Starting phenix.real_space_refine on Thu Jul 24 10:21:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ji3_22343/07_2025/7ji3_22343.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ji3_22343/07_2025/7ji3_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_22343/07_2025/7ji3_22343.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ji3_22343/07_2025/7ji3_22343.map" model { file = "/net/cci-nas-00/data/ceres_data/7ji3_22343/07_2025/7ji3_22343.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ji3_22343/07_2025/7ji3_22343.cif" } resolution = 3.46 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 1, 'PHE:plan': 2, '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: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 1, 'PHE:plan': 2, '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: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 1, 'PHE:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 43 Time building chain proxies: 3.73, per 1000 atoms: 0.62 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: 1.40 Conformation dependent library (CDL) restraints added in 826.0 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: 0.71 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: 1.55 Time building geometry restraints manager: 1.70 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.790 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: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 16.960 Find NCS groups from input model: 0.110 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:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.030 ------------------------------------------------------------------------------- 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 (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: -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 TRP 0.010 0.001 TRP A 241 HIS 0.002 0.001 HIS A 134 PHE 0.030 0.003 PHE C 234 TYR 0.021 0.002 TYR C 282 ARG 0.006 0.001 ARG A 239 Details of bonding type rmsd hydrogen bonds : bond 0.21650 ( 311) hydrogen bonds : angle 8.71332 ( 861) SS BOND : bond 0.01092 ( 3) SS BOND : angle 4.79473 ( 6) covalent geometry : bond 0.00535 ( 6135) covalent geometry : angle 0.79280 ( 8331) *********************** 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 : 0.694 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: 0.2366 time to fit residues: 40.0254 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 : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 63 optimal weight: 2.9990 chunk 56 optimal weight: 5.9990 chunk 31 optimal weight: 6.9990 chunk 19 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 58 optimal weight: 8.9990 chunk 22 optimal weight: 6.9990 chunk 35 optimal weight: 3.9990 chunk 43 optimal weight: 6.9990 chunk 68 optimal weight: 1.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- 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 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 = 0.3365 r_free = 0.3365 target = 0.068751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.049657 restraints weight = 21600.614| |-----------------------------------------------------------------------------| r_work (start): 0.2865 rms_B_bonded: 4.45 r_work: 0.2704 rms_B_bonded: 4.92 restraints_weight: 0.5000 r_work (final): 0.2704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.2533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 6138 Z= 0.172 Angle : 0.593 9.896 8337 Z= 0.298 Chirality : 0.043 0.202 933 Planarity : 0.005 0.051 1077 Dihedral : 4.604 23.434 831 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 2.08 % Allowed : 17.79 % Favored : 80.13 % 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: -2.65 (0.27), residues: 759 helix: -0.45 (0.31), residues: 252 sheet: -2.07 (0.25), residues: 306 loop : -2.46 (0.37), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 241 HIS 0.003 0.001 HIS A 131 PHE 0.014 0.001 PHE B 234 TYR 0.015 0.002 TYR B 292 ARG 0.002 0.000 ARG C 271 Details of bonding type rmsd hydrogen bonds : bond 0.03528 ( 311) hydrogen bonds : angle 4.76674 ( 861) SS BOND : bond 0.00351 ( 