 0.8027 moved from start: 0.1670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9079 Z= 0.178 Angle : 0.545 6.782 12303 Z= 0.290 Chirality : 0.041 0.151 1410 Planarity : 0.004 0.068 1555 Dihedral : 4.578 50.919 1245 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.29 % Allowed : 20.21 % Favored : 77.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.25), residues: 1127 helix: 0.91 (0.26), residues: 421 sheet: -0.26 (0.33), residues: 254 loop : -1.40 (0.28), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 169 HIS 0.006 0.001 HIS H 35 PHE 0.012 0.001 PHE A 323 TYR 0.011 0.001 TYR H 178 ARG 0.003 0.000 ARG B 68 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 41 time to evaluate : 1.091 Fit side-chains revert: symmetry clash outliers start: 22 outliers final: 7 residues processed: 60 average time/residue: 1.3396 time to fit residues: 86.5142 Evaluate side-chains 44 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 37 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain H residue 119 VAL Chi-restraints excluded: chain R residue 178 PHE Chi-restraints excluded: chain R residue 317 GLN Chi-restraints excluded: chain R residue 335 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 1.9990 chunk 52 optimal weight: 4.9990 chunk 11 optimal weight: 7.9990 chunk 48 optimal weight: 6.9990 chunk 68 optimal weight: 8.9990 chunk 102 optimal weight: 4.9990 chunk 108 optimal weight: 6.9990 chunk 53 optimal weight: 0.0980 chunk 96 optimal weight: 7.9990 chunk 29 optimal weight: 0.9980 chunk 90 optimal weight: 8.9990 overall best weight: 2.6186 ------------------------------------------------------------------------------- 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: 0.8044 moved from start: 0.1882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9079 Z= 0.211 Angle : 0.534 6.640 12303 Z= 0.285 Chirality : 0.041 0.152 1410 Planarity : 0.004 0.067 1555 Dihedral : 4.508 51.764 1245 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.50 % Allowed : 20.73 % Favored : 76.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.25), residues: 1127 helix: 1.12 (0.26), residues: 421 sheet: -0.43 (0.32), residues: 264 loop : -1.23 (0.29), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 169 HIS 0.006 0.001 HIS H 35 PHE 0.012 0.001 PHE R 141 TYR 0.015 0.001 TYR R 91 ARG 0.003 0.000 ARG B 68 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 39 time to evaluate : 1.011 Fit side-chains REVERT: R 89 LEU cc_start: 0.8849 (OUTLIER) cc_final: 0.8620 (mm) outliers start: 24 outliers final: 8 residues processed: 61 average time/residue: 1.2426 time to fit residues: 81.8037 Evaluate side-chains 46 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 37 time to evaluate : 1.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain H residue 119 VAL Chi-restraints excluded: chain R residue 89 LEU Chi-restraints excluded: chain R residue 91 TYR Chi-restraints excluded: chain R residue 178 PHE Chi-restraints excluded: chain R residue 317 GLN Chi-restraints excluded: chain R residue 335 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 6.9990 chunk 1 optimal weight: 2.9990 chunk 80 optimal weight: 9.9990 chunk 44 optimal weight: 10.0000 chunk 92 optimal weight: 4.9990 chunk 74 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 55 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 27 optimal weight: 5.9990 chunk 36 optimal weight: 4.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 18 GLN C 44 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.2041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 9079 Z= 0.279 Angle : 0.555 6.650 12303 Z= 0.295 Chirality : 0.041 0.155 1410 Planarity : 0.004 0.065 1555 Dihedral : 4.562 51.976 1245 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 2.60 % Allowed : 21.25 % Favored : 76.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.25), residues: 1127 helix: 1.18 (0.26), residues: 421 sheet: -0.34 (0.32), residues: 265 loop : -1.24 (0.29), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 169 HIS 0.006 0.001 HIS R 174 PHE 0.013 0.001 PHE R 141 TYR 0.015 0.001 TYR R 91 ARG 0.003 0.000 ARG B 68 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 39 time to evaluate : 1.148 Fit side-chains revert: symmetry clash REVERT: B 283 ARG cc_start: 0.8741 (OUTLIER) cc_final: 0.8504 (tpt90) REVERT: R 89 LEU cc_start: 0.8867 (OUTLIER) cc_final: 0.8633 (mm) outliers start: 25 outliers final: 8 residues processed: 62 average time/residue: 1.4442 time to fit residues: 95.5821 Evaluate side-chains 48 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 38 time to evaluate : 1.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 283 ARG Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain H residue 119 VAL Chi-restraints excluded: chain R residue 89 LEU Chi-restraints excluded: chain R residue 91 TYR Chi-restraints excluded: chain R residue 178 PHE Chi-restraints excluded: chain R residue 317 GLN Chi-restraints excluded: chain R residue 335 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 10.0000 chunk 21 optimal weight: 2.9990 chunk 63 optimal weight: 7.9990 chunk 26 optimal weight: 4.9990 chunk 108 optimal weight: 1.9990 chunk 89 optimal weight: 6.9990 chunk 50 optimal weight: 7.9990 chunk 9 optimal weight: 6.9990 chunk 35 optimal weight: 6.9990 chunk 56 optimal weight: 0.9980 chunk 104 optimal weight: 6.