Starting phenix.real_space_refine on Sat Sep 12 02:38:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7xjg_33226/09_2026/7xjg_33226.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xjg_33226/09_2026/7xjg_33226.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.51 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7xjg_33226/09_2026/7xjg_33226.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7xjg_33226/09_2026/7xjg_33226.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7xjg_33226/09_2026/7xjg_33226.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xjg_33226/09_2026/7xjg_33226.map" model { file = "/net/cci-nas-00/data/ceres_data/7xjg_33226/09_2026/7xjg_33226.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xjg_33226/09_2026/7xjg_33226.cif" } resolution = 2.51 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= 0.020 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: 6 Type Number sf(0) Gaussians P 216 5.49 5 Mg 2 5.21 5 S 34 5.16 5 C 7594 2.51 5 N 2367 2.21 5 O 2954 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13167 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 314, 2518 Classifications: {'peptide': 314} Link IDs: {'PTRANS': 12, 'TRANS': 301} Chain: "C" Number of atoms: 1096 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1096 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 2, 'TRANS': 129} Chain breaks: 2 Chain: "D" Number of atoms: 933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 933 Classifications: {'DNA': 45} Link IDs: {'rna3p': 44} Chain breaks: 1 Chain: "E" Number of atoms: 1225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 1225 Classifications: {'RNAv2': 58} Modifications used: {'rna2p_pur': 5, 'rna2p_pyr': 10, 'rna3p_pur': 20, 'rna3p_pyr': 23} Link IDs: {'rna2p': 15, 'rna3p': 42} Chain breaks: 1 Chain: "F" Number of atoms: 176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 176 Classifications: {'RNAv2': 8} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 5, 'rna3p_pyr': 2} Link IDs: {'rna3p': 7} Chain: "B" Number of atoms: 2518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 314, 2518 Classifications: {'peptide': 314} Link IDs: {'PTRANS': 12, 'TRANS': 301} Chain: "G" Number of atoms: 808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 808 Classifications: {'DNA': 39} Link IDs: {'rna3p': 38} Chain breaks: 1 Chain: "H" Number of atoms: 1225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 1225 Classifications: {'RNAv2': 58} Modifications used: {'rna2p_pur': 5, 'rna2p_pyr': 10, 'rna3p_pur': 20, 'rna3p_pyr': 23} Link IDs: {'rna2p': 15, 'rna3p': 42} Chain breaks: 1 Chain: "I" Number of atoms: 176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 176 Classifications: {'RNAv2': 8} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 5, 'rna3p_pyr': 2} Link IDs: {'rna3p': 7} Chain: "J" Number of atoms: 2490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2490 Classifications: {'peptide': 306} Link IDs: {'PTRANS': 6, 'TRANS': 299} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.68, per 1000 atoms: 0.20 Number of scatterers: 13167 At special positions: 0 Unit cell: (96.9, 122.4, 161.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 34 16.00 P 216 15.00 Mg 2 11.99 O 2954 8.00 N 2367 7.00 C 7594 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: 1.13 Conformation dependent library (CDL) restraints added in 578.6 milliseconds 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2020 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 10 sheets defined 60.1% alpha, 9.8% beta 68 base pairs and 120 stacking pairs defined. Time for finding SS restraints: 1.76 Creating SS restraints... Processing helix chain 'A' and resid 3 through 16 removed outlier: 3.576A pdb=" N PHE A 10 " --> pdb=" O TYR A 6 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LEU A 15 " --> pdb=" O ARG A 11 " (cutoff:3.500A) Processing helix chain 'A' and resid 22 through 31 removed outlier: 3.748A pdb=" N MET A 26 " --> pdb=" O ASN A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 33 through 43 Processing helix chain 'A' and resid 44 through 46 No H-bonds generated for 'chain 'A' and resid 44 through 46' Processing helix chain 'A' and resid 69 through 83 removed outlier: 3.616A pdb=" N LEU A 75 " --> pdb=" O GLU A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 87 Processing helix chain 'A' and resid 102 through 107 Processing helix chain 'A' and resid 