Starting phenix.real_space_refine on Tue Feb 11 01:33:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tmc_25995/02_2025/7tmc_25995.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tmc_25995/02_2025/7tmc_25995.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7tmc_25995/02_2025/7tmc_25995.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tmc_25995/02_2025/7tmc_25995.map" model { file = "/net/cci-nas-00/data/ceres_data/7tmc_25995/02_2025/7tmc_25995.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tmc_25995/02_2025/7tmc_25995.cif" } resolution = 3.25 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= 1.000 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 21 5.16 5 C 2178 2.51 5 N 531 2.21 5 O 696 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 3426 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1086 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 2, 'TRANS': 132} Chain: "B" Number of atoms: 1086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1086 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 2, 'TRANS': 132} Chain: "C" Number of atoms: 1086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1086 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 2, 'TRANS': 132} Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 3.15, per 1000 atoms: 0.92 Number of scatterers: 3426 At special positions: 0 Unit cell: (101.184, 110.67, 35.836, 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 21 16.00 O 696 8.00 N 531 7.00 C 2178 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 214 " - pdb=" SG CYS A 253 " distance=2.03 Simple disulfide: pdb=" SG CYS B 214 " - pdb=" SG CYS B 253 " distance=2.03 Simple disulfide: pdb=" SG CYS C 214 " - pdb=" SG CYS C 253 " distance=2.02 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 Links applied NAG-ASN " NAG A 301 " - " ASN A 151 " " NAG A 302 " - " ASN A 145 " " NAG A 303 " - " ASN A 164 " " NAG A 304 " - " ASN A 183 " " NAG B 301 " - " ASN B 151 " " NAG B 302 " - " ASN B 145 " " NAG B 303 " - " ASN B 164 " " NAG B 304 " - " ASN B 183 " " NAG C 301 " - " ASN C 151 " " NAG C 302 " - " ASN C 145 " " NAG C 303 " - " ASN C 164 " " NAG C 304 " - " ASN C 183 " Time building additional restraints: 0.84 Conformation dependent library (CDL) restraints added in 410.6 milliseconds 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 780 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 17 sheets defined 0.0% alpha, 44.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.58 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'B' and resid 124 through 126 removed outlier: 6.091A pdb=" N TYR A 125 " --> pdb=" O ILE C 126 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 129 through 130 removed outlier: 8.001A pdb=" N SER B 134 " --> pdb=" O ALA A 131 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N VAL A 133 " --> pdb=" O SER B 134 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 129 through 130 removed outlier: 9.113A pdb=" N SER A 130 " --> pdb=" O ALA C 131 " (cutoff:3.500A) removed outlier: 10.056A pdb=" N VAL C 133 " --> pdb=" O SER A 130 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N TYR A 132 " --> pdb=" O VAL C 133 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 141 through 143 removed outlier: 5.870A pdb=" N ILE A 142 " --> pdb=" O TYR C 143 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 152 through 153 removed outlier: 6.524A pdb=" N ILE A 152 " --> pdb=" O THR B 153 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 156 through 157 removed outlier: 6.522A pdb=" N ASN A 156 " --> pdb=" O TYR B 157 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 169 through 175 removed outlier: 6.217A pdb=" N GLN A 170 " --> pdb=" O PHE B 171 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N LYS B 173 " --> pdb=" O GLN A 170 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N SER A 172 " --> pdb=" O LYS B 173 " (cutoff:3.500A) removed outlier: 8.219A pdb=" N VAL B 175 " --> pdb=" O SER A 172 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N THR A 174 " --> pdb=" O VAL B 175 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N VAL A 169 " --> pdb=" O GLN C 170 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 169 through 175 removed outlier: 6.217A pdb=" N GLN A 170 " --> pdb=" O PHE B 171 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N LYS B 173 " --> pdb=" O GLN A 170 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N SER A 172 " --> pdb=" O LYS B 173 " (cutoff:3.500A) removed outlier: 8.219A pdb=" N VAL B 175 " --> pdb=" O SER A 172 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N THR A 174 " --> pdb=" O VAL B 175 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 184 through 186 removed outlier: 6.398A pdb=" N ILE A 184 " --> pdb=" O THR B 185 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 190 through 193 removed outlier: 6.878A pdb=" N LEU A 190 " --> pdb=" O ASP B 191 " (cutoff:3.500A) removed outlier: 8.447A pdb=" N LYS B 193 " --> pdb=" O LEU A 190 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N MET A 192 " --> pdb=" O LYS B 193 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 196 through 197 removed outlier: 6.082A pdb=" N ASP A 196 " --> pdb=" O TYR C 197 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 202 through 206 removed outlier: 6.317A pdb=" N VAL A 202 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N GLU C 205 " --> pdb=" O VAL A 202 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ALA A 204 " --> pdb=" O GLU C 205 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 