3) SS BOND : angle 2.55896 ( 6) covalent geometry : bond 0.00379 ( 6135) covalent geometry : angle 0.58895 ( 8331) *********************** 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 105 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 92 time to evaluate : 1.280 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 LYS cc_start: 0.9358 (mmmm) cc_final: 0.8861 (mmtm) REVERT: A 102 MET cc_start: 0.8112 (tpp) cc_final: 0.7883 (mmp) REVERT: A 218 LYS cc_start: 0.8517 (mmtt) cc_final: 0.8169 (mmtt) REVERT: A 290 ASP cc_start: 0.8644 (p0) cc_final: 0.7990 (p0) REVERT: A 292 TYR cc_start: 0.9155 (m-80) cc_final: 0.8847 (m-80) REVERT: B 96 LYS cc_start: 0.8601 (mptt) cc_final: 0.8384 (mmtp) REVERT: B 98 LYS cc_start: 0.9427 (tppp) cc_final: 0.9211 (ttmm) REVERT: B 150 ASP cc_start: 0.8767 (m-30) cc_final: 0.8431 (m-30) REVERT: B 184 MET cc_start: 0.9602 (ptp) cc_final: 0.9385 (ptp) REVERT: B 187 MET cc_start: 0.9064 (ptp) cc_final: 0.8859 (ptp) REVERT: B 218 LYS cc_start: 0.8509 (mmtt) cc_final: 0.8214 (mmtt) REVERT: B 290 ASP cc_start: 0.8777 (p0) cc_final: 0.8159 (p0) REVERT: C 96 LYS cc_start: 0.8598 (mptt) cc_final: 0.8286 (mmtp) REVERT: C 98 LYS cc_start: 0.9488 (mmmm) cc_final: 0.9066 (mmtm) REVERT: C 150 ASP cc_start: 0.8834 (m-30) cc_final: 0.8584 (m-30) REVERT: C 218 LYS cc_start: 0.8420 (mmtt) cc_final: 0.7805 (mmtt) outliers start: 13 outliers final: 6 residues processed: 100 average time/residue: 0.2813 time to fit residues: 35.0752 Evaluate side-chains 92 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 86 time to evaluate : 1.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 303 ASN 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 22 optimal weight: 3.9990 chunk 1 optimal weight: 5.9990 chunk 33 optimal weight: 7.9990 chunk 64 optimal weight: 0.0870 chunk 66 optimal weight: 4.9990 chunk 50 optimal weight: 40.0000 chunk 63 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 6 optimal weight: 4.9990 chunk 34 optimal weight: 5.9990 chunk 53 optimal weight: 4.9990 overall best weight: 2.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 131 HIS ** A 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 134 HIS ** 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 = 0.3343 r_free = 0.3343 target = 0.067410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.048598 restraints weight = 22043.627| |-----------------------------------------------------------------------------| r_work (start): 0.2842 rms_B_bonded: 4.42 r_work: 0.2680 rms_B_bonded: 4.90 restraints_weight: 0.5000 r_work (final): 0.2680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.3024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 6138 Z= 0.188 Angle : 0.580 10.532 8337 Z= 0.288 Chirality : 0.042 0.132 933 Planarity : 0.004 0.044 1077 Dihedral : 4.363 22.561 831 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.12 % Allowed : 17.95 % Favored : 80.93 % 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: -1.40 (0.30), residues: 759 helix: 1.12 (0.33), residues: 252 sheet: -1.61 (0.27), residues: 306 loop : -2.18 (0.39), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 305 HIS 0.002 0.001 HIS A 131 PHE 0.015 0.001 PHE B 234 TYR 0.013 0.001 TYR B 282 ARG 0.001 0.000 ARG C 180 Details of bonding type rmsd hydrogen bonds : bond 0.02952 ( 311) hydrogen bonds : angle 4.00607 ( 861) SS BOND : bond 0.00332 ( 3) SS BOND : angle 2.40860 ( 6) covalent geometry : bond 0.00421 ( 6135) covalent geometry : angle 0.57631 ( 8331) *********************** 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 90 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 83 time to evaluate : 1.252 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 96 LYS cc_start: 0.8627 (mptt) cc_final: 0.8390 (mmtp) REVERT: A 98 LYS cc_start: 0.9428 (mmmm) cc_final: 0.8929 (mmtm) REVERT: A 218 LYS cc_start: 0.8630 (mmtt) cc_final: 0.8289 (mmtt) REVERT: A 290 ASP cc_start: 0.8680 (p0) cc_final: 0.7968 (p0) REVERT: A 292 TYR cc_start: 0.9099 (m-80) cc_final: 0.8733 (m-80) REVERT: B 96 LYS cc_start: 0.8638 (mptt) cc_final: 0.8321 (mmtp) REVERT: B 150 ASP cc_start: 