108 through 110 No H-bonds generated for 'chain 'A' and resid 108 through 110' Processing helix chain 'A' and resid 122 through 127 removed outlier: 3.616A pdb=" N LEU A 127 " --> pdb=" O PHE A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 140 removed outlier: 3.946A pdb=" N VAL A 132 " --> pdb=" O THR A 128 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N PHE A 133 " --> pdb=" O ALA A 129 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU A 139 " --> pdb=" O VAL A 135 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N GLY A 140 " --> pdb=" O PHE A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 154 removed outlier: 3.557A pdb=" N SER A 147 " --> pdb=" O ARG A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 174 Processing helix chain 'A' and resid 174 through 186 Processing helix chain 'A' and resid 205 through 220 removed outlier: 3.550A pdb=" N VAL A 209 " --> pdb=" O SER A 205 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N SER A 218 " --> pdb=" O ASP A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 224 removed outlier: 3.598A pdb=" N GLY A 224 " --> pdb=" O PRO A 221 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 221 through 224' Processing helix chain 'A' and resid 256 through 272 Processing helix chain 'A' and resid 277 through 292 Processing helix chain 'A' and resid 292 through 311 Processing helix chain 'C' and resid 6 through 18 removed outlier: 3.726A pdb=" N GLN C 11 " --> pdb=" O ASP C 7 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLN C 12 " --> pdb=" O GLU C 8 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 213 Proline residue: C 208 - end of helix Processing helix chain 'C' and resid 217 through 230 removed outlier: 3.509A pdb=" N LEU C 221 " --> pdb=" O ASN C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 236 through 250 Processing helix chain 'C' and resid 263 through 274 Processing helix chain 'C' and resid 275 through 292 removed outlier: 3.585A pdb=" N LEU C 279 " --> pdb=" O ASP C 275 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ARG C 292 " --> pdb=" O ASN C 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 15 removed outlier: 3.888A pdb=" N LEU B 15 " --> pdb=" O ARG B 11 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 31 removed outlier: 3.510A pdb=" N MET B 26 " --> pdb=" O ASN B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 33 through 44 Processing helix chain 'B' and resid 69 through 83 removed outlier: 3.749A pdb=" N LEU B 75 " --> pdb=" O GLU B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 87 Processing helix chain 'B' and resid 102 through 107 Processing helix chain 'B' and resid 108 through 110 No H-bonds generated for 'chain 'B' and resid 108 through 110' Processing helix chain 'B' and resid 123 through 127 Processing helix chain 'B' and resid 128 through 139 removed outlier: 3.848A pdb=" N VAL B 132 " --> pdb=" O THR B 128 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU B 139 " --> pdb=" O VAL B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 154 Processing helix chain 'B' and resid 165 through 174 Processing helix chain 'B' and resid 175 through 186 Processing helix chain 'B' and resid 205 through 220 removed outlier: 3.600A pdb=" N VAL B 209 " --> pdb=" O SER B 205 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ASP B 214 " --> pdb=" O VAL B 210 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N SER B 218 " --> pdb=" O ASP B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 224 Processing helix chain 'B' and resid 257 through 273 Processing helix chain 'B' and resid 277 through 292 Processing helix chain 'B' and resid 292 through 310 removed outlier: 3.778A pdb=" N LYS B 308 " --> pdb=" O SER B 304 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LYS B 309 " --> pdb=" O LYS B 305 " (cutoff:3.500A) Processing helix chain 'J' and resid 6 through 14 Processing helix chain 'J' and resid 45 through 55 removed outlier: 3.759A pdb=" N LEU J 49 " --> pdb=" O TRP J 45 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LYS J 55 " --> pdb=" O GLN J 51 " (cutoff:3.500A) Processing helix chain 'J' and resid 67 through 72 Processing helix chain 'J' and resid 79 through 91 Processing helix chain 'J' and resid 100 through 111 Processing helix chain 'J' and resid 125 through 129 Processing helix chain 'J' and resid 133 through 138 Processing helix chain 'J' and resid 138 through 147 Processing helix chain 