Starting phenix.real_space_refine on Tue Mar 3 14:17:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ji3_22343/03_2026/7ji3_22343.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ji3_22343/03_2026/7ji3_22343.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ji3_22343/03_2026/7ji3_22343.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ji3_22343/03_2026/7ji3_22343.map" model { file = "/net/cci-nas-00/data/ceres_data/7ji3_22343/03_2026/7ji3_22343.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ji3_22343/03_2026/7ji3_22343.cif" } resolution = 3.46 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 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 36 5.16 5 C 3837 2.51 5 N 1005 2.21 5 O 1122 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 39 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6000 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 2000 Classifications: {'peptide': 259} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 12, 'TRANS': 246} Chain breaks: 2 Unresolved non-hydrogen bonds: 89 Unresolved non-hydrogen angles: 118 Unresolved non-hydrogen dihedrals: 74 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'ASN:plan1': 2, 'PHE:plan': 2, 'TYR:plan': 1, 'GLN:plan1': 1, 'TRP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 43 Chain: "B" Number of atoms: 2000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 2000 Classifications: {'peptide': 259} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 12, 'TRANS': 246} Chain breaks: 2 Unresolved non-hydrogen bonds: 89 Unresolved non-hydrogen angles: 118 Unresolved non-hydrogen dihedrals: 74 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'ASN:plan1': 2, 'PHE:plan': 2, 'TYR:plan': 1, 'GLN:plan1': 1, 'TRP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 43 Chain: "C" Number of atoms: 2000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 2000 Classifications: {'peptide': 259} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 12, 'TRANS': 246} Chain breaks: 2 Unresolved non-hydrogen bonds: 89 Unresolved non-hydrogen angles: 118 Unresolved non-hydrogen dihedrals: 74 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'ASN:plan1': 2, 'PHE:plan': 2, 'TYR:plan': 1, 'GLN:plan1': 1, 'TRP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 43 Time building chain proxies: 1.51, per 1000 atoms: 0.25 Number of scatterers: 6000 At special positions: 0 Unit cell: (84.7, 81.4, 127.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 36 16.00 O 1122 8.00 N 1005 7.00 C 3837 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 225 " - pdb=" SG CYS A 229 " distance=2.04 Simple disulfide: pdb=" SG CYS B 225 " - pdb=" SG CYS B 229 " distance=2.04 Simple disulfide: pdb=" SG CYS C 225 " - pdb=" SG CYS C 229 " distance=2.04 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: 0.43 Conformation dependent library (CDL) restraints added in 326.5 milliseconds 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1494 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 12 sheets defined 34.0% alpha, 32.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.15 Creating SS restraints... Processing helix chain 'A' and resid 66 through 99 removed outlier: 3.755A pdb=" N ILE A 90 " --> pdb=" O ALA A 86 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ASN A 99 " --> pdb=" O GLU A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 182 Processing helix chain 'A' and resid 209 through 214 removed outlier: 3.524A pdb=" N ILE A 213 " --> pdb=" O PHE A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 229 removed outlier: 3.946A pdb=" N PHE A 221 " --> pdb=" O ASN A 217 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N THR A 227 " --> pdb=" O GLY A 223 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ASN A 228 " --> pdb=" O GLU A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 332 removed outlier: 3.928A pdb=" N PHE A 319 " --> pdb=" O PHE A 315 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ALA A 322 " --> pdb=" O LEU A 318 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLN A 330 " --> pdb=" O LYS A 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 66 through 99 removed outlier: 3.755A pdb=" N ILE B 90 " --> pdb=" O ALA B 86 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ASN B 99 " --> pdb=" O GLU B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 182 Processing helix chain 'B' and resid 209 through 214 removed outlier: 3.525A pdb=" N ILE B 213 " --> pdb=" O PHE B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 229 removed outlier: 3.947A pdb=" N PHE B 221 " --> pdb=" O ASN B 217 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N THR B 227 " --> pdb=" O GLY B 223 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ASN B 228 " --> pdb=" O GLU B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 332 removed outlier: 3.927A pdb=" N PHE B 319 " --> pdb=" O PHE B 315 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ALA B 322 " --> pdb=" O LEU B 318 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLN B 330 " --> pdb=" O LYS B 326 " (cutoff:3.500A) Processing helix chain 'C' and resid 66 through 99 removed outlier: 3.754A pdb=" N ILE C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ASN C 99 " --> pdb=" O GLU C 95 " (cutoff:3.500A) Processing helix chain 'C' and resid 178 through 182 Processing helix chain 'C' and resid 209 through 214 removed outlier: 3.525A pdb=" N ILE C 213 " --> pdb=" O PHE C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 229 removed outlier: 3.947A pdb=" N PHE C 221 " --> pdb=" O ASN C 217 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N THR C 227 " --> pdb=" O GLY C 223 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ASN C 228 " --> pdb=" O GLU C 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 303 through 332 removed outlier: 3.928A pdb=" N PHE C 319 " --> pdb=" O PHE C 315 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ALA C 322 " --> pdb=" O LEU C 318 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLN C 330 " --> pdb=" O LYS C 326 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 101 through 108 removed outlier: 13.982A pdb=" N TYR A 292 " --> pdb=" O VAL A 242 " (cutoff:3.500A) removed outlier: 9.848A pdb=" N MET A 244 " --> pdb=" O TYR A 292 " (cutoff:3.500A) removed outlier: 9.713A pdb=" N GLN A 294 " --> pdb=" O MET A 244 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N LEU A 246 " --> pdb=" O GLN A 294 " (cutoff:3.500A) removed outlier: 8.124A pdb=" N ASN A 296 " --> pdb=" O LEU A 246 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N LYS A 248 " --> pdb=" O ASN A 296 " (cutoff:3.500A) removed outlier: 8.132A pdb=" N MET A 298 " --> pdb=" O LYS A 248 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LYS A 243 " --> pdb=" O GLU A 262 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 125 through 132 removed outlier: 6.336A pdb=" N GLN A 188 " --> pdb=" O LEU A 127 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N CYS A 129 " --> pdb=" O PHE A 186 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N PHE A 186 " --> pdb=" O CYS A 129 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N HIS A 131 " --> pdb=" O MET A 184 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N MET A 184 " --> pdb=" O HIS A 131 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N PHE A 286 " --> pdb=" O VAL A 185 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N PHE A 238 " --> pdb=" O LEU A 281 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N PHE A 283 " --> pdb=" O PHE A 238 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 152 through 156 removed outlier: 3.671A pdb=" N GLU A 155 " --> pdb=" O ALA A 170 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU A 119 " --> pdb=" O LEU A 171 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 200 through 203 Processing sheet with id=AA5, first strand: chain 'B' and resid 101 through 108 removed outlier: 13.980A pdb=" N TYR B 292 " --> pdb=" O VAL B 242 " (cutoff:3.500A) removed outlier: 9.847A pdb=" N MET B 244 " --> pdb=" O TYR B 292 " (cutoff:3.500A) removed outlier: 9.713A pdb=" N GLN B 294 " --> pdb=" O MET B 244 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N LEU B 246 " --> pdb=" O GLN B 294 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N ASN B 296 " --> pdb=" O LEU B 246 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N LYS B 248 " --> pdb=" O ASN B 296 " (cutoff:3.500A) removed outlier: 8.132A pdb=" N MET B 298 " --> pdb=" O LYS B 248 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 125 through 132 removed outlier: 6.335A pdb=" N GLN B 188 " --> pdb=" O LEU B 127 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N CYS B 129 " --> pdb=" O PHE B 186 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N PHE B 186 " --> pdb=" O CYS B 129 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N HIS B 131 " --> pdb=" O MET B 184 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N MET B 184 " --> pdb=" O HIS B 131 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N PHE B 286 " --> pdb=" O VAL B 185 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N PHE B 238 " --> pdb=" O LEU B 281 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N PHE B 283 " --> pdb=" O PHE B 238 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 152 through 156 removed outlier: 3.671A pdb=" N GLU B 155 " --> pdb=" O ALA B 170 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU B 119 " --> pdb=" O LEU B 171 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 200 through 203 Processing sheet with id=AA9, first strand: chain 'C' and resid 101 through 108 removed outlier: 13.981A pdb=" N TYR C 292 " --> pdb=" O VAL C 242 " (cutoff:3.500A) removed outlier: 9.847A pdb=" N MET C 244 " --> pdb=" O TYR C 292 " (cutoff:3.500A) removed outlier: 9.713A pdb=" N GLN C 294 " --> pdb=" O MET C 244 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N LEU C 246 " --> pdb=" O GLN C 294 " (cutoff:3.500A) removed outlier: 8.124A pdb=" N ASN C 296 " --> pdb=" O LEU C 246 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N LYS C 248 " --> pdb=" O ASN C 296 " (cutoff:3.500A) removed outlier: 8.131A pdb=" N MET C 298 " --> pdb=" O LYS C 248 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS C 243 " --> pdb=" O GLU C 262 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 125 through 132 removed outlier: 6.335A pdb=" N GLN C 188 " --> pdb=" O LEU C 127 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N CYS C 129 " --> pdb=" O PHE C 186 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N PHE C 186 " --> pdb=" O CYS C 129 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N HIS C 131 " --> pdb=" O MET C 184 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N MET C 184 " --> pdb=" O HIS C 131 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N PHE C 286 " --> pdb=" O VAL C 185 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N PHE C 238 " --> pdb=" O LEU C 281 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N PHE C 283 " --> pdb=" O PHE C 238 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 152 through 156 removed outlier: 3.672A pdb=" N GLU C 155 " --> pdb=" O ALA C 170 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU C 119 " --> pdb=" O LEU C 171 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 200 through 203 311 hydrogen bonds defined for protein. 861 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: 0.71 Time building geometry restraints manager: 0.