Starting phenix.real_space_refine on Tue Feb 11 23:26:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xk8_33247/02_2025/7xk8_33247.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xk8_33247/02_2025/7xk8_33247.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7xk8_33247/02_2025/7xk8_33247.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xk8_33247/02_2025/7xk8_33247.map" model { file = "/net/cci-nas-00/data/ceres_data/7xk8_33247/02_2025/7xk8_33247.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xk8_33247/02_2025/7xk8_33247.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 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 46 5.16 5 C 4352 2.51 5 N 1151 2.21 5 O 1247 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 6796 Number of models: 1 Model: "" Number of chains: 6 Chain: "P" Number of atoms: 202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 202 Classifications: {'peptide': 25} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 2, 'TRANS': 22} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 2115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2115 Classifications: {'peptide': 282} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PTRANS': 15, 'TRANS': 266} Chain breaks: 1 Unresolved non-hydrogen bonds: 184 Unresolved non-hydrogen angles: 230 Unresolved non-hydrogen dihedrals: 162 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1, 'PHE:plan': 7, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 99 Chain: "A" Number of atoms: 1673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1673 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 2, 'TRANS': 222} Chain breaks: 2 Unresolved non-hydrogen bonds: 140 Unresolved non-hydrogen angles: 165 Unresolved non-hydrogen dihedrals: 117 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 6, 'ASN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 8, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 77 Chain: "B" Number of atoms: 2432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2432 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 169 Unresolved non-hydrogen angles: 204 Unresolved non-hydrogen dihedrals: 134 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 7, 'ARG:plan': 10, 'ASN:plan1': 2, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 121 Chain: "C" Number of atoms: 373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 373 Classifications: {'peptide': 53} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 4, 'TRANS': 48} Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 16 Time building chain proxies: 4.36, per 1000 atoms: 0.64 Number of scatterers: 6796 At special positions: 0 Unit cell: (111.815, 127.49, 85.69, 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 46 16.00 O 1247 8.00 N 1151 7.00 C 4352 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 119 " - pdb=" SG CYS R 204 " distance=2.03 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.85 Conformation dependent library (CDL) restraints added in 1.2 seconds 1814 Ramachandran restraints generated. 907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1750 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 8 sheets defined 43.2% alpha, 16.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.72 Creating SS restraints... Processing helix chain 'R' and resid 45 through 72 Proline residue: R 54 - end of helix Processing helix chain 'R' and resid 78 through 108 Proline residue: R 100 - end of helix Processing helix chain 'R' and resid 115 through 150 Processing helix chain 'R' and resid 150 through 156 Processing helix chain 'R' and resid 157 through 159 No H-bonds generated for 'chain 'R' and resid 157 through 159' Processing helix chain 'R' and resid 160 through 184 Proline residue: R 180 - end of helix Processing helix chain 'R' and resid 209 through 247 removed outlier: 4.502A pdb=" N LEU R 227 " --> pdb=" O LEU R 223 " (cutoff:3.500A) Proline residue: R 228 - end of helix Processing helix chain 'R' and resid 259 through 282 Processing helix chain 'R' and resid 282 through 292 removed outlier: 3.987A pdb=" N ARG R 288 " --> pdb=" O PHE R 284 " (cutoff:3.500A) Processing helix chain 'R' and resid 299 through 328 Proline residue: R 324 - end of helix Processing helix chain 'A' and resid 6 through 33 removed outlier: 3.993A pdb=" N GLU A 33 " --> pdb=" O LYS A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 54 removed outlier: 3.624A pdb=" N ILE A 49 " --> pdb=" O GLY A 45 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N VAL A 50 " --> pdb=" O LYS A 46 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLN A 52 " --> pdb=" O THR A 48 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N MET A 53 " --> pdb=" O ILE A 49 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N LYS A 54 " --> pdb=" O VAL A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 216 Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 271 