'J' and resid 155 through 162 removed outlier: 3.768A pdb=" N LEU J 159 " --> pdb=" O SER J 155 " (cutoff:3.500A) Processing helix chain 'J' and resid 167 through 172 removed outlier: 3.742A pdb=" N ARG J 171 " --> pdb=" O ILE J 167 " (cutoff:3.500A) Processing helix chain 'J' and resid 173 through 190 Processing helix chain 'J' and resid 202 through 213 Proline residue: J 208 - end of helix Processing helix chain 'J' and resid 217 through 229 Processing helix chain 'J' and resid 233 through 235 No H-bonds generated for 'chain 'J' and resid 233 through 235' Processing helix chain 'J' and resid 236 through 250 removed outlier: 3.757A pdb=" N VAL J 240 " --> pdb=" O SER J 236 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ARG J 241 " --> pdb=" O LYS J 237 " (cutoff:3.500A) Processing helix chain 'J' and resid 263 through 274 Processing helix chain 'J' and resid 275 through 292 removed outlier: 3.814A pdb=" N LEU J 279 " --> pdb=" O ASP J 275 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ARG J 292 " --> pdb=" O ASN J 288 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 48 through 53 removed outlier: 3.604A pdb=" N ARG A 63 " --> pdb=" O VAL A 53 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 191 through 195 Processing sheet with id=AA3, first strand: chain 'A' and resid 242 through 243 Processing sheet with id=AA4, first strand: chain 'C' and resid 253 through 256 Processing sheet with id=AA5, first strand: chain 'B' and resid 48 through 52 Processing sheet with id=AA6, first strand: chain 'B' and resid 191 through 195 removed outlier: 4.570A pdb=" N VAL B 226 " --> pdb=" O GLU B 121 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 191 through 195 Processing sheet with id=AA8, first strand: chain 'B' and resid 242 through 243 Processing sheet with id=AA9, first strand: chain 'J' and resid 59 through 62 removed outlier: 6.601A pdb=" N ILE J 30 " --> pdb=" O ASP J 60 " (cutoff:3.500A) removed outlier: 8.035A pdb=" N PHE J 62 " --> pdb=" O ILE J 30 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N ILE J 32 " --> pdb=" O PHE J 62 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N ILE J 94 " --> pdb=" O ILE J 121 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N ILE J 123 " --> pdb=" O ILE J 94 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N LEU J 96 " --> pdb=" O ILE J 123 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N LEU J 152 " --> pdb=" O LEU J 120 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N CYS J 122 " --> pdb=" O LEU J 152 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'J' and resid 253 through 256 449 hydrogen bonds defined for protein. 1281 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 170 hydrogen bonds 308 hydrogen bond angles 0 basepair planarities 68 basepair parallelities 120 stacking parallelities Total time for adding SS restraints: 2.39 Time building geometry restraints manager: 1.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1964 1.33 - 1.45: 4683 1.45 - 1.57: 6743 1.57 - 1.69: 422 1.69 - 1.81: 50 Bond restraints: 13862 Sorted by residual: bond pdb=" CA SER B 218 " pdb=" CB SER B 218 " ideal model delta sigma weight residual 1.532 1.473 0.059 1.53e-02 4.27e+03 1.50e+01 bond pdb=" C3' DA D 8 " pdb=" C2' DA D 8 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.20e+01 bond pdb=" C3' DA G 8 " pdb=" C2' DA G 8 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.98e+00 bond pdb=" C3' DA G 9 " pdb=" C2' DA G 9 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.19e+00 bond pdb=" C3' DA D 11 " pdb=" C2' DA D 11 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.17e+00 ... (remaining 13857 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.06: 18702 2.06 - 4.13: 835 4.13 - 6.19: 120 6.19 - 8.26: 4 8.26 - 10.32: 4 Bond angle restraints: 19665 Sorted by residual: angle pdb=" C GLU B 59 " pdb=" CA GLU B 59 " pdb=" CB GLU B 59 " ideal model delta sigma weight residual 116.54 109.75 6.79 1.15e+00 7.56e-01 3.49e+01 angle pdb=" O4' DT D 82 " pdb=" C4' DT D 82 " pdb=" C3' DT D 82 " ideal model delta sigma weight residual 106.00 102.53 3.47 6.00e-01 2.78e+00 3.35e+01 angle pdb=" C ILE B 219 " pdb=" N ILE B 220 " pdb=" CA ILE B 220 " ideal model delta sigma weight residual 122.13 111.81 10.32 1.85e+00 2.92e-01 3.11e+01 angle pdb=" O4' DT G 82 " pdb=" C4' DT G 82 " pdb=" C3' DT G 82 " ideal model delta sigma weight residual 106.00 102.79 3.21 6.00e-01 