Starting phenix.real_space_refine on Wed Sep 17 08:18:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lwp_63455/09_2025/9lwp_63455.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lwp_63455/09_2025/9lwp_63455.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9lwp_63455/09_2025/9lwp_63455.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lwp_63455/09_2025/9lwp_63455.map" model { file = "/net/cci-nas-00/data/ceres_data/9lwp_63455/09_2025/9lwp_63455.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lwp_63455/09_2025/9lwp_63455.cif" } resolution = 2.93 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= -0.001 sd= 0.067 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 42 5.16 5 C 4371 2.51 5 N 1183 2.21 5 O 1248 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6844 Number of models: 1 Model: "" Number of chains: 4 Chain: "R" Number of atoms: 2165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2165 Classifications: {'peptide': 271} Link IDs: {'PTRANS': 10, 'TRANS': 260} Chain breaks: 4 Chain: "A" Number of atoms: 1650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1650 Classifications: {'peptide': 211} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 4, 'TRANS': 206} Chain breaks: 4 Unresolved non-hydrogen bonds: 85 Unresolved non-hydrogen angles: 100 Unresolved non-hydrogen dihedrals: 72 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 4, 'PHE:plan': 1, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 54 Chain: "B" Number of atoms: 2600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2600 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "G" Number of atoms: 429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 429 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 4, 'TRANS': 51} Time building chain proxies: 1.56, per 1000 atoms: 0.23 Number of scatterers: 6844 At special positions: 0 Unit cell: (77.112, 100.674, 127.449, 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 42 16.00 O 1248 8.00 N 1183 7.00 C 4371 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.39 Conformation dependent library (CDL) restraints added in 244.6 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1666 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 8 sheets defined 46.8% alpha, 18.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'R' and resid 48 through 75 removed outlier: 3.605A pdb=" N ILE R 52 " --> pdb=" O CYS R 48 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N THR R 53 " --> pdb=" O ALA R 49 " (cutoff:3.500A) Processing helix chain 'R' and resid 80 through 108 removed outlier: 3.552A pdb=" N ILE R 84 " --> pdb=" O THR R 80 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N PHE R 85 " --> pdb=" O VAL R 81 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ILE R 86 " --> pdb=" O PRO R 82 " (cutoff:3.500A) Proline residue: R 102 - end of helix Processing helix chain 'R' and resid 118 through 119 No H-bonds generated for 'chain 'R' and resid 118 through 119' Processing helix chain 'R' and resid 121 through 121 No H-bonds generated for 'chain 'R' and resid 121 through 121' Processing helix chain 'R' and resid 122 through 151 Processing helix chain 'R' and resid 160 through 180 Processing helix chain 'R' and resid 181 through 183 No H-bonds generated for 'chain 'R' and resid 181 through 183' Processing helix chain 'R' and resid 211 through 227 Processing helix chain 'R' and resid 227 through 248 Processing helix chain 'R' and resid 259 through 297 Proline residue: R 286 - end of helix Processing helix chain 'R' and resid 308 through 334 removed outlier: 4.012A pdb=" N ASN R 322 " --> pdb=" O LEU R 318 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N SER R 323 " --> pdb=" O ALA R 319 " (cutoff:3.500A) Proline residue: R 327 - end of helix removed outlier: 3.915A pdb=" N LEU R 330 " --> pdb=" O ASN R 326 " (cutoff:3.500A) Processing helix chain 'R' and resid 334 through 344 Processing helix chain 'A' and resid 6 through 31 Processing helix chain 'A' and resid 46 through 50 removed outlier: 3.560A pdb=" N ILE A 49 " --> pdb=" O LYS A 46 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N VAL A 50 " --> pdb=" O SER A 47 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 46 through 50' Processing helix chain 'A' and resid 95 through 100 removed outlier: 3.519A pdb=" N GLN A 98 " --> pdb=" O LYS A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 130 Processing helix chain 'A' and resid 145 through 156 Processing helix chain 'A' and resid 159 through 164 removed outlier: 4.164A pdb=" N TYR A 163 " --> pdb=" O LYS A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 168 Processing helix chain 'A' and resid 184 through 203 Processing helix chain 'A' and resid 222 through 243 Processing helix chain 'B' and resid 4 through 25 Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.580A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 8 through 24 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 45 through 48 removed outlier: 3.669A pdb=" N ASP G 48 " --> pdb=" O ALA G 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 45 through 48' Processing sheet with id=AA1, first strand: chain 'A' and resid 69 through 76 removed outlier: 4.725A pdb=" N VAL A 86 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ARG A 35 " --> pdb=" O ALA A 105 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N ILE A 107 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N LEU A 37 " --> pdb=" O ILE A 107 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N VAL A 109 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N ILE A 106 " --> pdb=" O ILE A 140 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N PHE A 142 " --> pdb=" O ILE A 106 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N PHE A 108 " --> pdb=" O PHE A 142 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ASN A 144 " --> pdb=" O PHE A 108 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N VAL A 110 " --> pdb=" O ASN A 144 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 52 removed outlier: 3.650A 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: 3.817A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.720A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 4.076A 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 153 removed outlier: 6.674A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.405A 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: 6.872A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.803A 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: 3.619A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.211A 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: 4.042A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) 373 hydrogen bonds defined for protein. 