Starting phenix.real_space_refine on Wed Mar 5 20:41:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tmc_25995/03_2025/7tmc_25995.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tmc_25995/03_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_25995/03_2025/7tmc_25995.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tmc_25995/03_2025/7tmc_25995.map" model { file = "/net/cci-nas-00/data/ceres_data/7tmc_25995/03_2025/7tmc_25995.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tmc_25995/03_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-5624/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: 3.04, per 1000 atoms: 0.89 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: 0.86 Conformation dependent library (CDL) restraints added in 406.6 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: 0.53 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: 1.03 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: 1.440 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: 0.030 Set scattering table: 0.050 Process input model: 13.810 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:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.600 ------------------------------------------------------------------------------- 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 : 0.370 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: 0.1610 time to fit residues: 19.8687 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 : 0.364 ------------------------------------------------------------------------------- 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: 3.59 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 : 0.377 Fit side-chains revert: symmetry clash REVERT: A 122 ASP cc_start: 0.6991 (t0) cc_final: 0.6761 (t0) REVERT: A 138 GLN cc_start: 0.6358 (mm110) cc_final: 0.6144 (mm110) REVERT: A 194 GLN cc_start: 0.7464 (mp10) cc_final: 0.6666 (mp10) REVERT: A 222 HIS cc_start: 0.6301 (m90) cc_final: 0.6066 (m-70) REVERT: B 194 GLN cc_start: 0.7168 (mt0) cc_final: 0.6817 (tp-100) REVERT: C 180 ARG cc_start: 0.6742 (mtt180) cc_final: 0.6368 (ptt-90) REVERT: C 194 GLN cc_start: 0.7418 (mt0) cc_final: 0.6923 (tp40) outliers start: 18 outliers final: 11 residues processed: 138 average time/residue: 0.1429 time to fit residues: 23.8683 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 : 0.344 ------------------------------------------------------------------------------- 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: 1.9990 chunk 3 optimal weight: 0.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- 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 = 0.4665 r_free = 0.4665 target = 0.154652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4509 r_free = 0.4509 target = 0.139337 restraints weight = 5823.497| |-----------------------------------------------------------------------------| r_work (start): 0.4519 rms_B_bonded: 3.26 r_work: 0.4437 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.4437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6243 moved from start: 1.2522 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= 0.287 Angle : 0.883 9.737 4731 Z= 0.436 Chirality : 0.070 0.533 603 Planarity : 0.005 0.050 570 Dihedral : 9.949 54.086 699 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.28 % Favored : 88.72 % Rotamer: Outliers : 5.82 % Allowed : 17.46 % Favored : 76.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.22 (0.33), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.21 (0.26), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 239 PHE 0.027 0.003 PHE B 171 TYR 0.024 0.002 TYR A 209 ARG 0.004 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 155 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 133 time to evaluate : 0.371 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 122 ASP cc_start: 0.7590 (t0) cc_final: 0.7339 (t0) REVERT: A 163 GLU cc_start: 0.8169 (mm-30) cc_final: 0.7692 (mm-30) REVERT: A 164 ASN cc_start: 0.7760 (OUTLIER) cc_final: 0.6454 (m110) REVERT: A 192 MET cc_start: 0.6358 (mmp) cc_final: 0.5798 (mmp) REVERT: A 228 MET cc_start: 0.7703 (OUTLIER) cc_final: 0.7423 (mtt) REVERT: B 194 GLN cc_start: 0.7600 (mt0) cc_final: 0.7106 (mp10) REVERT: B 246 GLU cc_start: 0.7386 (pt0) cc_final: 0.6788 (tp30) REVERT: C 180 ARG cc_start: 0.7188 (mtt180) cc_final: 0.6307 (ptt-90) REVERT: C 192 MET cc_start: 0.5872 (mpp) cc_final: 0.5615 (mtt) REVERT: C 194 GLN cc_start: 0.7886 (mt0) cc_final: 0.7102 (tp-100) REVERT: C 220 LYS cc_start: 0.7896 (ttmt) cc_final: 0.7679 (ttmm) REVERT: C 230 VAL cc_start: 0.7661 (t) cc_final: 0.7422 (t) REVERT: C 242 GLN cc_start: 0.7562 (tt0) cc_final: 0.6945 (tp40) outliers start: 22 outliers final: 14 residues processed: 145 average time/residue: 0.1455 time to fit residues: 25.5963 Evaluate side-chains 141 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 125 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 THR 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 24 optimal weight: 8.9990 chunk 33 optimal weight: 4.9990 chunk 3 optimal weight: 10.0000 chunk 7 optimal weight: 1.9990 chunk 21 optimal weight: 20.0000 chunk 1 optimal weight: 5.9990 chunk 15 optimal weight: 1.9990 chunk 22 optimal weight: 9.9990 chunk 9 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 chunk 8 optimal weight: 20.0000 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 249 GLN ** C 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4464 r_free = 0.4464 target = 0.134682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.121215 restraints weight = 6397.306| |-----------------------------------------------------------------------------| r_work (start): 0.4299 rms_B_bonded: 3.04 r_work: 0.4207 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.4207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7225 moved from start: 1.7302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 3480 Z= 0.366 Angle : 0.903 6.924 4731 Z= 0.463 Chirality : 0.069 0.454 603 Planarity : 0.007 0.083 570 Dihedral : 9.703 45.630 699 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 14.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.54 % Favored : 84.46 % Rotamer: Outliers : 5.03 % Allowed : 22.22 % Favored : 72.75 % 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: -4.37 (0.32), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.33 (0.25), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 222 PHE 0.021 0.003 PHE A 237 TYR 0.028 0.002 TYR A 248 ARG 0.004 0.001 ARG C 140 *********************** 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 155 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 136 time to evaluate : 0.320 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 122 ASP cc_start: 0.8581 (t0) cc_final: 0.8239 (t0) REVERT: A 124 LYS cc_start: 0.8764 (mttm) cc_final: 0.8545 (mmtp) REVERT: A 138 GLN cc_start: 0.8225 (mm110) cc_final: 0.7948 (mm-40) REVERT: A 171 PHE cc_start: 0.7474 (t80) cc_final: 0.7185 (t80) REVERT: A 192 MET cc_start: 0.7912 (mmp) cc_final: 0.7548 (mmp) REVERT: A 223 ASN cc_start: 0.8839 (t0) cc_final: 0.8584 (t0) REVERT: B 168 GLN cc_start: 0.8474 (tm-30) cc_final: 0.8202 (tm-30) REVERT: B 173 LYS cc_start: 0.8446 (mtmt) cc_final: 0.8162 (mtmt) REVERT: B 180 ARG cc_start: 0.2978 (mmp-170) cc_final: 0.2625 (mmp-170) REVERT: B 191 ASP cc_start: 0.8196 (m-30) cc_final: 0.7538 (t0) REVERT: B 194 GLN cc_start: 0.7780 (mt0) cc_final: 0.7551 (mp10) REVERT: B 228 MET cc_start: 0.8527 (OUTLIER) cc_final: 0.7959 (ptp) REVERT: B 229 GLN cc_start: 0.8863 (mp-120) cc_final: 0.7835 (mp10) REVERT: B 241 GLU cc_start: 0.7629 (mt-10) cc_final: 0.7304 (mt-10) REVERT: B 246 GLU cc_start: 0.8441 (pt0) cc_final: 0.7131 (tp30) REVERT: B 247 ARG cc_start: 0.8895 (ttt180) cc_final: 0.6329 (pmt-80) REVERT: C 124 LYS cc_start: 0.8142 (mttm) cc_final: 0.7898 (mmtt) REVERT: C 128 VAL cc_start: 0.8622 (OUTLIER) cc_final: 0.8408 (t) REVERT: C 180 ARG cc_start: 0.7301 (mtt180) cc_final: 0.6455 (ptt-90) REVERT: C 185 THR cc_start: 0.8541 (OUTLIER) cc_final: 0.8187 (p) REVERT: C 194 