Starting phenix.real_space_refine on Sat May 10 17:05:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ge7_29959/05_2025/8ge7_29959.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ge7_29959/05_2025/8ge7_29959.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ge7_29959/05_2025/8ge7_29959.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ge7_29959/05_2025/8ge7_29959.map" model { file = "/net/cci-nas-00/data/ceres_data/8ge7_29959/05_2025/8ge7_29959.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ge7_29959/05_2025/8ge7_29959.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.033 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 42 5.16 5 C 4245 2.51 5 N 1143 2.21 5 O 1187 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 6617 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1717 Classifications: {'peptide': 230} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 51} Link IDs: {'PTRANS': 5, 'TRANS': 224} Chain breaks: 3 Unresolved non-hydrogen bonds: 198 Unresolved non-hydrogen angles: 237 Unresolved non-hydrogen dihedrals: 161 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 4, 'ASN:plan1': 1, 'ASP:plan': 9, 'PHE:plan': 1, 'GLU:plan': 13, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 134 Chain: "B" Number of atoms: 2446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2446 Classifications: {'peptide': 331} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 5, 'TRANS': 325} Chain breaks: 1 Unresolved non-hydrogen bonds: 98 Unresolved non-hydrogen angles: 119 Unresolved non-hydrogen dihedrals: 77 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 4, 'ARG:plan': 6, 'ASN:plan1': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 77 Chain: "G" Number of atoms: 349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 349 Classifications: {'peptide': 52} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 4, 'TRANS': 47} Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "R" Number of atoms: 2090 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2090 Classifications: {'peptide': 282} Incomplete info: {'truncation_to_alanine': 49} Link IDs: {'PTRANS': 7, 'TRANS': 274} Chain breaks: 1 Unresolved non-hydrogen bonds: 182 Unresolved non-hydrogen angles: 226 Unresolved non-hydrogen dihedrals: 149 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 5, 'ASN:plan1': 2, 'TRP:plan': 1, 'HIS:plan': 2, 'GLU:plan': 9, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 103 Chain: "R" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'G1I': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.65, per 1000 atoms: 0.70 Number of scatterers: 6617 At special positions: 0 Unit cell: (69.96, 98.58, 129.32, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 42 16.00 O 1187 8.00 N 1143 7.00 C 4245 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 106 " - pdb=" SG CYS R 191 " 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: 1.88 Conformation dependent library (CDL) restraints added in 1.0 seconds 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1696 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 8 sheets defined 48.7% alpha, 18.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.84 Creating SS restraints... Processing helix chain 'A' and resid 12 through 40 removed outlier: 3.799A pdb=" N ALA A 39 " --> pdb=" O GLN A 35 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N THR A 40 " --> pdb=" O VAL A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 51 No H-bonds generated for 'chain 'A' and resid 49 through 51' Processing helix chain 'A' and resid 52 through 60 removed outlier: 3.633A pdb=" N ILE A 56 " --> pdb=" O GLY A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 238 Processing helix chain 'A' and resid 264 through 278 Processing helix chain 'A' and resid 293 through 304 Processing helix chain 'A' and resid 307 through 312 removed outlier: 4.006A pdb=" N TYR A 311 " --> pdb=" O LYS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 316 Processing helix chain 'A' and resid 331 through 353 removed outlier: 3.957A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLY A 353 " --> pdb=" O SER A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 Processing helix chain 'B' and resid 7 through 25 Processing helix chain 'B' and resid 29 through 35 removed outlier: 3.714A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 12 through 24 removed outlier: 3.569A 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 'R' and resid 31 through 61 Processing helix chain 'R' and resid 66 through 96 removed outlier: 3.664A pdb=" N PHE R 71 " --> pdb=" O VAL R 67 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N VAL R 87 " --> pdb=" O GLY R 83 " (cutoff:3.500A) Proline residue: R 88 - end of helix Processing helix chain 'R' and resid 102 through 137 Processing helix chain 'R' and resid 137 through 145 removed outlier: 4.525A pdb=" N GLN R 142 " --> pdb=" O