1095 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: 1.09 Time building geometry restraints manager: 0.54 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: 2210 1.34 - 1.46: 1621 1.46 - 1.58: 3088 1.58 - 1.69: 0 1.69 - 1.81: 57 Bond restraints: 6976 Sorted by residual: bond pdb=" CB ASN A 43 " pdb=" CG ASN A 43 " ideal model delta sigma weight residual 1.516 1.547 -0.031 2.50e-02 1.60e+03 1.57e+00 bond pdb=" C LEU R 180 " pdb=" N PRO R 181 " ideal model delta sigma weight residual 1.334 1.360 -0.027 2.34e-02 1.83e+03 1.29e+00 bond pdb=" CA ASN A 43 " pdb=" CB ASN A 43 " ideal model delta sigma weight residual 1.533 1.550 -0.016 1.66e-02 3.63e+03 9.47e-01 bond pdb=" C ILE R 251 " pdb=" N PRO R 252 " ideal model delta sigma weight residual 1.334 1.355 -0.021 2.34e-02 1.83e+03 8.06e-01 bond pdb=" CB VAL R 273 " pdb=" CG1 VAL R 273 " ideal model delta sigma weight residual 1.521 1.492 0.029 3.30e-02 9.18e+02 7.49e-01 ... (remaining 6971 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.88: 9356 1.88 - 3.75: 80 3.75 - 5.63: 12 5.63 - 7.50: 2 7.50 - 9.38: 1 Bond angle restraints: 9451 Sorted by residual: angle pdb=" CA LEU R 223 " pdb=" CB LEU R 223 " pdb=" CG LEU R 223 " ideal model delta sigma weight residual 116.30 125.68 -9.38 3.50e+00 8.16e-02 7.18e+00 angle pdb=" CA ASN A 43 " pdb=" CB ASN A 43 " pdb=" CG ASN A 43 " ideal model delta sigma weight residual 112.60 115.05 -2.45 1.00e+00 1.00e+00 6.01e+00 angle pdb=" C GLN R 256 " pdb=" N SER R 257 " pdb=" CA SER R 257 " ideal model delta sigma weight residual 125.66 129.64 -3.98 1.85e+00 2.92e-01 4.64e+00 angle pdb=" C ALA R 319 " pdb=" N PHE R 320 " pdb=" CA PHE R 320 " ideal model delta sigma weight residual 122.38 118.64 3.74 1.81e+00 3.05e-01 4.28e+00 angle pdb=" CA ASN B 155 " pdb=" C ASN B 155 " pdb=" O ASN B 155 " ideal model delta sigma weight residual 119.08 121.20 -2.12 1.03e+00 9.43e-01 4.23e+00 ... (remaining 9446 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.44: 3657 17.44 - 34.87: 388 34.87 - 52.30: 97 52.30 - 69.74: 6 69.74 - 87.17: 3 Dihedral angle restraints: 4151 sinusoidal: 1594 harmonic: 2557 Sorted by residual: dihedral pdb=" CG ARG A 188 " pdb=" CD ARG A 188 " pdb=" NE ARG A 188 " pdb=" CZ ARG A 188 " ideal model delta sinusoidal sigma weight residual 90.00 133.77 -43.77 2 1.50e+01 4.44e-03 1.02e+01 dihedral pdb=" CG ARG B 304 " pdb=" CD ARG B 304 " pdb=" NE ARG B 304 " pdb=" CZ ARG B 304 " ideal model delta sinusoidal sigma weight residual -90.00 -131.72 41.72 2 1.50e+01 4.44e-03 9.45e+00 dihedral pdb=" CA ARG R 271 " pdb=" CB ARG R 271 " pdb=" CG ARG R 271 " pdb=" CD ARG R 271 " ideal model delta sinusoidal sigma weight residual 180.00 127.45 52.55 3 1.50e+01 4.44e-03 9.13e+00 ... (remaining 4148 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 664 0.028 - 0.055: 273 0.055 - 0.082: 95 0.082 - 0.110: 46 0.110 - 0.137: 22 Chirality restraints: 1100 Sorted by residual: chirality pdb=" CA PRO R 252 " pdb=" N PRO R 252 " pdb=" C PRO R 252 " pdb=" CB PRO R 252 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.72e-01 chirality pdb=" CA ILE A 140 " pdb=" N ILE A 140 " pdb=" C ILE A 140 " pdb=" CB ILE A 140 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.20e-01 chirality pdb=" CA PRO R 102 " pdb=" N PRO R 102 " pdb=" C PRO R 102 " pdb=" CB PRO R 102 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.04e-01 ... (remaining 1097 not shown) Planarity restraints: 1186 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE R 251 " -0.028 5.00e-02 4.00e+02 4.22e-02 2.85e+00 pdb=" N PRO R 252 " 0.073 5.00e-02 4.00e+02 pdb=" CA PRO R 252 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO R 252 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU R 223 " 0.008 2.00e-02 2.50e+03 1.60e-02 2.57e+00 pdb=" C LEU R 223 " -0.028 2.00e-02 2.50e+03 pdb=" O LEU R 223 " 0.010 2.00e-02 2.50e+03 pdb=" N VAL R 224 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU R 180 " -0.022 5.00e-02 4.00e+02 3.39e-02 1.84e+00 pdb=" N PRO R 181 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO R 181 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO R 181 " -0.019 5.00e-02 4.00e+02 ... (remaining 1183 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 103 2.66 - 3.22: 6494 3.22 - 3.78: 10904 3.78 - 4.34: 14745 4.34 - 4.90: 24570 Nonbonded interactions: 56816 Sorted by model distance: nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.104 3.040 nonbonded pdb=" O CYS B 218 " pdb=" NE2 GLN G 18 " model vdw 2.202 3.120 nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 2.217 3.040 nonbonded pdb=" NH2 ARG R 268 " pdb=" O TRP R 332 " model vdw 2.239 3.120 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.245 3.040 ... (remaining 56811 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=0.00 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: 1.340 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: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.590 Find NCS groups from input model: 0.030 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:6.