209 through 218 removed outlier: 6.767A pdb=" N MET A 210 " --> pdb=" O TYR B 211 " (cutoff:3.500A) removed outlier: 8.022A pdb=" N PHE B 213 " --> pdb=" O MET A 210 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N ASP A 212 " --> pdb=" O PHE B 213 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N THR B 215 " --> pdb=" O ASP A 212 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N CYS A 214 " --> pdb=" O THR B 215 " (cutoff:3.500A) removed outlier: 10.343A pdb=" N ILE B 217 " --> pdb=" O CYS A 214 " (cutoff:3.500A) removed outlier: 9.147A pdb=" N LEU A 216 " --> pdb=" O ILE B 217 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N TYR A 209 " --> pdb=" O MET C 210 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N ASP C 212 " --> pdb=" O TYR A 209 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N TYR A 211 " --> pdb=" O ASP C 212 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'B' and resid 209 through 218 removed outlier: 6.767A pdb=" N MET A 210 " --> pdb=" O TYR B 211 " (cutoff:3.500A) removed outlier: 8.022A pdb=" N PHE B 213 " --> pdb=" O MET A 210 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N ASP A 212 " --> pdb=" O PHE B 213 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N THR B 215 " --> pdb=" O ASP A 212 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N CYS A 214 " --> pdb=" O THR B 215 " (cutoff:3.500A) removed outlier: 10.343A pdb=" N ILE B 217 " --> pdb=" O CYS A 214 " (cutoff:3.500A) removed outlier: 9.147A pdb=" N LEU A 216 " --> pdb=" O ILE B 217 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 224 through 228 removed outlier: 6.060A pdb=" N VAL A 225 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N MET B 228 " --> pdb=" O VAL A 225 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N MET A 227 " --> pdb=" O MET B 228 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 233 through 240 removed outlier: 6.641A pdb=" N THR A 233 " --> pdb=" O THR B 234 " (cutoff:3.500A) removed outlier: 8.104A pdb=" N TYR B 236 " --> pdb=" O THR A 233 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N THR A 235 " --> pdb=" O TYR B 236 " (cutoff:3.500A) removed outlier: 8.030A pdb=" N GLY B 238 " --> pdb=" O THR A 235 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N PHE A 237 " --> pdb=" O GLY B 238 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N SER B 240 " --> pdb=" O PHE A 237 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N HIS A 239 " --> pdb=" O SER B 240 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 243 through 246 removed outlier: 6.111A pdb=" N SER A 244 " --> pdb=" O GLN C 245 " (cutoff:3.500A) 37 hydrogen bonds defined for protein. 111 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.82 Time building geometry restraints manager: 1.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1050 1.34 - 1.46: 802 1.46 - 1.58: 1592 1.58 - 1.69: 0 1.69 - 1.81: 36 Bond restraints: 3480 Sorted by residual: bond pdb=" C1 NAG C 303 " pdb=" O5 NAG C 303 " ideal model delta sigma weight residual 1.406 1.489 -0.083 2.00e-02 2.50e+03 1.71e+01 bond pdb=" C1 NAG A 303 " pdb=" O5 NAG A 303 " ideal model delta sigma weight residual 1.406 1.486 -0.080 2.00e-02 2.50e+03 1.60e+01 bond pdb=" C1 NAG B 303 " pdb=" O5 NAG B 303 " ideal model delta sigma weight residual 1.406 1.480 -0.074 2.00e-02 2.50e+03 1.38e+01 bond pdb=" C1 NAG A 302 " pdb=" O5 NAG A 302 " ideal model delta sigma weight residual 1.406 1.443 -0.037 2.00e-02 2.50e+03 3.39e+00 bond pdb=" C1 NAG C 302 " pdb=" O5 NAG C 302 " ideal model delta sigma weight residual 1.406 1.443 -0.037 2.00e-02 2.50e+03 3.34e+00 ... (remaining 3475 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.10: 4252 1.10 - 2.20: 390 2.20 - 3.29: 68 3.29 - 4.39: 10 4.39 - 5.49: 11 Bond angle restraints: 4731 Sorted by residual: angle pdb=" N GLY C 238 " pdb=" CA GLY C 238 " pdb=" C GLY C 238 " ideal model delta sigma weight residual 110.29 114.60 -4.31 1.28e+00 6.10e-01 1.14e+01 angle pdb=" N ILE C 219 " pdb=" CA ILE C 219 " pdb=" C ILE C 219 " ideal model delta sigma weight residual 109.34 103.85 5.49 2.08e+00 2.31e-01 6.96e+00 angle pdb=" N ILE A 219 " pdb=" CA ILE A 219 " pdb=" C ILE A 219 " ideal model delta sigma weight residual 109.34 103.92 5.42 2.08e+00 2.31e-01 6.78e+00 angle pdb=" N GLN C 138 " pdb=" CA GLN C 138 " pdb=" C GLN C 138 " ideal model delta sigma weight residual 109.65 113.65 -4.00 1.56e+00 4.11e-01 6.59e+00 angle pdb=" N ILE B 219 " pdb=" CA ILE B 219 " pdb=" C ILE B 219 " ideal model delta sigma weight residual 109.34 104.08 5.26 2.08e+00 2.31e-01 6.40e+00 ... (remaining 4726 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.85: 2092 24.85 - 49.69: 114 49.69 - 74.54: 27 74.54 - 99.39: 7 99.39 - 124.23: 7 Dihedral angle restraints: 2247 sinusoidal: 1029 harmonic: 1218 Sorted by residual: dihedral pdb=" CB CYS A 214 " pdb=" SG CYS A 214 " pdb=" SG CYS A 253 " pdb=" CB CYS A 253 " ideal model delta sinusoidal sigma weight residual 93.00 167.93 -74.93 1 1.00e+01 1.00e-02 7.10e+01 dihedral pdb=" CB CYS C 214 " pdb=" SG CYS C 214 " pdb=" SG CYS C 253 " pdb=" CB CYS C 253 " ideal model delta sinusoidal sigma weight residual 93.00 163.42 -70.42 1 1.00e+01 1.00e-02 6.38e+01 dihedral pdb=" CA TYR A 143 " pdb=" C TYR A 143 " pdb=" N LEU A 144 " pdb=" CA LEU A 144 " ideal model delta harmonic sigma weight residual 180.00 -154.88 -25.12 0 5.00e+00 4.00e-02 2.52e+01 ... (remaining 2244 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 491 0.080 - 0.159: 102 0.159 - 0.239: 3 0.239 - 0.319: 2 0.319 - 0.399: 5 Chirality restraints: 603 Sorted by residual: chirality pdb=" C1 NAG C 304 " pdb=" ND2 ASN C 183 " pdb=" C2 NAG C 304 " pdb=" O5 NAG C 304 " both_signs ideal model delta sigma weight residual False -2.40 -2.00 -0.40 2.00e-01 2.50e+01 3.97e+00 chirality pdb=" C1 NAG B 304 " pdb=" ND2 ASN B 183 " pdb=" C2 NAG B 304 " pdb=" O5 NAG B 304 " both_signs ideal model delta sigma weight residual False -2.40 -2.00 -0.40 2.00e-01 2.50e+01 3.94e+00 chirality pdb=" C1 NAG A 304 " pdb=" ND2 ASN A 183 " pdb=" C2 NAG A 304 " pdb=" O5 NAG A 304 " both_signs ideal model delta sigma weight residual False -2.40 -2.01 -0.39 2.00e-01 2.50e+01 3.89e+00 ... (remaining 600 not shown) Planarity restraints: 582 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL C 199 " 0.056 5.00e-02 4.00e+02 8.53e-02 1.16e+01 pdb=" N PRO C 200 " -0.148 5.00e-02 4.00e+02 pdb=" CA PRO C 200 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRO C 200 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 145 " 0.026 2.00e-02 2.50e+03 2.41e-02 7.28e+00 pdb=" CG ASN B 145 " -0.032 2.00e-02 2.50e+03 pdb=" OD1 ASN B 145 " 0.004 2.00e-02 2.50e+03 pdb=" ND2 ASN B 145 " -0.024 2.00e-02 2.50e+03 pdb=" C1 NAG B 302 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL B 199 " 0.040 5.00e-02 4.00e+02 6.10e-02 5.95e+00 pdb=" N PRO B 200 " -0.105 5.00e-02 4.00e+02 pdb=" CA PRO B 200 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 200 " 0.034 5.00e-02 4.00e+02 ... (remaining 579 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 99 2.70 - 3.25: 3219 3.25 - 3.80: 5135 3.80 - 4.35: 6307 4.35 - 4.90: 11312 Nonbonded interactions: 26072 Sorted by model distance: nonbonded pdb=" OG1 THR C 231 " pdb=" OG1 THR C 234 " model vdw 2.152 3.040 nonbonded pdb=" OD2 ASP A 196 " pdb=" OG1 THR A 198 " model vdw 2.193 3.040 nonbonded pdb=" NZ LYS B 129 " pdb=" OD2 ASP B 136 " model vdw 2.201 3.120 nonbonded pdb=" OD1 ASP B 212 " pdb=" OG1 THR B 215 " model vdw 2.214 3.040 nonbonded pdb=" NE2 GLN C 249 " pdb=" OD2 ASP C 252 " model vdw 2.225 3.120 ... (remaining 26067 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.050 Process input model: 13.490 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3031 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 0.083 3480 Z= 0.332 Angle : 0.722 5.489 4731 Z= 0.382 Chirality : 0.066 0.399 603 Planarity : 0.006 0.085 570 Dihedral : 18.016 124.235 1458 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 13.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.52 % Favored : 90.48 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.08 (0.34), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.10 (0.26), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 239 PHE 0.005 0.001 PHE A 237 TYR 0.022 0.002 TYR B 250 ARG 0.001 0.000 ARG B 247 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 0.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 135 TYR cc_start: 0.2725 (m-80) cc_final: 0.2105 (p90) outliers start: 0 outliers final: 0 residues processed: 102 average time/residue: 0.1556 time to fit residues: 19.2105 Evaluate side-chains 65 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 32 optimal weight: 4.9990 chunk 29 optimal weight: 0.0970 chunk 16 optimal weight: 7.9990 chunk 10 optimal weight: 5.9990 chunk 19 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 30 optimal weight: 7.9990 chunk 11 optimal weight: 6.9990 chunk 18 optimal weight: 9.9990 chunk 22 optimal weight: 6.9990 chunk 35 optimal weight: 1.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 ASN ** A 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 249 GLN ** B 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 249 GLN C 155 ASN C 170 GLN ** C 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4673 r_free = 0.4673 target = 0.161663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4535 r_free = 0.4535 target = 0.147323 restraints weight = 5481.118| |-----------------------------------------------------------------------------| r_work (start): 0.4523 rms_B_bonded: 3.27 r_work: 0.4432 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.4432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5541 moved from start: 0.9544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 3480 Z= 0.365 Angle : 1.136 15.508 4731 Z= 0.538 Chirality : 0.084 0.612 603 Planarity : 0.007 0.065 570 Dihedral : 12.362 59.589 699 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.28 % Favored : 87.72 % Rotamer: Outliers : 4.76 % Allowed : 16.14 % Favored : 79.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.12 (0.34), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.13 (0.26), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS C 222 PHE 0.014 0.002 PHE C 213 TYR 0.029 0.003 TYR A 197 ARG 0.006 0.001 ARG C 140 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 127 time to evaluate : 0.385 Fit side-chains revert: symmetry clash REVERT: A 122 ASP cc_start: 0.6988 (t0) cc_final: 0.6759 (t0) REVERT: A 138 GLN cc_start: 0.6359 (mm110) cc_final: 0.6144 (mm110) REVERT: A 194 GLN cc_start: 0.7462 (mp10) cc_final: 0.6663 (mp10) REVERT: A 222 HIS cc_start: 0.6300 (m90) cc_final: 0.6067 (m-70) REVERT: B 194 GLN cc_start: 0.7166 (mt0) cc_final: 0.6813 (tp-100) REVERT: C 180 ARG cc_start: 0.6736 (mtt180) cc_final: 0.6365 (ptt-90) REVERT: C 194 GLN cc_start: 0.7413 (mt0) cc_final: 0.6919 (tp40) outliers start: 18 outliers final: 11 residues processed: 138 average time/residue: 0.1474 time to fit residues: 24.7177 Evaluate side-chains 120 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 109 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 135 TYR Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 208 SER Chi-restraints excluded: chain C residue 216 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 25 optimal weight: 2.9990 chunk 34 optimal weight: 10.0000 chunk 30 optimal weight: 1.9990 chunk 22 optimal weight: 10.0000 chunk 0 optimal weight: 6.9990 chunk 16 optimal weight: 8.9990 chunk 2 optimal weight: 9.9990 chunk 37 optimal weight: 9.9990 chunk 32 optimal weight: 0.9980 chunk 13 optimal weight: 0.9990 chunk 3 optimal weight: 0.