GLN cc_start: 0.8638 (mt0) cc_final: 0.7741 (mp10) REVERT: C 220 LYS cc_start: 0.9062 (ttmt) cc_final: 0.8776 (ttmm) REVERT: C 227 MET cc_start: 0.8741 (mpp) cc_final: 0.8479 (mpp) outliers start: 19 outliers final: 11 residues processed: 149 average time/residue: 0.1759 time to fit residues: 30.8719 Evaluate side-chains 135 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 121 time to evaluate : 0.441 ------------------------------------------------------------------------------- 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 216 LEU Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 228 MET 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 215 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 20 optimal weight: 1.9990 chunk 16 optimal weight: 5.9990 chunk 37 optimal weight: 8.9990 chunk 36 optimal weight: 5.9990 chunk 24 optimal weight: 8.9990 chunk 4 optimal weight: 8.9990 chunk 17 optimal weight: 9.9990 chunk 28 optimal weight: 0.8980 chunk 21 optimal weight: 10.0000 chunk 33 optimal weight: 1.9990 chunk 11 optimal weight: 7.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 GLN A 155 ASN C 148 ASN C 155 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4431 r_free = 0.4431 target = 0.135625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.122729 restraints weight = 6185.681| |-----------------------------------------------------------------------------| r_work (start): 0.4273 rms_B_bonded: 3.04 r_work: 0.4193 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.4193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7303 moved from start: 1.9203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 3480 Z= 0.363 Angle : 0.838 8.653 4731 Z= 0.435 Chirality : 0.071 0.588 603 Planarity : 0.007 0.083 570 Dihedral : 9.067 53.320 699 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 13.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.53 % Favored : 87.47 % Rotamer: Outliers : 6.08 % Allowed : 23.54 % Favored : 70.37 % 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: -4.39 (0.32), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.34 (0.25), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS C 222 PHE 0.032 0.003 PHE B 171 TYR 0.018 0.002 TYR A 248 ARG 0.006 0.001 ARG A 180 *********************** 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 138 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 115 time to evaluate : 0.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 185 THR cc_start: 0.8473 (OUTLIER) cc_final: 0.7954 (p) REVERT: A 192 MET cc_start: 0.8119 (mmt) cc_final: 0.7775 (mmp) REVERT: A 193 LYS cc_start: 0.8740 (mtmm) cc_final: 0.7904 (mtmm) REVERT: A 194 GLN cc_start: 0.8331 (mp10) cc_final: 0.7717 (mp10) REVERT: A 212 ASP cc_start: 0.6977 (m-30) cc_final: 0.6689 (m-30) REVERT: A 216 LEU cc_start: 0.8660 (OUTLIER) cc_final: 0.8412 (pp) REVERT: B 136 ASP cc_start: 0.7482 (t0) cc_final: 0.7037 (t0) REVERT: B 138 GLN cc_start: 0.8582 (mt0) cc_final: 0.8085 (mm-40) REVERT: B 168 GLN cc_start: 0.8857 (tm-30) cc_final: 0.8448 (tm-30) REVERT: B 173 LYS cc_start: 0.8468 (mtmt) cc_final: 0.8217 (mtmt) REVERT: B 180 ARG cc_start: 0.3328 (mmp-170) cc_final: 0.3054 (mmp-170) REVERT: B 185 THR cc_start: 0.8675 (OUTLIER) cc_final: 0.8354 (p) REVERT: B 194 GLN cc_start: 0.8436 (mt0) cc_final: 0.7789 (mp10) REVERT: B 207 MET cc_start: 0.7916 (tpt) cc_final: 0.7663 (ttp) REVERT: B 209 TYR cc_start: 0.4288 (OUTLIER) cc_final: 0.2694 (t80) REVERT: B 228 MET cc_start: 0.8401 (ptm) cc_final: 0.8132 (ptp) REVERT: B 229 GLN cc_start: 0.8788 (mp-120) cc_final: 0.7755 (mp10) REVERT: B 240 SER cc_start: 0.8473 (OUTLIER) cc_final: 0.8181 (p) REVERT: B 241 GLU cc_start: 0.7447 (mt-10) cc_final: 0.6853 (mt-10) REVERT: B 246 GLU cc_start: 0.8696 (pt0) cc_final: 0.7043 (tp30) REVERT: C 128 VAL cc_start: 0.8230 (OUTLIER) cc_final: 0.7983 (t) REVERT: C 161 GLU cc_start: 0.8194 (mm-30) cc_final: 0.7897 (mm-30) REVERT: C 187 ILE cc_start: 0.8313 (mm) cc_final: 0.7807 (pt) REVERT: C 193 LYS cc_start: 0.8728 (mtpt) cc_final: 