0.8715 (m-30) cc_final: 0.8442 (m-30) REVERT: B 187 MET cc_start: 0.9168 (ptp) cc_final: 0.8941 (ptp) REVERT: B 218 LYS cc_start: 0.8655 (mmtt) cc_final: 0.8343 (mmtt) REVERT: B 290 ASP cc_start: 0.8696 (p0) cc_final: 0.7944 (p0) REVERT: B 292 TYR cc_start: 0.9098 (m-10) cc_final: 0.8814 (m-10) REVERT: C 98 LYS cc_start: 0.9484 (mmmm) cc_final: 0.9017 (mmtm) REVERT: C 171 LEU cc_start: 0.9317 (OUTLIER) cc_final: 0.8802 (tt) outliers start: 7 outliers final: 4 residues processed: 89 average time/residue: 0.3335 time to fit residues: 37.2800 Evaluate side-chains 82 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 77 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 179 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 42 optimal weight: 0.9990 chunk 65 optimal weight: 4.9990 chunk 43 optimal weight: 3.9990 chunk 46 optimal weight: 0.9990 chunk 69 optimal weight: 8.9990 chunk 14 optimal weight: 7.9990 chunk 1 optimal weight: 6.9990 chunk 24 optimal weight: 4.9990 chunk 49 optimal weight: 5.9990 chunk 34 optimal weight: 1.9990 chunk 4 optimal weight: 0.0030 overall best weight: 1.5998 ------------------------------------------------------------------------------- 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 134 HIS ** B 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.067703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.048789 restraints weight = 22209.642| |-----------------------------------------------------------------------------| r_work (start): 0.2853 rms_B_bonded: 4.46 r_work: 0.2689 rms_B_bonded: 4.94 restraints_weight: 0.5000 r_work (final): 0.2689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.3227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 6138 Z= 0.138 Angle : 0.554 10.804 8337 Z= 0.270 Chirality : 0.042 0.230 933 Planarity : 0.004 0.043 1077 Dihedral : 4.158 21.103 831 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 1.12 % Allowed : 17.95 % Favored : 80.93 % 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: -0.78 (0.30), residues: 759 helix: 1.75 (0.34), residues: 252 sheet: -1.31 (0.27), residues: 306 loop : -1.95 (0.41), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 305 HIS 0.003 0.001 HIS A 131 PHE 0.014 0.001 PHE C 234 TYR 0.010 0.001 TYR B 282 ARG 0.001 0.000 ARG A 272 Details of bonding type rmsd hydrogen bonds : bond 0.02622 ( 311) hydrogen bonds : angle 3.67790 ( 861) SS BOND : bond 0.00366 ( 3) SS BOND : angle 2.21536 ( 6) covalent geometry : bond 0.00315 ( 6135) covalent geometry : angle 0.55102 ( 8331) *********************** 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 91 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 84 time to evaluate : 0.829 Fit side-chains revert: symmetry clash REVERT: A 98 LYS cc_start: 0.9457 (mmmm) cc_final: 0.8956 (mmtm) REVERT: A 218 LYS cc_start: 0.8657 (mmtt) cc_final: 0.8294 (mmtt) REVERT: A 290 ASP cc_start: 0.8645 (p0) cc_final: 0.8089 (p0) REVERT: A 292 TYR cc_start: 0.9085 (m-80) cc_final: 0.8851 (m-10) REVERT: B 150 ASP cc_start: 0.8714 (m-30) cc_final: 0.8478 (m-30) REVERT: B 218 LYS cc_start: 0.8717 (mmtt) cc_final: 0.8434 (mmtt) REVERT: B 290 ASP cc_start: 0.8637 (p0) cc_final: 0.7886 (p0) REVERT: B 292 TYR cc_start: 0.9095 (m-10) cc_final: 0.8782 (m-10) REVERT: C 98 LYS cc_start: 0.9515 (mmmm) cc_final: 0.9078 (mmtm) REVERT: C 171 LEU cc_start: 0.9321 (OUTLIER) cc_final: 0.8786 (tt) REVERT: C 218 LYS cc_start: 0.8677 (mmtt) cc_final: 0.8067 (mmtt) outliers start: 7 outliers final: 3 residues processed: 89 average time/residue: 0.2285 time to fit residues: 25.6789 Evaluate side-chains 81 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 77 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 179 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 20 optimal weight: 4.9990 chunk 3 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 6 optimal weight: 4.9990 chunk 31 optimal weight: 0.2980 chunk 28 optimal weight: 6.9990 chunk 70 optimal weight: 7.9990 chunk 47 optimal weight: 1.9990 chunk 63 optimal weight: 4.9990 chunk 1 optimal weight: 7.9990 chunk 73 optimal weight: 0.6980 overall best weight: 1.9986 ------------------------------------------------------------------------------- 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 188 GLN ** A 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.067036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.048273 restraints weight = 21983.623| |-----------------------------------------------------------------------------| r_work (start): 0.2837 rms_B_bonded: 4.42 r_work: 0.2673 rms_B_bonded: 4.91 restraints_weight: 0.5000 r_work (final): 0.2673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.3400 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= 0.164 Angle : 0.586 11.681 8337 Z= 0.283 Chirality : 0.042 0.179 933 Planarity : 0.004 0.043 1077 Dihedral : 4.140 21.014 831 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.28 % Allowed : 16.99 % Favored : 81.73 % 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: -0.51 (0.31), residues: 759 helix: 1.99 (0.34), residues: 252 sheet: -1.14 (0.27), residues: 306 loop : -1.84 (0.43), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 305 HIS 0.002 0.001 HIS A 131 PHE 0.014 0.001 PHE B 234 TYR 0.011 0.001 TYR B 282 ARG 0.001 0.000 ARG A 272 Details of bonding type rmsd hydrogen bonds : bond 0.02663 ( 311) hydrogen bonds : angle 3.71875 ( 861) SS BOND : bond 0.00405 ( 3) SS BOND : angle 2.24081 ( 6) covalent geometry : bond 0.00371 ( 6135) covalent geometry : angle 0.58314 ( 8331) *********************** 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 85 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 77 time to evaluate : 0.722 Fit side-chains revert: symmetry clash REVERT: A 218 LYS cc_start: 0.8721 (mmtt) cc_final: 0.8362 (mmtt) REVERT: A 290 ASP cc_start: 0.8632 (p0) cc_final: 0.7991 (p0) REVERT: A 292 TYR cc_start: 0.9088 (m-80) cc_final: 0.8706 (m-80) REVERT: B 218 LYS cc_start: 0.8769 (mmtt) cc_final: 0.8457 (mmtt) REVERT: B 290 ASP cc_start: 0.8687 (p0) cc_final: 0.7866 (p0) REVERT: B 292 TYR cc_start: 0.9075 (m-10) cc_final: 0.8738 (m-10) REVERT: B 297 LYS cc_start: 0.8715 (mmmm) cc_final: 0.8348 (mmmm) REVERT: C 98 LYS cc_start: 0.9519 (mmmm) cc_final: 0.9107 (mmtm) REVERT: C 102 MET cc_start: 0.8790 (tpp) cc_final: 0.8536 (tpp) REVERT: C 171 LEU cc_start: 0.9335 (OUTLIER) cc_final: 0.8786 (tt) REVERT: C 197 ASP cc_start: 0.9575 (p0) cc_final: 0.9367 (p0) REVERT: C 218 LYS cc_start: 0.8731 (mmtt) cc_final: 0.8012 (mmtt) outliers start: 8 outliers final: 5 residues processed: 83 average time/residue: 0.2042 time to fit residues: 21.7819 Evaluate side-chains 78 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 72 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 229 CYS Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 229 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 61 optimal weight: 4.9990 chunk 3 optimal weight: 4.9990 chunk 26 optimal weight: 5.9990 chunk 19 optimal weight: 8.9990 chunk 14 optimal weight: 0.0050 chunk 59 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 71 optimal weight: 4.9990 chunk 64 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 overall best weight: 1.5600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 131 HIS B 188 GLN ** B 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3345 r_free = 0.3345 target = 0.067455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.048549 restraints weight = 21859.706| |-----------------------------------------------------------------------------| r_work (start): 0.2845 rms_B_bonded: 4.40 r_work: 0.2683 rms_B_bonded: 4.91 restraints_weight: 0.5000 r_work (final): 0.2683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.3537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 6138 Z= 0.138 Angle : 0.596 12.125 8337 Z= 0.282 Chirality : 0.044 0.350 933 Planarity : 0.004 0.043 1077 Dihedral : 4.053 20.354 831 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.76 % Allowed : 17.15 % Favored : 81.09 % 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: -0.32 (0.31), residues: 759 helix: 2.12 (0.34), residues: 252 sheet: -0.99 (0.27), residues: 306 loop : -1.81 (0.43), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 