2.78e+00 2.87e+01 angle pdb=" O4' DC D 83 " pdb=" C4' DC D 83 " pdb=" C3' DC D 83 " ideal model delta sigma weight residual 106.00 102.98 3.02 6.00e-01 2.78e+00 2.53e+01 ... (remaining 19660 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.95: 7110 35.95 - 71.89: 790 71.89 - 107.84: 19 107.84 - 143.78: 3 143.78 - 179.73: 4 Dihedral angle restraints: 7926 sinusoidal: 4799 harmonic: 3127 Sorted by residual: dihedral pdb=" C4' C E 39 " pdb=" C3' C E 39 " pdb=" C2' C E 39 " pdb=" C1' C E 39 " ideal model delta sinusoidal sigma weight residual 36.34 -38.42 74.76 1 3.10e+00 1.04e-01 7.36e+02 dihedral pdb=" C4' C H 39 " pdb=" C3' C H 39 " pdb=" C2' C H 39 " pdb=" C1' C H 39 " ideal model delta sinusoidal sigma weight residual 36.34 -37.71 74.06 1 3.10e+00 1.04e-01 7.25e+02 dihedral pdb=" C4' C H 40 " pdb=" C3' C H 40 " pdb=" C2' C H 40 " pdb=" C1' C H 40 " ideal model delta sinusoidal sigma weight residual 36.34 -37.09 73.44 1 3.10e+00 1.04e-01 7.14e+02 ... (remaining 7923 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.103: 2000 0.103 - 0.206: 145 0.206 - 0.309: 163 0.309 - 0.412: 6 0.412 - 0.515: 5 Chirality restraints: 2319 Sorted by residual: chirality pdb=" P G F 1 " pdb=" OP1 G F 1 " pdb=" OP2 G F 1 " pdb=" O5' G F 1 " both_signs ideal model delta sigma weight residual True 2.17 -2.69 -0.51 2.00e-01 2.50e+01 6.63e+00 chirality pdb=" P G I 1 " pdb=" OP1 G I 1 " pdb=" OP2 G I 1 " pdb=" O5' G I 1 " both_signs ideal model delta sigma weight residual True 2.17 -2.63 -0.46 2.00e-01 2.50e+01 5.26e+00 chirality pdb=" P G E 14 " pdb=" OP1 G E 14 " pdb=" OP2 G E 14 " pdb=" O5' G E 14 " both_signs ideal model delta sigma weight residual True 2.17 -2.60 -0.43 2.00e-01 2.50e+01 4.54e+00 ... (remaining 2316 not shown) Planarity restraints: 1697 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU J 223 " 0.012 2.00e-02 2.50e+03 2.46e-02 6.05e+00 pdb=" CD GLU J 223 " -0.043 2.00e-02 2.50e+03 pdb=" OE1 GLU J 223 " 0.015 2.00e-02 2.50e+03 pdb=" OE2 GLU J 223 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE J 302 " 0.040 5.00e-02 4.00e+02 6.02e-02 5.80e+00 pdb=" N PRO J 303 " -0.104 5.00e-02 4.00e+02 pdb=" CA PRO J 303 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO J 303 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 124 " 0.039 5.00e-02 4.00e+02 5.85e-02 5.48e+00 pdb=" N PRO A 125 " -0.101 5.00e-02 4.00e+02 pdb=" CA PRO A 125 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 125 " 0.033 5.00e-02 4.00e+02 ... (remaining 1694 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 60 2.55 - 3.14: 9033 3.14 - 3.72: 21354 3.72 - 4.31: 31367 4.31 - 4.90: 47292 Nonbonded interactions: 109106 Sorted by model distance: nonbonded pdb=" O LEU A 39 " pdb=" OG1 THR A 43 " model vdw 1.962 3.040 nonbonded pdb=" NZ LYS B 60 " pdb=" OE2 GLU B 121 " model vdw 2.010 3.120 nonbonded pdb=" N2 G E 20 " pdb=" O2 U E 41 " model vdw 2.209 3.120 nonbonded pdb=" OP1 DG D 14 " pdb=" NH2 ARG J 276 " model vdw 2.211 3.120 nonbonded pdb=" O TYR C 211 " pdb=" NH2 ARG B 31 " model vdw 2.234 3.120 ... (remaining 109101 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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = (chain 'D' and (resid 1 through 19 or resid 66 through 85)) selection = chain 'G' } ncs_group { reference = chain 'E' selection = chain 'H' } ncs_group { reference = chain 'F' selection = chain 'I' } 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: 2.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.270 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 14.700 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 13862 Z= 0.364 Angle : 0.886 10.322 19665 Z= 0.519 Chirality : 0.086 0.515 2319 Planarity : 0.005 0.060 1697 Dihedral : 23.157 179.725 5906 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 3.44 % Allowed : 26.38 % Favored : 70.18 % 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 are not related in a simple way. whole: -0.23 (0.25), residues: 1054 helix: 0.43 (0.23), residues: 547 sheet: 1.77 (0.53), residues: 87 loop : -1.32 (0.28), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 31 TYR 0.024 0.002 TYR B 184 PHE 0.015 0.002 PHE B 96 TRP 0.007 0.002 TRP B 78 HIS 0.007 0.001 HIS B 280 Details of bonding type rmsd/Z covalent geometry : bond 0.00535 / 0.36 (13862) covalent geometry : angle 0.88602 / 0.52 (19665) hydrogen bonds : bond 0.16129 / 10.74 ( 607) hydrogen bonds : angle 5.30362 / 3.72 ( 