through 281 removed outlier: 4.172A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N LYS A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 310 Processing helix chain 'A' and resid 327 through 352 removed outlier: 4.264A pdb=" N ASN A 331 " --> pdb=" O THR A 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 25 Processing helix chain 'B' and resid 29 through 33 Processing helix chain 'C' and resid 12 through 21 Processing helix chain 'C' and resid 29 through 44 Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 190 removed outlier: 3.747A pdb=" N VAL A 185 " --> pdb=" O ASP A 200 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LYS A 197 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU A 36 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N PHE A 199 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 4.224A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 4.832A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA B 73 " --> pdb=" O ALA B 60 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 104 through 105 removed outlier: 3.863A pdb=" N SER B 122 " --> pdb=" O CYS B 114 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ASN B 125 " --> pdb=" O ARG B 134 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 4.271A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.988A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 8.026A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N SER B 201 " --> pdb=" O LYS B 209 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LYS B 209 " --> pdb=" O SER B 201 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.672A pdb=" N SER B 245 " --> pdb=" O THR B 249 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.802A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) 368 hydrogen bonds defined for protein. 1068 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.89 Time building geometry restraints manager: 2.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1099 1.31 - 1.44: 1926 1.44 - 1.56: 3855 1.56 - 1.69: 0 1.69 - 1.82: 62 Bond restraints: 6942 Sorted by residual: bond pdb=" CG ASN P 25 " pdb=" ND2 ASN P 25 " ideal model delta sigma weight residual 1.328 1.452 -0.124 2.10e-02 2.27e+03 3.46e+01 bond pdb=" CG ASN P 25 " pdb=" OD1 ASN P 25 " ideal model delta sigma weight residual 1.231 1.185 0.046 1.90e-02 2.77e+03 5.92e+00 bond pdb=" C ASN P 25 " pdb=" O ASN P 25 " ideal model delta sigma weight residual 1.231 1.184 0.047 2.00e-02 2.50e+03 5.42e+00 bond pdb=" C SER P 9 " pdb=" N PRO P 10 " ideal model delta sigma weight residual 1.334 1.359 -0.025 2.34e-02 1.83e+03 1.12e+00 bond pdb=" N PRO R 193 " pdb=" CA PRO R 193 " ideal model delta sigma weight residual 1.469 1.475 -0.006 7.40e-03 1.83e+04 7.36e-01 ... (remaining 6937 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.23: 9231 1.23 - 2.46: 184 2.46 - 3.68: 41 3.68 - 4.91: 11 4.91 - 6.14: 8 Bond angle restraints: 9475 Sorted by residual: angle pdb=" N ILE B 33 " pdb=" CA ILE B 33 " pdb=" C ILE B 33 " ideal model delta sigma weight residual 112.96 109.56 3.40 1.00e+00 1.00e+00 1.16e+01 angle pdb=" N GLY R 186 " pdb=" CA GLY R 186 " pdb=" C GLY R 186 " ideal model delta sigma weight residual 110.80 115.68 -4.88 1.71e+00 3.42e-01 8.15e+00 angle pdb=" OD1 ASN P 25 " pdb=" CG ASN P 25 " pdb=" ND2 ASN P 25 " ideal model delta sigma weight residual 122.60 119.99 2.61 1.00e+00 1.00e+00 6.82e+00 angle pdb=" N THR B 196 " pdb=" CA THR B 196 " pdb=" CB THR B 196 " ideal model delta sigma weight residual 113.65 110.02 3.63 1.47e+00 4.63e-01 6.11e+00 angle pdb=" CB ASN P 25 " pdb=" CG ASN P 25 " pdb=" ND2 ASN P 25 " ideal model delta sigma weight residual 116.40 120.02 -3.62 1.50e+00 4.44e-01 5.81e+00 ... (remaining 9470 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.57: 3698 15.57 - 31.14: 291 31.14 - 46.70: 57 46.70 - 62.27: 7 62.27 - 77.84: 1 Dihedral angle restraints: 4054 sinusoidal: 1361 harmonic: 2693 Sorted by residual: dihedral pdb=" CA PHE R 189 " pdb=" C PHE R 189 " pdb=" N HIS R 190 " pdb=" CA HIS R 190 " ideal model delta harmonic sigma weight residual 180.00 160.50 19.50 0 5.00e+00 4.00e-02 1.52e+01 dihedral pdb=" CB CYS R 119 " pdb=" SG CYS R 119 " pdb=" SG CYS R 204 " pdb=" CB CYS R 204 " ideal model delta sinusoidal sigma weight residual 93.00 65.34 27.66 1 1.00e+01 1.00e-02 1.10e+01 dihedral pdb=" CA ASP B 38 " pdb=" CB ASP B 38 " pdb=" CG ASP B 38 " pdb=" OD1 ASP B 38 " ideal model delta sinusoidal sigma weight residual -30.00 -83.44 53.44 1 2.00e+01 2.50e-03 9.71e+00 ... (remaining 4051 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 756 0.030 - 0.059: 243 0.059 - 0.089: 79 0.089 - 0.119: 44 0.119 - 0.149: 3 Chirality restraints: 1125 Sorted by residual: chirality pdb=" CA THR B 164 " pdb=" N THR B 164 " pdb=" C THR B 164 " pdb=" CB THR B 164 " both_signs ideal model delta sigma weight residual False 2.53 2.38 0.15 2.00e-01 2.50e+01 5.52e-01 chirality pdb=" CA ILE