305 HIS 0.002 0.000 HIS A 131 PHE 0.014 0.001 PHE C 234 TYR 0.010 0.001 TYR B 282 ARG 0.001 0.000 ARG C 272 Details of bonding type rmsd hydrogen bonds : bond 0.02617 ( 311) hydrogen bonds : angle 3.69802 ( 861) SS BOND : bond 0.00432 ( 3) SS BOND : angle 2.08308 ( 6) covalent geometry : bond 0.00315 ( 6135) covalent geometry : angle 0.59382 ( 8331) *********************** 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 91 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 80 time to evaluate : 0.731 Fit side-chains revert: symmetry clash REVERT: A 98 LYS cc_start: 0.9486 (mmmm) cc_final: 0.9008 (mmtm) REVERT: A 218 LYS cc_start: 0.8772 (mmtt) cc_final: 0.8379 (mmtt) REVERT: A 244 MET cc_start: 0.9422 (ptt) cc_final: 0.9104 (ptp) REVERT: A 290 ASP cc_start: 0.8605 (p0) cc_final: 0.7980 (p0) REVERT: A 292 TYR cc_start: 0.9074 (m-80) cc_final: 0.8706 (m-80) REVERT: A 315 PHE cc_start: 0.9459 (m-10) cc_final: 0.9060 (t80) REVERT: B 218 LYS cc_start: 0.8769 (mmtt) cc_final: 0.8436 (mmtt) REVERT: B 290 ASP cc_start: 0.8622 (p0) cc_final: 0.7732 (p0) REVERT: B 292 TYR cc_start: 0.9048 (m-10) cc_final: 0.8689 (m-10) REVERT: B 315 PHE cc_start: 0.9403 (m-10) cc_final: 0.8979 (t80) REVERT: C 98 LYS cc_start: 0.9533 (mmmm) cc_final: 0.9105 (mmtm) REVERT: C 171 LEU cc_start: 0.9325 (OUTLIER) cc_final: 0.8758 (tt) REVERT: C 184 MET cc_start: 0.9365 (ptp) cc_final: 0.9131 (ptp) REVERT: C 218 LYS cc_start: 0.8748 (mmtt) cc_final: 0.8012 (mmtt) REVERT: C 298 MET cc_start: 0.8921 (mmm) cc_final: 0.8578 (mmm) outliers start: 11 outliers final: 6 residues processed: 88 average time/residue: 0.2141 time to fit residues: 24.1466 Evaluate side-chains 79 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 72 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 229 CYS Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 229 CYS 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 8 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 11 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 7 optimal weight: 7.9990 chunk 41 optimal weight: 0.7980 chunk 74 optimal weight: 3.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 217 ASN ** 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 = 0.3342 r_free = 0.3342 target = 0.067254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.048338 restraints weight = 22055.793| |-----------------------------------------------------------------------------| r_work (start): 0.2843 rms_B_bonded: 4.42 r_work: 0.2680 rms_B_bonded: 4.93 restraints_weight: 0.5000 r_work (final): 0.2680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.3651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 6138 Z= 0.149 Angle : 0.606 12.300 8337 Z= 0.287 Chirality : 0.044 0.308 933 Planarity : 0.004 0.043 1077 Dihedral : 3.997 19.434 831 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.44 % Allowed : 17.79 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.31), residues: 759 helix: 2.20 (0.33), residues: 255 sheet: -0.83 (0.27), residues: 306 loop : -1.80 (0.43), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 305 HIS 0.001 0.001 HIS A 131 PHE 0.014 0.001 PHE C 234 TYR 0.010 0.001 TYR B 282 ARG 0.001 0.000 ARG A 272 Details of bonding type rmsd hydrogen bonds : bond 0.02575 ( 311) hydrogen bonds : angle 3.64856 ( 861) SS BOND : bond 0.00380 ( 3) SS BOND : angle 2.14217 ( 6) covalent geometry : bond 0.00341 ( 6135) covalent geometry : angle 0.60361 ( 8331) *********************** 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 82 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 73 time to evaluate : 0.632 Fit side-chains revert: symmetry clash REVERT: A 98 LYS cc_start: 0.9506 (mmmm) cc_final: 0.9002 (mmtm) REVERT: A 290 ASP cc_start: 0.8610 (p0) cc_final: 0.8002 (p0) REVERT: A 292 TYR cc_start: 0.9052 (m-80) cc_final: 0.8696 (m-80) REVERT: A 315 PHE cc_start: 0.9448 (m-10) cc_final: 0.9100 (t80) REVERT: B 290 ASP cc_start: 0.8574 (p0) cc_final: 0.7742 (p0) REVERT: B 292 TYR cc_start: 0.9042 (m-10) cc_final: 0.8822 (m-10) REVERT: B 297 LYS cc_start: 0.8805 (mmmm) cc_final: 0.8468 (mmmm) REVERT: C 98 LYS