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 1947 1.35 - 1.48: 1562 1.48 - 1.61: 2566 1.61 - 1.74: 0 1.74 - 1.86: 60 Bond restraints: 6135 Sorted by residual: bond pdb=" N ILE C 299 " pdb=" CA ILE C 299 " ideal model delta sigma weight residual 1.458 1.496 -0.038 1.14e-02 7.69e+03 1.14e+01 bond pdb=" N ILE A 299 " pdb=" CA ILE A 299 " ideal model delta sigma weight residual 1.458 1.495 -0.037 1.14e-02 7.69e+03 1.07e+01 bond pdb=" N ILE B 299 " pdb=" CA ILE B 299 " ideal model delta sigma weight residual 1.458 1.495 -0.037 1.14e-02 7.69e+03 1.06e+01 bond pdb=" N ILE C 308 " pdb=" CA ILE C 308 " ideal model delta sigma weight residual 1.461 1.495 -0.034 1.19e-02 7.06e+03 8.14e+00 bond pdb=" N ILE B 308 " pdb=" CA ILE B 308 " ideal model delta sigma weight residual 1.461 1.494 -0.034 1.19e-02 7.06e+03 8.11e+00 ... (remaining 6130 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.29: 7549 1.29 - 2.57: 641 2.57 - 3.86: 107 3.86 - 5.14: 28 5.14 - 6.43: 6 Bond angle restraints: 8331 Sorted by residual: angle pdb=" N GLY B 223 " pdb=" CA GLY B 223 " pdb=" C GLY B 223 " ideal model delta sigma weight residual 112.50 107.99 4.51 1.16e+00 7.43e-01 1.51e+01 angle pdb=" N GLY A 223 " pdb=" CA GLY A 223 " pdb=" C GLY A 223 " ideal model delta sigma weight residual 112.50 108.00 4.50 1.16e+00 7.43e-01 1.51e+01 angle pdb=" N CYS C 225 " pdb=" CA CYS C 225 " pdb=" C CYS C 225 " ideal model delta sigma weight residual 112.54 116.65 -4.11 1.22e+00 6.72e-01 1.14e+01 angle pdb=" N MET A 316 " pdb=" CA MET A 316 " pdb=" C MET A 316 " ideal model delta sigma weight residual 112.45 107.77 4.68 1.39e+00 5.18e-01 1.13e+01 angle pdb=" N CYS B 225 " pdb=" CA CYS B 225 " pdb=" C CYS B 225 " ideal model delta sigma weight residual 112.54 116.65 -4.11 1.22e+00 6.72e-01 1.13e+01 ... (remaining 8326 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.48: 3332 16.48 - 32.97: 266 32.97 - 49.45: 60 49.45 - 65.94: 7 65.94 - 82.42: 10 Dihedral angle restraints: 3675 sinusoidal: 1386 harmonic: 2289 Sorted by residual: dihedral pdb=" CB CYS C 225 " pdb=" SG CYS C 225 " pdb=" SG CYS C 229 " pdb=" CB CYS C 229 " ideal model delta sinusoidal sigma weight residual -86.00 -123.22 37.22 1 1.00e+01 1.00e-02 1.96e+01 dihedral pdb=" CB CYS A 225 " pdb=" SG CYS A 225 " pdb=" SG CYS A 229 " pdb=" CB CYS A 229 " ideal model delta sinusoidal sigma weight residual -86.00 -123.22 37.22 1 1.00e+01 1.00e-02 1.95e+01 dihedral pdb=" CB CYS B 225 " pdb=" SG CYS B 225 " pdb=" SG CYS B 229 " pdb=" CB CYS B 229 " ideal model delta sinusoidal sigma weight residual -86.00 -123.20 37.20 1 1.00e+01 1.00e-02 1.95e+01 ... (remaining 3672 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 623 0.043 - 0.085: 182 0.085 - 0.127: 92 0.127 - 0.170: 28 0.170 - 0.212: 8 Chirality restraints: 933 Sorted by residual: chirality pdb=" CA MET B 316 " pdb=" N MET B 316 " pdb=" C MET B 316 " pdb=" CB MET B 316 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" CA MET A 316 " pdb=" N MET A 316 " pdb=" C MET A 316 " pdb=" CB MET A 316 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" CA MET C 316 " pdb=" N MET C 316 " pdb=" C MET C 316 " pdb=" CB MET C 316 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.07e+00 ... (remaining 930 not shown) Planarity restraints: 1077 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A 142 " 0.045 5.00e-02 4.00e+02 6.80e-02 7.39e+00 pdb=" N PRO A 143 " -0.118 5.00e-02 4.00e+02 pdb=" CA PRO A 143 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 143 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU C 142 " 0.045 5.00e-02 4.00e+02 6.78e-02 7.36e+00 pdb=" N PRO C 143 " -0.117 5.00e-02 4.00e+02 pdb=" CA PRO C 143 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO C 143 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU B 142 " 0.045 5.00e-02 4.00e+02 6.77e-02 7.33e+00 pdb=" N PRO B 143 " -0.117 5.00e-02 4.00e+02 pdb=" CA PRO B 143 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO B 143 " 0.037 5.00e-02 4.00e+02 ... (remaining 1074 not shown) Histogram of nonbonded interaction distances: 2.37 - 2.87: 2164 2.87 - 3.38: 4914 3.38 - 3.89: 9427 3.89 - 4.39: 9936 4.39 - 4.90: 18361 Nonbonded interactions: 44802 Sorted by model distance: nonbonded pdb=" O PHE A 324 " pdb=" OG1 THR A 328 " model vdw 2.365 3.040 nonbonded pdb=" O PHE C 324 " pdb=" OG1 THR C 328 " model vdw 2.365 3.040 nonbonded pdb=" O PHE B 324 " pdb=" OG1 THR B 328 " model vdw 2.366 3.040 nonbonded pdb=" O PRO B 176 " pdb=" NE1 TRP B 288 " model vdw 2.416 3.120 nonbonded pdb=" O PRO A 176 " pdb=" NE1 TRP A 288 " model vdw 2.416 3.120 ... (remaining 44797 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.000 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: 0.000 Extract box with map and model: 0.070 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 6.960 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 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:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7122 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 6138 Z= 0.305 Angle : 0.803 6.738 8337 Z= 0.514 Chirality : 0.055 0.212 933 Planarity : 0.008 0.068 1077 Dihedral : 13.456 82.424 2172 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 0.00 % Allowed : 14.74 % Favored : 85.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.13 (0.22), residues: 759 helix: -3.58 (0.21), residues: 255 sheet: -2.95 (0.22), residues: 312 loop : -2.99 (0.32), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 239 TYR 0.021 0.002 TYR C 282 PHE 0.030 0.003 PHE C 234 TRP 0.010 0.001 TRP A 241 HIS 0.002 0.001 HIS A 134 Details of bonding type rmsd covalent geometry : bond 0.00535 ( 6135) covalent geometry : angle 0.79280 ( 8331) SS BOND : bond 0.01092 ( 3) SS BOND : angle 4.79473 ( 6) hydrogen bonds : bond 0.21650 ( 311) hydrogen bonds : angle 8.71332 ( 861) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 0.215 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 290 ASP cc_start: 0.6077 (p0) cc_final: 0.5719 (p0) outliers start: 0 outliers final: 0 residues processed: 137 average time/residue: 0.0978 time to fit residues: 16.6902 Evaluate side-chains 76 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 49 optimal weight: 7.9990 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 8.9990 chunk 62 optimal weight: 7.9990 chunk 51 optimal weight: 6.9990 chunk 38 optimal weight: 5.9990 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 74 optimal weight: 8.