R 187 " pdb=" N ILE R 187 " pdb=" C ILE R 187 " pdb=" CB ILE R 187 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.35e-01 chirality pdb=" CB ILE R 184 " pdb=" CA ILE R 184 " pdb=" CG1 ILE R 184 " pdb=" CG2 ILE R 184 " both_signs ideal model delta sigma weight residual False 2.64 2.51 0.13 2.00e-01 2.50e+01 4.28e-01 ... (remaining 1122 not shown) Planarity restraints: 1203 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR R 78 " -0.019 5.00e-02 4.00e+02 2.88e-02 1.33e+00 pdb=" N PRO R 79 " 0.050 5.00e-02 4.00e+02 pdb=" CA PRO R 79 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO R 79 " -0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA R 282 " 0.018 5.00e-02 4.00e+02 2.64e-02 1.12e+00 pdb=" N PRO R 283 " -0.046 5.00e-02 4.00e+02 pdb=" CA PRO R 283 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO R 283 " 0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.015 5.00e-02 4.00e+02 2.26e-02 8.20e-01 pdb=" N PRO B 236 " -0.039 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.013 5.00e-02 4.00e+02 ... (remaining 1200 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1396 2.78 - 3.31: 6603 3.31 - 3.84: 11498 3.84 - 4.37: 12427 4.37 - 4.90: 22105 Nonbonded interactions: 54029 Sorted by model distance: nonbonded pdb=" O LEU R 289 " pdb=" OG SER R 292 " model vdw 2.248 3.040 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.252 3.040 nonbonded pdb=" OG1 THR R 78 " pdb=" OD1 ASP A 350 " model vdw 2.270 3.040 nonbonded pdb=" OG SER B 108 " pdb=" OD1 ASN B 110 " model vdw 2.278 3.040 nonbonded pdb=" O SER B 67 " pdb=" OG SER B 67 " model vdw 2.306 3.040 ... (remaining 54024 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: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 19.100 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6270 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 : 0.002 0.124 6942 Z= 0.142 Angle : 0.479 6.142 9475 Z= 0.271 Chirality : 0.038 0.149 1125 Planarity : 0.003 0.029 1203 Dihedral : 11.624 77.838 2301 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.25), residues: 907 helix: 0.38 (0.24), residues: 371 sheet: -0.45 (0.38), residues: 154 loop : -2.23 (0.26), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.000 TRP B 99 HIS 0.003 0.000 HIS R 285 PHE 0.010 0.001 PHE R 291 TYR 0.004 0.001 TYR B 289 ARG 0.001 0.000 ARG B 251 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1814 Ramachandran restraints generated. 907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1814 Ramachandran restraints generated. 907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 160 time to evaluate : 0.780 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 127 GLU cc_start: 0.6422 (tp30) cc_final: 0.6077 (tp30) REVERT: R 333 ARG cc_start: 0.4321 (pmt170) cc_final: 0.3932 (tpp-160) REVERT: A 9 ASP cc_start: 0.7360 (t70) cc_final: 0.6993 (t0) REVERT: B 188 MET cc_start: 0.7046 (mmm) cc_final: 0.6843 (mmm) REVERT: C 62 ARG cc_start: 0.6621 (mtm-85) cc_final: 0.6392 (mtm110) outliers start: 0 outliers final: 0 residues processed: 160 average time/residue: 0.2207 time to fit residues: 45.1072 Evaluate side-chains 99 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 99 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 75 optimal weight: 0.0870 chunk 68 optimal weight: 4.9990 chunk 37 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 46 optimal weight: 5.9990 chunk 36 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 42 optimal weight: 0.8980 chunk 52 optimal weight: 8.9990 chunk 81 optimal weight: 1.9990 overall best weight: 0.9560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 43 HIS R 285 HIS A 57 HIS A 294 ASN A 304 GLN A 347 ASN B 340 ASN C 18 GLN C 44 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4728 r_free = 0.4728 target = 0.213468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.171568 restraints weight = 7545.180| |-----------------------------------------------------------------------------| r_work (start): 0.4329 rms_B_bonded: 3.24 r_work: 0.3977 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6860 moved from start: 0.1950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6942 Z= 0.235 Angle : 0.592 7.509 9475 Z= 0.305 Chirality : 0.042 0.237 1125 Planarity : 0.003 0.028 1203 Dihedral : 3.657 29.105 978 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 2.24 % Allowed : 14.93 % Favored : 82.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.27), residues: 907 helix: 1.56 (0.26), residues: 373 sheet: -0.41 (0.39), residues: 145 loop : -1.72 (0.28), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 169 HIS 0.005 0.001 HIS B 142 PHE 0.023 0.002 PHE R 316 TYR 0.019 0.002 TYR R 213 ARG 0.005 0.001 ARG R 288 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1814 Ramachandran restraints generated. 907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1814 Ramachandran restraints generated. 