Starting phenix.real_space_refine on Tue Feb 13 12:02:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ji3_22343/02_2024/7ji3_22343.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ji3_22343/02_2024/7ji3_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ji3_22343/02_2024/7ji3_22343.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ji3_22343/02_2024/7ji3_22343.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ji3_22343/02_2024/7ji3_22343.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ji3_22343/02_2024/7ji3_22343.pdb" } 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 Residue "A GLU 108": "OE1" <-> "OE2" Residue "A PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 136": "OD1" <-> "OD2" Residue "A ARG 169": "NH1" <-> "NH2" Residue "A GLU 193": "OE1" <-> "OE2" Residue "A GLU 196": "OE1" <-> "OE2" Residue "A ARG 220": "NH1" <-> "NH2" Residue "A GLU 224": "OE1" <-> "OE2" Residue "A PHE 234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 239": "NH1" <-> "NH2" Residue "A TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 290": "OD1" <-> "OD2" Residue "B GLU 108": "OE1" <-> "OE2" Residue "B PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 136": "OD1" <-> "OD2" Residue "B ARG 169": "NH1" <-> "NH2" Residue "B GLU 193": "OE1" <-> "OE2" Residue "B GLU 196": "OE1" <-> "OE2" Residue "B ARG 220": "NH1" <-> "NH2" Residue "B GLU 224": "OE1" <-> "OE2" Residue "B PHE 234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 239": "NH1" <-> "NH2" Residue "B TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 290": "OD1" <-> "OD2" Residue "C GLU 108": "OE1" <-> "OE2" Residue "C PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 136": "OD1" <-> "OD2" Residue "C ARG 169": "NH1" <-> "NH2" Residue "C GLU 193": "OE1" <-> "OE2" Residue "C GLU 196": "OE1" <-> "OE2" Residue "C ARG 220": "NH1" <-> "NH2" Residue "C GLU 224": "OE1" <-> "OE2" Residue "C PHE 234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 239": "NH1" <-> "NH2" Residue "C TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 290": "OD1" <-> "OD2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 3.66, per 1000 atoms: 0.61 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.23 Conformation dependent library (CDL) restraints added in 1.3 seconds 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: 0.64 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: 1.87 Time building geometry restraints manager: 2.42 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: 99.49 - 106.45: 180 106.45 - 113.40: 3237 113.40 - 120.36: 2408 120.36 - 127.32: 2452 127.32 - 134.27: 54 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 2.440 nonbonded pdb=" O PHE C 324 " pdb=" OG1 THR C 328 " model vdw 2.365 2.440 nonbonded pdb=" O PHE B 324 " pdb=" OG1 THR B 328 " model vdw 2.366 2.440 nonbonded pdb=" O PRO B 176 " pdb=" NE1 TRP B 288 " model vdw 2.416 2.520 nonbonded pdb=" O PRO A 176 " pdb=" NE1 TRP A 288 " model vdw 2.416 2.520 ... (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 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: 0.520 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: 2.480 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 20.330 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.030 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: 0.010 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.560 ------------------------------------------------------------------------------- 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 6135 Z= 0.347 Angle : 0.793 6.426 8331 Z= 0.511 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 *********************** 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 fitting. rotamer outliers: 0 poor density : 137 time to evaluate : 0.756 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: 0.2360 time to fit residues: 39.9461 Evaluate side-chains 76 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 76 time to evaluate : 0.671 ------------------------------------------------------------------------------- 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: 1.9990 chunk 56 optimal weight: 4.9990 chunk 31 optimal weight: 6.9990 chunk 19 optimal weight: 4.9990 chunk 38 optimal weight: 0.8980 chunk 30 optimal weight: 0.9990 chunk 58 optimal weight: 8.9990 chunk 22 optimal weight: 5.9990 chunk 35 optimal weight: 4.9990 chunk 43 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 261 GLN A 280 GLN B 88 GLN ** B 107 GLN ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7306 moved from start: 0.2455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6135 Z= 