PRO R 138 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N SER R 143 " --> pdb=" O PHE R 139 " (cutoff:3.500A) Processing helix chain 'R' and resid 146 through 171 removed outlier: 4.303A pdb=" N LEU R 167 " --> pdb=" O LEU R 163 " (cutoff:3.500A) Proline residue: R 168 - end of helix removed outlier: 3.868A pdb=" N MET R 171 " --> pdb=" O LEU R 167 " (cutoff:3.500A) Processing helix chain 'R' and resid 178 through 187 Processing helix chain 'R' and resid 196 through 208 Processing helix chain 'R' and resid 208 through 237 Processing helix chain 'R' and resid 270 through 299 removed outlier: 3.695A pdb=" N PHE R 282 " --> pdb=" O ILE R 278 " (cutoff:3.500A) Proline residue: R 288 - end of helix removed outlier: 4.004A pdb=" N VAL R 297 " --> pdb=" O ASN R 293 " (cutoff:3.500A) Processing helix chain 'R' and resid 304 through 327 removed outlier: 3.755A pdb=" N ASN R 318 " --> pdb=" O ILE R 314 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N SER R 319 " --> pdb=" O GLY R 315 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N GLY R 320 " --> pdb=" O TYR R 316 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N PHE R 321 " --> pdb=" O VAL R 317 " (cutoff:3.500A) Proline residue: R 323 - end of helix Processing helix chain 'R' and resid 329 through 340 Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214 removed outlier: 6.433A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N VAL A 224 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N LEU A 45 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.511A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 4.043A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.614A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.841A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.879A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.711A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 5.613A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) 391 hydrogen bonds defined for protein. 1137 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.79 Time building geometry restraints manager: 2.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2142 1.34 - 1.46: 1573 1.46 - 1.58: 2984 1.58 - 1.70: 0 1.70 - 1.81: 58 Bond restraints: 6757 Sorted by residual: bond pdb=" CAC G1I R 501 " pdb=" CAD G1I R 501 " ideal model delta sigma weight residual 1.397 1.449 -0.052 2.00e-02 2.50e+03 6.63e+00 bond pdb=" CAI G1I R 501 " pdb=" CAJ G1I R 501 " ideal model delta sigma weight residual 1.523 1.566 -0.043 2.00e-02 2.50e+03 4.70e+00 bond pdb=" CAD G1I R 501 " pdb=" CAE G1I R 501 " ideal model delta sigma weight residual 1.394 1.437 -0.043 2.00e-02 2.50e+03 4.67e+00 bond pdb=" CAG G1I R 501 " pdb=" CAH G1I R 501 " ideal model delta sigma weight residual 1.520 1.562 -0.042 2.00e-02 2.50e+03 4.36e+00 bond pdb=" CAI G1I R 501 " pdb=" NAN G1I R 501 " ideal model delta sigma weight residual 1.451 1.484 -0.033 2.00e-02 2.50e+03 2.72e+00 ... (remaining 6752 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.13: 8833 1.13 - 2.26: 308 2.26 - 3.39: 62 3.39 - 4.52: 13 4.52 - 5.65: 10 Bond angle restraints: 9226 Sorted by residual: angle pdb=" C HIS B 183 " pdb=" N THR B 184 " pdb=" CA THR B 184 " ideal model delta sigma weight residual 122.79 118.37 4.42 1.70e+00 3.46e-01 6.76e+00 angle pdb=" N GLN A 227 " pdb=" CA GLN A 227 " pdb=" C GLN A 227 " ideal model delta sigma weight residual 111.81 108.60 3.21 1.44e+00 4.82e-01 4.98e+00 angle pdb=" CA GLU G 47 " pdb=" CB GLU G 47 " pdb=" CG GLU G 47 " ideal model delta sigma weight residual 114.10 118.54 -4.44 2.00e+00 2.50e-01 4.92e+00 angle pdb=" C TYR B 59 " pdb=" N ALA B 60 " pdb=" CA ALA B 60 " ideal model delta sigma weight residual 121.75 118.36 3.39 1.73e+00 3.34e-01 3.84e+00 angle pdb=" N PHE B 335 " pdb=" CA PHE B 335 " pdb=" C PHE B 335 " ideal model delta sigma weight residual 109.24 112.41 -3.17 1.63e+00 3.76e-01 3.79e+00 ... (remaining 9221 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.98: 3557 15.98 - 31.95: 292 31.95 - 47.93: 68 47.93 - 63.90: 9 63.90 - 79.88: 3 Dihedral angle restraints: 3929 sinusoidal: 1319 harmonic: 2610 Sorted by residual: dihedral pdb=" CA THR B 165 " pdb=" C THR B 165 " pdb=" N CYS B 166 " pdb=" CA CYS B 166 " ideal model delta harmonic sigma weight residual 180.00 158.02 21.98 0 5.00e+00 4.00e-02 1.93e+01 dihedral pdb=" CA ASP B 291 " pdb=" C ASP B 291 " pdb=" N PHE B 292 " pdb=" CA PHE B 292 " ideal model delta harmonic sigma weight residual 180.00 -160.87 -19.13 0 5.00e+00 4.00e-02 1.46e+01 dihedral pdb=" CA TRP B 332 " pdb=" C TRP B 332 " pdb=" N ASP B 333 " pdb=" CA ASP B 333 " ideal model delta harmonic sigma weight residual 180.00 161.73 18.27 0 5.00e+00 4.00e-02 1.33e+01 ... (remaining 3926 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 757 0.034 - 0.069: 248 0.069 - 0.103: 71 0.103 - 0.137: 22 0.137 - 0.171: 1 Chirality restraints: 1099 Sorted by