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 249 GLN B 170 GLN B 229 GLN B 249 GLN C 170 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4690 r_free = 0.4690 target = 0.157202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4535 r_free = 0.4535 target = 0.142177 restraints weight = 5775.359| |-----------------------------------------------------------------------------| r_work (start): 0.4529 rms_B_bonded: 3.22 r_work: 0.4446 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.4446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6141 moved from start: 1.1963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 3480 Z= 0.264 Angle : 0.839 8.953 4731 Z= 0.417 Chirality : 0.069 0.545 603 Planarity : 0.005 0.048 570 Dihedral : 9.658 53.710 699 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.03 % Favored : 88.97 % Rotamer: Outliers : 5.29 % Allowed : 18.78 % Favored : 75.93 % 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: -4.18 (0.33), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.18 (0.26), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 239 PHE 0.026 0.002 PHE B 171 TYR 0.021 0.002 TYR A 209 ARG 0.005 0.001 ARG A 180 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 131 time to evaluate : 0.377 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 122 ASP cc_start: 0.7451 (t0) cc_final: 0.7194 (t0) REVERT: A 164 ASN cc_start: 0.7552 (OUTLIER) cc_final: 0.6918 (m110) REVERT: A 228 MET cc_start: 0.7405 (OUTLIER) cc_final: 0.7136 (mtt) REVERT: B 194 GLN cc_start: 0.7567 (mt0) cc_final: 0.7037 (tp-100) REVERT: B 226 LEU cc_start: 0.6648 (mt) cc_final: 0.6426 (mt) REVERT: B 227 MET cc_start: 0.6615 (mmm) cc_final: 0.6362 (mmm) REVERT: B 246 GLU cc_start: 0.7159 (pt0) cc_final: 0.6649 (tp30) REVERT: C 180 ARG cc_start: 0.7153 (mtt180) cc_final: 0.6316 (ptt-90) REVERT: C 193 LYS cc_start: 0.7732 (mtmm) cc_final: 0.7509 (mtpt) REVERT: C 194 GLN cc_start: 0.7686 (mt0) cc_final: 0.7023 (tp-100) REVERT: C 216 LEU cc_start: 0.6608 (OUTLIER) cc_final: 0.6297 (pp) REVERT: C 242 GLN cc_start: 0.7293 (tt0) cc_final: 0.6691 (tp40) outliers start: 20 outliers final: 13 residues processed: 143 average time/residue: 0.1546 time to fit residues: 26.6042 Evaluate side-chains 134 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 118 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 228 MET Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 240 SER Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 216 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 24 optimal weight: 0.8980 chunk 33 optimal weight: 0.9990 chunk 3 optimal weight: 9.9990 chunk 7 optimal weight: 2.9990 chunk 21 optimal weight: 0.4980 chunk 1 optimal weight: 2.9990 chunk 15 optimal weight: 4.9990 chunk 22 optimal weight: 5.9990 chunk 9 optimal weight: 0.9990 chunk 31 optimal weight: 9.9990 chunk 8 optimal weight: 7.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- 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 = 0.4678 r_free = 0.4678 target = 0.156695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4528 r_free = 0.4528 target = 0.141468 restraints weight = 5863.349| |-----------------------------------------------------------------------------| r_work (start): 0.4512 rms_B_bonded: 3.25 r_work: 0.4429 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.4429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6448 moved from start: 1.3618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3480 Z= 0.220 Angle : 0.731 5.953 4731 Z= 0.380 Chirality : 0.062 0.393 603 Planarity : 0.005 0.078 570 Dihedral : 8.767 50.239 699 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.27 % Favored : 90.73 % Rotamer: Outliers : 5.82 % Allowed : 20.63 % Favored : 73.54 % 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: -4.15 (0.33), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.15 (0.25), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 222 PHE 0.018 0.002 PHE A 237 TYR 0.014 0.002 TYR B 250 ARG 0.005 0.001 ARG A 180 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 144 time to evaluate : 0.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 192 MET cc_start: 0.7254 (mmp) cc_final: 0.6870 (mmp) REVERT: A 220 LYS cc_start: 0.7748 (ttpt) cc_final: 0.7482 (ttmm) REVERT: B 191 ASP cc_start: 0.7479 (m-30) cc_final: 0.7053 (t0) REVERT: B 194 GLN cc_start: 0.7689 (mt0) cc_final: 0.7279 (mp10) REVERT: B 246 GLU cc_start: 0.7710 (pt0) cc_final: 0.6952 (tp30) REVERT: C 180 ARG cc_start: 0.6726 (mtt180) cc_final: 0.6176 (ptt-90) REVERT: C 194 GLN cc_start: 0.8099 (mt0) cc_final: 0.7246 (mp10) outliers start: 22 outliers final: 16 residues processed: 154 average time/residue: 0.1496 time to fit residues: 27.7593 Evaluate side-chains 150 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 134 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 240 SER Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 231 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 20 