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 88 GLN A 99 ASN A 107 GLN ** A 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 135 ASN A 188 GLN ** A 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 280 GLN B 88 GLN B 99 ASN B 107 GLN ** B 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 135 ASN B 188 GLN ** B 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 280 GLN C 88 GLN C 107 GLN ** C 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 135 ASN C 188 GLN ** C 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 280 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.066002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.047326 restraints weight = 22319.845| |-----------------------------------------------------------------------------| r_work (start): 0.2802 rms_B_bonded: 4.40 r_work: 0.2640 rms_B_bonded: 4.90 restraints_weight: 0.5000 r_work (final): 0.2640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.2791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.036 6138 Z= 0.307 Angle : 0.663 9.216 8337 Z= 0.343 Chirality : 0.044 0.169 933 Planarity : 0.006 0.056 1077 Dihedral : 4.864 24.242 831 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 2.08 % Allowed : 18.75 % Favored : 79.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.76 (0.27), residues: 759 helix: -0.41 (0.30), residues: 252 sheet: -2.22 (0.26), residues: 306 loop : -2.53 (0.36), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 145 TYR 0.019 0.002 TYR B 282 PHE 0.017 0.002 PHE B 234 TRP 0.006 0.001 TRP C 305 HIS 0.002 0.001 HIS C 134 Details of bonding type rmsd covalent geometry : bond 0.00680 ( 6135) covalent geometry : angle 0.65875 ( 8331) SS BOND : bond 0.00288 ( 3) SS BOND : angle 2.97277 ( 6) hydrogen bonds : bond 0.03942 ( 311) hydrogen bonds : angle 4.87471 ( 861) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 89 time to evaluate : 0.220 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 98 LYS cc_start: 0.9351 (mmmm) cc_final: 0.8888 (mmtm) REVERT: A 102 MET cc_start: 0.8175 (tpp) cc_final: 0.7881 (mmp) REVERT: A 171 LEU cc_start: 0.9348 (OUTLIER) cc_final: 0.9146 (tt) REVERT: A 187 MET cc_start: 0.9180 (ptp) cc_final: 0.8975 (ptp) REVERT: A 218 LYS cc_start: 0.8654 (mmtt) cc_final: 0.8352 (mmtt) REVERT: A 290 ASP cc_start: 0.8758 (p0) cc_final: 0.8121 (p0) REVERT: A 292 TYR cc_start: 0.9124 (m-80) cc_final: 0.8812 (m-80) REVERT: B 96 LYS cc_start: 0.8664 (mptt) cc_final: 0.8352 (mmtp) REVERT: B 150 ASP cc_start: 0.8673 (m-30) cc_final: 0.8390 (m-30) REVERT: B 171 LEU cc_start: 0.9392 (OUTLIER) cc_final: 0.9177 (tt) REVERT: B 290 ASP cc_start: 0.8802 (p0) cc_final: 0.8323 (p0) REVERT: C 96 LYS cc_start: 0.8688 (mptt) cc_final: 0.8365 (mmtp) REVERT: C 98 LYS cc_start: 0.9505 (mmmm) cc_final: 0.9028 (mmtm) REVERT: C 218 LYS cc_start: 0.8604 (mmtt) cc_final: 0.7972 (mmtt) outliers start: 13 outliers final: 6 residues processed: 97 average time/residue: 0.1004 time to fit residues: 12.0664 Evaluate side-chains 87 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 79 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 303 ASN Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 303 ASN Chi-restraints excluded: chain C residue 179 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 61 optimal weight: 0.9980 chunk 46 optimal weight: 4.9990 chunk 60 optimal weight: 0.9990 chunk 17 optimal weight: 3.9990 chunk 3 optimal weight: 4.9990 chunk 50 optimal weight: 40.0000 chunk 54 optimal weight: 4.9990 chunk 44 optimal weight: 0.0770 chunk 39 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 overall best weight: 1.2144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 HIS ** A 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 134 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.067565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.048766 restraints weight = 21906.137| |-----------------------------------------------------------------------------| r_work (start): 0.2850 rms_B_bonded: 4.43 r_work: 0.2687 rms_B_bonded: 4.93 restraints_weight: 0.5000 r_work (final): 0.2687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.3146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6138 Z= 0.127 Angle : 0.563 10.670 8337 Z= 0.278 Chirality : 0.043 0.233 933 Planarity : 0.004 0.051 1077 Dihedral : 4.436 23.178 831 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.92 % Allowed : 17.31 % Favored : 80.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.42 (0.30), residues: 759 helix: 1.10 (0.33), residues: 252 sheet: -1.63 (0.27), residues: 306 loop : -2.16 (0.39), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 180 TYR 0.010 0.001 TYR B 282 PHE 0.014 0.001 PHE B 234 TRP 0.004 0.001 TRP B 241 HIS 0.002 0.001 HIS B 131 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 6135) covalent geometry : angle 0.55992 ( 8331) SS BOND : bond 0.00477 ( 3) SS BOND : angle 2.28763 ( 6) hydrogen bonds : bond 0.03000 ( 311) hydrogen bonds : angle 4.07376 ( 861) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 83 time to evaluate : 0.220 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 96 LYS cc_start: 0.8628 (mptt) cc_final: 0.8383 (mmtp) REVERT: A 98 LYS cc_start: 0.9426 (mmmm) cc_final: 0.8924 (mmtm) REVERT: A 218 LYS cc_start: 0.8626 (mmtt) cc_final: 0.8277 (mmtt) REVERT: A 290 ASP cc_start: 0.8629 (p0) cc_final: 0.7907 (p0) REVERT: A 292 TYR cc_start: 0.9110 (m-80) cc_final: 0.8739 (m-80) REVERT: A 298 MET cc_start: 0.9320 (tpp) cc_final: 0.9042 (mmm) REVERT: B 98 LYS cc_start: 0.9520 (tppp) cc_final: 0.9315 (ttmm) REVERT: B 150 ASP cc_start: 0.8764 (m-30) cc_final: 0.8476 (m-30) REVERT: B 184 MET cc_start: 0.9613 (ptp) cc_final: 0.9394 (ptp) REVERT: B 204 MET cc_start: 0.8998 (OUTLIER) cc_final: 0.8596 (ttt) REVERT: B 290 ASP cc_start: 0.8680 (p0) cc_final: 0.8203 (p0) REVERT: C 98 LYS cc_start: 0.9478 (mmmm) cc_final: 0.9013 (mmtm) REVERT: C 171 LEU cc_start: 0.9341 (OUTLIER) cc_final: 0.8858 (tt) REVERT: C 218 LYS cc_start: 0.8518 (mmtt) cc_final: 0.7810 (mmtt) outliers start: 12 outliers final: 7 residues processed: 91 average time/residue: 0.0917 time to fit residues: 10.5814 Evaluate side-chains 88 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 79 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 229 CYS Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 204 MET Chi-restraints excluded: chain B residue 229 CYS Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 311 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 43 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 58 optimal weight: 9.9990 chunk 13 optimal weight: 0.7980 chunk 70 optimal weight: 7.9990 chunk 57 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 61 optimal weight: 4.9990 chunk 71 optimal weight: 4.9990 chunk 39 optimal weight: 0.0980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.068528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.049693 restraints weight = 21692.067| |-----------------------------------------------------------------------------| r_work (start): 0.2881 rms_B_bonded: 4.47 r_work: 0.2717 rms_B_bonded: 4.95 restraints_weight: 0.5000 r_work (final): 0.2717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.3385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 6138 Z= 0.098 Angle : 0.557 11.081 8337 Z= 0.267 Chirality : 0.043 0.271 933 Planarity : 0.004 0.042 1077 Dihedral : 4.082 21.683 831 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 1.44 % Allowed : 18.75 % Favored : 79.