residual: chirality pdb=" CAJ G1I R 501 " pdb=" CAF G1I R 501 " pdb=" CAI G1I R 501 " pdb=" OAM G1I R 501 " both_signs ideal model delta sigma weight residual False 2.40 2.57 -0.17 2.00e-01 2.50e+01 7.33e-01 chirality pdb=" CA ILE B 58 " pdb=" N ILE B 58 " pdb=" C ILE B 58 " pdb=" CB ILE B 58 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.54e-01 chirality pdb=" CA VAL B 327 " pdb=" N VAL B 327 " pdb=" C VAL B 327 " pdb=" CB VAL B 327 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.17e-01 ... (remaining 1096 not shown) Planarity restraints: 1163 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN G 59 " 0.024 5.00e-02 4.00e+02 3.59e-02 2.07e+00 pdb=" N PRO G 60 " -0.062 5.00e-02 4.00e+02 pdb=" CA PRO G 60 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO G 60 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR G 52 " -0.021 5.00e-02 4.00e+02 3.24e-02 1.67e+00 pdb=" N PRO G 53 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO G 53 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO G 53 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 320 " -0.020 5.00e-02 4.00e+02 3.04e-02 1.48e+00 pdb=" N PRO A 321 " 0.053 5.00e-02 4.00e+02 pdb=" CA PRO A 321 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 321 " -0.017 5.00e-02 4.00e+02 ... (remaining 1160 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 488 2.74 - 3.28: 6779 3.28 - 3.82: 11192 3.82 - 4.36: 12602 4.36 - 4.90: 22962 Nonbonded interactions: 54023 Sorted by model distance: nonbonded pdb=" OG SER B 281 " pdb=" O HIS G 44 " model vdw 2.197 3.040 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.209 3.040 nonbonded pdb=" O ARG B 68 " pdb=" OG SER B 84 " model vdw 2.210 3.040 nonbonded pdb=" NZ LYS A 233 " pdb=" OD2 ASP B 228 " model vdw 2.212 3.120 nonbonded pdb=" OD1 ASP B 247 " pdb=" OG1 THR B 249 " model vdw 2.226 3.040 ... (remaining 54018 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=0.00 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: 1.110 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: 0.260 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 19.710 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 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:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 6758 Z= 0.150 Angle : 0.532 5.652 9228 Z= 0.295 Chirality : 0.039 0.171 1099 Planarity : 0.004 0.039 1163 Dihedral : 12.646 79.878 2230 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % 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: 0.95 (0.28), residues: 877 helix: 2.16 (0.26), residues: 389 sheet: 0.22 (0.42), residues: 155 loop : -1.03 (0.30), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 99 HIS 0.012 0.001 HIS B 183 PHE 0.015 0.001 PHE B 234 TYR 0.019 0.001 TYR B 59 ARG 0.010 0.000 ARG A 347 Details of bonding type rmsd hydrogen bonds : bond 0.15968 ( 391) hydrogen bonds : angle 6.10427 ( 1137) SS BOND : bond 0.00351 ( 1) SS BOND : angle 1.09807 ( 2) covalent geometry : bond 0.00317 ( 6757) covalent geometry : angle 0.53224 ( 9226) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 0.766 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 101 average time/residue: 0.1615 time to fit residues: 22.7464 Evaluate side-chains 81 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 75 optimal weight: 1.9990 chunk 67 optimal weight: 0.8980 chunk 37 optimal weight: 0.5980 chunk 23 optimal weight: 7.9990 chunk 45 optimal weight: 0.0770 chunk 36 optimal weight: 1.9990 chunk 69 optimal weight: 0.7980 chunk 26 optimal weight: 7.9990 chunk 42 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 overall best weight: 0.6740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 ASN B 237 ASN G 18 GLN R 231 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.147473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.130390 restraints weight = 9508.836| |-----------------------------------------------------------------------------| r_work (start): 0.3626 rms_B_bonded: 1.88 r_work: 0.3483 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3336 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3373 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3373 r_free = 0.3373 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3373 r_free = 0.3373 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3373 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.0940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6758 Z= 0.143 Angle : 0.511 5.653 9228 Z= 0.283 Chirality : 0.040 0.142 1099 Planarity : 0.004 0.034 1163 Dihedral : 4.713 33.108 969 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 0.63 % Allowed : 9.29 % Favored : 90.08 % 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: 1.04 (0.28), residues: 877 helix: 2.25 (0.26), residues: 388 sheet: 0.18 (0.36), residues: 179 loop : -1.04 (0.32), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 211 HIS 0.008 0.001 