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- 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: 0.8069 moved from start: 0.2139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 9079 Z= 0.266 Angle : 0.572 7.495 12303 Z= 0.300 Chirality : 0.041 0.157 1410 Planarity : 0.004 0.066 1555 Dihedral : 4.541 51.768 1245 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 2.29 % Allowed : 21.67 % Favored : 76.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.25), residues: 1127 helix: 1.17 (0.26), residues: 421 sheet: -0.31 (0.32), residues: 252 loop : -1.24 (0.29), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 169 HIS 0.006 0.001 HIS R 174 PHE 0.013 0.001 PHE R 141 TYR 0.015 0.001 TYR R 91 ARG 0.003 0.000 ARG C 13 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 39 time to evaluate : 1.064 Fit side-chains REVERT: B 283 ARG cc_start: 0.8730 (OUTLIER) cc_final: 0.8491 (tpt90) REVERT: R 89 LEU cc_start: 0.8869 (OUTLIER) cc_final: 0.8634 (mm) outliers start: 22 outliers final: 8 residues processed: 59 average time/residue: 1.5654 time to fit residues: 98.2379 Evaluate side-chains 48 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 38 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 283 ARG Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain R residue 89 LEU Chi-restraints excluded: chain R residue 91 TYR Chi-restraints excluded: chain R residue 178 PHE Chi-restraints excluded: chain R residue 317 GLN Chi-restraints excluded: chain R residue 335 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 3.9990 chunk 61 optimal weight: 5.9990 chunk 79 optimal weight: 1.9990 chunk 91 optimal weight: 7.9990 chunk 60 optimal weight: 0.8980 chunk 107 optimal weight: 1.9990 chunk 67 optimal weight: 10.0000 chunk 65 optimal weight: 0.7980 chunk 49 optimal weight: 10.0000 chunk 66 optimal weight: 6.9990 chunk 43 optimal weight: 3.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- 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: 0.8040 moved from start: 0.2224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9079 Z= 0.180 Angle : 0.561 8.598 12303 Z= 0.292 Chirality : 0.041 0.151 1410 Planarity : 0.004 0.066 1555 Dihedral : 4.466 52.412 1245 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 1.98 % Allowed : 22.40 % Favored : 75.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.26), residues: 1127 helix: 1.24 (0.26), residues: 422 sheet: -0.39 (0.32), residues: 260 loop : -1.12 (0.29), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 169 HIS 0.006 0.001 HIS R 174 PHE 0.012 0.001 PHE R 141 TYR 0.014 0.001 TYR R 91 ARG 0.003 0.000 ARG C 13 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 42 time to evaluate : 1.079 Fit side-chains REVERT: B 283 ARG cc_start: 0.8721 (OUTLIER) cc_final: 0.8478 (tpt90) REVERT: R 89 LEU cc_start: 0.8850 (OUTLIER) cc_final: 0.8603 (mm) outliers start: 19 outliers final: 8 residues processed: 59 average time/residue: 1.4521 time to fit residues: 91.6687 Evaluate side-chains 48 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 38 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 283 ARG Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain R residue 89 LEU Chi-restraints excluded: chain R residue 91 TYR Chi-restraints excluded: chain R residue 178 PHE Chi-restraints excluded: chain R residue 317 GLN Chi-restraints excluded: chain R residue 335 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 2.9990 chunk 32 optimal weight: 8.9990 chunk 21 optimal weight: 4.9990 chunk 20 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 chunk 73 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 chunk 10 optimal weight: 0.0980 chunk 84 optimal weight: 10.0000 chunk 98 optimal weight: 0.9980 chunk 103 optimal weight: 10.0000 overall best weight: 1.4186 ------------------------------------------------------------------------------- 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: 0.8025 moved from start: 0.2314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9079 Z= 0.158 Angle : 0.561 9.648 12303 Z= 0.292 Chirality : 0.040 0.150 1410 Planarity : 0.004 0.066 1555 Dihedral : 4.391 53.324 1245 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 1.67 % Allowed : 22.81 % Favored : 75.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.26), residues: 1127 helix: 1.28 (0.26), residues: 422 sheet: -0.58 (0.31), residues: 272 loop : -0.99 (0.30), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 169 HIS 0.005 0.001 HIS R 174 PHE 0.012 0.001 PHE R 141 TYR 0.014 0.001 TYR R 91 ARG 0.002 0.000 ARG H 206 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 40 time to evaluate : 0.977 Fit side-chains REVERT: R 89 LEU cc_start: 0.8854 (OUTLIER) cc_final: 0.8633 (mm) outliers start: 16 outliers final: 8 residues processed: 55 average time/residue: 1.3998 time to fit residues: 82.5095 Evaluate side-chains 47 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 38 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain R residue 89 LEU Chi-restraints excluded: chain R residue 91 TYR Chi-restraints excluded: chain R residue 178 PHE Chi-restraints excluded: chain R residue 317 GLN