1589) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 172 time to evaluate : 0.460 Fit side-chains REVERT: C 282 LEU cc_start: 0.7679 (mt) cc_final: 0.7461 (mt) REVERT: C 292 ARG cc_start: 0.7893 (mtp-110) cc_final: 0.7652 (mtm180) outliers start: 33 outliers final: 30 residues processed: 204 average time/residue: 0.6136 time to fit residues: 136.6616 Evaluate side-chains 209 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 179 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 60 LYS Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain J residue 49 LEU Chi-restraints excluded: chain J residue 53 LEU Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain J residue 115 ASN Chi-restraints excluded: chain J residue 135 ILE Chi-restraints excluded: chain J residue 145 LYS Chi-restraints excluded: chain J residue 149 LYS Chi-restraints excluded: chain J residue 153 ARG Chi-restraints excluded: chain J residue 156 SER Chi-restraints excluded: chain J residue 169 VAL Chi-restraints excluded: chain J residue 179 LEU Chi-restraints excluded: chain J residue 188 LYS Chi-restraints excluded: chain J residue 192 VAL Chi-restraints excluded: chain J residue 194 LYS Chi-restraints excluded: chain J residue 195 ASP Chi-restraints excluded: chain J residue 207 LEU Chi-restraints excluded: chain J residue 216 VAL Chi-restraints excluded: chain J residue 220 THR Chi-restraints excluded: chain J residue 229 ILE Chi-restraints excluded: chain J residue 234 VAL Chi-restraints excluded: chain J residue 295 SER Chi-restraints excluded: chain J residue 306 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 108 optimal weight: 10.0000 chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 9.9990 chunk 113 optimal weight: 0.6980 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 0.1980 chunk 62 optimal weight: 0.0050 chunk 51 optimal weight: 2.9990 chunk 117 optimal weight: 0.4980 overall best weight: 0.4194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 157 ASN ** J 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 198 ASN J 298 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.189136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.153217 restraints weight = 16059.926| |-----------------------------------------------------------------------------| r_work (start): 0.3762 rms_B_bonded: 1.28 r_work: 0.3566 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3414 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.0892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13862 Z= 0.198 Angle : 1.277 23.674 19665 Z= 0.523 Chirality : 0.134 1.369 2319 Planarity : 0.005 0.050 1697 Dihedral : 21.889 178.309 3784 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 5.53 % Allowed : 23.77 % Favored : 70.70 % 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 are not related in a simple way. whole: 0.14 (0.25), residues: 1054 helix: 0.76 (0.22), residues: 557 sheet: 1.97 (0.54), residues: 87 loop : -1.24 (0.29), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 31 TYR 0.013 0.001 TYR B 179 PHE 0.011 0.001 PHE A 92 TRP 0.005 0.001 TRP B 78 HIS 0.005 0.001 HIS B 280 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.20 (13862) covalent geometry : angle 1.27685 / 0.52 (19665) hydrogen bonds : bond 0.05399 / 3.50 ( 607) hydrogen bonds : angle 4.01143 / 2.79 ( 1589) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 176 time to evaluate : 0.357 Fit side-chains revert: symmetry clash REVERT: C 292 ARG cc_start: 0.7948 (mtp-110) cc_final: 0.7574 (mtm180) REVERT: J 30 ILE cc_start: 0.7100 (OUTLIER) cc_final: 0.6875 (pp) outliers start: 53 outliers final: 30 residues processed: 211 average time/residue: 0.6279 time to fit residues: 144.2073 Evaluate side-chains 205 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 174 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 86 LYS Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain C residue 256 MET Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain J residue 6 THR Chi-restraints excluded: chain J residue 30 ILE Chi-restraints excluded: chain J residue 49 LEU Chi-restraints excluded: chain J residue 53 LEU Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain J residue 115 ASN Chi-restraints excluded: chain J residue 135 ILE Chi-restraints excluded: chain J residue 149 LYS Chi-restraints excluded: chain J residue 169 VAL Chi-restraints excluded: chain J residue 179 LEU Chi-restraints excluded: chain J residue 184 LYS Chi-restraints excluded: chain J residue 189 GLU Chi-restraints excluded: chain J residue 194 LYS Chi-restraints excluded: chain J residue 205 PHE Chi-restraints excluded: chain J residue 207 LEU Chi-restraints excluded: chain J residue 216 VAL Chi-restraints excluded: chain J residue 229 ILE Chi-restraints excluded: chain J residue 234 VAL Chi-restraints excluded: chain J residue 239 ILE Chi-restraints excluded: chain J residue 262 VAL Chi-restraints excluded: chain J residue 273 VAL Chi-restraints excluded: chain J residue 295 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 13 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 45 optimal weight: 7.9990 chunk 15 optimal weight: 0.8980 chunk 115 optimal weight: 0.5980 chunk 104 optimal weight: 7.9990 chunk 102 optimal weight: 5.9990 chunk 3 optimal weight: 0.8980 chunk 110 optimal weight: 20.0000 chunk 1 optimal weight: 0.4980 chunk 82 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 296 HIS B 76 GLN B 157 ASN ** J 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 198 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.188997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.153573 restraints weight = 16031.410| |-----------------------------------------------------------------------------| r_work (start): 0.3769 rms_B_bonded: 1.21 r_work: 0.3572 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3417 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.1220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 13862 Z= 0.189 Angle : 0.991 13.492 19665 Z= 0.431 Chirality : 0.092 1.119 2319 Planarity : 0.005 0.045 1697 Dihedral : 22.025 179.373 3752 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 5.21 % Allowed : 23.04 % Favored : 71.74 % 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 are not related in a simple way. whole: 0.23 (0.25), residues: 1054 helix: 0.88 (0.22), residues: 563 sheet: 1.75 (0.53), residues: 90 loop : -1.27 (0.29), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 49 TYR 0.017 0.001 TYR B 179 PHE 0.013 0.002 PHE B 96 TRP 0.005 0.002 TRP B 78 HIS 0.006 0.001 HIS B 280 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.19 (13862) covalent geometry : angle 0.99072 / 0.43 (19665) hydrogen bonds : bond 0.05673 / 3.64 ( 607) hydrogen bonds : angle 3.82185 / 2.66 ( 1589) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 173 time to evaluate : 0.478 Fit side-chains REVERT: C 292 ARG cc_start: 0.7889 (mtp-110) cc_final: 0.7514 (mtm180) REVERT: B 62 MET cc_start: 0.5299 (mpp) cc_final: 0.5076 (mpp) REVERT: B 139 LEU cc_start: 0.8048 (OUTLIER) cc_final: 0.7753 (mp) REVERT: J 30 ILE cc_start: 0.7146 (OUTLIER) cc_final: 0.6945 (pt) REVERT: J 298 ASN cc_start: 0.8643 (t0) cc_final: 0.8406 (t0) outliers start: 50 outliers final: 30 residues processed: 203 average time/residue: 0.6087 time to fit residues: 134.6234 Evaluate side-chains 203 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 171 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 LYS Chi-restraints excluded: chain A residue 151 LYS Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 242 LYS Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain C residue 256 MET Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain J residue 6 THR Chi-restraints excluded: chain J residue 30 ILE Chi-restraints excluded: chain J residue 49 LEU Chi-restraints excluded: chain J residue 53 LEU Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain J residue 115 ASN Chi-restraints excluded: chain J residue 119 LYS Chi-restraints excluded: chain J residue 149 LYS Chi-restraints excluded: chain J residue 169 VAL Chi-restraints excluded: chain J residue 179 LEU Chi-restraints excluded: chain J residue 184 LYS Chi-restraints excluded: chain J residue 194 LYS Chi-restraints excluded: chain J residue 205 PHE Chi-restraints excluded: chain J residue 207 LEU Chi-restraints excluded: chain J residue 216 VAL Chi-restraints excluded: chain J residue 229 ILE Chi-restraints excluded: chain J residue 239 ILE Chi-restraints excluded: chain J residue 261 GLN Chi-restraints excluded: chain J residue 262 VAL Chi-restraints excluded: chain J residue 273 VAL Chi-restraints excluded: chain J residue 277 LYS Chi-restraints excluded: chain J residue 295 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 71 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 95 