907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 118 time to evaluate : 0.827 Fit side-chains revert: symmetry clash REVERT: R 104 TYR cc_start: 0.3860 (m-80) cc_final: 0.3420 (m-80) REVERT: R 333 ARG cc_start: 0.5044 (pmt170) cc_final: 0.3727 (tpp-160) REVERT: A 9 ASP cc_start: 0.7296 (t70) cc_final: 0.6942 (t0) REVERT: A 52 GLN cc_start: 0.6976 (pp30) cc_final: 0.6236 (pp30) REVERT: C 62 ARG cc_start: 0.6794 (mtm-85) cc_final: 0.6315 (mtm110) outliers start: 15 outliers final: 7 residues processed: 128 average time/residue: 0.1976 time to fit residues: 33.6169 Evaluate side-chains 109 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 102 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 78 THR Chi-restraints excluded: chain R residue 307 LEU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 189 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 33 optimal weight: 2.9990 chunk 18 optimal weight: 9.9990 chunk 62 optimal weight: 0.8980 chunk 59 optimal weight: 0.9990 chunk 66 optimal weight: 0.7980 chunk 30 optimal weight: 8.9990 chunk 20 optimal weight: 0.9990 chunk 67 optimal weight: 3.9990 chunk 87 optimal weight: 0.7980 chunk 78 optimal weight: 4.9990 chunk 42 optimal weight: 1.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 285 HIS A 294 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4689 r_free = 0.4689 target = 0.209770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.167499 restraints weight = 7720.697| |-----------------------------------------------------------------------------| r_work (start): 0.4279 rms_B_bonded: 3.23 r_work: 0.3925 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6914 moved from start: 0.2467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6942 Z= 0.223 Angle : 0.569 6.824 9475 Z= 0.293 Chirality : 0.041 0.175 1125 Planarity : 0.003 0.031 1203 Dihedral : 3.839 36.674 978 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 3.28 % Allowed : 18.06 % Favored : 78.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.27), residues: 907 helix: 1.89 (0.27), residues: 376 sheet: -0.50 (0.40), residues: 146 loop : -1.43 (0.29), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.007 0.001 HIS R 285 PHE 0.017 0.001 PHE R 316 TYR 0.015 0.001 TYR R 213 ARG 0.007 0.000 ARG B 49 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1814 Ramachandran restraints generated. 907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1814 Ramachandran restraints generated. 907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 118 time to evaluate : 0.730 Fit side-chains REVERT: R 104 TYR cc_start: 0.4096 (m-80) cc_final: 0.3638 (m-80) REVERT: R 281 TRP cc_start: 0.5101 (m100) cc_final: 0.4713 (m100) REVERT: R 333 ARG cc_start: 0.4877 (pmt170) cc_final: 0.3649 (tpp-160) REVERT: A 9 ASP cc_start: 0.7254 (t70) cc_final: 0.6922 (t0) REVERT: A 197 LYS cc_start: 0.8292 (ptpt) cc_final: 0.8085 (ptmt) REVERT: B 152 LEU cc_start: 0.8754 (mt) cc_final: 0.8549 (mt) REVERT: C 62 ARG cc_start: 0.6807 (mtm-85) cc_final: 0.6479 (mtm110) outliers start: 22 outliers final: 16 residues processed: 130 average time/residue: 0.1808 time to fit residues: 31.5476 Evaluate side-chains 117 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 101 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 78 THR Chi-restraints excluded: chain R residue 220 THR Chi-restraints excluded: chain R residue 307 LEU Chi-restraints excluded: chain R residue 311 VAL Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 89 LYS Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain C residue 28 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 22 optimal weight: 7.9990 chunk 83 optimal weight: 2.9990 chunk 18 optimal weight: 7.9990 chunk 68 optimal weight: 2.9990 chunk 54 optimal weight: 20.0000 chunk 38 optimal weight: 0.0030 chunk 0 optimal weight: 20.0000 chunk 71 optimal weight: 2.9990 chunk 30 optimal weight: 6.9990 chunk 47 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 overall best weight: 1.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 285 HIS A 294 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4618 r_free = 0.4618 target = 0.202178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.145269 restraints weight = 7856.825| |-----------------------------------------------------------------------------| r_work (start): 0.4012 rms_B_bonded: 2.43 r_work: 0.3874 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7019 moved from start: 0.3175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 6942 Z= 0.333 Angle : 0.632 8.320 9475 Z= 0.324 Chirality : 0.043 0.166 1125 Planarity : 0.004 0.035 1203 Dihedral : 4.303 41.926 978 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 5.22 % Allowed : 19.70 % Favored : 75.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.28), residues: 907 helix: 1.91 (0.26), residues: 376 sheet: -0.65 (0.37), residues: 175 loop : -1.44 (0.31), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 99 HIS 0.008 0.002 HIS R 285 PHE 0.019 0.002 PHE R 316 TYR 0.012 0.002 TYR B 59 ARG 0.004 0.000 ARG B 49 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1814 Ramachandran restraints generated. 