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 36 optimal weight: 4.9990 chunk 24 optimal weight: 6.9990 chunk 4 optimal weight: 10.0000 chunk 17 optimal weight: 3.9990 chunk 28 optimal weight: 9.9990 chunk 21 optimal weight: 0.0570 chunk 33 optimal weight: 0.8980 chunk 11 optimal weight: 0.9990 overall best weight: 0.7702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 242 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 = 0.4706 r_free = 0.4706 target = 0.160211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4552 r_free = 0.4552 target = 0.144496 restraints weight = 5840.415| |-----------------------------------------------------------------------------| r_work (start): 0.4553 rms_B_bonded: 3.29 r_work: 0.4462 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.4462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6588 moved from start: 1.4482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3480 Z= 0.181 Angle : 0.659 5.539 4731 Z= 0.352 Chirality : 0.061 0.412 603 Planarity : 0.006 0.081 570 Dihedral : 7.620 54.725 699 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.27 % Favored : 90.73 % Rotamer: Outliers : 4.76 % Allowed : 23.81 % Favored : 71.43 % 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: -4.10 (0.33), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.11 (0.25), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS C 239 PHE 0.020 0.002 PHE B 171 TYR 0.015 0.001 TYR B 143 ARG 0.006 0.001 ARG A 140 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 136 time to evaluate : 0.359 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 192 MET cc_start: 0.7174 (mmp) cc_final: 0.6773 (mmp) REVERT: A 193 LYS cc_start: 0.7517 (mtmm) cc_final: 0.7246 (mtmm) REVERT: A 228 MET cc_start: 0.7948 (mtt) cc_final: 0.7616 (mtt) REVERT: B 194 GLN cc_start: 0.7715 (mt0) cc_final: 0.7392 (mp10) REVERT: B 227 MET cc_start: 0.6693 (mmt) cc_final: 0.6393 (mmm) REVERT: B 246 GLU cc_start: 0.7610 (pt0) cc_final: 0.6981 (tp30) REVERT: C 180 ARG cc_start: 0.6717 (mtt180) cc_final: 0.6117 (ptt-90) REVERT: C 193 LYS cc_start: 0.8101 (mtmm) cc_final: 0.7056 (mtpt) REVERT: C 194 GLN cc_start: 0.8334 (mt0) cc_final: 0.7424 (mp10) REVERT: C 224 ILE cc_start: 0.8074 (mm) cc_final: 0.7782 (mm) outliers start: 18 outliers final: 15 residues processed: 146 average time/residue: 0.1467 time to fit residues: 26.0003 Evaluate side-chains 146 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 131 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 240 SER Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 231 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 36 optimal weight: 5.9990 chunk 9 optimal weight: 9.9990 chunk 12 optimal weight: 9.9990 chunk 28 optimal weight: 5.9990 chunk 0 optimal weight: 7.9990 chunk 13 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 chunk 20 optimal weight: 0.3980 chunk 32 optimal weight: 5.9990 chunk 35 optimal weight: 4.9990 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 138 GLN A 249 GLN B 242 GLN B 249 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4539 r_free = 0.4539 target = 0.147421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4380 r_free = 0.4380 target = 0.133551 restraints weight = 6254.384| |-----------------------------------------------------------------------------| r_work (start): 0.4403 rms_B_bonded: 3.22 r_work: 0.4428 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.4332 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.4332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 moved from start: 1.7628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 3480 Z= 0.314 Angle : 0.817 13.433 4731 Z= 0.424 Chirality : 0.066 0.437 603 Planarity : 0.007 0.088 570 Dihedral : 7.743 50.524 699 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 13.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.78 % Favored : 88.22 % Rotamer: Outliers : 6.61 % Allowed : 24.87 % Favored : 68.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.15 (0.33), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.15 (0.25), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 222 PHE 0.014 0.002 PHE B 171 TYR 0.025 0.002 TYR A 143 ARG 0.006 0.001 ARG A 180 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 137 time to evaluate : 0.373 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 124 LYS cc_start: 0.9022 (mttm) cc_final: 0.8811 (mmtp) REVERT: A 138 GLN cc_start: 0.8649 (mm-40) cc_final: 0.7988 (mm110) REVERT: A 185 THR cc_start: 0.8547 (OUTLIER) cc_final: 0.7977 (p) REVERT: A 193 LYS cc_start: 0.8357 (mtmm) cc_final: 0.7638 (mppt) REVERT: A 207 MET cc_start: 0.7382 (tpt) cc_final: 0.7029 (tpp) REVERT: A 247 ARG cc_start: 0.8950 (OUTLIER) cc_final: 0.8600 (ttt180) REVERT: B 163 GLU cc_start: 0.8355 (mm-30) cc_final: 0.6504 (mp0) REVERT: B 180 ARG cc_start: 0.3594 (mmp-170) cc_final: 0.3210 (mmp-170) REVERT: B 185 THR cc_start: 0.8570 (OUTLIER) cc_final: 0.8123 (p) REVERT: B 194 GLN cc_start: 0.8191 (mt0) cc_final: 0.7735 (mp10) REVERT: B 229 GLN cc_start: 0.8965 (mp-120) cc_final: 0.8176 (mp10) REVERT: B 241 GLU cc_start: 0.7890 (mt-10) cc_final: 0.7666 (mt-10) REVERT: B 246 GLU cc_start: 0.8487 (pt0) cc_final: 0.7230 (tp30) REVERT: B 247 ARG cc_start: 0.8934 (ttt180) cc_final: 0.6642 (pmt-80) REVERT: C 136 ASP cc_start: 0.8802 (p0) cc_final: 0.8596 (p0) REVERT: C 180 ARG cc_start: 0.7423 (mtt180) cc_final: 0.6406 (ptt-90) REVERT: C 193 LYS cc_start: 0.8582 (mtmm) cc_final: 0.8027 (mttp) REVERT: C 194 GLN cc_start: 0.8743 (mt0) cc_final: 0.8087 (mp10) outliers