HIS B 183 PHE 0.017 0.001 PHE B 199 TYR 0.015 0.001 TYR B 59 ARG 0.005 0.000 ARG A 347 Details of bonding type rmsd hydrogen bonds : bond 0.04471 ( 391) hydrogen bonds : angle 4.52465 ( 1137) SS BOND : bond 0.00316 ( 1) SS BOND : angle 0.36464 ( 2) covalent geometry : bond 0.00318 ( 6757) covalent geometry : angle 0.51107 ( 9226) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 93 time to evaluate : 0.776 Fit side-chains revert: symmetry clash REVERT: A 29 GLN cc_start: 0.8783 (tp40) cc_final: 0.8498 (tp40) REVERT: A 343 ASP cc_start: 0.7990 (m-30) cc_final: 0.7630 (m-30) REVERT: G 18 GLN cc_start: 0.8711 (OUTLIER) cc_final: 0.8430 (tp40) outliers start: 4 outliers final: 3 residues processed: 96 average time/residue: 0.1657 time to fit residues: 22.1033 Evaluate side-chains 86 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 82 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain G residue 18 GLN Chi-restraints excluded: chain R residue 86 VAL Chi-restraints excluded: chain R residue 314 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 9 optimal weight: 0.9990 chunk 86 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 67 optimal weight: 4.9990 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 74 optimal weight: 0.0470 chunk 55 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 overall best weight: 0.9684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 225 HIS B 237 ASN R 231 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.145885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.128613 restraints weight = 9675.949| |-----------------------------------------------------------------------------| r_work (start): 0.3603 rms_B_bonded: 1.91 r_work: 0.3459 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3311 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3344 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3344 r_free = 0.3344 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3344 r_free = 0.3344 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3344 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.1134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6758 Z= 0.168 Angle : 0.506 5.433 9228 Z= 0.279 Chirality : 0.040 0.145 1099 Planarity : 0.004 0.036 1163 Dihedral : 4.720 31.368 969 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.26 % Allowed : 11.65 % Favored : 87.09 % 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: 0.95 (0.28), residues: 877 helix: 2.25 (0.26), residues: 388 sheet: -0.01 (0.36), residues: 180 loop : -1.09 (0.32), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 211 HIS 0.005 0.001 HIS B 183 PHE 0.017 0.001 PHE B 199 TYR 0.013 0.001 TYR B 59 ARG 0.003 0.000 ARG B 49 Details of bonding type rmsd hydrogen bonds : bond 0.04320 ( 391) hydrogen bonds : angle 4.36135 ( 1137) SS BOND : bond 0.00319 ( 1) SS BOND : angle 0.26488 ( 2) covalent geometry : bond 0.00391 ( 6757) covalent geometry : angle 0.50555 ( 9226) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 88 time to evaluate : 0.740 Fit side-chains revert: symmetry clash REVERT: A 29 GLN cc_start: 0.8781 (tp40) cc_final: 0.8537 (tp40) REVERT: A 317 ARG cc_start: 0.8404 (mtm-85) cc_final: 0.7985 (ptp90) REVERT: A 343 ASP cc_start: 0.8092 (m-30) cc_final: 0.7700 (m-30) REVERT: B 246 ASP cc_start: 0.7905 (m-30) cc_final: 0.7634 (m-30) outliers start: 8 outliers final: 5 residues processed: 93 average time/residue: 0.1770 time to fit residues: 22.6080 Evaluate side-chains 86 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 81 time to evaluate : 0.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain R residue 86 VAL Chi-restraints excluded: chain R residue 100 THR Chi-restraints excluded: chain R residue 314 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 67 optimal weight: 4.9990 chunk 76 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 57 optimal weight: 5.9990 chunk 21 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 81 optimal weight: 0.6980 chunk 77 optimal weight: 0.6980 chunk 50 optimal weight: 0.4980 chunk 61 optimal weight: 10.0000 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 231 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.144532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.126629 restraints weight = 9773.721| |-----------------------------------------------------------------------------| r_work (start): 0.3587 rms_B_bonded: 1.98 r_work: 0.3438 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3287 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3330 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3330 r_free = 0.3330 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3330 r_free = 0.3330 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3330 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.1303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 6758 Z= 0.163 Angle : 0.493 5.405 9228 Z= 0.273 Chirality : 0.040 0.136 1099 Planarity : 0.003 0.036 1163 Dihedral : 4.683 29.376 969 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.36 % Allowed : 11.97 % Favored : 85.