907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1814 Ramachandran restraints generated. 907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 113 time to evaluate : 0.823 Fit side-chains REVERT: R 169 ILE cc_start: 0.4451 (OUTLIER) cc_final: 0.4138 (tp) REVERT: R 239 MET cc_start: 0.5543 (mtp) cc_final: 0.5234 (ttm) REVERT: R 333 ARG cc_start: 0.4838 (pmt170) cc_final: 0.3474 (tmt170) outliers start: 35 outliers final: 21 residues processed: 136 average time/residue: 0.1696 time to fit residues: 31.6907 Evaluate side-chains 120 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 98 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 78 THR Chi-restraints excluded: chain R residue 169 ILE Chi-restraints excluded: chain R residue 177 PHE Chi-restraints excluded: chain R residue 182 THR Chi-restraints excluded: chain R residue 214 ASN Chi-restraints excluded: chain R residue 307 LEU Chi-restraints excluded: chain R residue 311 VAL Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 89 LYS Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 294 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 75 optimal weight: 0.3980 chunk 74 optimal weight: 1.9990 chunk 80 optimal weight: 0.5980 chunk 64 optimal weight: 0.9990 chunk 8 optimal weight: 10.0000 chunk 15 optimal weight: 0.9980 chunk 58 optimal weight: 0.8980 chunk 89 optimal weight: 0.9990 chunk 35 optimal weight: 3.9990 chunk 16 optimal weight: 9.9990 chunk 51 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4647 r_free = 0.4647 target = 0.205356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.147791 restraints weight = 7665.361| |-----------------------------------------------------------------------------| r_work (start): 0.4045 rms_B_bonded: 2.57 r_work: 0.3896 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6974 moved from start: 0.3220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6942 Z= 0.215 Angle : 0.588 9.379 9475 Z= 0.300 Chirality : 0.041 0.148 1125 Planarity : 0.003 0.033 1203 Dihedral : 4.101 41.047 978 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 4.78 % Allowed : 22.39 % Favored : 72.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.28), residues: 907 helix: 2.04 (0.26), residues: 376 sheet: -0.71 (0.39), residues: 165 loop : -1.39 (0.30), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.004 0.001 HIS B 183 PHE 0.019 0.001 PHE R 316 TYR 0.010 0.001 TYR A 287 ARG 0.004 0.000 ARG A 15 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1814 Ramachandran restraints generated. 907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1814 Ramachandran restraints generated. 907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 109 time to evaluate : 0.749 Fit side-chains REVERT: R 210 MET cc_start: 0.3889 (tpp) cc_final: 0.3444 (tpp) REVERT: R 239 MET cc_start: 0.5750 (mtp) cc_final: 0.5451 (ttm) REVERT: R 333 ARG cc_start: 0.4820 (pmt170) cc_final: 0.3505 (tmt170) REVERT: A 197 LYS cc_start: 0.8483 (ptpt) cc_final: 0.8222 (ptmt) outliers start: 32 outliers final: 20 residues processed: 129 average time/residue: 0.1760 time to fit residues: 30.8412 Evaluate side-chains 124 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 104 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 78 THR Chi-restraints excluded: chain R residue 82 TYR Chi-restraints excluded: chain R residue 104 TYR Chi-restraints excluded: chain R residue 177 PHE Chi-restraints excluded: chain R residue 214 ASN Chi-restraints excluded: chain R residue 311 VAL Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 180 PHE Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 285 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 57 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 15 optimal weight: 0.4980 chunk 84 optimal weight: 0.8980 chunk 80 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 12 optimal weight: 10.0000 chunk 58 optimal weight: 0.7980 chunk 86 optimal weight: 6.9990 chunk 79 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4636 r_free = 0.4636 target = 0.204365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.147256 restraints weight = 7650.900| |-----------------------------------------------------------------------------| r_work (start): 0.4036 rms_B_bonded: 2.57 r_work: 0.3888 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6987 moved from start: 0.3381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 6942 Z= 0.241 Angle : 0.595 8.712 9475 Z= 0.303 Chirality : 0.042 0.278 1125 Planarity : 0.003 0.034 1203 Dihedral : 4.106 39.076 978 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 5.37 % Allowed : 22.24 % Favored : 72.