start: 25 outliers final: 15 residues processed: 150 average time/residue: 0.1618 time to fit residues: 29.2163 Evaluate side-chains 139 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 121 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 247 ARG Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 233 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 32 optimal weight: 6.9990 chunk 18 optimal weight: 10.0000 chunk 8 optimal weight: 2.9990 chunk 24 optimal weight: 6.9990 chunk 27 optimal weight: 5.9990 chunk 3 optimal weight: 9.9990 chunk 34 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 chunk 31 optimal weight: 0.4980 chunk 4 optimal weight: 10.0000 chunk 11 optimal weight: 1.9990 overall best weight: 3.0988 ------------------------------------------------------------------------------- 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 = 0.4460 r_free = 0.4460 target = 0.137562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.124648 restraints weight = 6282.561| |-----------------------------------------------------------------------------| r_work (start): 0.4306 rms_B_bonded: 3.06 r_work: 0.4227 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.4227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7339 moved from start: 1.9468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 3480 Z= 0.351 Angle : 0.827 7.859 4731 Z= 0.429 Chirality : 0.066 0.429 603 Planarity : 0.007 0.088 570 Dihedral : 8.112 53.642 699 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 14.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.03 % Favored : 88.97 % Rotamer: Outliers : 5.56 % Allowed : 27.51 % Favored : 66.93 % 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: -4.28 (0.33), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.26 (0.25), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS C 239 PHE 0.013 0.002 PHE B 213 TYR 0.020 0.002 TYR A 143 ARG 0.005 0.001 ARG A 180 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 110 time to evaluate : 0.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 LYS cc_start: 0.8647 (mttm) cc_final: 0.8362 (mmtp) REVERT: A 136 ASP cc_start: 0.7677 (t0) cc_final: 0.7317 (t0) REVERT: A 138 GLN cc_start: 0.8564 (mm-40) cc_final: 0.8062 (mm110) REVERT: A 185 THR cc_start: 0.8444 (OUTLIER) cc_final: 0.7816 (p) REVERT: A 193 LYS cc_start: 0.8512 (mtmm) cc_final: 0.7545 (mppt) REVERT: A 206 GLU cc_start: 0.7165 (mt-10) cc_final: 0.6963 (mt-10) REVERT: A 212 ASP cc_start: 0.7259 (m-30) cc_final: 0.6881 (m-30) REVERT: A 241 GLU cc_start: 0.8192 (mt-10) cc_final: 0.7773 (mt-10) REVERT: A 247 ARG cc_start: 0.8744 (OUTLIER) cc_final: 0.8396 (ttt180) REVERT: B 163 GLU cc_start: 0.8079 (mm-30) cc_final: 0.7838 (mm-30) REVERT: B 168 GLN cc_start: 0.8376 (tt0) cc_final: 0.8125 (tt0) REVERT: B 180 ARG cc_start: 0.3454 (mmp-170) cc_final: 0.3134 (mmp-170) REVERT: B 185 THR cc_start: 0.8696 (OUTLIER) cc_final: 0.8365 (p) REVERT: B 194 GLN cc_start: 0.8552 (mt0) cc_final: 0.8246 (mp10) REVERT: B 209 TYR cc_start: 0.4453 (OUTLIER) cc_final: 0.2863 (t80) REVERT: B 229 GLN cc_start: 0.8862 (mp-120) cc_final: 0.8021 (mp10) REVERT: B 241 GLU cc_start: 0.7732 (mt-10) cc_final: 0.7237 (mt-10) REVERT: B 246 GLU cc_start: 0.8593 (pt0) cc_final: 0.7028 (tp30) REVERT: B 247 ARG cc_start: 0.8994 (ttt180) cc_final: 0.6366 (pmt-80) REVERT: C 194 GLN cc_start: 0.8942 (mt0) cc_final: 0.8593 (mp10) REVERT: C 211 TYR cc_start: 0.4200 (p90) cc_final: 0.3811 (p90) REVERT: C 212 ASP cc_start: 0.7772 (m-30) cc_final: 0.7346 (m-30) outliers start: 21 outliers final: 15 residues processed: 123 average time/residue: 0.1638 time to fit residues: 24.1240 Evaluate side-chains 123 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 104 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 247 ARG Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 209 TYR Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 233 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 22 optimal weight: 20.0000 chunk 26 optimal weight: 7.9990 chunk 33 optimal weight: 5.9990 chunk 1 optimal weight: 6.9990 chunk 4 optimal weight: 8.9990 chunk 32 optimal weight: 1.9990 chunk 27 optimal weight: 0.0970 chunk 24 optimal weight: 0.5980 chunk 5 optimal weight: 10.0000 chunk 7 optimal weight: 0.8980 chunk 38 optimal weight: 3.9990 overall best weight: 1.5182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 170 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4502 r_free = 0.4502 target = 0.140598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.127545 restraints weight = 6100.421| |-----------------------------------------------------------------------------| r_work (start): 0.4350 rms_B_bonded: 2.98 r_work: 0.4274 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.4274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7288 moved from start: 1.9855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3480 Z= 0.223 Angle : 0.742 8.186 4731 Z= 0.380 Chirality : 0.063 0.392 603 Planarity : 0.007 0.079 570 Dihedral : 7.665 51.473 699 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.03 % Favored : 89.97 % Rotamer: Outliers : 6.08 % Allowed : 28.04 % Favored : 65.87 % 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: -4.19 (0.33), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.18 (0.25), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS C 239 PHE 0.013 0.002 PHE B 213 TYR 0.016 0.001 TYR B 248 ARG 0.004 0.001 ARG A 140 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 111 time to evaluate : 0.