cc_start: 0.9532 (mmmm) cc_final: 0.9126 (mmtm) REVERT: C 171 LEU cc_start: 0.9337 (OUTLIER) cc_final: 0.8770 (tt) REVERT: C 204 MET cc_start: 0.8730 (tmm) cc_final: 0.8296 (tmm) outliers start: 9 outliers final: 6 residues processed: 79 average time/residue: 0.1822 time to fit residues: 18.9722 Evaluate side-chains 76 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 69 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 229 CYS Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 229 CYS 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 21 optimal weight: 4.9990 chunk 25 optimal weight: 40.0000 chunk 49 optimal weight: 0.0170 chunk 51 optimal weight: 5.9990 chunk 73 optimal weight: 0.5980 chunk 14 optimal weight: 0.0980 chunk 37 optimal weight: 7.9990 chunk 56 optimal weight: 0.2980 chunk 57 optimal weight: 4.9990 chunk 46 optimal weight: 0.7980 chunk 22 optimal weight: 4.9990 overall best weight: 0.3618 ------------------------------------------------------------------------------- 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 = 0.3377 r_free = 0.3377 target = 0.068717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.049972 restraints weight = 21498.704| |-----------------------------------------------------------------------------| r_work (start): 0.2893 rms_B_bonded: 4.43 r_work: 0.2730 rms_B_bonded: 4.93 restraints_weight: 0.5000 r_work (final): 0.2730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.3760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 6138 Z= 0.095 Angle : 0.609 12.614 8337 Z= 0.281 Chirality : 0.045 0.357 933 Planarity : 0.004 0.043 1077 Dihedral : 3.862 19.872 831 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.12 % Allowed : 18.59 % Favored : 80.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.31), residues: 759 helix: 2.32 (0.33), residues: 255 sheet: -0.60 (0.28), residues: 306 loop : -1.75 (0.44), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.000 TRP B 305 HIS 0.002 0.000 HIS A 131 PHE 0.014 0.001 PHE A 234 TYR 0.007 0.001 TYR B 203 ARG 0.001 0.000 ARG A 239 Details of bonding type rmsd hydrogen bonds : bond 0.02439 ( 311) hydrogen bonds : angle 3.50673 ( 861) SS BOND : bond 0.00420 ( 3) SS BOND : angle 1.79289 ( 6) covalent geometry : bond 0.00223 ( 6135) covalent geometry : angle 0.60706 ( 8331) *********************** 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 93 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 86 time to evaluate : 0.651 Fit side-chains REVERT: A 98 LYS cc_start: 0.9509 (mmmm) cc_final: 0.8979 (mmtm) REVERT: A 290 ASP cc_start: 0.8576 (p0) cc_final: 0.8047 (p0) REVERT: A 292 TYR cc_start: 0.9047 (m-80) cc_final: 0.8770 (m-10) REVERT: A 297 LYS cc_start: 0.8190 (mmmm) cc_final: 0.7780 (mmtm) REVERT: A 315 PHE cc_start: 0.9411 (m-10) cc_final: 0.9071 (t80) REVERT: B 290 ASP cc_start: 0.8560 (p0) cc_final: 0.7737 (p0) REVERT: B 292 TYR cc_start: 0.9039 (m-10) cc_final: 0.8814 (m-10) REVERT: C 98 LYS cc_start: 0.9531 (mmmm) cc_final: 0.9135 (mmtm) REVERT: C 171 LEU cc_start: 0.9330 (OUTLIER) cc_final: 0.8785 (tt) REVERT: C 184 MET cc_start: 0.9449 (ptp) cc_final: 0.9188 (ptp) REVERT: C 197 ASP cc_start: 0.9554 (p0) cc_final: 0.9315 (p0) REVERT: C 204 MET cc_start: 0.8685 (tmm) cc_final: 0.8201 (tmm) REVERT: C 218 LYS cc_start: 0.8737 (mmtt) cc_final: 0.7957 (mmtt) REVERT: C 222 MET cc_start: 0.9413 (tpt) cc_final: 0.9147 (tpt) REVERT: C 243 LYS cc_start: 0.8985 (mtpt) cc_final: 0.8578 (mtpp) REVERT: C 248 LYS cc_start: 0.9271 (mtpp) cc_final: 0.8881 (ttmm) REVERT: C 298 MET cc_start: 0.8906 (mmm) cc_final: 0.8576 (mmm) outliers start: 7 outliers final: 5 residues processed: 91 average time/residue: 0.1942 time to fit residues: 22.9513 Evaluate side-chains 83 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 77 time to evaluate : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 CYS Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 229 CYS 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 3 optimal weight: 7.9990 chunk 6 optimal weight: 4.9990 chunk 56 optimal weight: 7.9990 chunk 27 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 41 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 chunk 67 optimal weight: 4.9990 chunk 69 optimal weight: 5.9990 chunk 8 optimal weight: 4.