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.28), residues: 877 helix: 2.30 (0.26), residues: 388 sheet: -0.06 (0.37), residues: 179 loop : -1.11 (0.32), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 211 HIS 0.003 0.001 HIS A 357 PHE 0.017 0.001 PHE B 199 TYR 0.013 0.001 TYR B 59 ARG 0.002 0.000 ARG B 49 Details of bonding type rmsd hydrogen bonds : bond 0.04148 ( 391) hydrogen bonds : angle 4.24557 ( 1137) SS BOND : bond 0.00293 ( 1) SS BOND : angle 0.24216 ( 2) covalent geometry : bond 0.00379 ( 6757) covalent geometry : angle 0.49263 ( 9226) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 86 time to evaluate : 0.783 Fit side-chains REVERT: A 29 GLN cc_start: 0.8775 (tp40) cc_final: 0.8555 (tp40) REVERT: A 317 ARG cc_start: 0.8372 (mtm-85) cc_final: 0.8106 (ptp-170) REVERT: A 343 ASP cc_start: 0.8071 (m-30) cc_final: 0.7663 (m-30) REVERT: B 59 TYR cc_start: 0.8573 (OUTLIER) cc_final: 0.8313 (m-80) REVERT: B 117 LEU cc_start: 0.8649 (OUTLIER) cc_final: 0.8350 (tt) REVERT: B 228 ASP cc_start: 0.7648 (p0) cc_final: 0.7269 (p0) REVERT: B 246 ASP cc_start: 0.7769 (m-30) cc_final: 0.7468 (m-30) outliers start: 15 outliers final: 9 residues processed: 95 average time/residue: 0.1657 time to fit residues: 21.6240 Evaluate side-chains 91 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 80 time to evaluate : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain R residue 86 VAL Chi-restraints excluded: chain R residue 94 ILE Chi-restraints excluded: chain R residue 100 THR Chi-restraints excluded: chain R residue 314 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 60 optimal weight: 0.1980 chunk 31 optimal weight: 1.9990 chunk 57 optimal weight: 5.9990 chunk 16 optimal weight: 4.9990 chunk 37 optimal weight: 0.9990 chunk 54 optimal weight: 0.9980 chunk 73 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 71 optimal weight: 0.9980 chunk 5 optimal weight: 3.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 231 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.144745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.126761 restraints weight = 9735.269| |-----------------------------------------------------------------------------| r_work (start): 0.3592 rms_B_bonded: 2.00 r_work: 0.3441 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3292 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3323 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3323 r_free = 0.3323 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3323 r_free = 0.3323 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3323 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.1384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 6758 Z= 0.151 Angle : 0.485 5.982 9228 Z= 0.268 Chirality : 0.040 0.133 1099 Planarity : 0.003 0.035 1163 Dihedral : 4.632 28.079 969 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.20 % Allowed : 13.07 % Favored : 84.72 % 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: 0.97 (0.28), residues: 877 helix: 2.35 (0.26), residues: 388 sheet: -0.07 (0.37), residues: 179 loop : -1.16 (0.32), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 211 HIS 0.003 0.001 HIS A 357 PHE 0.017 0.001 PHE B 199 TYR 0.012 0.001 TYR B 59 ARG 0.002 0.000 ARG B 251 Details of bonding type rmsd hydrogen bonds : bond 0.04022 ( 391) hydrogen bonds : angle 4.16073 ( 1137) SS BOND : bond 0.00255 ( 1) SS BOND : angle 0.20549 ( 2) covalent geometry : bond 0.00350 ( 6757) covalent geometry : angle 0.48507 ( 9226) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 89 time to evaluate : 0.816 Fit side-chains REVERT: A 29 GLN cc_start: 0.8776 (tp40) cc_final: 0.8564 (tp40) REVERT: A 317 ARG cc_start: 0.8326 (mtm-85) cc_final: 0.8036 (ptp90) REVERT: A 343 ASP cc_start: 0.8074 (m-30) cc_final: 0.7676 (m-30) REVERT: B 59 TYR cc_start: 0.8582 (OUTLIER) cc_final: 0.8195 (m-80) REVERT: B 117 LEU cc_start: 0.8621 (OUTLIER) cc_final: 0.8336 (tt) REVERT: B 246 ASP cc_start: 0.7637 (m-30) cc_final: 0.7333 (m-30) outliers start: 14 outliers final: 8 residues processed: 96 average time/residue: 0.1758 time to fit residues: 23.3198 Evaluate side-chains 91 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 81 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain R residue 86 VAL Chi-restraints excluded: chain R residue 100 THR Chi-restraints excluded: chain R residue 314 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 51 optimal weight: 0.9980 chunk 82 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 34 optimal weight: 0.4980 chunk 36 optimal weight: 0.8980 chunk 17 optimal weight: 0.8980 chunk 73 optimal weight: 0.7980 chunk 80 optimal weight: 0.7980 chunk 57 optimal weight: 7.9990 chunk 86 