0.256 Angle : 0.588 9.853 8331 Z= 0.294 Chirality : 0.042 0.198 933 Planarity : 0.006 0.054 1077 Dihedral : 4.559 23.044 831 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 2.24 % Allowed : 20.35 % Favored : 77.40 % 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: -2.66 (0.27), residues: 759 helix: -0.39 (0.31), residues: 252 sheet: -2.07 (0.25), residues: 306 loop : -2.57 (0.37), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 232 HIS 0.002 0.001 HIS A 131 PHE 0.014 0.001 PHE B 234 TYR 0.015 0.002 TYR B 292 ARG 0.001 0.000 ARG A 145 *********************** 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 106 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 92 time to evaluate : 0.653 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 MET cc_start: 0.6372 (tpp) cc_final: 0.5674 (mmp) REVERT: A 290 ASP cc_start: 0.6104 (p0) cc_final: 0.5817 (p0) REVERT: B 211 ASP cc_start: 0.7031 (p0) cc_final: 0.6760 (p0) outliers start: 14 outliers final: 7 residues processed: 100 average time/residue: 0.2472 time to fit residues: 30.5557 Evaluate side-chains 83 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 76 time to evaluate : 0.750 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain C residue 303 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 37 optimal weight: 6.9990 chunk 21 optimal weight: 0.9980 chunk 56 optimal weight: 0.6980 chunk 46 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 68 optimal weight: 0.0670 chunk 73 optimal weight: 0.6980 chunk 60 optimal weight: 4.9990 chunk 67 optimal weight: 0.9980 chunk 23 optimal weight: 0.9980 chunk 54 optimal weight: 2.9990 overall best weight: 0.6918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 134 HIS ** A 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 134 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7262 moved from start: 0.2927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 6135 Z= 0.152 Angle : 0.553 11.156 8331 Z= 0.265 Chirality : 0.041 0.143 933 Planarity : 0.004 0.042 1077 Dihedral : 4.160 21.335 831 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.44 % Allowed : 20.35 % Favored : 78.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.30), residues: 759 helix: 1.18 (0.33), residues: 252 sheet: -1.49 (0.27), residues: 306 loop : -2.21 (0.39), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP B 241 HIS 0.002 0.001 HIS B 131 PHE 0.012 0.001 PHE B 234 TYR 0.009 0.001 TYR B 282 ARG 0.001 0.000 ARG A 145 *********************** 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 fitting. rotamer outliers: 9 poor density : 81 time to evaluate : 0.679 Fit side-chains REVERT: B 211 ASP cc_start: 0.7087 (p0) cc_final: 0.6846 (p0) outliers start: 9 outliers final: 6 residues processed: 87 average time/residue: 0.2171 time to fit residues: 23.9762 Evaluate side-chains 80 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 74 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 229 CYS Chi-restraints excluded: chain C residue 99 ASN 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 67 optimal weight: 3.9990 chunk 51 optimal weight: 5.9990 chunk 35 optimal weight: 7.9990 chunk 7 optimal weight: 6.9990 chunk 32 optimal weight: 4.9990 chunk 45 optimal weight: 5.9990 chunk 68 optimal weight: 3.9990 chunk 72 optimal weight: 0.8980 chunk 64 optimal weight: 1.9990 chunk 19 optimal weight: 6.9990 chunk 60 optimal weight: 0.6980 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN ** A 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 287 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 moved from start: 0.3266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 6135 Z= 0.269 Angle : 0.601 11.225 8331 Z= 0.291 Chirality : 0.042 0.213 933 Planarity : 0.004 0.041 1077 Dihedral : 4.166 20.460 831 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 1.60 % Allowed : 20.51 % Favored : 77.88 % 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: -0.75 (0.31), residues: 759 helix: 1.79 (0.34), residues: 252 sheet: -1.20 (0.27), residues: 306 loop : -2.12 (0.41), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 305 HIS 0.004 0.001 HIS B 131 PHE 0.014 0.001 PHE B 234 TYR 0.012 0.001 TYR A 282 ARG 0.001 0.000 ARG B 272 *********************** 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 86 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 76 time to evaluate : 0.686 Fit side-chains REVERT: B 96 LYS cc_start: 0.7735 (mptt) cc_final: 0.7500 (mmtm) REVERT: B 204 MET cc_start: 0.6776 (tmm) cc_final: 0.6128 (ttt) REVERT: B 211 ASP cc_start: 0.7073 (p0) cc_final: 0.6749 (p0) outliers start: 