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 ASN ** C 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.067653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.048706 restraints weight = 22097.259| |-----------------------------------------------------------------------------| r_work (start): 0.2856 rms_B_bonded: 4.45 r_work: 0.2695 rms_B_bonded: 4.94 restraints_weight: 0.5000 r_work (final): 0.2695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.3836 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 : 0.646 16.976 8337 Z= 0.299 Chirality : 0.044 0.325 933 Planarity : 0.004 0.043 1077 Dihedral : 3.897 19.195 831 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.44 % Allowed : 18.43 % Favored : 80.13 % 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: 0.22 (0.31), residues: 759 helix: 2.33 (0.33), residues: 255 sheet: -0.52 (0.28), residues: 300 loop : -1.50 (0.42), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 305 HIS 0.003 0.001 HIS A 131 PHE 0.015 0.001 PHE C 234 TYR 0.020 0.001 TYR C 203 ARG 0.001 0.000 ARG A 272 Details of bonding type rmsd hydrogen bonds : bond 0.02613 ( 311) hydrogen bonds : angle 3.59330 ( 861) SS BOND : bond 0.00388 ( 3) SS BOND : angle 2.00213 ( 6) covalent geometry : bond 0.00323 ( 6135) covalent geometry : angle 0.64406 ( 8331) *********************** 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 87 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 78 time to evaluate : 0.647 Fit side-chains revert: symmetry clash REVERT: A 98 LYS cc_start: 0.9502 (mmmm) cc_final: 0.8992 (mmtm) REVERT: A 290 ASP cc_start: 0.8623 (p0) cc_final: 0.8112 (p0) REVERT: A 292 TYR cc_start: 0.9032 (m-80) cc_final: 0.8778 (m-10) REVERT: A 315 PHE cc_start: 0.9365 (m-10) cc_final: 0.9035 (t80) REVERT: B 290 ASP cc_start: 0.8621 (p0) cc_final: 0.7776 (p0) REVERT: B 292 TYR cc_start: 0.9040 (m-10) cc_final: 0.8807 (m-10) REVERT: C 98 LYS cc_start: 0.9531 (mmmm) cc_final: 0.9135 (mmtm) REVERT: C 171 LEU cc_start: 0.9336 (OUTLIER) cc_final: 0.8768 (tt) REVERT: C 197 ASP cc_start: 0.9551 (p0) cc_final: 0.9282 (p0) REVERT: C 204 MET cc_start: 0.8737 (tmm) cc_final: 0.8280 (tmm) REVERT: C 218 LYS cc_start: 0.8805 (mmtt) cc_final: 0.8064 (mmtt) REVERT: C 222 MET cc_start: 0.9392 (tpt) cc_final: 0.9110 (tpt) REVERT: C 243 LYS cc_start: 0.8997 (mtpt) cc_final: 0.8597 (mtpp) REVERT: C 298 MET cc_start: 0.8762 (mmm) cc_final: 0.8527 (mmm) outliers start: 9 outliers final: 7 residues processed: 84 average time/residue: 0.1858 time to fit residues: 20.3706 Evaluate side-chains 85 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 77 time to evaluate : 0.705 ------------------------------------------------------------------------------- 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 303 ASN Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 229 CYS 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 71 optimal weight: 5.9990 chunk 41 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 chunk 42 optimal weight: 6.9990 chunk 44 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 39 optimal weight: 0.1980 chunk 38 optimal weight: 4.9990 chunk 63 optimal weight: 0.9980 chunk 50 optimal weight: 40.0000 chunk 32 optimal weight: 0.5980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 296 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 = 0.3346 r_free = 0.3346 target = 0.067790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.048922 restraints weight = 21719.991| |-----------------------------------------------------------------------------| r_work (start): 0.2845 rms_B_bonded: 4.44 r_work: 0.2681 rms_B_bonded: 4.95 restraints_weight: 0.5000 r_work (final): 0.2681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.3920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6138 Z= 0.123 Angle : 0.663 16.694 8337 Z= 0.304 Chirality : 0.044 0.372 933 Planarity : 0.004 0.043 1077 Dihedral : 3.893 19.517 831 