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 231 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.145148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.127440 restraints weight = 9589.088| |-----------------------------------------------------------------------------| r_work (start): 0.3605 rms_B_bonded: 1.95 r_work: 0.3458 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3309 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3339 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3339 r_free = 0.3339 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3339 r_free = 0.3339 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3339 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.1505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6758 Z= 0.140 Angle : 0.475 6.153 9228 Z= 0.264 Chirality : 0.040 0.162 1099 Planarity : 0.003 0.034 1163 Dihedral : 4.557 26.883 969 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.05 % Allowed : 14.02 % Favored : 83.94 % 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: 0.98 (0.28), residues: 877 helix: 2.41 (0.26), residues: 388 sheet: -0.13 (0.37), residues: 179 loop : -1.19 (0.32), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 169 HIS 0.004 0.001 HIS A 220 PHE 0.017 0.001 PHE B 199 TYR 0.011 0.001 TYR R 199 ARG 0.002 0.000 ARG B 251 Details of bonding type rmsd hydrogen bonds : bond 0.03900 ( 391) hydrogen bonds : angle 4.09474 ( 1137) SS BOND : bond 0.00182 ( 1) SS BOND : angle 0.10586 ( 2) covalent geometry : bond 0.00320 ( 6757) covalent geometry : angle 0.47536 ( 9226) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 84 time to evaluate : 0.773 Fit side-chains REVERT: A 29 GLN cc_start: 0.8765 (tp40) cc_final: 0.8557 (tp40) REVERT: A 317 ARG cc_start: 0.8278 (mtm-85) cc_final: 0.8032 (ptp-170) REVERT: A 343 ASP cc_start: 0.8026 (m-30) cc_final: 0.7630 (m-30) REVERT: B 59 TYR cc_start: 0.8602 (OUTLIER) cc_final: 0.8165 (m-80) REVERT: B 117 LEU cc_start: 0.8580 (OUTLIER) cc_final: 0.8300 (tt) REVERT: B 246 ASP cc_start: 0.7528 (m-30) cc_final: 0.7173 (m-30) outliers start: 13 outliers final: 9 residues processed: 91 average time/residue: 0.1650 time to fit residues: 20.9748 Evaluate side-chains 92 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 81 time to evaluate : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain R residue 86 VAL Chi-restraints excluded: chain R residue 100 THR Chi-restraints excluded: chain R residue 314 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 85 optimal weight: 0.0570 chunk 25 optimal weight: 0.9990 chunk 61 optimal weight: 9.9990 chunk 48 optimal weight: 0.0770 chunk 57 optimal weight: 0.6980 chunk 35 optimal weight: 2.9990 chunk 6 optimal weight: 0.8980 chunk 74 optimal weight: 0.6980 chunk 5 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 chunk 73 optimal weight: 0.6980 overall best weight: 0.4456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 231 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.147680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.130030 restraints weight = 9590.689| |-----------------------------------------------------------------------------| r_work (start): 0.3635 rms_B_bonded: 1.96 r_work: 0.3490 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3342 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3379 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3379 r_free = 0.3379 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3379 r_free = 0.3379 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3379 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.1635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 6758 Z= 0.109 Angle : 0.451 6.577 9228 Z= 0.250 Chirality : 0.039 0.151 1099 Planarity : 0.003 0.033 1163 Dihedral : 4.382 25.520 969 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.73 % Allowed : 14.96 % Favored : 83.31 % 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: 1.07 (0.28), residues: 877 helix: 2.55 (0.26), residues: 388 sheet: -0.16 (0.38), residues: 175 loop : -1.16 (0.32), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 169 HIS 0.003 0.001 HIS A 357 PHE 0.016 0.001 PHE B 199 TYR 0.009 0.001 TYR R 199 ARG 0.002 0.000 ARG B 49 Details of bonding type rmsd hydrogen bonds : bond 0.03572 ( 391) hydrogen bonds : angle 3.96469 ( 1137) SS BOND : bond 0.00127 ( 1) SS BOND : angle 0.11794 ( 2) covalent geometry : bond 0.00241 ( 6757) covalent geometry : angle 0.45128 ( 9226) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 92 time to evaluate : 0.712 Fit side-chains REVERT: A 29 GLN cc_start: 0.8730 (tp40) cc_final: 0.8524 (tp40) REVERT: B 59 TYR cc_start: 0.8505 (OUTLIER) cc_final: 0.8060 (m-80) REVERT: B 117 LEU cc_start: 0.8488 (OUTLIER) cc_final: 0.8227 (tt) REVERT: R 232 LYS cc_start: 0.9101 (ttmm) cc_final: 0.8883 (ttmt) outliers start: 11 outliers final: 6 residues processed: 98 average time/residue: 