0.8090 (mttp) REVERT: C 194 GLN cc_start: 0.8966 (mt0) cc_final: 0.8047 (mp10) REVERT: C 212 ASP cc_start: 0.7579 (m-30) cc_final: 0.7067 (m-30) REVERT: C 239 HIS cc_start: 0.6682 (t70) cc_final: 0.6366 (t-170) REVERT: C 246 GLU cc_start: 0.8178 (pt0) cc_final: 0.7937 (pt0) outliers start: 23 outliers final: 13 residues processed: 130 average time/residue: 0.1617 time to fit residues: 25.0302 Evaluate side-chains 125 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 106 time to evaluate : 0.350 ------------------------------------------------------------------------------- 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 215 THR Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 209 TYR 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 146 ILE 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 215 THR Chi-restraints excluded: chain C residue 233 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: 8.9990 chunk 12 optimal weight: 5.9990 chunk 28 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 13 optimal weight: 0.8980 chunk 21 optimal weight: 0.0000 chunk 16 optimal weight: 9.9990 chunk 20 optimal weight: 0.9990 chunk 32 optimal weight: 6.9990 chunk 35 optimal weight: 0.9990 overall best weight: 0.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 GLN B 249 GLN C 170 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4544 r_free = 0.4544 target = 0.145160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 22)----------------| | r_work = 0.4395 r_free = 0.4395 target = 0.131307 restraints weight = 6072.276| |-----------------------------------------------------------------------------| r_work (start): 0.4376 rms_B_bonded: 3.17 r_work: 0.4287 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.4287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7243 moved from start: 1.9451 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= 0.185 Angle : 0.698 8.587 4731 Z= 0.362 Chirality : 0.063 0.375 603 Planarity : 0.006 0.074 570 Dihedral : 7.924 49.791 699 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.28 % Favored : 89.72 % Rotamer: Outliers : 5.29 % Allowed : 26.19 % 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: -4.20 (0.33), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.20 (0.25), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS C 222 PHE 0.023 0.003 PHE B 171 TYR 0.021 0.001 TYR A 143 ARG 0.004 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 141 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 121 time to evaluate : 0.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 TYR cc_start: 0.8323 (m-80) cc_final: 0.8021 (m-80) REVERT: A 136 ASP cc_start: 0.7272 (t0) cc_final: 0.7009 (t0) REVERT: A 185 THR cc_start: 0.8385 (OUTLIER) cc_final: 0.7851 (p) REVERT: A 192 MET cc_start: 0.8192 (mmt) cc_final: 0.7755 (mmp) REVERT: A 193 LYS cc_start: 0.8633 (mtmm) cc_final: 0.8055 (mtmm) REVERT: A 216 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8406 (pp) REVERT: A 223 ASN cc_start: 0.8896 (t0) cc_final: 0.8572 (t0) REVERT: B 136 ASP cc_start: 0.7420 (t0) cc_final: 0.6813 (t0) REVERT: B 163 GLU cc_start: 0.8129 (mm-30) cc_final: 0.6040 (pm20) REVERT: B 168 GLN cc_start: 0.8663 (tm-30) cc_final: 0.8240 (tm-30) REVERT: B 173 LYS cc_start: 0.8388 (mtmt) cc_final: 0.8166 (mtmt) REVERT: B 180 ARG cc_start: 0.3362 (mmp-170) cc_final: 0.2521 (mmp-170) REVERT: B 194 GLN cc_start: 0.8571 (mt0) cc_final: 0.7866 (mp10) REVERT: B 216 LEU cc_start: 0.9121 (pt) cc_final: 0.8845 (pp) REVERT: B 246 GLU cc_start: 0.8457 (pt0) cc_final: 0.6773 (tp30) REVERT: B 247 ARG cc_start: 0.8995 (ttt180) cc_final: 0.6397 (pmt-80) REVERT: C 163 GLU cc_start: 0.6662 (mp0) cc_final: 0.6380 (mp0) REVERT: C 193 LYS cc_start: 0.8796 (mtpt) cc_final: 0.8178 (mttp) REVERT: C 194 GLN cc_start: 0.8931 (mt0) cc_final: 0.7994 (mp10) REVERT: C 199 VAL cc_start: 0.6741 (p) cc_final: 0.6528 (p) REVERT: C 212 ASP cc_start: 0.7678 (m-30) cc_final: 0.7180 (m-30) REVERT: C 239 HIS cc_start: 0.6695 (t70) cc_final: 0.6406 (t70) REVERT: C 241 GLU