10 outliers final: 8 residues processed: 82 average time/residue: 0.2012 time to fit residues: 21.4234 Evaluate side-chains 77 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 69 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 303 ASN Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 229 CYS Chi-restraints excluded: chain B residue 303 ASN Chi-restraints excluded: chain C residue 99 ASN 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 41 optimal weight: 0.7980 chunk 1 optimal weight: 5.9990 chunk 53 optimal weight: 5.9990 chunk 29 optimal weight: 0.5980 chunk 61 optimal weight: 6.9990 chunk 50 optimal weight: 40.0000 chunk 0 optimal weight: 5.9990 chunk 37 optimal weight: 0.9980 chunk 65 optimal weight: 8.9990 chunk 18 optimal weight: 5.9990 chunk 24 optimal weight: 1.9990 overall best weight: 2.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN ** A 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7350 moved from start: 0.3425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 6135 Z= 0.242 Angle : 0.603 11.330 8331 Z= 0.287 Chirality : 0.041 0.134 933 Planarity : 0.004 0.043 1077 Dihedral : 4.075 20.610 831 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.44 % Allowed : 20.51 % Favored : 78.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.31), residues: 759 helix: 2.06 (0.34), residues: 252 sheet: -1.05 (0.27), residues: 306 loop : -2.01 (0.41), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 305 HIS 0.002 0.001 HIS B 131 PHE 0.013 0.001 PHE B 234 TYR 0.010 0.001 TYR B 282 ARG 0.001 0.000 ARG C 272 *********************** 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 fitting. rotamer outliers: 9 poor density : 76 time to evaluate : 0.739 Fit side-chains REVERT: B 96 LYS cc_start: 0.7790 (mptt) cc_final: 0.7495 (mmtm) REVERT: C 102 MET cc_start: 0.6704 (tpp) cc_final: 0.6346 (tpp) outliers start: 9 outliers final: 7 residues processed: 81 average time/residue: 0.2016 time to fit residues: 21.5193 Evaluate side-chains 76 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 69 time to evaluate : 0.744 ------------------------------------------------------------------------------- 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 99 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 65 optimal weight: 5.9990 chunk 14 optimal weight: 0.0770 chunk 42 optimal weight: 6.9990 chunk 17 optimal weight: 3.9990 chunk 72 optimal weight: 5.9990 chunk 60 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 6 optimal weight: 4.9990 chunk 24 optimal weight: 5.9990 chunk 38 optimal weight: 4.9990 chunk 69 optimal weight: 7.9990 overall best weight: 2.6144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 GLN ** A 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 moved from start: 0.3617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.025 6135 Z= 0.290 Angle : 0.617 11.967 8331 Z= 0.298 Chirality : 0.044 0.313 933 Planarity : 0.004 0.043 1077 Dihedral : 4.167 20.307 831 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 2.40 % Allowed : 18.91 % Favored : 78.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.31), residues: 759 helix: 2.11 (0.33), residues: 255 sheet: -1.06 (0.27), residues: 306 loop : -2.00 (0.42), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 305 HIS 0.002 0.001 HIS B 131 PHE 0.014 0.001 PHE B 234 TYR 0.011 0.001 TYR A 282 ARG 0.001 0.000 ARG A 272 *********************** 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 83 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 68 time to evaluate : 0.721 Fit side-chains REVERT: A 316 MET cc_start: 0.7173 (ppp) cc_final: 0.6902 (ppp) REVERT: B 96 LYS cc_start: 0.7778 (mptt) cc_final: 0.7531 (mmtm) REVERT: B 204 MET cc_start: 0.6665 (tmm) cc_final: 0.5953 (ttt) REVERT: B 211 ASP cc_start: 0.7120 (p0) cc_final: 0.6863 (p0) REVERT: C 102 MET cc_start: 0.6812 (tpp) cc_final: 0.6520 (tpp) REVERT: C 214 ASP cc_start: 0.6073 (p0) cc_final: 0.5718 (p0) outliers start: 15 outliers final: 9 residues processed: 79 average time/residue: 0.1785 time to fit residues: 19.0460 Evaluate side-chains 73 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 64 time to evaluate : 0.767 ------------------------------------------------------------------------------- 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 99 ASN Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 229 CYS Chi-restraints excluded: chain B residue 303 ASN Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 229 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 8 optimal weight: 10.0000 chunk 41 optimal weight: 0.8980 chunk 52 optimal