0.1690 time to fit residues: 22.8183 Evaluate side-chains 90 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 82 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain R residue 86 VAL Chi-restraints excluded: chain R residue 314 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 14 optimal weight: 0.9980 chunk 54 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 6 optimal weight: 0.8980 chunk 85 optimal weight: 3.9990 chunk 65 optimal weight: 0.9990 chunk 60 optimal weight: 0.4980 chunk 37 optimal weight: 0.9980 chunk 20 optimal weight: 0.6980 chunk 69 optimal weight: 0.5980 chunk 3 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 231 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.135071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.115996 restraints weight = 10330.018| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 2.24 r_work: 0.3267 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3290 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3290 r_free = 0.3290 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3290 r_free = 0.3290 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3290 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.1715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6758 Z= 0.135 Angle : 0.469 6.035 9228 Z= 0.259 Chirality : 0.040 0.172 1099 Planarity : 0.003 0.033 1163 Dihedral : 4.426 25.486 969 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.57 % Allowed : 15.75 % Favored : 82.68 % 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: 1.12 (0.29), residues: 877 helix: 2.54 (0.26), residues: 392 sheet: -0.28 (0.37), residues: 186 loop : -1.03 (0.33), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 211 HIS 0.003 0.001 HIS A 357 PHE 0.016 0.001 PHE B 199 TYR 0.011 0.001 TYR R 199 ARG 0.002 0.000 ARG A 231 Details of bonding type rmsd hydrogen bonds : bond 0.03729 ( 391) hydrogen bonds : angle 3.98785 ( 1137) SS BOND : bond 0.00127 ( 1) SS BOND : angle 0.08730 ( 2) covalent geometry : bond 0.00310 ( 6757) covalent geometry : angle 0.46884 ( 9226) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 87 time to evaluate : 0.794 Fit side-chains REVERT: A 343 ASP cc_start: 0.8013 (m-30) cc_final: 0.7722 (m-30) REVERT: B 59 TYR cc_start: 0.8467 (OUTLIER) cc_final: 0.8043 (m-80) REVERT: B 117 LEU cc_start: 0.8367 (OUTLIER) cc_final: 0.8087 (tt) REVERT: R 231 GLN cc_start: 0.8199 (OUTLIER) cc_final: 0.7977 (mp10) outliers start: 10 outliers final: 6 residues processed: 93 average time/residue: 0.1582 time to fit residues: 20.7487 Evaluate side-chains 93 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 84 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain R residue 86 VAL Chi-restraints excluded: chain R residue 231 GLN Chi-restraints excluded: chain R residue 314 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 40 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 chunk 69 optimal weight: 0.5980 chunk 1 optimal weight: 0.9990 chunk 78 optimal weight: 0.9980 chunk 53 optimal weight: 0.4980 chunk 32 optimal weight: 1.9990 chunk 66 optimal weight: 0.7980 chunk 85 optimal weight: 4.9990 chunk 19 optimal weight: 0.1980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 231 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.135279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.116187 restraints weight = 10335.942| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 2.24 r_work: 0.3275 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3297 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3297 r_free = 0.3297 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3297 r_free = 0.3297 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3297 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.1751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6758 Z= 0.128 Angle : 0.472 5.987 9228 Z= 0.260 Chirality : 0.039 0.170 1099 Planarity : 0.003 0.033 1163 Dihedral : 4.413 25.198 969 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.42 % Allowed : 16.06 % Favored : 82.52 % 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: 1.12 (0.29), residues: 877 helix: 2.61 (0.26), residues: 387 sheet: -0.29 (0.37), residues: 186 loop : -1.08 (0.33), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 211 HIS 0.003 0.001 HIS A 357 PHE 0.016 0.001 PHE B 199 TYR 0.010 0.001 TYR R 199 ARG 0.002 0.000 ARG R 228 Details of bonding type rmsd hydrogen bonds : bond 0.03670 ( 391) hydrogen bonds : angle 3.96811 ( 1137) SS BOND : bond 0.00122 ( 1) SS BOND : angle 0.05413 ( 2) covalent geometry : bond 0.00293 ( 6757) covalent geometry : angle 0.47218 ( 9226) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 83 time to evaluate : 0.682 Fit side-chains REVERT: A 343 ASP cc_start: 0.8032 (m-30) cc_final: 0.7744 (m-30) REVERT: B 59 TYR cc_start: 0.8441 (OUTLIER) cc_final: 0.7986 (m-80) REVERT: B 117 LEU cc_start: 0.8350 (OUTLIER) cc_final: 0.8063 (tt) REVERT: R 231 GLN cc_start: 0.8277 (OUTLIER) cc_final: 0.8028 (mp10) outliers start: 9 outliers final: 5 residues processed: 89 average time/residue: 0.1688 time to fit residues: 21.1218 Evaluate side-chains 89 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 81 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain R residue 86 VAL Chi-restraints excluded: chain R residue 231 GLN Chi-restraints excluded: chain R residue 314 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 54 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 86 optimal weight: 0.7980 chunk 56 optimal weight: 0.2980 chunk 84 optimal weight: 0.6980 chunk 34 optimal weight: 0.6980 chunk 43 optimal weight: 0.0970 chunk 28 optimal weight: 0.9990 chunk 83 optimal weight: 0.8980 chunk 74 optimal weight: 0.5980 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 231 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.134615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.116158 restraints weight = 10272.375| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 2.17 r_work: 0.3291 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3312 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3312 r_free = 0.3312 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3312 r_free = 0.3312 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3312 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.1826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6758 Z= 0.115 Angle : 0.467 6.117 9228 Z= 0.256 Chirality : 0.039 0.166 1099 Planarity : 0.003 0.034 1163 Dihedral : 4.363 25.044 969 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.89 % Allowed : 15.91 % Favored : 82.20 % 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: 1.17 (0.29), residues: 877 helix: 2.65 (0.26), residues: 387 sheet: -0.24 (0.37), residues: 185 loop : -1.06 (0.33), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 211 HIS 0.003 0.001 HIS A 357 PHE 0.016 0.001 PHE B 199 TYR 0.010 0.001 TYR R 199 ARG 0.004 0.000 ARG R 228 Details of bonding type rmsd hydrogen bonds : bond 0.03586 ( 391) hydrogen bonds : angle 3.92938 ( 1137) SS BOND : bond 0.00110 ( 1) SS BOND : angle 0.07342 ( 2) covalent geometry : bond 0.00260 ( 6757) covalent geometry : angle 0.46692 ( 9226) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 90 time to evaluate : 0.735 Fit side-chains REVERT: A 343 ASP cc_start: 0.8027 (m-30) cc_final: 0.7741 (m-30) REVERT: B 59 TYR cc_start: 0.8389 (OUTLIER) cc_final: 0.7900 (m-80) REVERT: B 117 LEU cc_start: 0.8313 (OUTLIER) cc_final: 0.8043 (tt) REVERT: R 231 GLN cc_start: 0.8286 (OUTLIER) cc_final: 0.8022 (mp10) outliers start: 12 outliers final: 7 residues processed: 98 average time/residue: 0.1576 time to fit residues: 21.8002 Evaluate side-chains 96 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 86 time to evaluate : 0.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain R residue 86 VAL Chi-restraints excluded: chain R residue 231 GLN Chi-restraints excluded: chain R residue 314 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 85 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 23 optimal weight: 6.9990 chunk 46 optimal weight: 0.7980 chunk 59 optimal weight: 0.6980 chunk 15 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 51 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 231 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.134393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.115190 restraints weight = 10456.370| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 2.24 r_work: 0.3261 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3281 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3281 r_free = 0.3281 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3281 r_free = 0.3281 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3281 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.1797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 6758 Z= 0.156 Angle : 0.492 6.616 9228 Z= 0.271 Chirality : 0.040 0.166 1099 Planarity : 0.003 0.034 1163 Dihedral : 4.446 25.123 969 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.89 % Allowed : 15.91 % Favored : 82.20 % 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: 1.09 (0.28), residues: 877 helix: 2.57 (0.26), residues: 387 sheet: -0.33 (0.37), residues: 186 loop : -1.05 (0.33), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 211 HIS 0.003 0.001 HIS A 357 PHE 0.016 0.001 PHE B 199 TYR 0.012 0.001 TYR R 199 ARG 0.005 0.000 ARG R 228 Details of bonding type rmsd hydrogen bonds : bond 0.03800 ( 391) hydrogen bonds : angle 3.98882 ( 1137) SS BOND : bond 0.00154 ( 1) SS BOND : angle 0.04771 ( 2) covalent geometry : bond 0.00366 ( 6757) covalent geometry : angle 0.49167 ( 9226) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3370.66 seconds wall clock time: 59 minutes 17.57 seconds (3557.57 seconds total)