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7006 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 0.031 6976 Z= 0.118 Angle : 0.504 9.379 9451 Z= 0.279 Chirality : 0.040 0.137 1100 Planarity : 0.004 0.042 1186 Dihedral : 14.803 87.172 2485 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.23 % Allowed : 3.17 % Favored : 96.60 % Rotamer: Outliers : 0.95 % Allowed : 14.91 % Favored : 84.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.93 (0.28), residues: 852 helix: 1.82 (0.26), residues: 381 sheet: 0.34 (0.38), residues: 188 loop : -0.81 (0.35), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 132 TYR 0.015 0.001 TYR B 59 PHE 0.022 0.001 PHE R 320 TRP 0.011 0.001 TRP R 332 HIS 0.004 0.001 HIS R 308 Details of bonding type rmsd covalent geometry : bond 0.00238 ( 6976) covalent geometry : angle 0.50445 ( 9451) hydrogen bonds : bond 0.13840 ( 373) hydrogen bonds : angle 5.66140 ( 1095) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 73 time to evaluate : 0.261 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 78 MET cc_start: 0.6771 (ptm) cc_final: 0.6492 (ptp) REVERT: R 147 LYS cc_start: 0.8034 (ttmm) cc_final: 0.7572 (ttpt) REVERT: R 210 LYS cc_start: 0.5315 (mmtt) cc_final: 0.3968 (mptp) REVERT: R 220 LEU cc_start: 0.7416 (tt) cc_final: 0.6752 (tp) REVERT: A 32 ARG cc_start: 0.6674 (mmt-90) cc_final: 0.5749 (mtm180) REVERT: B 110 ASN cc_start: 0.8393 (m-40) cc_final: 0.8139 (m-40) REVERT: B 217 MET cc_start: 0.6570 (pmm) cc_final: 0.6183 (pmt) REVERT: B 262 MET cc_start: 0.7331 (tpt) cc_final: 0.7071 (tpp) REVERT: B 325 MET cc_start: 0.8297 (ttm) cc_final: 0.7991 (tpt) outliers start: 7 outliers final: 3 residues processed: 74 average time/residue: 0.5458 time to fit residues: 42.7265 Evaluate side-chains 69 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 66 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain B residue 146 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 49 optimal weight: 6.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 9.9990 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 74 optimal weight: 0.8980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 ASN B 220 GLN B 268 ASN B 340 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.197098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.157240 restraints weight = 7258.048| |-----------------------------------------------------------------------------| r_work (start): 0.3752 rms_B_bonded: 2.03 r_work: 0.3557 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3422 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7106 moved from start: 0.0916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 6976 Z= 0.166 Angle : 0.537 7.841 9451 Z= 0.291 Chirality : 0.043 0.159 1100 Planarity : 0.004 0.049 1186 Dihedral : 4.251 40.280 945 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.23 % Allowed : 3.40 % Favored : 96.36 % Rotamer: Outliers : 3.66 % Allowed : 13.96 % Favored : 82.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.75 (0.28), residues: 852 helix: 1.67 (0.25), residues: 375 sheet: 0.39 (0.39), residues: 185 loop : -0.95 (0.34), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 132 TYR 0.023 0.001 TYR B 59 PHE 0.019 0.002 PHE R 320 TRP 0.018 0.002 TRP B 82 HIS 0.004 0.001 HIS R 294 Details of bonding type rmsd covalent geometry : bond 0.00384 ( 6976) covalent geometry : angle 0.53697 ( 9451) hydrogen bonds : bond 0.04665 ( 373) hydrogen bonds : angle 4.71645 ( 1095) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 79 time to evaluate : 0.283 Fit side-chains revert: symmetry clash REVERT: R 78 MET cc_start: 0.6653 (ptm) cc_final: 0.6077 (ptp) REVERT: R 127 ARG cc_start: 0.5508 (ttp80) cc_final: 0.4894 (ttp-170) REVERT: R 147 LYS cc_start: 0.8112 (ttmm) cc_final: 0.7628 (ttmm) REVERT: R 210 LYS cc_start: 0.5481 (mmtt) cc_final: 0.4002 (mptp) REVERT: R 220 LEU cc_start: 0.7518 (tt) cc_final: 0.6898 (tp) REVERT: A 32 ARG cc_start: 0.6849 (mmt-90) cc_final: 0.5828 (mtm180) REVERT: B 137 ARG cc_start: 0.7010 (tpp-160) cc_final: 0.6741 (tpp-160) REVERT: B 200 VAL cc_start: 0.8945 (p) cc_final: 0.8641 (m) REVERT: B 217 MET cc_start: 0.6372 (pmm) cc_final: 0.5957 (pmt) REVERT: B 219 ARG cc_start: 0.7466 (OUTLIER) cc_final: 0.6799 (mpt90) REVERT: B 304 ARG cc_start: 0.7330 (ttp-110) cc_final: 0.7006 (ttm170) REVERT: B 325 MET cc_start: 0.8261 (ttm) cc_final: 0.7935 (tpt) outliers start: 27 outliers final: 11 residues processed: 95 average time/residue: 0.5592 time to fit residues: 56.1070 Evaluate side-chains 85 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 73 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 53 THR Chi-restraints excluded: chain R residue 218 SER Chi-restraints excluded: chain R residue 307 MET Chi-restraints excluded: chain R residue 325 VAL Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 275 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 68 optimal weight: 1.9990 chunk 58 optimal weight: 0.5980 chunk 71 optimal weight: 0.8980 chunk 61 optimal weight: 3.9990 chunk 35 optimal weight: 0.8980 chunk 23 optimal weight: 6.9990 chunk 0 optimal weight: 7.9990 chunk 82 optimal weight: 3.9990 chunk 55 optimal weight: 0.0270 chunk 45 optimal weight: 0.9990 chunk 38 optimal weight: 0.8980 overall best weight: 0.6638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 ASN B 119 ASN B 220 GLN B 268 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.196160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.157126 restraints weight = 7185.477| |-----------------------------------------------------------------------------| r_work (start): 0.3761 rms_B_bonded: 1.99 r_work: 0.3569 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3434 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7085 moved from start: 0.1205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6976 Z= 0.136 Angle : 0.498 7.438 9451 Z= 0.270 Chirality : 0.042 0.154 1100 Planarity : 0.004 0.051 1186 Dihedral : 4.198 39.275 944 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.29 % Favored : 96.60 % Rotamer: Outliers : 3.52 % Allowed : 16.26 % Favored : 80.