cc_start: 0.7774 (mt-10) cc_final: 0.6744 (mt-10) outliers start: 20 outliers final: 14 residues processed: 137 average time/residue: 0.1607 time to fit residues: 26.2430 Evaluate side-chains 124 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 108 time to evaluate : 0.382 ------------------------------------------------------------------------------- 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 215 THR Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain B residue 193 LYS Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 240 SER 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 233 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 32 optimal weight: 8.9990 chunk 18 optimal weight: 6.9990 chunk 8 optimal weight: 5.9990 chunk 24 optimal weight: 10.0000 chunk 27 optimal weight: 0.0060 chunk 3 optimal weight: 10.0000 chunk 34 optimal weight: 5.9990 chunk 10 optimal weight: 8.9990 chunk 31 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 11 optimal weight: 0.9990 overall best weight: 1.9802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 249 GLN C 222 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4445 r_free = 0.4445 target = 0.136071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.122683 restraints weight = 6137.097| |-----------------------------------------------------------------------------| r_work (start): 0.4278 rms_B_bonded: 2.93 r_work: 0.4193 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.4193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7401 moved from start: 1.9983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 3480 Z= 0.248 Angle : 0.732 7.394 4731 Z= 0.377 Chirality : 0.064 0.423 603 Planarity : 0.006 0.076 570 Dihedral : 7.875 51.760 699 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 13.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.78 % Favored : 88.22 % Rotamer: Outliers : 5.29 % Allowed : 28.31 % Favored : 66.40 % 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: -4.15 (0.34), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.16 (0.26), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 239 PHE 0.022 0.003 PHE B 171 TYR 0.020 0.001 TYR A 143 ARG 0.007 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 128 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 108 time to evaluate : 0.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 185 THR cc_start: 0.8502 (OUTLIER) cc_final: 0.8068 (p) REVERT: A 192 MET cc_start: 0.8271 (mmt) cc_final: 0.8047 (mmt) REVERT: A 193 LYS cc_start: 0.8889 (mtmm) cc_final: 0.8282 (mtmm) REVERT: A 194 GLN cc_start: 0.8432 (mp10) cc_final: 0.7925 (mp10) REVERT: A 206 GLU cc_start: 0.7411 (mt-10) cc_final: 0.7196 (mt-10) REVERT: A 216 LEU cc_start: 0.8797 (OUTLIER) cc_final: 0.8587 (pp) REVERT: A 239 HIS cc_start: 0.8470 (t70) cc_final: 0.8252 (t-170) REVERT: B 163 GLU cc_start: 0.8288 (mm-30) cc_final: 0.6096 (pm20) REVERT: B 168 GLN cc_start: 0.8715 (tm-30) cc_final: 0.8308 (tm-30) REVERT: B 180 ARG cc_start: 0.3711 (mmp-170) cc_final: 0.2997 (mmp-170) REVERT: B 194 GLN cc_start: 0.8569 (mt0) cc_final: 0.8336 (mp10) REVERT: B 216 LEU cc_start: 0.9130 (pt) cc_final: 0.8862 (pp) REVERT: B 229 GLN cc_start: 0.8727 (mp-120) cc_final: 0.7687 (mp10) REVERT: B 241 GLU cc_start: 0.7296 (mt-10) cc_final: 0.6721 (mt-10) REVERT: B 246 GLU cc_start: 0.8563 (pt0) cc_final: 0.6984 (tp30) REVERT: B 247 ARG cc_start: 0.9044 (ttt180) cc_final: 0.6498 (pmt-80) REVERT: C 163 GLU cc_start: 0.6929 (mp0) cc_final: 0.6590 (mp0) REVERT: C 193 LYS cc_start: 0.8805 (mtpt) cc_final: 0.8587 (mttp) REVERT: C 194 GLN cc_start: 0.9026 (mt0) cc_final: 0.8574 (mp10) REVERT: C 199 VAL cc_start: 0.7164 (OUTLIER) cc_final: 0.6884 (p) REVERT: C 207 MET cc_start: 0.7324 (tpt) cc_final: 0.6935 (ttp) REVERT: C 212 ASP cc_start: 0.7807 (m-30) cc_final: 0.7430 (m-30) REVERT: C 239 HIS cc_start: 0.6847 (t70) cc_final: 0.6614 (t70) outliers start: 20 outliers final: 11 residues processed: 124 average time/residue: 0.1637 time to fit residues: 24.1788 Evaluate