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.73 (0.31), residues: 759 helix: 1.75 (0.34), residues: 252 sheet: -1.25 (0.27), residues: 306 loop : -1.91 (0.42), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 272 TYR 0.008 0.001 TYR B 282 PHE 0.013 0.001 PHE B 234 TRP 0.003 0.000 TRP C 305 HIS 0.001 0.000 HIS B 131 Details of bonding type rmsd covalent geometry : bond 0.00226 ( 6135) covalent geometry : angle 0.55440 ( 8331) SS BOND : bond 0.00456 ( 3) SS BOND : angle 1.96039 ( 6) hydrogen bonds : bond 0.02568 ( 311) hydrogen bonds : angle 3.65417 ( 861) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 87 time to evaluate : 0.202 Fit side-chains revert: symmetry clash REVERT: A 98 LYS cc_start: 0.9502 (mmmm) cc_final: 0.8984 (mmtm) REVERT: A 218 LYS cc_start: 0.8642 (mmtt) cc_final: 0.8257 (mmtt) REVERT: A 290 ASP cc_start: 0.8609 (p0) cc_final: 0.8049 (p0) REVERT: A 292 TYR cc_start: 0.9090 (m-80) cc_final: 0.8848 (m-80) REVERT: B 102 MET cc_start: 0.9296 (mmm) cc_final: 0.9010 (tpt) REVERT: B 204 MET cc_start: 0.8902 (OUTLIER) cc_final: 0.8638 (tmm) REVERT: B 218 LYS cc_start: 0.8721 (mmtt) cc_final: 0.8326 (mmtt) REVERT: B 290 ASP cc_start: 0.8643 (p0) cc_final: 0.8158 (p0) REVERT: C 98 LYS cc_start: 0.9515 (mmmm) cc_final: 0.9078 (mmtm) REVERT: C 171 LEU cc_start: 0.9326 (OUTLIER) cc_final: 0.8816 (tt) REVERT: C 197 ASP cc_start: 0.9591 (p0) cc_final: 0.9193 (p0) REVERT: C 218 LYS cc_start: 0.8568 (mmtt) cc_final: 0.7847 (mmtt) outliers start: 9 outliers final: 5 residues processed: 92 average time/residue: 0.0917 time to fit residues: 10.6115 Evaluate side-chains 84 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 77 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 204 MET Chi-restraints excluded: chain B residue 229 CYS Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 311 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 11 optimal weight: 6.9990 chunk 24 optimal weight: 5.9990 chunk 69 optimal weight: 5.9990 chunk 39 optimal weight: 5.9990 chunk 72 optimal weight: 1.9990 chunk 63 optimal weight: 5.9990 chunk 73 optimal weight: 0.9990 chunk 22 optimal weight: 9.9990 chunk 34 optimal weight: 9.9990 chunk 23 optimal weight: 5.9990 chunk 25 optimal weight: 40.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 GLN ** A 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 134 HIS B 188 GLN ** B 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 294 GLN B 296 ASN ** C 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.065134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.046501 restraints weight = 22885.755| |-----------------------------------------------------------------------------| r_work (start): 0.2781 rms_B_bonded: 4.42 r_work: 0.2616 rms_B_bonded: 4.93 restraints_weight: 0.5000 r_work (final): 0.2616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.3633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.037 6138 Z= 0.310 Angle : 0.660 11.425 8337 Z= 0.327 Chirality : 0.044 0.179 933 Planarity : 0.004 0.043 1077 Dihedral : 4.414 21.462 831 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 1.76 % Allowed : 18.27 % Favored : 79.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.73 (0.30), residues: 759 helix: 1.85 (0.33), residues: 252 sheet: -1.44 (0.26), residues: 300 loop : -1.69 (0.41), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 180 TYR 0.016 0.002 TYR B 282 PHE 0.020 0.002 PHE C 206 TRP 0.011 0.001 TRP B 305 HIS 0.002 0.001 HIS B 131 Details of bonding type rmsd covalent geometry : bond 0.00694 ( 6135) covalent geometry : angle 0.65670 ( 8331) SS BOND : bond 0.00364 ( 3) SS BOND : angle 2.56377 ( 6) hydrogen bonds : bond 0.03112 ( 311) hydrogen bonds : angle 4.04593 ( 861) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 73 time to evaluate : 0.233 Fit side-chains revert: symmetry clash REVERT: A 290 ASP cc_start: 0.8679 (p0) cc_final: 0.7980 (p0) REVERT: A 292 TYR cc_start: 0.9053 (m-80) cc_final: 0.8692 (m-80) REVERT: B 184 MET cc_start: 0.9631 (ptp) cc_final: 0.9414 (ptp) REVERT: B 204 MET cc_start: 0.9122 (OUTLIER) cc_final: 0.8746 (tmm) REVERT: B 248 LYS cc_start: 0.9254 (ttmm) cc_final: 0.8943 (ttmm) REVERT: B 290 ASP cc_start: 0.8678 (p0) cc_final: 0.8207 (p0) REVERT: B 298 MET cc_start: 0.8697 (mmm) cc_final: 0.8415 (mmm) REVERT: C 98 LYS cc_start: 0.9524 (mmmm) cc_final: 0.9112 (mmtm) outliers start: 11 outliers final: 9 residues processed: 79 average time/residue: 0.0800 time to fit residues: 8.4570 Evaluate side-chains 79 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 69 time to evaluate : 0.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 303 ASN Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 204 MET Chi-restraints excluded: chain B residue 229 CYS Chi-restraints excluded: chain B residue 296 ASN Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 311 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 50 optimal weight: 40.0000 chunk 10 optimal weight: 2.9990 chunk 70 optimal weight: 0.9980 chunk 74 optimal weight: 8.9990 chunk 64 optimal weight: 3.9990 chunk 5 optimal weight: 6.9990 chunk 51 optimal weight: 5.9990 chunk 69 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 131 HIS ** A 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 188 GLN ** C 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.066188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.047571 restraints weight = 22280.055| |-----------------------------------------------------------------------------| r_work (start): 0.2816 rms_B_bonded: 4.39 r_work: 0.2647 rms_B_bonded: 4.90 restraints_weight: 0.5000 r_work (final): 0.2647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.3689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 6138 Z= 0.178 Angle : 0.586 12.011 8337 Z= 0.284 Chirality : 0.044 0.284 933 Planarity : 0.004 0.045 1077 Dihedral : 4.225 21.207 831 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.76 % Allowed : 17.79 % Favored : 80.