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.88 (0.28), residues: 852 helix: 1.77 (0.25), residues: 376 sheet: 0.53 (0.38), residues: 190 loop : -0.96 (0.35), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 132 TYR 0.018 0.001 TYR B 59 PHE 0.019 0.001 PHE R 320 TRP 0.017 0.001 TRP B 82 HIS 0.004 0.001 HIS R 294 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 6976) covalent geometry : angle 0.49753 ( 9451) hydrogen bonds : bond 0.04245 ( 373) hydrogen bonds : angle 4.49804 ( 1095) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 79 time to evaluate : 0.265 Fit side-chains revert: symmetry clash REVERT: R 78 MET cc_start: 0.6730 (ptm) cc_final: 0.6079 (ptp) REVERT: R 147 LYS cc_start: 0.8104 (ttmm) cc_final: 0.7711 (ttpm) REVERT: R 210 LYS cc_start: 0.5529 (mmtt) cc_final: 0.4031 (mptp) REVERT: R 220 LEU cc_start: 0.7728 (tt) cc_final: 0.7051 (tp) REVERT: A 25 GLU cc_start: 0.7436 (tt0) cc_final: 0.7029 (tt0) REVERT: A 32 ARG cc_start: 0.6831 (mmt-90) cc_final: 0.5982 (ptp90) REVERT: A 136 THR cc_start: 0.8831 (t) cc_final: 0.8566 (m) REVERT: B 200 VAL cc_start: 0.8988 (p) cc_final: 0.8687 (m) REVERT: B 217 MET cc_start: 0.6506 (pmm) cc_final: 0.6130 (pmt) REVERT: B 219 ARG cc_start: 0.7465 (OUTLIER) cc_final: 0.6705 (mpt90) REVERT: B 262 MET cc_start: 0.7499 (tpt) cc_final: 0.7240 (tpp) REVERT: B 300 LEU cc_start: 0.8434 (mt) cc_final: 0.8234 (OUTLIER) REVERT: B 325 MET cc_start: 0.8304 (ttm) cc_final: 0.7964 (tpt) outliers start: 26 outliers final: 14 residues processed: 93 average time/residue: 0.4891 time to fit residues: 48.4480 Evaluate side-chains 89 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 75 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 128 LEU Chi-restraints excluded: chain R residue 218 SER Chi-restraints excluded: chain R residue 248 THR Chi-restraints excluded: chain R residue 307 MET Chi-restraints excluded: chain R residue 325 VAL Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 275 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 63 optimal weight: 0.0370 chunk 55 optimal weight: 0.5980 chunk 62 optimal weight: 0.9980 chunk 73 optimal weight: 0.7980 chunk 83 optimal weight: 7.9990 chunk 22 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 60 optimal weight: 0.1980 chunk 7 optimal weight: 0.8980 chunk 12 optimal weight: 0.8980 chunk 76 optimal weight: 2.9990 overall best weight: 0.5058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 ASN B 220 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.196956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.158087 restraints weight = 7250.748| |-----------------------------------------------------------------------------| r_work (start): 0.3729 rms_B_bonded: 2.00 r_work: 0.3536 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3401 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7118 moved from start: 0.1382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6976 Z= 0.121 Angle : 0.480 7.555 9451 Z= 0.260 Chirality : 0.041 0.153 1100 Planarity : 0.004 0.051 1186 Dihedral : 4.117 38.924 944 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.64 % Favored : 96.24 % Rotamer: Outliers : 3.79 % Allowed : 17.21 % Favored : 79.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.01 (0.28), residues: 852 helix: 1.88 (0.25), residues: 376 sheet: 0.58 (0.38), residues: 192 loop : -0.91 (0.35), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 268 TYR 0.013 0.001 TYR B 59 PHE 0.019 0.001 PHE R 320 TRP 0.016 0.001 TRP B 82 HIS 0.003 0.001 HIS R 294 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 6976) covalent geometry : angle 0.47952 ( 9451) hydrogen bonds : bond 0.03962 ( 373) hydrogen bonds : angle 4.36831 ( 1095) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 80 time to evaluate : 0.200 Fit side-chains revert: symmetry clash REVERT: R 78 MET cc_start: 0.6802 (ptm) cc_final: 0.6148 (ptp) REVERT: R 99 THR cc_start: 0.6976 (m) cc_final: 0.6517 (p) REVERT: R 147 LYS cc_start: 0.8099 (ttmm) cc_final: 0.7683 (ttpm) REVERT: R 210 LYS cc_start: 0.5729 (mmtt) cc_final: 0.4275 (mptp) REVERT: R 220 LEU cc_start: 0.7792 (tt) cc_final: 0.7139 (tp) REVERT: A 25 GLU cc_start: 0.7457 (tt0) cc_final: 0.7069 (tt0) REVERT: A 32 ARG cc_start: 0.6896 (mmt-90) cc_final: 0.6040 (ptp90) REVERT: A 72 THR cc_start: 0.8987 (OUTLIER) cc_final: 0.8523 (p) REVERT: A 136 THR cc_start: 0.8845 (t) cc_final: 0.8586 (m) REVERT: B 137 ARG cc_start: 0.7232 (tpp-160) cc_final: 0.6966 (tpp-160) REVERT: B 171 ILE cc_start: 0.7518 (OUTLIER) cc_final: 0.7264 (mp) REVERT: B 200 VAL cc_start: 0.8958 (p) cc_final: 0.8613 (m) REVERT: B 217 MET cc_start: 0.6601 (pmm) cc_final: 0.6233 (pmt) REVERT: B 219 ARG cc_start: 0.7502 (OUTLIER) cc_final: 0.6549 (mpt90) REVERT: B 234 PHE cc_start: 0.9184 (OUTLIER) cc_final: 0.8045 (m-80) REVERT: B 262 MET cc_start: 0.7489 (tpt) cc_final: 0.7224 (tpp) REVERT: B 325 MET cc_start: 0.8331 (ttm) cc_final: 0.8001 (tpt) outliers start: 28 outliers final: 14 residues processed: 98 average time/residue: 0.4916 time to fit residues: 51.3224 Evaluate side-chains 98 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 80 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 63 LEU Chi-restraints excluded: chain R residue 87 THR Chi-restraints excluded: chain R residue 128 LEU Chi-restraints excluded: chain R residue 218 SER Chi-restraints excluded: chain R residue 248 THR Chi-restraints excluded: chain R residue 307 MET Chi-restraints excluded: chain R residue 325 VAL Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 261 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 74 optimal weight: 2.9990 chunk 64 optimal weight: 4.9990 chunk 2 optimal weight: 0.6980 chunk 52 optimal weight: 0.0870 chunk 82 optimal weight: 8.9990 chunk 23 optimal weight: 4.9990 chunk 29 optimal weight: 0.8980 chunk 41 optimal weight: 0.5980 chunk 5 optimal weight: 0.0670 chunk 47 optimal weight: 0.4980 chunk 13 optimal weight: 0.2980 overall best weight: 0.3096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 288 HIS A 101 ASN B 220 GLN ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.199906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.160746 restraints weight = 7245.719| |-----------------------------------------------------------------------------| r_work (start): 0.3787 rms_B_bonded: 1.95 r_work: 0.3597 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3461 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7062 moved from start: 0.1559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 6976 Z= 0.104 Angle : 0.466 8.612 9451 Z= 0.251 Chirality : 0.041 0.149 1100 Planarity : 0.004 0.051 1186 Dihedral : 3.997 38.167 944 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.29 % Favored : 96.60 % Rotamer: Outliers : 3.79 % Allowed : 17.89 % Favored : 78.