weight: 0.9990 chunk 61 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 44 optimal weight: 0.6980 chunk 33 optimal weight: 9.9990 chunk 28 optimal weight: 7.9990 chunk 43 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 GLN ** B 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 GLN C 107 GLN C 188 GLN C 295 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7339 moved from start: 0.3731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 6135 Z= 0.189 Angle : 0.632 12.731 8331 Z= 0.293 Chirality : 0.044 0.292 933 Planarity : 0.004 0.044 1077 Dihedral : 4.009 19.913 831 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.60 % Allowed : 19.87 % Favored : 78.53 % 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: -0.15 (0.31), residues: 759 helix: 2.23 (0.33), residues: 255 sheet: -0.81 (0.27), residues: 306 loop : -1.90 (0.43), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 305 HIS 0.001 0.001 HIS B 131 PHE 0.013 0.001 PHE B 234 TYR 0.008 0.001 TYR A 292 ARG 0.001 0.000 ARG A 289 *********************** 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 85 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 75 time to evaluate : 0.786 Fit side-chains REVERT: B 96 LYS cc_start: 0.7747 (mptt) cc_final: 0.7525 (mmtm) REVERT: B 204 MET cc_start: 0.6912 (tmm) cc_final: 0.6213 (ttt) REVERT: C 102 MET cc_start: 0.6785 (tpp) cc_final: 0.6558 (tpp) outliers start: 10 outliers final: 9 residues processed: 82 average time/residue: 0.1759 time to fit residues: 19.4349 Evaluate side-chains 75 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 66 time to evaluate : 0.787 ------------------------------------------------------------------------------- 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 B residue 229 CYS Chi-restraints excluded: chain B residue 303 ASN 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: 0.8980 chunk 14 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 49 optimal weight: 5.9990 chunk 35 optimal weight: 6.9990 chunk 6 optimal weight: 2.9990 chunk 56 optimal weight: 0.0060 chunk 65 optimal weight: 5.9990 chunk 69 optimal weight: 3.9990 chunk 63 optimal weight: 0.8980 chunk 67 optimal weight: 1.9990 overall best weight: 1.3600 ------------------------------------------------------------------------------- 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** A 295 GLN ** B 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7337 moved from start: 0.3864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6135 Z= 0.195 Angle : 0.630 12.545 8331 Z= 0.294 Chirality : 0.045 0.367 933 Planarity : 0.004 0.043 1077 Dihedral : 4.010 19.705 831 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.60 % Allowed : 20.51 % Favored : 77.88 % 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: 0.02 (0.31), residues: 759 helix: 2.26 (0.33), residues: 255 sheet: -0.63 (0.27), residues: 306 loop : -1.83 (0.43), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 305 HIS 0.002 0.001 HIS B 131 PHE 0.013 0.001 PHE B 234 TYR 0.008 0.001 TYR B 282 ARG 0.001 0.000 ARG A 272 *********************** 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 80 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 70 time to evaluate : 0.728 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 9 residues processed: 77 average time/residue: 0.1761 time to fit residues: 18.4606 Evaluate side-chains 78 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 69 time to evaluate : 0.817 ------------------------------------------------------------------------------- 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 B residue 229 CYS Chi-restraints excluded: chain B residue 303 ASN 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 69 optimal weight: 7.9990 chunk 40 optimal weight: 7.9990 chunk 29 optimal weight: 3.9990 chunk 52 optimal weight: 5.9990 chunk 20 optimal weight: 0.9990 chunk 60 optimal weight: 3.9990 chunk 63 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 chunk 71 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- 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 107 GLN ** 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: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7351 moved from start: 0.3978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 6135 Z= 0.229 Angle : 0.646 12.837 8331 Z= 0.303 Chirality : 0.045 0.379 933 Planarity : 0.004 0.044 1077 Dihedral : 4.084 20.037 831 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.76 % Allowed : 20.03 % Favored : 78.