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % 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 (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: 0.38 (0.31), residues: 759 helix: 2.46 (0.33), residues: 255 sheet: -0.43 (0.28), residues: 300 loop : -1.45 (0.42), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 305 HIS 0.002 0.001 HIS A 131 PHE 0.014 0.001 PHE C 234 TYR 0.009 0.001 TYR B 282 ARG 0.001 0.000 ARG A 272 Details of bonding type rmsd hydrogen bonds : bond 0.02568 ( 311) hydrogen bonds : angle 3.59795 ( 861) SS BOND : bond 0.00390 ( 3) SS BOND : angle 1.89890 ( 6) covalent geometry : bond 0.00287 ( 6135) covalent geometry : angle 0.66082 ( 8331) ********************** 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 88 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 80 time to evaluate : 0.720 Fit side-chains REVERT: A 98 LYS cc_start: 0.9487 (mmmm) cc_final: 0.8991 (mmtm) REVERT: A 290 ASP cc_start: 0.8604 (p0) cc_final: 0.8095 (p0) REVERT: A 292 TYR cc_start: 0.9018 (m-80) cc_final: 0.8766 (m-10) REVERT: A 315 PHE cc_start: 0.9382 (m-10) cc_final: 0.9071 (t80) REVERT: B 218 LYS cc_start: 0.8846 (mmtt) cc_final: 0.8389 (mmtt) REVERT: B 290 ASP cc_start: 0.8564 (p0) cc_final: 0.7703 (p0) REVERT: B 292 TYR cc_start: 0.9040 (m-10) cc_final: 0.8823 (m-10) REVERT: C 98 LYS cc_start: 0.9528 (mmmm) cc_final: 0.9105 (mmtm) REVERT: C 171 LEU cc_start: 0.9313 (OUTLIER) cc_final: 0.8923 (tt) REVERT: C 184 MET cc_start: 0.9295 (ptp) cc_final: 0.9015 (ptp) REVERT: C 197 ASP cc_start: 0.9543 (p0) cc_final: 0.9291 (p0) REVERT: C 204 MET cc_start: 0.8734 (tmm) cc_final: 0.8239 (tmm) REVERT: C 218 LYS cc_start: 0.8819 (mmtt) cc_final: 0.8055 (mmtt) REVERT: C 222 MET cc_start: 0.9443 (tpt) cc_final: 0.9152 (tpt) REVERT: C 243 LYS cc_start: 0.8936 (mtpt) cc_final: 0.8532 (mtpp) REVERT: C 298 MET cc_start: 0.8765 (mmm) cc_final: 0.8497 (mmm) outliers start: 8 outliers final: 6 residues processed: 86 average time/residue: 0.1981 time to fit residues: 22.2902 Evaluate side-chains 85 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 78 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 229 CYS Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 229 CYS 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 31 optimal weight: 3.9990 chunk 53 optimal weight: 8.9990 chunk 30 optimal weight: 3.9990 chunk 57 optimal weight: 8.9990 chunk 32 optimal weight: 0.8980 chunk 39 optimal weight: 3.9990 chunk 68 optimal weight: 5.9990 chunk 47 optimal weight: 7.9990 chunk 27 optimal weight: 0.9980 chunk 51 optimal weight: 6.9990 chunk 66 optimal weight: 1.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 217 ASN ** 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** ** C 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.066635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.047873 restraints weight = 22351.530| |-----------------------------------------------------------------------------| r_work (start): 0.2831 rms_B_bonded: 4.41 r_work: 0.2664 rms_B_bonded: 4.94 restraints_weight: 0.5000 r_work (final): 0.2664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.3942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 6138 Z= 0.190 Angle : 0.674 15.408 8337 Z= 0.316 Chirality : 0.044 0.357 933 Planarity : 0.004 0.043 1077 Dihedral : 4.009 18.985 831 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 0.96 % Allowed : 19.39 % Favored : 79.65 % 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: 0.39 (0.31), residues: 759 helix: 2.51 (0.33), residues: 255 sheet: -0.47 (0.29), residues: 300 loop : -1.43 (0.42), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 305 HIS 0.003 0.001 HIS A 131 PHE 0.016 0.001 PHE C 234 TYR 0.012 0.001 TYR B 282 ARG 0.001 0.000 ARG A 272 Details of bonding type rmsd hydrogen bonds : bond 0.02712 ( 311) hydrogen bonds : angle 3.72622 ( 861) SS BOND : bond 0.00442 ( 3) SS BOND : angle 2.31400 ( 6) covalent geometry : bond 0.00433 ( 6135) covalent geometry : angle 0.67180 ( 8331) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3905.82 seconds wall clock time: 69 minutes 30.44 seconds (4170.44 seconds total)