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.15 (0.29), residues: 852 helix: 2.03 (0.25), residues: 378 sheet: 0.59 (0.38), residues: 192 loop : -0.86 (0.36), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 197 TYR 0.008 0.001 TYR B 59 PHE 0.021 0.001 PHE R 320 TRP 0.015 0.001 TRP B 82 HIS 0.002 0.001 HIS R 294 Details of bonding type rmsd covalent geometry : bond 0.00219 ( 6976) covalent geometry : angle 0.46625 ( 9451) hydrogen bonds : bond 0.03650 ( 373) hydrogen bonds : angle 4.23318 ( 1095) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 82 time to evaluate : 0.224 Fit side-chains revert: symmetry clash REVERT: R 78 MET cc_start: 0.6759 (ptm) cc_final: 0.6080 (ptp) REVERT: R 99 THR cc_start: 0.6878 (m) cc_final: 0.6464 (p) REVERT: R 138 LEU cc_start: 0.7377 (mt) cc_final: 0.7126 (mt) REVERT: R 147 LYS cc_start: 0.8053 (ttmm) cc_final: 0.7648 (ttpm) REVERT: R 210 LYS cc_start: 0.5258 (mmtt) cc_final: 0.3913 (mptp) REVERT: R 220 LEU cc_start: 0.7714 (tt) cc_final: 0.7033 (tp) REVERT: A 25 GLU cc_start: 0.7396 (tt0) cc_final: 0.6999 (tt0) REVERT: A 72 THR cc_start: 0.8886 (OUTLIER) cc_final: 0.8442 (p) REVERT: A 73 LYS cc_start: 0.8113 (mtpp) cc_final: 0.7786 (mmmt) REVERT: A 136 THR cc_start: 0.8737 (t) cc_final: 0.8476 (m) REVERT: B 78 LYS cc_start: 0.8549 (tppp) cc_final: 0.8251 (tppt) REVERT: B 171 ILE cc_start: 0.7433 (OUTLIER) cc_final: 0.7231 (mp) REVERT: B 200 VAL cc_start: 0.8987 (p) cc_final: 0.8705 (m) REVERT: B 217 MET cc_start: 0.6592 (pmm) cc_final: 0.6225 (pmt) REVERT: B 219 ARG cc_start: 0.7405 (OUTLIER) cc_final: 0.6470 (mpt90) REVERT: B 262 MET cc_start: 0.7470 (tpt) cc_final: 0.7227 (tpp) REVERT: B 284 LEU cc_start: 0.8533 (OUTLIER) cc_final: 0.8184 (mp) REVERT: B 325 MET cc_start: 0.8273 (ttm) cc_final: 0.7935 (mmt) outliers start: 28 outliers final: 15 residues processed: 102 average time/residue: 0.3922 time to fit residues: 43.0011 Evaluate side-chains 95 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 76 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 63 LEU Chi-restraints excluded: chain R residue 87 THR Chi-restraints excluded: chain R residue 128 LEU Chi-restraints excluded: chain R residue 180 LEU Chi-restraints excluded: chain R residue 248 THR Chi-restraints excluded: chain R residue 289 LEU Chi-restraints excluded: chain R residue 307 MET Chi-restraints excluded: chain R residue 318 LEU Chi-restraints excluded: chain R residue 324 CYS Chi-restraints excluded: chain R residue 325 VAL Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 284 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 18 optimal weight: 7.9990 chunk 13 optimal weight: 0.8980 chunk 49 optimal weight: 8.9990 chunk 10 optimal weight: 0.9980 chunk 42 optimal weight: 0.5980 chunk 67 optimal weight: 0.0980 chunk 68 optimal weight: 0.5980 chunk 14 optimal weight: 6.9990 chunk 47 optimal weight: 0.7980 chunk 51 optimal weight: 0.0060 chunk 52 optimal weight: 3.9990 overall best weight: 0.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 ASN A 144 ASN B 220 GLN ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.199184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.159706 restraints weight = 7221.643| |-----------------------------------------------------------------------------| r_work (start): 0.3759 rms_B_bonded: 1.97 r_work: 0.3564 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3428 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7076 moved from start: 0.1683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 6976 Z= 0.111 Angle : 0.470 7.989 9451 Z= 0.252 Chirality : 0.041 0.149 1100 Planarity : 0.003 0.051 1186 Dihedral : 3.982 39.188 944 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.76 % Favored : 96.13 % Rotamer: Outliers : 3.93 % Allowed : 18.97 % Favored : 77.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.15 (0.28), residues: 852 helix: 2.02 (0.25), residues: 378 sheet: 0.62 (0.38), residues: 192 loop : -0.88 (0.36), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 197 TYR 0.011 0.001 TYR B 59 PHE 0.020 0.001 PHE R 320 TRP 0.015 0.001 TRP B 82 HIS 0.002 0.001 HIS R 294 Details of bonding type rmsd covalent geometry : bond 0.00241 ( 6976) covalent geometry : angle 0.47007 ( 9451) hydrogen bonds : bond 0.03701 ( 373) hydrogen bonds : angle 4.19572 ( 1095) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 75 time to evaluate : 0.297 Fit side-chains revert: symmetry clash REVERT: R 78 MET cc_start: 0.6773 (ptm) cc_final: 0.6081 (ptp) REVERT: R 99 THR cc_start: 0.7096 (m) cc_final: 0.6616 (p) REVERT: R 138 LEU cc_start: 0.7392 (mt) cc_final: 0.7155 (mt) REVERT: R 147 LYS cc_start: 0.8124 (ttmm) cc_final: 0.7690 (ttpm) REVERT: R 210 LYS cc_start: 0.5445 (mmtt) cc_final: 0.4072 (mptp) REVERT: R 220 LEU cc_start: 0.7725 (tt) cc_final: 0.7036 (tp) REVERT: A 25 GLU cc_start: 0.7402 (tt0) cc_final: 0.6998 (tt0) REVERT: A 72 THR cc_start: 0.8768 (OUTLIER) cc_final: 0.8375 (p) REVERT: A 136 THR cc_start: 0.8723 (t) cc_final: 0.8473 (m) REVERT: B 46 ARG cc_start: 0.7406 (OUTLIER) cc_final: 0.7197 (mtp-110) REVERT: B 78 LYS cc_start: 0.8557 (tppp) cc_final: 0.8264 (tppt) REVERT: B 200 VAL cc_start: 0.8993 (p) cc_final: 0.8711 (m) REVERT: B 217 MET cc_start: 