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.48 (0.31), residues: 759 helix: 2.06 (0.33), residues: 252 sheet: -1.27 (0.27), residues: 300 loop : -1.64 (0.42), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 272 TYR 0.011 0.001 TYR B 282 PHE 0.014 0.001 PHE B 234 TRP 0.009 0.001 TRP B 305 HIS 0.001 0.001 HIS A 134 Details of bonding type rmsd covalent geometry : bond 0.00401 ( 6135) covalent geometry : angle 0.58333 ( 8331) SS BOND : bond 0.00408 ( 3) SS BOND : angle 2.17765 ( 6) hydrogen bonds : bond 0.02763 ( 311) hydrogen bonds : angle 3.81002 ( 861) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 77 time to evaluate : 0.245 Fit side-chains revert: symmetry clash REVERT: A 98 LYS cc_start: 0.9496 (mmmm) cc_final: 0.9011 (mmtm) REVERT: A 290 ASP cc_start: 0.8634 (p0) cc_final: 0.8007 (p0) REVERT: A 292 TYR cc_start: 0.9037 (m-80) cc_final: 0.8677 (m-80) REVERT: B 129 CYS cc_start: 0.8783 (t) cc_final: 0.8505 (t) REVERT: B 204 MET cc_start: 0.9057 (OUTLIER) cc_final: 0.8719 (tmm) REVERT: B 248 LYS cc_start: 0.9263 (ttmm) cc_final: 0.8951 (ttmm) REVERT: B 290 ASP cc_start: 0.8617 (p0) cc_final: 0.8047 (p0) REVERT: B 298 MET cc_start: 0.8520 (mmm) cc_final: 0.8204 (mmm) REVERT: C 98 LYS cc_start: 0.9507 (mmmm) cc_final: 0.9113 (mmtm) REVERT: C 171 LEU cc_start: 0.9352 (OUTLIER) cc_final: 0.8810 (tt) REVERT: C 197 ASP cc_start: 0.9561 (p0) cc_final: 0.9353 (p0) outliers start: 11 outliers final: 7 residues processed: 83 average time/residue: 0.0723 time to fit residues: 8.0295 Evaluate side-chains 81 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 72 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 HIS Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 204 MET Chi-restraints excluded: chain B residue 229 CYS Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 311 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 42 optimal weight: 1.9990 chunk 74 optimal weight: 5.9990 chunk 49 optimal weight: 7.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 8.9990 chunk 57 optimal weight: 0.2980 chunk 67 optimal weight: 0.9980 chunk 8 optimal weight: 7.9990 chunk 53 optimal weight: 3.9990 chunk 37 optimal weight: 5.9990 chunk 71 optimal weight: 1.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.066443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.047803 restraints weight = 22100.988| |-----------------------------------------------------------------------------| r_work (start): 0.2826 rms_B_bonded: 4.37 r_work: 0.2659 rms_B_bonded: 4.87 restraints_weight: 0.5000 r_work (final): 0.2659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.3756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 6138 Z= 0.156 Angle : 0.590 12.293 8337 Z= 0.283 Chirality : 0.043 0.230 933 Planarity : 0.004 0.043 1077 Dihedral : 4.173 21.112 831 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.92 % Allowed : 18.11 % Favored : 79.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.31), residues: 759 helix: 2.15 (0.33), residues: 252 sheet: -1.13 (0.27), residues: 300 loop : -1.59 (0.42), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 272 TYR 0.010 0.001 TYR B 282 PHE 0.015 0.001 PHE B 234 TRP 0.007 0.001 TRP C 305 HIS 0.007 0.001 HIS A 131 Details of bonding type rmsd covalent geometry : bond 0.00357 ( 6135) covalent geometry : angle 0.58737 ( 8331) SS BOND : bond 0.00489 ( 3) SS BOND : angle 2.16297 ( 6) hydrogen bonds : bond 0.02697 ( 311) hydrogen bonds : angle 3.73500 ( 861) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 78 time to evaluate : 0.188 Fit side-chains revert: symmetry clash REVERT: A 98 LYS cc_start: 0.9499 (mmmm) cc_final: 0.8976 (mmtm) REVERT: A 290 ASP cc_start: 0.8632 (p0) cc_final: 0.8007 (p0) REVERT: A 292 TYR cc_start: 0.9009 (m-80) cc_final: 0.8666 (m-80) REVERT: A 295 GLN cc_start: 0.9179 (OUTLIER) cc_final: 0.8443 (mp10) REVERT: B 129 CYS cc_start: 0.8842 (t) cc_final: 0.8522 (t) REVERT: B 204 MET cc_start: 0.9022 (OUTLIER) cc_final: 0.8726 (tmm) REVERT: B 218 LYS cc_start: 0.8832 (mmtt) cc_final: 0.8391 (mmtt) REVERT: B 248 LYS cc_start: 0.9215 (ttmm) cc_final: 0.8908 (ttmm) REVERT: B 290 ASP cc_start: 0.8603 (p0) cc_final: 0.7767 (p0) REVERT: B 315 PHE cc_start: 0.9415 (m-10) cc_final: 0.9039 (t80) REVERT: C 98 LYS cc_start: 0.9510 (mmmm) cc_final: 0.9114 (mmtm) REVERT: C 102 MET cc_start: 0.9361 (ttm) cc_final: 0.8908 (tpp) REVERT: C 171 LEU cc_start: 0.9348 (OUTLIER) cc_final: 0.8810 (tt) REVERT: C 197 ASP cc_start: 0.9573 (p0) cc_final: 0.9362 (p0) outliers start: 12 outliers final: 7 residues processed: 86 average time/residue: 0.0699 time to fit residues: 8.1001 Evaluate side-chains 84 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 74 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 229 CYS Chi-restraints excluded: chain A residue 295 GLN Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 204 MET Chi-restraints excluded: chain B residue 229 CYS Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 311 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 8 optimal weight: 9.9990 chunk 49 optimal weight: 6.9990 chunk 16 optimal weight: 1.9990 chunk 57 optimal weight: 10.0000 chunk 70 optimal weight: 0.5980 chunk 19 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 17 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.067406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.048724 restraints weight = 21875.359| |-----------------------------------------------------------------------------| r_work (start): 0.2854 rms_B_bonded: 4.40 r_work: 0.2686 rms_B_bonded: 4.89 restraints_weight: 0.5000 r_work (final): 0.2686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.3833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6138 Z= 0.116 Angle : 0.597 12.447 8337 Z= 0.279 Chirality : 0.045 0.365 933 Planarity : 0.004 0.044 1077 Dihedral : 4.023 20.874 831 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.76 % Allowed : 18.27 % Favored : 79.