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.31), residues: 759 helix: 2.33 (0.33), residues: 255 sheet: -0.56 (0.28), residues: 300 loop : -1.59 (0.42), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 305 HIS 0.002 0.001 HIS B 131 PHE 0.013 0.001 PHE B 234 TYR 0.010 0.001 TYR B 282 ARG 0.001 0.000 ARG A 272 *********************** 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 83 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 72 time to evaluate : 0.750 Fit side-chains revert: symmetry clash REVERT: B 204 MET cc_start: 0.6848 (tmm) cc_final: 0.6094 (ttt) REVERT: C 204 MET cc_start: 0.6845 (tmm) cc_final: 0.6486 (ttt) outliers start: 11 outliers final: 11 residues processed: 80 average time/residue: 0.1667 time to fit residues: 18.2296 Evaluate side-chains 76 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 65 time to evaluate : 0.737 ------------------------------------------------------------------------------- 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 99 ASN Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 229 CYS Chi-restraints excluded: chain B residue 303 ASN 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 33 optimal weight: 5.9990 chunk 49 optimal weight: 10.0000 chunk 74 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 59 optimal weight: 0.8980 chunk 6 optimal weight: 0.4980 chunk 45 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 47 optimal weight: 4.9990 chunk 63 optimal weight: 0.6980 chunk 18 optimal weight: 3.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7314 moved from start: 0.4093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6135 Z= 0.183 Angle : 0.680 12.720 8331 Z= 0.311 Chirality : 0.045 0.393 933 Planarity : 0.004 0.044 1077 Dihedral : 4.013 19.813 831 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.76 % Allowed : 20.99 % Favored : 77.24 % 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: 0.36 (0.31), residues: 759 helix: 2.39 (0.33), residues: 255 sheet: -0.36 (0.28), residues: 300 loop : -1.52 (0.42), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.000 TRP B 305 HIS 0.001 0.000 HIS B 131 PHE 0.013 0.001 PHE A 234 TYR 0.008 0.001 TYR A 292 ARG 0.001 0.000 ARG A 272 ********************** 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 fitting. rotamer outliers: 11 poor density : 77 time to evaluate : 0.795 Fit side-chains revert: symmetry clash REVERT: B 204 MET cc_start: 0.6950 (tmm) cc_final: 0.6234 (ttt) REVERT: C 204 MET cc_start: 0.6909 (tmm) cc_final: 0.6669 (ttt) outliers start: 11 outliers final: 11 residues processed: 85 average time/residue: 0.1656 time to fit residues: 19.4094 Evaluate side-chains 83 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 72 time to evaluate : 0.742 ------------------------------------------------------------------------------- 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 99 ASN Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 229 CYS Chi-restraints excluded: chain B residue 303 ASN 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 54 optimal weight: 5.9990 chunk 8 optimal weight: 5.9990 chunk 16 optimal weight: 3.9990 chunk 59 optimal weight: 0.8980 chunk 24 optimal weight: 10.0000 chunk 61 optimal weight: 0.9990 chunk 7 optimal weight: 0.0370 chunk 10 optimal weight: 0.3980 chunk 52 optimal weight: 1.9990 chunk 3 optimal weight: 6.9990 chunk 43 optimal weight: 3.9990 overall best weight: 0.8662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 107 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 = 0.3377 r_free = 0.3377 target = 0.068830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.050301 restraints weight = 21620.766| |-----------------------------------------------------------------------------| r_work (start): 0.2891 rms_B_bonded: 4.41 r_work: 0.2729 rms_B_bonded: 4.91 restraints_weight: 0.5000 r_work (final): 0.2729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.4191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6135 Z= 0.181 Angle : 0.687 12.921 8331 Z= 0.311 Chirality : 0.045 0.401 933 Planarity : 0.004 0.044 1077 Dihedral : 3.928 19.614 831 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.76 % Allowed : 21.47 % Favored : 76.76 % 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: 0.52 (0.31), residues: 759 helix: 2.49 (0.33), residues: 255 sheet: -0.22 (0.29), residues: 300 loop : -1.47 (0.42), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.000 TRP B 305 HIS 0.001 0.001 HIS B 131 PHE 0.013 0.001 PHE C 234 TYR 0.021 0.001 TYR C 203 ARG 0.001 0.000 ARG A 272 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1593.08 seconds wall clock time: 29 minutes 38.43 seconds (1778.43 seconds total)