0.6540 (pmm) cc_final: 0.6195 (pmt) REVERT: B 219 ARG cc_start: 0.7425 (OUTLIER) cc_final: 0.6329 (mpt90) REVERT: B 262 MET cc_start: 0.7443 (tpt) cc_final: 0.7193 (tpp) REVERT: B 284 LEU cc_start: 0.8512 (OUTLIER) cc_final: 0.8179 (mp) REVERT: B 325 MET cc_start: 0.8291 (ttm) cc_final: 0.7949 (mmt) outliers start: 29 outliers final: 18 residues processed: 97 average time/residue: 0.4177 time to fit residues: 43.3988 Evaluate side-chains 95 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 73 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 63 LEU Chi-restraints excluded: chain R residue 87 THR Chi-restraints excluded: chain R residue 128 LEU Chi-restraints excluded: chain R residue 180 LEU Chi-restraints excluded: chain R residue 248 THR Chi-restraints excluded: chain R residue 289 LEU Chi-restraints excluded: chain R residue 307 MET Chi-restraints excluded: chain R residue 318 LEU Chi-restraints excluded: chain R residue 324 CYS Chi-restraints excluded: chain R residue 325 VAL Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 284 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 41 optimal weight: 4.9990 chunk 29 optimal weight: 0.8980 chunk 42 optimal weight: 0.5980 chunk 58 optimal weight: 0.8980 chunk 50 optimal weight: 4.9990 chunk 77 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 chunk 52 optimal weight: 0.5980 chunk 33 optimal weight: 2.9990 chunk 46 optimal weight: 0.6980 chunk 22 optimal weight: 5.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 ASN B 220 GLN ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.196452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.156786 restraints weight = 7136.644| |-----------------------------------------------------------------------------| r_work (start): 0.3725 rms_B_bonded: 1.97 r_work: 0.3529 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3392 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7109 moved from start: 0.1830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6976 Z= 0.139 Angle : 0.501 7.849 9451 Z= 0.268 Chirality : 0.042 0.150 1100 Planarity : 0.004 0.051 1186 Dihedral : 4.157 45.536 944 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.64 % Favored : 96.24 % Rotamer: Outliers : 4.34 % Allowed : 19.24 % Favored : 76.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.10 (0.28), residues: 852 helix: 1.97 (0.25), residues: 377 sheet: 0.66 (0.38), residues: 190 loop : -0.91 (0.35), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 197 TYR 0.015 0.001 TYR B 59 PHE 0.018 0.001 PHE R 320 TRP 0.015 0.001 TRP B 82 HIS 0.003 0.001 HIS R 294 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 6976) covalent geometry : angle 0.50076 ( 9451) hydrogen bonds : bond 0.04082 ( 373) hydrogen bonds : angle 4.29773 ( 1095) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 81 time to evaluate : 0.198 Fit side-chains revert: symmetry clash REVERT: R 78 MET cc_start: 0.6727 (ptm) cc_final: 0.6499 (ptm) REVERT: R 99 THR cc_start: 0.7151 (m) cc_final: 0.6469 (p) REVERT: R 121 LYS cc_start: 0.7047 (mtpt) cc_final: 0.6427 (mmmt) REVERT: R 147 LYS cc_start: 0.8174 (ttmm) cc_final: 0.7740 (ttpm) REVERT: R 220 LEU cc_start: 0.7675 (tt) cc_final: 0.7026 (tp) REVERT: A 25 GLU cc_start: 0.7435 (tt0) cc_final: 0.7021 (tt0) REVERT: A 32 ARG cc_start: 0.6777 (mmt-90) cc_final: 0.5982 (ptp90) REVERT: A 72 THR cc_start: 0.8691 (OUTLIER) cc_final: 0.8290 (p) REVERT: A 136 THR cc_start: 0.8702 (t) cc_final: 0.8475 (m) REVERT: A 153 VAL cc_start: 0.7580 (p) cc_final: 0.7255 (m) REVERT: B 46 ARG cc_start: 0.7495 (OUTLIER) cc_final: 0.7293 (mtp-110) REVERT: B 78 LYS cc_start: 0.8555 (tppp) cc_final: 0.8272 (tppt) REVERT: B 200 VAL cc_start: 0.9001 (p) cc_final: 0.8737 (m) REVERT: B 217 MET cc_start: 0.6631 (pmm) cc_final: 0.6270 (pmt) REVERT: B 219 ARG cc_start: 0.7383 (OUTLIER) cc_final: 0.6360 (mpt90) REVERT: B 262 MET cc_start: 0.7434 (tpt) cc_final: 0.7189 (tpp) REVERT: B 284 LEU cc_start: 0.8514 (OUTLIER) cc_final: 0.8163 (mp) REVERT: B 325 MET cc_start: 0.8331 (ttm) cc_final: 0.7994 (mmt) outliers start: 32 outliers final: 19 residues processed: 104 average time/residue: 0.4745 time to fit residues: 52.6403 Evaluate side-chains 98 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 75 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 63 LEU Chi-restraints excluded: chain R residue 87 THR Chi-restraints excluded: chain R residue 128 LEU Chi-restraints excluded: chain R residue 171 VAL Chi-restraints excluded: chain R residue 180 LEU Chi-restraints excluded: chain R residue 218 SER Chi-restraints excluded: chain R residue 248 THR Chi-restraints excluded: chain R residue 289 LEU Chi-restraints excluded: chain R residue 307 MET Chi-restraints excluded: chain R residue 318 LEU Chi-restraints excluded: chain R residue 324 CYS Chi-restraints excluded: chain R residue 325 VAL Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 284 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 49 optimal weight: 0.8980 chunk 55 optimal weight: 1.9990 chunk 81 optimal weight: 9.9990 chunk 66 optimal weight: 2.9990 chunk 73 optimal weight: 0.2980 chunk 74 optimal weight: 0.5980 chunk 36 optimal weight: 0.8980 chunk 63 optimal weight: 0.8980 chunk 61 optimal weight: 0.6980 chunk 79 optimal weight: 0.9990 chunk 70 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 258 HIS A 80 ASN A 101 ASN B 220 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.196675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.156710 restraints weight = 7250.519| |-----------------------------------------------------------------------------| r_work (start): 0.3731 rms_B_bonded: 1.99 r_work: 0.3539 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3403 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7143 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6976 Z= 0.131 Angle : 0.491 8.162 9451 Z= 0.263 Chirality : 0.042 0.148 1100 Planarity : 0.004 0.051 1186 Dihedral : 4.183 50.839 944 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.76 % Favored : 96.13 % Rotamer: Outliers : 4.07 % Allowed : 19.92 % Favored : 76.