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.31), residues: 759 helix: 2.21 (0.33), residues: 255 sheet: -0.93 (0.28), residues: 300 loop : -1.49 (0.43), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 272 TYR 0.008 0.001 TYR B 282 PHE 0.014 0.001 PHE B 234 TRP 0.007 0.001 TRP B 305 HIS 0.002 0.000 HIS A 134 Details of bonding type rmsd covalent geometry : bond 0.00270 ( 6135) covalent geometry : angle 0.59471 ( 8331) SS BOND : bond 0.00516 ( 3) SS BOND : angle 1.95760 ( 6) hydrogen bonds : bond 0.02501 ( 311) hydrogen bonds : angle 3.55632 ( 861) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 84 time to evaluate : 0.207 Fit side-chains REVERT: A 98 LYS cc_start: 0.9508 (mmmm) cc_final: 0.9003 (mmtm) REVERT: A 218 LYS cc_start: 0.8835 (mmtt) cc_final: 0.8441 (mmtt) REVERT: A 290 ASP cc_start: 0.8588 (p0) cc_final: 0.7980 (p0) REVERT: A 292 TYR cc_start: 0.9012 (m-80) cc_final: 0.8679 (m-80) REVERT: A 295 GLN cc_start: 0.9175 (OUTLIER) cc_final: 0.8435 (mp10) REVERT: A 315 PHE cc_start: 0.9455 (m-10) cc_final: 0.9095 (t80) REVERT: B 129 CYS cc_start: 0.8826 (t) cc_final: 0.8447 (t) REVERT: B 204 MET cc_start: 0.8944 (OUTLIER) cc_final: 0.8659 (tmm) REVERT: B 218 LYS cc_start: 0.8850 (mmtt) cc_final: 0.8419 (mmtt) REVERT: B 248 LYS cc_start: 0.9216 (ttmm) cc_final: 0.8924 (ttmm) REVERT: B 290 ASP cc_start: 0.8618 (p0) cc_final: 0.7760 (p0) REVERT: B 315 PHE cc_start: 0.9348 (m-10) cc_final: 0.8984 (t80) REVERT: C 98 LYS cc_start: 0.9488 (mmmm) cc_final: 0.9112 (mmtm) REVERT: C 102 MET cc_start: 0.9410 (ttm) cc_final: 0.8995 (tpp) REVERT: C 171 LEU cc_start: 0.9342 (OUTLIER) cc_final: 0.8784 (tt) REVERT: C 204 MET cc_start: 0.8731 (tmm) cc_final: 0.8339 (tmm) REVERT: C 218 LYS cc_start: 0.8785 (mmtt) cc_final: 0.7980 (mmtt) REVERT: C 222 MET cc_start: 0.9407 (tpt) cc_final: 0.9114 (tpt) REVERT: C 243 LYS cc_start: 0.8980 (mtpt) cc_final: 0.8700 (mtpp) REVERT: C 297 LYS cc_start: 0.8605 (mmmm) cc_final: 0.7882 (mmtm) REVERT: C 315 PHE cc_start: 0.9441 (m-10) cc_final: 0.9044 (t80) outliers start: 11 outliers final: 7 residues processed: 91 average time/residue: 0.0765 time to fit residues: 9.2187 Evaluate side-chains 87 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 77 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 229 CYS Chi-restraints excluded: chain A residue 295 GLN Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 204 MET Chi-restraints excluded: chain B residue 229 CYS Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 311 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 12 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 42 optimal weight: 5.9990 chunk 32 optimal weight: 0.0070 chunk 22 optimal weight: 3.9990 chunk 58 optimal weight: 6.9990 chunk 29 optimal weight: 5.9990 chunk 62 optimal weight: 5.9990 chunk 71 optimal weight: 3.9990 chunk 8 optimal weight: 0.8980 chunk 17 optimal weight: 3.9990 overall best weight: 1.7602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.066810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.048244 restraints weight = 22142.224| |-----------------------------------------------------------------------------| r_work (start): 0.2840 rms_B_bonded: 4.37 r_work: 0.2675 rms_B_bonded: 4.87 restraints_weight: 0.5000 r_work (final): 0.2675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.3892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6138 Z= 0.150 Angle : 0.619 13.248 8337 Z= 0.291 Chirality : 0.045 0.411 933 Planarity : 0.004 0.044 1077 Dihedral : 4.036 20.460 831 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.60 % Allowed : 19.07 % Favored : 79.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.31), residues: 759 helix: 2.33 (0.33), residues: 255 sheet: -0.87 (0.28), residues: 300 loop : -1.46 (0.43), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 272 TYR 0.020 0.001 TYR C 203 PHE 0.015 0.001 PHE C 234 TRP 0.009 0.001 TRP B 305 HIS 0.001 0.000 HIS C 134 Details of bonding type rmsd covalent geometry : bond 0.00346 ( 6135) covalent geometry : angle 0.61620 ( 8331) SS BOND : bond 0.00454 ( 3) SS BOND : angle 2.13537 ( 6) hydrogen bonds : bond 0.02652 ( 311) hydrogen bonds : angle 3.66417 ( 861) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 81 time to evaluate : 0.269 Fit side-chains REVERT: A 98 LYS cc_start: 0.9501 (mmmm) cc_final: 0.8986 (mmtp) REVERT: A 204 MET cc_start: 0.9044 (ttp) cc_final: 0.8715 (tmm) REVERT: A 218 LYS cc_start: 0.8888 (mmtt) cc_final: 0.8490 (mmtt) REVERT: A 290 ASP cc_start: 0.8618 (p0) cc_final: 0.8013 (p0) REVERT: A 292 TYR cc_start: 0.8992 (m-80) cc_final: 0.8660 (m-80) REVERT: A 295 GLN cc_start: 0.9229 (OUTLIER) cc_final: 0.8480 (mp10) REVERT: A 315 PHE cc_start: 0.9455 (m-10) cc_final: 0.9102 (t80) REVERT: B 129 CYS cc_start: 0.8825 (t) cc_final: 0.8410 (t) REVERT: B 204 MET cc_start: 0.8984 (OUTLIER) cc_final: 0.8667 (tmm) REVERT: B 218 LYS cc_start: 0.8881 (mmtt) cc_final: 0.8446 (mmtt) REVERT: B 248 LYS cc_start: 0.9210 (ttmm) cc_final: 0.8917 (ttmm) REVERT: B 290 ASP cc_start: 0.8616 (p0) cc_final: 0.7666 (p0) REVERT: B 292 TYR cc_start: 0.9094 (m-10) cc_final: 0.8793 (m-10) REVERT: B 315 PHE cc_start: 0.9351 (m-10) cc_final: 0.8960 (t80) REVERT: C 98 LYS cc_start: 0.9471 (mmmm) cc_final: 0.9083 (mmtm) REVERT: C 102 MET cc_start: 0.9379 (ttm) cc_final: 0.8893 (tpp) REVERT: C 171 LEU cc_start: 0.9338 (OUTLIER) cc_final: 0.8778 (tt) REVERT: C 204 MET cc_start: 0.8678 (tmm) cc_final: 0.8239 (tmm) REVERT: C 218 LYS cc_start: 0.8837 (mmtt) cc_final: 0.8065 (mmtt) REVERT: C 222 MET cc_start: 0.9448 (tpt) cc_final: 0.9151 (tpt) REVERT: C 243 LYS cc_start: 0.8998 (mtpt) cc_final: 0.8608 (mtpp) REVERT: C 315 PHE cc_start: 0.9432 (m-10) cc_final: 0.9050 (t80) outliers start: 10 outliers final: 6 residues processed: 87 average time/residue: 0.0786 time to fit residues: 9.0499 Evaluate side-chains 88 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 79 time to evaluate : 0.