side-chains 121 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 107 time to evaluate : 0.359 ------------------------------------------------------------------------------- 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 A residue 221 VAL Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 232 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 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: 10.0000 chunk 26 optimal weight: 9.9990 chunk 33 optimal weight: 5.9990 chunk 1 optimal weight: 7.9990 chunk 4 optimal weight: 0.9990 chunk 32 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 5 optimal weight: 5.9990 chunk 7 optimal weight: 1.9990 chunk 38 optimal weight: 10.0000 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 138 GLN ** B 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.126379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.113821 restraints weight = 6315.932| |-----------------------------------------------------------------------------| r_work (start): 0.4192 rms_B_bonded: 2.96 r_work: 0.4106 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.4106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 2.0923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 3480 Z= 0.314 Angle : 0.764 7.022 4731 Z= 0.399 Chirality : 0.067 0.426 603 Planarity : 0.006 0.081 570 Dihedral : 8.268 49.227 699 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.03 % Favored : 87.97 % 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: -4.08 (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 0.002 0.001 HIS A 239 PHE 0.022 0.003 PHE B 171 TYR 0.017 0.002 TYR A 143 ARG 0.003 0.000 ARG C 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 121 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 100 time to evaluate : 0.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 PHE cc_start: 0.8373 (t80) cc_final: 0.8046 (t80) REVERT: A 185 THR cc_start: 0.8516 (OUTLIER) cc_final: 0.8200 (p) REVERT: A 193 LYS cc_start: 0.8709 (mtmm) cc_final: 0.8192 (mtpp) REVERT: A 194 GLN cc_start: 0.8442 (mp10) cc_final: 0.7835 (mp10) REVERT: B 138 GLN cc_start: 0.8452 (mm-40) cc_final: 0.8183 (mm-40) REVERT: B 163 GLU cc_start: 0.8345 (mm-30) cc_final: 0.5695 (pt0) REVERT: B 168 GLN cc_start: 0.8812 (tm-30) cc_final: 0.8453 (tm-30) REVERT: B 180 ARG cc_start: 0.3326 (mmp-170) cc_final: 0.2616 (mmp-170) REVERT: B 182 ASN cc_start: 0.7827 (m-40) cc_final: 0.7479 (t0) REVERT: B 209 TYR cc_start: 0.4703 (OUTLIER) cc_final: 0.3816 (t80) REVERT: B 216 LEU cc_start: 0.9239 (pt) cc_final: 0.8989 (pp) REVERT: B 229 GLN cc_start: 0.8612 (mp-120) cc_final: 0.7975 (mp10) REVERT: B 246 GLU cc_start: 0.8583 (pt0) cc_final: 0.6948 (tp30) REVERT: C 187 ILE cc_start: 0.3861 (pt) cc_final: 0.3536 (pt) REVERT: C 193 LYS cc_start: 0.8795 (mtpt) cc_final: 0.8568 (mtpp) REVERT: C 194 GLN cc_start: 0.9070 (mt0) cc_final: 0.8572 (mp10) REVERT: C 207 MET cc_start: 0.7568 (tpt) cc_final: 0.7283 (ttp) REVERT: C 212 ASP cc_start: 0.7791 (m-30) cc_final: 0.7536 (m-30) REVERT: C 241 GLU cc_start: 0.8025 (mt-10) cc_final: 0.7660 (mt-10) outliers start: 21 outliers final: 14 residues processed: 115 average time/residue: 0.1604 time to fit residues: 22.3498 Evaluate side-chains 108 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 92 time to evaluate : 0.414 ------------------------------------------------------------------------------- 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 215 THR Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 209 TYR 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 215 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: 0.9990 chunk 30 optimal weight: 0.1980 chunk 6 optimal weight: 5.9990 chunk 5 optimal weight: 0.0870 chunk 9 optimal weight: 8.9990 chunk 12 optimal weight: 4.9990 chunk 1 optimal weight: 8.9990 chunk 28 optimal weight: 6.9990 chunk 3 optimal weight: 9.9990 chunk 18 optimal weight: 6.9990 chunk 35 optimal weight: 3.9990 overall best weight: 2.0564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 249 GLN C 168 