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.09 (0.28), residues: 852 helix: 1.98 (0.25), residues: 377 sheet: 0.58 (0.38), residues: 192 loop : -0.90 (0.35), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 256 TYR 0.014 0.001 TYR B 59 PHE 0.019 0.001 PHE R 320 TRP 0.015 0.001 TRP B 82 HIS 0.003 0.001 HIS R 294 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 6976) covalent geometry : angle 0.49094 ( 9451) hydrogen bonds : bond 0.03996 ( 373) hydrogen bonds : angle 4.28292 ( 1095) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 76 time to evaluate : 0.266 Fit side-chains revert: symmetry clash REVERT: R 99 THR cc_start: 0.7165 (m) cc_final: 0.6520 (p) REVERT: R 121 LYS cc_start: 0.6990 (mtpt) cc_final: 0.6250 (mmmt) REVERT: R 147 LYS cc_start: 0.8185 (ttmm) cc_final: 0.7758 (ttpm) REVERT: R 220 LEU cc_start: 0.7666 (tt) cc_final: 0.7040 (tp) REVERT: A 25 GLU cc_start: 0.7469 (tt0) cc_final: 0.7055 (tt0) REVERT: A 32 ARG cc_start: 0.6848 (mmt-90) cc_final: 0.6048 (ptp90) REVERT: A 72 THR cc_start: 0.8764 (OUTLIER) cc_final: 0.8332 (p) REVERT: A 136 THR cc_start: 0.8701 (t) cc_final: 0.8482 (m) REVERT: A 153 VAL cc_start: 0.7691 (p) cc_final: 0.7359 (m) REVERT: B 78 LYS cc_start: 0.8585 (tppp) cc_final: 0.8299 (tppt) REVERT: B 200 VAL cc_start: 0.8997 (p) cc_final: 0.8740 (m) REVERT: B 217 MET cc_start: 0.6691 (pmm) cc_final: 0.6433 (pmm) REVERT: B 219 ARG cc_start: 0.7366 (OUTLIER) cc_final: 0.6311 (mpt90) REVERT: B 262 MET cc_start: 0.7456 (tpt) cc_final: 0.7220 (tpp) REVERT: B 284 LEU cc_start: 0.8511 (OUTLIER) cc_final: 0.8158 (mp) REVERT: B 325 MET cc_start: 0.8352 (ttm) cc_final: 0.8006 (mmt) outliers start: 30 outliers final: 19 residues processed: 97 average time/residue: 0.4713 time to fit residues: 48.6251 Evaluate side-chains 96 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 74 time to evaluate : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 63 LEU Chi-restraints excluded: chain R residue 87 THR Chi-restraints excluded: chain R residue 128 LEU Chi-restraints excluded: chain R residue 171 VAL Chi-restraints excluded: chain R residue 180 LEU Chi-restraints excluded: chain R residue 218 SER Chi-restraints excluded: chain R residue 248 THR Chi-restraints excluded: chain R residue 289 LEU Chi-restraints excluded: chain R residue 307 MET Chi-restraints excluded: chain R residue 318 LEU Chi-restraints excluded: chain R residue 324 CYS Chi-restraints excluded: chain R residue 325 VAL Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 284 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 12 optimal weight: 0.9990 chunk 5 optimal weight: 0.6980 chunk 77 optimal weight: 0.9990 chunk 60 optimal weight: 0.8980 chunk 17 optimal weight: 0.8980 chunk 73 optimal weight: 3.9990 chunk 13 optimal weight: 0.4980 chunk 25 optimal weight: 0.7980 chunk 82 optimal weight: 9.9990 chunk 31 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.196109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.156010 restraints weight = 7191.564| |-----------------------------------------------------------------------------| r_work (start): 0.3709 rms_B_bonded: 1.99 r_work: 0.3524 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3387 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7110 moved from start: 0.2024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 6976 Z= 0.141 Angle : 0.504 8.084 9451 Z= 0.270 Chirality : 0.042 0.148 1100 Planarity : 0.004 0.051 1186 Dihedral : 4.302 58.747 944 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.40 % Favored : 96.48 % Rotamer: Outliers : 3.39 % Allowed : 20.46 % Favored : 76.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.06 (0.28), residues: 852 helix: 1.96 (0.25), residues: 377 sheet: 0.57 (0.38), residues: 192 loop : -0.91 (0.35), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 256 TYR 0.009 0.001 TYR R 54 PHE 0.018 0.001 PHE R 320 TRP 0.015 0.001 TRP B 82 HIS 0.003 0.001 HIS A 82 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 6976) covalent geometry : angle 0.50363 ( 9451) hydrogen bonds : bond 0.04125 ( 373) hydrogen bonds : angle 4.31885 ( 1095) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 75 time to evaluate : 0.276 Fit side-chains revert: symmetry clash REVERT: R 78 MET cc_start: 0.6773 (ptm) cc_final: 0.6292 (ptp) REVERT: R 99 THR cc_start: 0.7123 (m) cc_final: 0.6485 (p) REVERT: R 121 LYS cc_start: 0.7090 (mtpt) cc_final: 0.6335 (mmmt) REVERT: R 147 LYS cc_start: 0.8121 (ttmm) cc_final: 0.7678 (ttpm) REVERT: R 210 LYS cc_start: 0.5100 (mmtt) cc_final: 0.4737 (mmtt) REVERT: R 220 LEU cc_start: 0.7658 (tt) cc_final: 0.7042 (tp) REVERT: A 25 GLU cc_start: 0.7420 (tt0) cc_final: 0.6999 (tt0) REVERT: A 32 ARG cc_start: 0.6764 (mmt-90) cc_final: 0.5915 (ptp90) REVERT: A 72 THR cc_start: 0.8810 (OUTLIER) cc_final: 0.8494 (p) REVERT: A 136 THR cc_start: 0.8680 (t) cc_final: 0.8469 (m) REVERT: A 153 VAL cc_start: 0.7666 (p) cc_final: 0.7344 (m) REVERT: B 78 LYS cc_start: 0.8592 (tppp) cc_final: 0.8297 (tppt) REVERT: B 200 VAL cc_start: 0.8960 (p) cc_final: 0.8647 (m) REVERT: B 217 MET cc_start: 0.6642 (pmm) cc_final: 0.6375 (pmm) REVERT: B 219 ARG cc_start: 0.7340 (OUTLIER) cc_final: 0.6264 (mpt90) REVERT: B 234 PHE cc_start: 0.9168 (OUTLIER) cc_final: 0.8196 (m-80) REVERT: B 262 MET cc_start: 0.7427 (tpt) cc_final: 0.7180 (tpp) REVERT: B 284 LEU cc_start: 0.8484 (OUTLIER) cc_final: 0.8127 (mp) REVERT: B 325 MET cc_start: 0.8340 (ttm) cc_final: 0.8124 (mmt) outliers start: 25 outliers final: 19 residues processed: 93 average time/residue: 0.4898 time to fit residues: 48.4765 Evaluate side-chains 98 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 75 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 63 LEU Chi-restraints excluded: chain R residue 87 THR Chi-restraints excluded: chain R residue 128 LEU Chi-restraints excluded: chain R residue 171 VAL Chi-restraints excluded: chain R residue 180 LEU Chi-restraints excluded: chain R residue 218 SER Chi-restraints excluded: chain R residue 248 THR Chi-restraints excluded: chain R residue 289 LEU Chi-restraints excluded: chain R residue 307 MET Chi-restraints excluded: chain R residue 318 LEU Chi-restraints excluded: chain R residue 324 CYS Chi-restraints excluded: chain R residue 325 VAL Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 284 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 34 optimal weight: 2.9990 chunk 18 optimal weight: 10.0000 chunk 74 optimal weight: 0.7980 chunk 41 optimal weight: 3.9990 chunk 7 optimal weight: 0.9990 chunk 55 optimal weight: 0.7980 chunk 52 optimal weight: 0.6980 chunk 71 optimal weight: 0.8980 chunk 3 optimal weight: 0.3980 chunk 39 optimal weight: 0.8980 chunk 70 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.195036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.155537 restraints weight = 7163.763| |-----------------------------------------------------------------------------| r_work (start): 0.3750 rms_B_bonded: 1.96 r_work: 0.3558 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3421 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7109 moved from start: 0.2115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 6976 Z= 0.137 Angle : 0.499 8.018 9451 Z= 0.268 Chirality : 0.042 0.148 1100 Planarity : 0.004 0.051 1186 Dihedral : 4.299 59.909 944 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.40 % Favored : 96.48 % Rotamer: Outliers : 3.39 % Allowed : 20.60 % Favored : 76.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.06 (0.28), residues: 852 helix: 2.00 (0.25), residues: 377 sheet: 0.50 (0.38), residues: 192 loop : -0.93 (0.35), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 256 TYR 0.009 0.001 TYR R 54 PHE 0.019 0.001 PHE R 320 TRP 0.015 0.001 TRP B 82 HIS 0.009 0.001 HIS A 82 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 6976) covalent geometry : angle 0.49898 ( 9451) hydrogen bonds : bond 0.04082 ( 373) hydrogen bonds : angle 4.31027 ( 1095) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 75 time to evaluate : 0.237 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 78 MET cc_start: 0.6737 (ptm) cc_final: 0.6195 (ptp) REVERT: R 99 THR cc_start: 0.7103 (m) cc_final: 0.6476 (p) REVERT: R 121 LYS cc_start: 0.7089 (mtpt) cc_final: 0.6348 (mmmt) REVERT: R 147 LYS cc_start: 0.8121 (ttmm) cc_final: 0.7679 (ttpm) REVERT: R 220 LEU cc_start: 0.7559 (tt) cc_final: 0.6963 (tp) REVERT: A 25 GLU cc_start: 0.7415 (tt0) cc_final: 0.7019 (tt0) REVERT: A 32 ARG cc_start: 0.6766 (mmt-90) cc_final: 0.5914 (ptp90) REVERT: A 72 THR cc_start: 0.8803 (OUTLIER) cc_final: 0.8513 (p) REVERT: A 136 THR cc_start: 0.8677 (t) cc_final: 0.8469 (m) REVERT: A 153 VAL cc_start: 0.7668 (p) cc_final: 0.7364 (m) REVERT: B 78 LYS cc_start: 0.8582 (tppp) cc_final: 0.8301 (tppt) REVERT: B 137 ARG cc_start: 0.6978 (tpp-160) cc_final: 0.6756 (tpp-160) REVERT: B 200 VAL cc_start: 0.8998 (p) cc_final: 0.8662 (m) REVERT: B 217 MET cc_start: 0.6727 (pmm) cc_final: 0.6343 (pmt) REVERT: B 219 ARG cc_start: 0.7413 (OUTLIER) cc_final: 0.6348 (mpt90) REVERT: B 234 PHE cc_start: 0.9174 (OUTLIER) cc_final: 0.8201 (m-80) REVERT: B 262 MET cc_start: 0.7434 (tpt) cc_final: 0.7188 (tpp) REVERT: B 284 LEU cc_start: 0.8484 (OUTLIER) cc_final: 0.8121 (mp) REVERT: B 325 MET cc_start: 0.8336 (ttm) cc_final: 0.7989 (mmt) outliers start: 25 outliers final: 17 residues processed: 92 average time/residue: 0.5187 time to fit residues: 50.5011 Evaluate side-chains 96 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 75 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 63 LEU Chi-restraints excluded: chain R residue 87 THR Chi-restraints excluded: chain R residue 128 LEU Chi-restraints excluded: chain R residue 171 VAL Chi-restraints excluded: chain R residue 218 SER Chi-restraints excluded: chain R residue 248 THR Chi-restraints excluded: chain R residue 289 LEU Chi-restraints excluded: chain R residue 318 LEU Chi-restraints excluded: chain R residue 324 CYS Chi-restraints excluded: chain R residue 325 VAL Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 284 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 41 optimal weight: 3.9990 chunk 61 optimal weight: 0.9990 chunk 10 optimal weight: 0.7980 chunk 69 optimal weight: 1.9990 chunk 7 optimal weight: 0.0980 chunk 66 optimal weight: 0.8980 chunk 65 optimal weight: 0.9990 chunk 21 optimal weight: 0.7980 chunk 33 optimal weight: 3.9990 chunk 84 optimal weight: 0.9980 chunk 82 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 HIS A 101 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.194827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.155104 restraints weight = 7164.189| |-----------------------------------------------------------------------------| r_work (start): 0.3731 rms_B_bonded: 1.97 r_work: 0.3541 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3406 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7151 moved from start: 0.2170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 6976 Z= 0.138 Angle : 0.503 8.007 9451 Z= 0.270 Chirality : 0.042 0.148 1100 Planarity : 0.004 0.051 1186 Dihedral : 4.264 56.505 944 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.52 % Favored : 96.36 % Rotamer: Outliers : 3.52 % Allowed : 20.33 % Favored : 76.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.03 (0.28), residues: 852 helix: 1.98 (0.25), residues: 377 sheet: 0.48 (0.38), residues: 192 loop : -0.96 (0.35), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 256 TYR 0.009 0.001 TYR R 54 PHE 0.019 0.001 PHE R 320 TRP 0.015 0.001 TRP B 82 HIS 0.013 0.001 HIS A 82 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 6976) covalent geometry : angle 0.50268 ( 9451) hydrogen bonds : bond 0.04103 ( 373) hydrogen bonds : angle 4.31931 ( 1095) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2575.58 seconds wall clock time: 44 minutes 45.42 seconds (2685.42 seconds total)