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 LYS cc_start: 0.8448 (mttm) cc_final: 0.8109 (mmtp) REVERT: A 135 TYR cc_start: 0.8040 (m-80) cc_final: 0.7833 (m-80) REVERT: A 136 ASP cc_start: 0.7531 (t0) cc_final: 0.7018 (t0) REVERT: A 138 GLN cc_start: 0.8634 (mm-40) cc_final: 0.7901 (mm110) REVERT: A 185 THR cc_start: 0.8497 (OUTLIER) cc_final: 0.7936 (p) REVERT: A 193 LYS cc_start: 0.8469 (mtmm) cc_final: 0.7604 (mppt) REVERT: A 212 ASP cc_start: 0.7440 (m-30) cc_final: 0.7022 (m-30) REVERT: A 223 ASN cc_start: 0.8832 (t0) cc_final: 0.8397 (t0) REVERT: A 247 ARG cc_start: 0.8752 (OUTLIER) cc_final: 0.8414 (ttt180) REVERT: B 136 ASP cc_start: 0.7409 (t0) cc_final: 0.6884 (t0) REVERT: B 138 GLN cc_start: 0.8625 (mm-40) cc_final: 0.8300 (mm110) REVERT: B 180 ARG cc_start: 0.3266 (mmp-170) cc_final: 0.2601 (mmp-170) REVERT: B 185 THR cc_start: 0.8736 (OUTLIER) cc_final: 0.8484 (p) REVERT: B 194 GLN cc_start: 0.8561 (mt0) cc_final: 0.8263 (mp10) REVERT: B 228 MET cc_start: 0.8043 (ptm) cc_final: 0.7789 (ptp) REVERT: B 229 GLN cc_start: 0.8765 (mp-120) cc_final: 0.7760 (mp10) REVERT: B 235 THR cc_start: 0.8752 (m) cc_final: 0.8526 (t) REVERT: B 241 GLU cc_start: 0.7640 (mt-10) cc_final: 0.7170 (mt-10) REVERT: B 245 GLN cc_start: 0.8776 (mt0) cc_final: 0.8541 (mt0) REVERT: B 246 GLU cc_start: 0.8552 (pt0) cc_final: 0.6957 (tp30) REVERT: B 247 ARG cc_start: 0.8935 (ttt180) cc_final: 0.6383 (pmt-80) REVERT: C 124 LYS cc_start: 0.8869 (mtpp) cc_final: 0.7929 (mmtt) REVERT: C 194 GLN cc_start: 0.8946 (mt0) cc_final: 0.8069 (mp10) REVERT: C 199 VAL cc_start: 0.7168 (OUTLIER) cc_final: 0.6926 (p) REVERT: C 207 MET cc_start: 0.7248 (tpt) cc_final: 0.6770 (mtp) REVERT: C 211 TYR cc_start: 0.3911 (p90) cc_final: 0.3589 (p90) REVERT: C 212 ASP cc_start: 0.7813 (m-30) cc_final: 0.7367 (m-30) outliers start: 23 outliers final: 15 residues processed: 125 average time/residue: 0.1656 time to fit residues: 24.7210 Evaluate side-chains 124 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 105 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 228 MET Chi-restraints excluded: chain A residue 247 ARG Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 233 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 25 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 chunk 6 optimal weight: 6.9990 chunk 5 optimal weight: 5.9990 chunk 9 optimal weight: 10.0000 chunk 12 optimal weight: 0.7980 chunk 1 optimal weight: 6.9990 chunk 28 optimal weight: 0.8980 chunk 3 optimal weight: 6.9990 chunk 18 optimal weight: 7.9990 chunk 35 optimal weight: 8.9990 overall best weight: 3.3386 ------------------------------------------------------------------------------- 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 = 0.4350 r_free = 0.4350 target = 0.125986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.113509 restraints weight = 6228.953| |-----------------------------------------------------------------------------| r_work (start): 0.4183 rms_B_bonded: 2.85 r_work: 0.4096 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.4096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 2.0687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 3480 Z= 0.359 Angle : 0.811 6.541 4731 Z= 0.422 Chirality : 0.066 0.439 603 Planarity : 0.007 0.077 570 Dihedral : 8.154 50.536 699 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 15.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.03 % Favored : 86.97 % Rotamer: Outliers : 5.56 % Allowed : 28.31 % Favored : 66.14 % 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: -4.22 (0.33), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.21 (0.25), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 239 PHE 0.015 0.002 PHE B 213 TYR 0.019 0.002 TYR B 143 ARG 0.004 0.001 ARG A 140 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 102 time to evaluate : 0.371 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 122 ASP cc_start: 0.8633 (t0) cc_final: 0.8427 (t0) REVERT: A 124 LYS cc_start: 0.8687 (mttm) cc_final: 0.8399 (mmtp) REVERT: A 171 PHE cc_start: 0.8454 (t80) cc_final: 0.8136 (t80) REVERT: A 192 MET cc_start: 0.8267 (mmm) cc_final: 0.7919 (mpp) REVERT: A 194 GLN cc_start: 0.8561 (mp10) cc_final: 0.7961 (mp10) REVERT: A 212 ASP cc_start: 0.7585 (m-30) cc_final: 0.7140 (m-30) REVERT: A 247 ARG cc_start: 0.8768 (OUTLIER) cc_final: 0.8393 (ttt180) REVERT: B 138 GLN cc_start: 0.8654 (mm-40) cc_final: 0.8369 (mm110) REVERT: B 180 ARG cc_start: 0.3446 (mmp-170) cc_final: 0.2626 (mmp-170) REVERT: B 182 ASN cc_start: 0.7999 (m-40) cc_final: 0.7669 (t0) REVERT: B 207 MET cc_start: 0.8271 (tpp) cc_final: 0.8025 (ttp) REVERT: B 209 TYR cc_start: 0.5198 (OUTLIER) cc_final: 0.4424 (t80) REVERT: B 229 GLN cc_start: 0.8631 (mp-120) cc_final: 0.7901 (mp10) REVERT: B 241 GLU cc_start: 0.7504 (mt-10) cc_final: 0.7124 (mt-10) REVERT: B 246 GLU cc_start: 0.8597 (pt0) cc_final: 0.6949 (tp30) REVERT: B 247 ARG cc_start: 0.9006 (ttt180) cc_final: 0.6557 (pmt-80) REVERT: C 124 LYS cc_start: 0.8571 (mtpp) cc_final: 0.7843 (mmtt) REVERT: C 163 GLU cc_start: 0.7768 (mp0) cc_final: 0.7262 (mp0) REVERT: C 187 ILE cc_start: 0.3747 (pt) cc_final: 0.3332 (pt) REVERT: C 194 GLN cc_start: 0.9068 (mt0) cc_final: 0.8671 (mp10) REVERT: C 207 MET cc_start: 0.7564 (tpt) cc_final: 0.7214 (ttp) REVERT: C 212 ASP cc_start: 0.7729 (m-30) cc_final: 0.7473 (m-30) outliers start: 21 outliers final: 17 residues processed: 115 average time/residue: 0.1716 time to fit residues: 23.4325 Evaluate side-chains 117 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 98 