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4407 r_free = 0.4407 target = 0.132299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.119592 restraints weight = 6077.577| |-----------------------------------------------------------------------------| r_work (start): 0.4271 rms_B_bonded: 2.95 r_work: 0.4193 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.4193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7389 moved from start: 2.1139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3480 Z= 0.248 Angle : 0.739 7.595 4731 Z= 0.377 Chirality : 0.064 0.415 603 Planarity : 0.005 0.076 570 Dihedral : 8.281 50.518 699 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.53 % Favored : 88.47 % Rotamer: Outliers : 4.50 % Allowed : 29.10 % Favored : 66.40 % 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: -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 0.003 0.001 HIS A 239 PHE 0.027 0.003 PHE B 171 TYR 0.019 0.001 TYR A 143 ARG 0.002 0.000 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 121 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 104 time to evaluate : 0.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 LYS cc_start: 0.8550 (mmtp) cc_final: 0.8265 (mmtp) REVERT: A 182 ASN cc_start: 0.8552 (m-40) cc_final: 0.8003 (t0) REVERT: A 193 LYS cc_start: 0.8573 (mtmm) cc_final: 0.8069 (mtpp) REVERT: A 194 GLN cc_start: 0.8349 (mp10) cc_final: 0.7742 (mp10) REVERT: A 223 ASN cc_start: 0.8898 (t0) cc_final: 0.8576 (t0) REVERT: B 163 GLU cc_start: 0.8332 (mm-30) cc_final: 0.5762 (pm20) REVERT: B 168 GLN cc_start: 0.8746 (tm-30) cc_final: 0.8345 (tm-30) REVERT: B 180 ARG cc_start: 0.3388 (mmp-170) cc_final: 0.2741 (mmp-170) REVERT: B 182 ASN cc_start: 0.7851 (m-40) cc_final: 0.7619 (t0) REVERT: B 209 TYR cc_start: 0.4760 (OUTLIER) cc_final: 0.3876 (t80) REVERT: B 229 GLN cc_start: 0.8618 (mp-120) cc_final: 0.7523 (mp10) REVERT: B 246 GLU cc_start: 0.8521 (pt0) cc_final: 0.6762 (tp30) REVERT: C 124 LYS cc_start: 0.8621 (mtpp) cc_final: 0.7847 (mmtt) REVERT: C 187 ILE cc_start: 0.4362 (pt) cc_final: 0.3899 (pt) REVERT: C 194 GLN cc_start: 0.9026 (mt0) cc_final: 0.8525 (mp10) REVERT: C 199 VAL cc_start: 0.7807 (OUTLIER) cc_final: 0.7528 (p) REVERT: C 207 MET cc_start: 0.7560 (tpt) cc_final: 0.7298 (mtp) REVERT: C 212 ASP cc_start: 0.7921 (m-30) cc_final: 0.7719 (m-30) REVERT: C 241 GLU cc_start: 0.7931 (mt-10) cc_final: 0.7552 (mt-10) outliers start: 17 outliers final: 11 residues processed: 117 average time/residue: 0.1521 time to fit residues: 21.4531 Evaluate side-chains 111 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 98 time to evaluate : 0.354 ------------------------------------------------------------------------------- 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 199 VAL Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 209 TYR 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 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: 7.9990 chunk 20 optimal weight: 0.3980 chunk 12 optimal weight: 7.9990 chunk 9 optimal weight: 10.0000 chunk 26 optimal weight: 0.7980 chunk 29 optimal weight: 0.0980 chunk 24 optimal weight: 2.9990 chunk 31 optimal weight: 10.0000 chunk 36 optimal weight: 3.9990 chunk 33 optimal weight: 0.9980 chunk 27 optimal weight: 9.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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 = 0.4489 r_free = 0.4489 target = 0.139839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4344 r_free = 0.4344 target = 0.126732 restraints weight = 5991.673| |-----------------------------------------------------------------------------| r_work (start): 0.4323 rms_B_bonded: 3.08 r_work: 0.4237 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.4237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7343 moved from start: 2.1259 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= 0.194 Angle : 0.728 7.536 4731 Z= 0.367 Chirality : 0.063 0.393 603 Planarity : 0.005 0.072 570 Dihedral : 7.935 50.774 699 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.28 % Favored : 89.72 % Rotamer: Outliers : 3.17 % Allowed : 30.16 % Favored : 66.