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.28), residues: 907 helix: 2.12 (0.26), residues: 375 sheet: -0.97 (0.38), residues: 160 loop : -1.38 (0.30), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 169 HIS 0.004 0.001 HIS B 183 PHE 0.019 0.001 PHE R 316 TYR 0.012 0.001 TYR B 59 ARG 0.004 0.000 ARG B 49 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1814 Ramachandran restraints generated. 907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1814 Ramachandran restraints generated. 907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 107 time to evaluate : 0.706 Fit side-chains revert: symmetry clash REVERT: R 210 MET cc_start: 0.3713 (tpp) cc_final: 0.3260 (tpp) REVERT: R 239 MET cc_start: 0.5630 (mtp) cc_final: 0.5312 (ttm) REVERT: R 333 ARG cc_start: 0.4736 (pmt170) cc_final: 0.3442 (tmt170) REVERT: A 247 MET cc_start: 0.7714 (OUTLIER) cc_final: 0.7403 (ptp) outliers start: 36 outliers final: 24 residues processed: 131 average time/residue: 0.1753 time to fit residues: 31.1917 Evaluate side-chains 122 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 97 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 78 THR Chi-restraints excluded: chain R residue 104 TYR Chi-restraints excluded: chain R residue 177 PHE Chi-restraints excluded: chain R residue 214 ASN Chi-restraints excluded: chain R residue 307 LEU Chi-restraints excluded: chain R residue 311 VAL Chi-restraints excluded: chain R residue 322 VAL Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 180 PHE Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 294 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 77 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 chunk 86 optimal weight: 9.9990 chunk 51 optimal weight: 0.4980 chunk 80 optimal weight: 0.9980 chunk 14 optimal weight: 5.9990 chunk 76 optimal weight: 1.9990 chunk 89 optimal weight: 0.0980 chunk 18 optimal weight: 5.9990 chunk 62 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4649 r_free = 0.4649 target = 0.205882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.149262 restraints weight = 7535.529| |-----------------------------------------------------------------------------| r_work (start): 0.4063 rms_B_bonded: 2.56 r_work: 0.3917 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6947 moved from start: 0.3424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6942 Z= 0.200 Angle : 0.586 8.240 9475 Z= 0.297 Chirality : 0.042 0.282 1125 Planarity : 0.003 0.034 1203 Dihedral : 4.000 38.934 978 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 5.22 % Allowed : 23.28 % Favored : 71.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.28), residues: 907 helix: 2.16 (0.26), residues: 376 sheet: -0.87 (0.36), residues: 169 loop : -1.34 (0.30), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 169 HIS 0.004 0.001 HIS B 183 PHE 0.020 0.001 PHE R 316 TYR 0.026 0.001 TYR B 59 ARG 0.003 0.000 ARG B 49 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1814 Ramachandran restraints generated. 907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1814 Ramachandran restraints generated. 907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 106 time to evaluate : 0.796 Fit side-chains revert: symmetry clash REVERT: R 84 LEU cc_start: 0.6192 (OUTLIER) cc_final: 0.5860 (mp) REVERT: R 169 ILE cc_start: 0.4836 (OUTLIER) cc_final: 0.4565 (tp) REVERT: R 210 MET cc_start: 0.4015 (tpp) cc_final: 0.3613 (tpp) REVERT: R 333 ARG cc_start: 0.4736 (pmt170) cc_final: 0.3431 (tmt170) REVERT: A 247 MET cc_start: 0.7877 (ptp) cc_final: 0.7639 (ptt) outliers start: 35 outliers final: 27 residues processed: 130 average time/residue: 0.1639 time to fit residues: 29.4592 Evaluate side-chains 128 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 99 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 78 THR Chi-restraints excluded: chain R residue 82 TYR Chi-restraints excluded: chain R residue 84 LEU Chi-restraints excluded: chain R residue 104 TYR Chi-restraints excluded: chain R residue 169 ILE Chi-restraints excluded: chain R residue 177 PHE Chi-restraints excluded: chain R residue 214 ASN Chi-restraints excluded: chain R residue 307 LEU Chi-restraints excluded: chain R residue 311 VAL Chi-restraints excluded: chain R residue 322 VAL Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 294 ASN Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 180 PHE Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 294 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 25 optimal weight: 7.9990 chunk 54 optimal weight: 0.8980 chunk 36 optimal weight: 0.7980 chunk 44 optimal weight: 5.9990 chunk 20 optimal weight: 0.9980 chunk 14 optimal weight: 6.9990 chunk 63 optimal weight: 0.3980 chunk 78 optimal weight: 0.6980 chunk 48 optimal weight: 0.6980 chunk 72 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4646 r_free = 0.4646 target = 0.205628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.149182 restraints weight = 7573.231| |-----------------------------------------------------------------------------| r_work (start): 0.4063 rms_B_bonded: 2.56 r_work: 0.3918 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6947 moved from start: 0.3492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6942 Z= 0.208 Angle : 0.587 7.963 9475 Z= 0.298 Chirality : 0.042 0.279 1125 Planarity : 0.003 0.033 1203 Dihedral : 3.976 38.238 978 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 5.67 % Allowed : 23.28 % Favored : 71.