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 247 ARG Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 209 TYR Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 233 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 1 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 chunk 12 optimal weight: 4.9990 chunk 9 optimal weight: 9.9990 chunk 26 optimal weight: 7.9990 chunk 29 optimal weight: 4.9990 chunk 24 optimal weight: 0.0010 chunk 31 optimal weight: 0.0670 chunk 36 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 27 optimal weight: 6.9990 overall best weight: 2.0130 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 194 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4430 r_free = 0.4430 target = 0.133591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.121098 restraints weight = 6192.964| |-----------------------------------------------------------------------------| r_work (start): 0.4279 rms_B_bonded: 2.94 r_work: 0.4201 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.4201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7389 moved from start: 2.0921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3480 Z= 0.256 Angle : 0.765 6.559 4731 Z= 0.394 Chirality : 0.064 0.407 603 Planarity : 0.006 0.075 570 Dihedral : 7.996 50.531 699 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 13.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.28 % Favored : 89.72 % Rotamer: Outliers : 4.76 % Allowed : 29.37 % Favored : 65.87 % 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: -4.18 (0.33), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.18 (0.25), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS C 239 PHE 0.012 0.002 PHE B 213 TYR 0.017 0.001 TYR B 248 ARG 0.004 0.001 ARG A 140 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 105 time to evaluate : 0.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 ASP cc_start: 0.8550 (t0) cc_final: 0.8321 (t0) REVERT: A 124 LYS cc_start: 0.8580 (mttm) cc_final: 0.8280 (mmtp) REVERT: A 171 PHE cc_start: 0.8327 (t80) cc_final: 0.7985 (t80) REVERT: A 192 MET cc_start: 0.8183 (mmm) cc_final: 0.7829 (mpp) REVERT: A 194 GLN cc_start: 0.8467 (mp10) cc_final: 0.8208 (mp10) REVERT: A 212 ASP cc_start: 0.7568 (m-30) cc_final: 0.7130 (m-30) REVERT: A 247 ARG cc_start: 0.8773 (OUTLIER) cc_final: 0.8459 (ttt180) REVERT: B 136 ASP cc_start: 0.7497 (t0) cc_final: 0.6798 (t0) REVERT: B 138 GLN cc_start: 0.8718 (mm-40) cc_final: 0.8282 (mm110) REVERT: B 180 ARG cc_start: 0.3384 (mmp-170) cc_final: 0.2600 (mmp-170) REVERT: B 182 ASN cc_start: 0.7948 (m-40) cc_final: 0.7666 (t0) REVERT: B 193 LYS cc_start: 0.8932 (mtpt) cc_final: 0.8589 (mtpp) REVERT: B 216 LEU cc_start: 0.9225 (pt) cc_final: 0.8890 (pp) REVERT: B 229 GLN cc_start: 0.8657 (mp-120) cc_final: 0.7976 (mp10) REVERT: B 241 GLU cc_start: 0.7312 (mt-10) cc_final: 0.6866 (mt-10) REVERT: B 246 GLU cc_start: 0.8630 (pt0) cc_final: 0.6894 (tp30) REVERT: B 247 ARG cc_start: 0.8978 (ttt180) cc_final: 0.6361 (pmt-80) REVERT: C 124 LYS cc_start: 0.8590 (mtpp) cc_final: 0.7693 (mmtt) REVERT: C 163 GLU cc_start: 0.7757 (mp0) cc_final: 0.7274 (mp0) REVERT: C 187 ILE cc_start: 0.3704 (pt) cc_final: 0.3283 (pt) REVERT: C 194 GLN cc_start: 0.8948 (mt0) cc_final: 0.8580 (mp10) REVERT: C 199 VAL cc_start: 0.7825 (OUTLIER) cc_final: 0.7575 (p) REVERT: C 207 MET cc_start: 0.7552 (tpt) cc_final: 0.7204 (mtp) REVERT: C 212 ASP cc_start: 0.7842 (m-30) cc_final: 0.7453 (m-30) REVERT: C 239 HIS cc_start: 0.8248 (t-170) cc_final: 0.7878 (t-90) outliers start: 18 outliers final: 13 residues processed: 117 average time/residue: 0.1717 time to fit residues: 23.8739 Evaluate side-chains 117 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 102 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 228 MET Chi-restraints excluded: chain A residue 247 ARG Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 233 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 33 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 18 optimal weight: 7.9990 chunk 15 optimal weight: 5.9990 chunk 29 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 36 optimal weight: 10.0000 chunk 4 optimal weight: 5.9990 chunk 9 optimal weight: 9.9990 chunk 37 optimal weight: 0.0470 chunk 14 optimal weight: 9.9990 overall best weight: 1.5684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 194 GLN B 249 GLN C 168 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4469 r_free = 0.4469 target = 0.136588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.123650 restraints weight = 6062.827| |-----------------------------------------------------------------------------| r_work (start): 0.4311 rms_B_bonded: 3.03 r_work: 0.4224 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.4224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7392 moved from start: 2.1089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3480 Z= 0.234 Angle : 0.768 7.261 4731 Z= 0.397 Chirality : 0.063 0.403 603 Planarity : 0.006 0.073 570 Dihedral : 7.925 50.808 699 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.03 % Favored : 88.97 % Rotamer: Outliers : 3.44 % Allowed : 32.01 % Favored : 64.55 % 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: -4.10 (0.34), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.12 (0.26), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 239 PHE 0.012 0.002 PHE B 213 TYR 0.018 0.001 TYR B 248 ARG 0.004 0.001 ARG A 140 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2009.91 seconds wall clock time: 36 minutes 23.38 seconds (2183.38 seconds total)