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.96 (0.35), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.01 (0.26), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS A 239 PHE 0.024 0.003 PHE B 171 TYR 0.020 0.001 TYR A 143 ARG 0.004 0.001 ARG C 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 115 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 103 time to evaluate : 0.473 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 LYS cc_start: 0.8572 (mmtp) cc_final: 0.8348 (mmtp) REVERT: A 193 LYS cc_start: 0.8570 (mtmm) cc_final: 0.8226 (mtpp) REVERT: A 194 GLN cc_start: 0.8374 (mp10) cc_final: 0.7865 (mp10) REVERT: A 223 ASN cc_start: 0.8921 (t0) cc_final: 0.8557 (t0) REVERT: B 136 ASP cc_start: 0.7557 (t0) cc_final: 0.6972 (t0) REVERT: B 138 GLN cc_start: 0.8713 (mm-40) cc_final: 0.8465 (mm-40) REVERT: B 168 GLN cc_start: 0.8634 (tm-30) cc_final: 0.8181 (tm-30) REVERT: B 170 GLN cc_start: 0.7857 (mt0) cc_final: 0.7388 (mm-40) REVERT: B 180 ARG cc_start: 0.3433 (mmp-170) cc_final: 0.2808 (mmp-170) REVERT: B 182 ASN cc_start: 0.7784 (m-40) cc_final: 0.7539 (t0) REVERT: B 207 MET cc_start: 0.8346 (ttp) cc_final: 0.7661 (tpt) REVERT: B 216 LEU cc_start: 0.8792 (pp) cc_final: 0.6922 (mt) REVERT: B 229 GLN cc_start: 0.8685 (mp-120) cc_final: 0.7593 (mp10) REVERT: B 246 GLU cc_start: 0.8514 (pt0) cc_final: 0.6561 (tp30) REVERT: B 247 ARG cc_start: 0.8983 (ttt180) cc_final: 0.6442 (pmt-80) REVERT: C 124 LYS cc_start: 0.8646 (mtpp) cc_final: 0.7734 (mmtt) REVERT: C 171 PHE cc_start: 0.8579 (t80) cc_final: 0.8287 (t80) REVERT: C 187 ILE cc_start: 0.4265 (pt) cc_final: 0.3813 (pt) REVERT: C 194 GLN cc_start: 0.8993 (mt0) cc_final: 0.8597 (mp10) REVERT: C 199 VAL cc_start: 0.7579 (OUTLIER) cc_final: 0.7354 (p) REVERT: C 207 MET cc_start: 0.7605 (tpt) cc_final: 0.7286 (mtp) REVERT: C 241 GLU cc_start: 0.7856 (mt-10) cc_final: 0.7532 (mt-10) REVERT: C 245 GLN cc_start: 0.8962 (mt0) cc_final: 0.8713 (mt0) outliers start: 12 outliers final: 10 residues processed: 113 average time/residue: 0.1650 time to fit residues: 22.3541 Evaluate side-chains 110 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 99 time to evaluate : 0.389 ------------------------------------------------------------------------------- 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 199 VAL Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 160 VAL 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: 0.9980 chunk 25 optimal weight: 5.9990 chunk 18 optimal weight: 3.9990 chunk 15 optimal weight: 0.8980 chunk 29 optimal weight: 4.9990 chunk 23 optimal weight: 8.9990 chunk 36 optimal weight: 5.9990 chunk 4 optimal weight: 4.9990 chunk 9 optimal weight: 10.0000 chunk 37 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- 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 = 0.4438 r_free = 0.4438 target = 0.135623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.122660 restraints weight = 6130.340| |-----------------------------------------------------------------------------| r_work (start): 0.4272 rms_B_bonded: 3.05 r_work: 0.4186 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.4186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 moved from start: 2.1357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3480 Z= 0.225 Angle : 0.738 7.508 4731 Z= 0.374 Chirality : 0.064 0.405 603 Planarity : 0.005 0.071 570 Dihedral : 8.004 50.683 699 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.03 % Favored : 87.97 % Rotamer: Outliers : 2.91 % Allowed : 30.95 % 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: -3.94 (0.35), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.00 (0.26), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS A 239 PHE 0.024 0.003 PHE B 171 TYR 0.018 0.001 TYR A 143 ARG 0.004 0.000 ARG C 140 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1989.73 seconds wall clock time: 35 minutes 2.72 seconds (2102.72 seconds total)