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.28), residues: 907 helix: 2.16 (0.26), residues: 377 sheet: -0.90 (0.36), residues: 169 loop : -1.30 (0.31), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 169 HIS 0.004 0.001 HIS B 183 PHE 0.020 0.001 PHE R 316 TYR 0.014 0.001 TYR A 287 ARG 0.003 0.000 ARG B 49 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1814 Ramachandran restraints generated. 907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1814 Ramachandran restraints generated. 907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 106 time to evaluate : 0.747 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 84 LEU cc_start: 0.6074 (OUTLIER) cc_final: 0.5760 (mp) REVERT: R 169 ILE cc_start: 0.4815 (OUTLIER) cc_final: 0.4537 (tp) REVERT: R 210 MET cc_start: 0.4023 (tpp) cc_final: 0.3616 (tpp) REVERT: R 333 ARG cc_start: 0.4763 (pmt170) cc_final: 0.3473 (tmt170) outliers start: 38 outliers final: 26 residues processed: 130 average time/residue: 0.1697 time to fit residues: 30.6816 Evaluate side-chains 132 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 104 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 78 THR Chi-restraints excluded: chain R residue 84 LEU Chi-restraints excluded: chain R residue 104 TYR Chi-restraints excluded: chain R residue 169 ILE Chi-restraints excluded: chain R residue 177 PHE Chi-restraints excluded: chain R residue 214 ASN Chi-restraints excluded: chain R residue 307 LEU Chi-restraints excluded: chain R residue 311 VAL Chi-restraints excluded: chain R residue 322 VAL Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 180 PHE Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 294 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 20 optimal weight: 0.9990 chunk 19 optimal weight: 0.9990 chunk 5 optimal weight: 0.0030 chunk 1 optimal weight: 5.9990 chunk 82 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 70 optimal weight: 0.9990 chunk 34 optimal weight: 0.9980 chunk 48 optimal weight: 0.0980 chunk 10 optimal weight: 0.7980 overall best weight: 0.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 285 HIS A 294 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4657 r_free = 0.4657 target = 0.206926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.163425 restraints weight = 7569.145| |-----------------------------------------------------------------------------| r_work (start): 0.4230 rms_B_bonded: 3.23 r_work: 0.3896 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6960 moved from start: 0.3541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6942 Z= 0.188 Angle : 0.592 10.372 9475 Z= 0.296 Chirality : 0.042 0.278 1125 Planarity : 0.003 0.032 1203 Dihedral : 3.900 37.458 978 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 5.22 % Allowed : 24.33 % Favored : 70.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.28), residues: 907 helix: 2.19 (0.26), residues: 378 sheet: -0.89 (0.38), residues: 165 loop : -1.27 (0.30), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 169 HIS 0.007 0.001 HIS R 285 PHE 0.031 0.001 PHE R 316 TYR 0.020 0.001 TYR B 59 ARG 0.002 0.000 ARG A 205 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1814 Ramachandran restraints generated. 907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1814 Ramachandran restraints generated. 907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 108 time to evaluate : 0.750 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 49 SER cc_start: 0.5183 (t) cc_final: 0.4520 (p) REVERT: R 84 LEU cc_start: 0.6151 (OUTLIER) cc_final: 0.5818 (mp) REVERT: R 169 ILE cc_start: 0.4748 (OUTLIER) cc_final: 0.4481 (tp) REVERT: R 210 MET cc_start: 0.4037 (tpp) cc_final: 0.3465 (tpp) REVERT: R 333 ARG cc_start: 0.4754 (pmt170) cc_final: 0.3458 (tmt170) outliers start: 35 outliers final: 28 residues processed: 129 average time/residue: 0.1658 time to fit residues: 29.6298 Evaluate side-chains 135 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 105 time to evaluate : 0.