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 295 GLN Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 204 MET Chi-restraints excluded: chain B residue 229 CYS Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 311 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 68 optimal weight: 1.9990 chunk 49 optimal weight: 10.0000 chunk 14 optimal weight: 0.8980 chunk 10 optimal weight: 5.9990 chunk 8 optimal weight: 6.9990 chunk 6 optimal weight: 6.9990 chunk 65 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 7 optimal weight: 0.0870 chunk 64 optimal weight: 0.9980 chunk 72 optimal weight: 3.9990 overall best weight: 0.9560 ------------------------------------------------------------------------------- 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 = 0.3356 r_free = 0.3356 target = 0.067724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.049000 restraints weight = 22070.978| |-----------------------------------------------------------------------------| r_work (start): 0.2868 rms_B_bonded: 4.43 r_work: 0.2701 rms_B_bonded: 4.93 restraints_weight: 0.5000 r_work (final): 0.2701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.3970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6138 Z= 0.113 Angle : 0.631 13.994 8337 Z= 0.293 Chirality : 0.046 0.418 933 Planarity : 0.004 0.045 1077 Dihedral : 3.947 20.298 831 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.28 % Allowed : 19.23 % Favored : 79.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.31), residues: 759 helix: 2.43 (0.33), residues: 255 sheet: -0.66 (0.28), residues: 300 loop : -1.43 (0.42), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 272 TYR 0.008 0.001 TYR B 282 PHE 0.014 0.001 PHE C 234 TRP 0.007 0.001 TRP B 305 HIS 0.001 0.000 HIS A 131 Details of bonding type rmsd covalent geometry : bond 0.00266 ( 6135) covalent geometry : angle 0.62925 ( 8331) SS BOND : bond 0.00461 ( 3) SS BOND : angle 1.99079 ( 6) hydrogen bonds : bond 0.02514 ( 311) hydrogen bonds : angle 3.53150 ( 861) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 85 time to evaluate : 0.202 Fit side-chains REVERT: A 98 LYS cc_start: 0.9502 (mmmm) cc_final: 0.9021 (mmtm) REVERT: A 204 MET cc_start: 0.9057 (ttp) cc_final: 0.8743 (tmm) REVERT: A 212 LEU cc_start: 0.9247 (tt) cc_final: 0.8879 (tt) REVERT: A 218 LYS cc_start: 0.8901 (mmtt) cc_final: 0.8209 (mmtt) REVERT: A 290 ASP cc_start: 0.8598 (p0) cc_final: 0.8005 (p0) REVERT: A 292 TYR cc_start: 0.8992 (m-80) cc_final: 0.8687 (m-80) REVERT: A 297 LYS cc_start: 0.8457 (mmmm) cc_final: 0.8138 (mmtm) REVERT: A 315 PHE cc_start: 0.9447 (m-10) cc_final: 0.9087 (t80) REVERT: B 129 CYS cc_start: 0.8875 (t) cc_final: 0.8450 (t) REVERT: B 204 MET cc_start: 0.8916 (OUTLIER) cc_final: 0.8640 (tmm) REVERT: B 218 LYS cc_start: 0.8877 (mmtt) cc_final: 0.8438 (mmtt) REVERT: B 248 LYS cc_start: 0.9197 (ttmm) cc_final: 0.8909 (ttmm) REVERT: B 290 ASP cc_start: 0.8589 (p0) cc_final: 0.7665 (p0) REVERT: B 292 TYR cc_start: 0.9095 (m-10) cc_final: 0.8791 (m-10) REVERT: B 315 PHE cc_start: 0.9377 (m-10) cc_final: 0.8960 (t80) REVERT: C 98 LYS cc_start: 0.9462 (mmmm) cc_final: 0.9061 (mmtm) REVERT: C 102 MET cc_start: 0.9409 (ttm) cc_final: 0.8886 (tpp) REVERT: C 171 LEU cc_start: 0.9346 (OUTLIER) cc_final: 0.8794 (tt) REVERT: C 184 MET cc_start: 0.9280 (ptp) cc_final: 0.8953 (ptp) REVERT: C 204 MET cc_start: 0.8739 (tmm) cc_final: 0.8343 (tmm) REVERT: C 218 LYS cc_start: 0.8864 (mmtt) cc_final: 0.8092 (mmtt) REVERT: C 222 MET cc_start: 0.9437 (tpt) cc_final: 0.9127 (tpt) REVERT: C 243 LYS cc_start: 0.8992 (mtpt) cc_final: 0.8587 (mtpp) REVERT: C 297 LYS cc_start: 0.8579 (mmmm) cc_final: 0.7910 (mmtm) REVERT: C 315 PHE cc_start: 0.9443 (m-10) cc_final: 0.9070 (t80) outliers start: 8 outliers final: 5 residues processed: 90 average time/residue: 0.0717 time to fit residues: 8.5466 Evaluate side-chains 90 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 83 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 204 MET Chi-restraints excluded: chain B residue 229 CYS Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 311 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 56 optimal weight: 7.9990 chunk 24 optimal weight: 2.9990 chunk 50 optimal weight: 40.0000 chunk 64 optimal weight: 0.7980 chunk 40 optimal weight: 7.9990 chunk 26 optimal weight: 6.9990 chunk 20 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 31 optimal weight: 6.9990 chunk 11 optimal weight: 1.9990 chunk 4 optimal weight: 0.0770 overall best weight: 1.5744 ------------------------------------------------------------------------------- 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 = 0.3344 r_free = 0.3344 target = 0.067242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.048617 restraints weight = 22224.299| |-----------------------------------------------------------------------------| r_work (start): 0.2855 rms_B_bonded: 4.43 r_work: 0.2686 rms_B_bonded: 4.95 restraints_weight: 0.5000 r_work (final): 0.2686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.3999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6138 Z= 0.140 Angle : 0.642 13.369 8337 Z= 0.298 Chirality : 0.045 0.419 933 Planarity : 0.004 0.044 1077 Dihedral : 3.953 20.236 831 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.44 % Allowed : 19.39 % Favored : 79.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.31), residues: 759 helix: 2.51 (0.33), residues: 255 sheet: -0.61 (0.28), residues: 300 loop : -1.39 (0.42), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 272 TYR 0.010 0.001 TYR B 282 PHE 0.015 0.001 PHE C 234 TRP 0.007 0.001 TRP B 305 HIS 0.001 0.000 HIS B 134 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 6135) covalent geometry : angle 0.64004 ( 8331) SS BOND : bond 0.00442 ( 3) SS BOND : angle 2.02993 ( 6) hydrogen bonds : bond 0.02552 ( 311) hydrogen bonds : angle 3.58585 ( 861) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1478.31 seconds wall clock time: 26 minutes 0.67 seconds (1560.67 seconds total)