Chi-restraints excluded: chain R residue 335 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 9.9990 chunk 100 optimal weight: 0.2980 chunk 103 optimal weight: 9.9990 chunk 60 optimal weight: 9.9990 chunk 43 optimal weight: 6.9990 chunk 78 optimal weight: 7.9990 chunk 30 optimal weight: 4.9990 chunk 90 optimal weight: 9.9990 chunk 95 optimal weight: 2.9990 chunk 66 optimal weight: 5.9990 chunk 106 optimal weight: 10.0000 overall best weight: 4.2588 ------------------------------------------------------------------------------- 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: 0.8074 moved from start: 0.2295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 9079 Z= 0.305 Angle : 0.602 11.514 12303 Z= 0.313 Chirality : 0.042 0.155 1410 Planarity : 0.004 0.065 1555 Dihedral : 4.557 52.983 1245 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 1.56 % Allowed : 23.23 % Favored : 75.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.26), residues: 1127 helix: 1.23 (0.26), residues: 421 sheet: -0.53 (0.31), residues: 270 loop : -1.04 (0.30), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 169 HIS 0.006 0.001 HIS R 174 PHE 0.013 0.001 PHE R 141 TYR 0.015 0.001 TYR R 91 ARG 0.012 0.000 ARG H 206 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 38 time to evaluate : 1.109 Fit side-chains REVERT: R 89 LEU cc_start: 0.8874 (OUTLIER) cc_final: 0.8634 (mm) outliers start: 15 outliers final: 9 residues processed: 52 average time/residue: 1.2136 time to fit residues: 68.4840 Evaluate side-chains 46 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 36 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain R residue 89 LEU Chi-restraints excluded: chain R residue 91 TYR Chi-restraints excluded: chain R residue 173 VAL Chi-restraints excluded: chain R residue 178 PHE Chi-restraints excluded: chain R residue 317 GLN Chi-restraints excluded: chain R residue 335 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 0.9980 chunk 50 optimal weight: 10.0000 chunk 73 optimal weight: 2.9990 chunk 111 optimal weight: 5.9990 chunk 102 optimal weight: 0.7980 chunk 88 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 68 optimal weight: 0.5980 chunk 54 optimal weight: 1.9990 chunk 70 optimal weight: 4.9990 chunk 94 optimal weight: 2.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- 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: 0.8030 moved from start: 0.2383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9079 Z= 0.166 Angle : 0.595 12.803 12303 Z= 0.304 Chirality : 0.041 0.163 1410 Planarity : 0.004 0.065 1555 Dihedral : 4.473 53.382 1245 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 1.35 % Allowed : 23.54 % Favored : 75.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.26), residues: 1127 helix: 1.29 (0.26), residues: 422 sheet: -0.49 (0.31), residues: 275 loop : -0.97 (0.30), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 169 HIS 0.006 0.001 HIS H 35 PHE 0.012 0.001 PHE R 141 TYR 0.014 0.001 TYR R 91 ARG 0.006 0.000 ARG H 206 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 40 time to evaluate : 1.000 Fit side-chains REVERT: R 89 LEU cc_start: 0.8841 (OUTLIER) cc_final: 0.8608 (mm) outliers start: 13 outliers final: 9 residues processed: 53 average time/residue: 1.3150 time to fit residues: 75.1265 Evaluate side-chains 48 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 38 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain R residue 89 LEU Chi-restraints excluded: chain R residue 91 TYR Chi-restraints excluded: chain R residue 173 VAL Chi-restraints excluded: chain R residue 178 PHE Chi-restraints excluded: chain R residue 317 GLN Chi-restraints excluded: chain R residue 335 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 6.9990 chunk 81 optimal weight: 3.9990 chunk 13 optimal weight: 10.0000 chunk 24 optimal weight: 6.9990 chunk 88 optimal weight: 2.9990 chunk 37 optimal weight: 0.0870 chunk 91 optimal weight: 0.9980 chunk 11 optimal weight: 8.9990 chunk 16 optimal weight: 7.9990 chunk 78 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 overall best weight: 2.4164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2595 r_free = 0.2595 target = 0.039950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2355 r_free = 0.2355 target = 0.032340 restraints weight = 56989.624| |-----------------------------------------------------------------------------| r_work (start): 0.2303 rms_B_bonded: 2.94 r_work: 0.2222 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9134 moved from start: 0.2390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9079 Z= 0.209 Angle : 0.595 11.849 12303 Z= 0.306 Chirality : 0.041 0.164 1410 Planarity : 0.004 0.066 1555 Dihedral : 4.478 53.615 1245 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.15 % Allowed : 23.85 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.26), residues: 1127 helix: 1.24 (0.26), residues: 422 sheet: -0.48 (0.31), residues: 267 loop : -1.00 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 169 HIS 0.006 0.001 HIS R 174 PHE 0.012 0.001 PHE R 141 TYR 0.014 0.001 TYR R 91 ARG 0.005 0.000 ARG H 206 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2406.33 seconds wall clock time: 44 minutes 33.79 seconds (2673.79 seconds total)