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 78 THR Chi-restraints excluded: chain R residue 84 LEU Chi-restraints excluded: chain R residue 104 TYR Chi-restraints excluded: chain R residue 169 ILE Chi-restraints excluded: chain R residue 177 PHE Chi-restraints excluded: chain R residue 214 ASN Chi-restraints excluded: chain R residue 307 LEU Chi-restraints excluded: chain R residue 311 VAL Chi-restraints excluded: chain R residue 322 VAL Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 294 ASN Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 180 PHE Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain C residue 28 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 50 optimal weight: 3.9990 chunk 9 optimal weight: 5.9990 chunk 36 optimal weight: 2.9990 chunk 78 optimal weight: 4.9990 chunk 32 optimal weight: 0.9980 chunk 79 optimal weight: 0.8980 chunk 66 optimal weight: 0.0570 chunk 31 optimal weight: 0.6980 chunk 6 optimal weight: 3.9990 chunk 39 optimal weight: 0.9980 chunk 40 optimal weight: 0.0770 overall best weight: 0.5456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 ASN B 340 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4661 r_free = 0.4661 target = 0.207303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.163610 restraints weight = 7613.191| |-----------------------------------------------------------------------------| r_work (start): 0.4226 rms_B_bonded: 3.26 r_work: 0.3891 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6954 moved from start: 0.3587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6942 Z= 0.186 Angle : 0.598 9.404 9475 Z= 0.299 Chirality : 0.042 0.278 1125 Planarity : 0.003 0.032 1203 Dihedral : 3.891 37.773 978 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 4.48 % Allowed : 25.37 % Favored : 70.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.28), residues: 907 helix: 2.24 (0.26), residues: 377 sheet: -0.89 (0.38), residues: 169 loop : -1.23 (0.30), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 169 HIS 0.004 0.001 HIS B 183 PHE 0.031 0.001 PHE R 316 TYR 0.015 0.001 TYR B 59 ARG 0.003 0.000 ARG R 263 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1814 Ramachandran restraints generated. 907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1814 Ramachandran restraints generated. 907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 108 time to evaluate : 0.754 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 49 SER cc_start: 0.5186 (t) cc_final: 0.4517 (p) REVERT: R 84 LEU cc_start: 0.6166 (OUTLIER) cc_final: 0.5831 (mp) REVERT: R 169 ILE cc_start: 0.4788 (OUTLIER) cc_final: 0.4507 (tp) REVERT: R 210 MET cc_start: 0.4018 (tpp) cc_final: 0.3451 (tpp) REVERT: R 263 ARG cc_start: 0.4901 (tmm160) cc_final: 0.4164 (tmm160) REVERT: R 333 ARG cc_start: 0.4799 (pmt170) cc_final: 0.3531 (tmt170) REVERT: A 197 LYS cc_start: 0.8622 (ptpt) cc_final: 0.8296 (ptmt) REVERT: A 247 MET cc_start: 0.7755 (ptt) cc_final: 0.7453 (ptp) outliers start: 30 outliers final: 26 residues processed: 129 average time/residue: 0.1620 time to fit residues: 28.8538 Evaluate side-chains 136 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 108 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 78 THR Chi-restraints excluded: chain R residue 84 LEU Chi-restraints excluded: chain R residue 104 TYR Chi-restraints excluded: chain R residue 169 ILE Chi-restraints excluded: chain R residue 177 PHE Chi-restraints excluded: chain R residue 214 ASN Chi-restraints excluded: chain R residue 307 LEU Chi-restraints excluded: chain R residue 311 VAL Chi-restraints excluded: chain R residue 322 VAL Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 294 ASN Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 180 PHE Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain C residue 28 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 29 optimal weight: 0.8980 chunk 48 optimal weight: 2.9990 chunk 53 optimal weight: 20.0000 chunk 57 optimal weight: 0.0770 chunk 86 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 81 optimal weight: 3.9990 chunk 64 optimal weight: 0.0470 chunk 5 optimal weight: 8.9990 chunk 9 optimal weight: 5.9990 chunk 51 optimal weight: 4.9990 overall best weight: 1.6040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4606 r_free = 0.4606 target = 0.201361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.158376 restraints weight = 7750.000| |-----------------------------------------------------------------------------| r_work (start): 0.4164 rms_B_bonded: 3.16 r_work: 0.3809 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7045 moved from start: 0.3837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 6942 Z= 0.328 Angle : 0.654 9.455 9475 Z= 0.332 Chirality : 0.044 0.276 1125 Planarity : 0.004 0.036 1203 Dihedral : 4.186 39.657 978 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 4.93 % Allowed : 24.48 % Favored : 70.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.27), residues: 907 helix: 2.11 (0.26), residues: 376 sheet: -1.27 (0.35), residues: 181 loop : -1.27 (0.31), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 99 HIS 0.005 0.002 HIS A 188 PHE 0.033 0.002 PHE R 316 TYR 0.018 0.002 TYR B 59 ARG 0.003 0.000 ARG B 49 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4596.44 seconds wall clock time: 82 minutes 1.34 seconds (4921.34 seconds total)