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 79 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 60 optimal weight: 0.6980 chunk 80 optimal weight: 0.9980 chunk 100 optimal weight: 3.9990 chunk 34 optimal weight: 0.6980 chunk 91 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 117 ASN A 240 GLN B 104 ASN B 157 ASN ** J 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 198 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.180402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.145502 restraints weight = 16000.800| |-----------------------------------------------------------------------------| r_work (start): 0.3772 rms_B_bonded: 1.21 r_work: 0.3577 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3424 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.1367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13862 Z= 0.186 Angle : 0.940 13.225 19665 Z= 0.412 Chirality : 0.085 1.026 2319 Planarity : 0.004 0.043 1697 Dihedral : 21.897 179.822 3749 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 4.69 % Allowed : 23.88 % Favored : 71.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.25), residues: 1054 helix: 0.98 (0.22), residues: 565 sheet: 1.67 (0.54), residues: 90 loop : -1.32 (0.29), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 31 TYR 0.015 0.001 TYR A 179 PHE 0.013 0.002 PHE B 96 TRP 0.006 0.002 TRP B 78 HIS 0.006 0.001 HIS B 280 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.19 (13862) covalent geometry : angle 0.93980 / 0.41 (19665) hydrogen bonds : bond 0.05259 / 3.39 ( 607) hydrogen bonds : angle 3.74583 / 2.60 ( 1589) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 175 time to evaluate : 0.446 Fit side-chains REVERT: C 292 ARG cc_start: 0.7901 (mtp-110) cc_final: 0.7545 (mtm180) REVERT: B 62 MET cc_start: 0.5166 (mpp) cc_final: 0.4938 (mpp) REVERT: J 30 ILE cc_start: 0.7155 (OUTLIER) cc_final: 0.6931 (pt) REVERT: J 298 ASN cc_start: 0.8635 (t0) cc_final: 0.8405 (t0) outliers start: 45 outliers final: 32 residues processed: 203 average time/residue: 0.6125 time to fit residues: 135.5889 Evaluate side-chains 209 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 176 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 151 LYS Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain C residue 14 ILE Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain C residue 256 MET Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain J residue 6 THR Chi-restraints excluded: chain J residue 30 ILE Chi-restraints excluded: chain J residue 49 LEU Chi-restraints excluded: chain J residue 53 LEU Chi-restraints excluded: chain J residue 115 ASN Chi-restraints excluded: chain J residue 169 VAL Chi-restraints excluded: chain J residue 179 LEU Chi-restraints excluded: chain J residue 184 LYS Chi-restraints excluded: chain J residue 189 GLU Chi-restraints excluded: chain J residue 194 LYS Chi-restraints excluded: chain J residue 196 ILE Chi-restraints excluded: chain J residue 205 PHE Chi-restraints excluded: chain J residue 207 LEU Chi-restraints excluded: chain J residue 216 VAL Chi-restraints excluded: chain J residue 229 ILE Chi-restraints excluded: chain J residue 239 ILE Chi-restraints excluded: chain J residue 261 GLN Chi-restraints excluded: chain J residue 262 VAL Chi-restraints excluded: chain J residue 273 VAL Chi-restraints excluded: chain J residue 277 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 93 optimal weight: 0.9990 chunk 3 optimal weight: 0.9980 chunk 117 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 102 optimal weight: 6.9990 chunk 91 optimal weight: 2.9990 chunk 9 optimal weight: 0.0870 chunk 59 optimal weight: 2.9990 chunk 54 optimal weight: 0.0470 chunk 60 optimal weight: 0.6980 chunk 14 optimal weight: 0.7980 overall best weight: 0.5256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 157 ASN ** J 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 136 ASN J 198 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.182032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.148029 restraints weight = 16290.351| |-----------------------------------------------------------------------------| r_work (start): 0.3807 rms_B_bonded: 1.27 r_work: 0.3607 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3454 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.1643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13862 Z= 0.152 Angle : 0.867 12.515 19665 Z= 0.381 Chirality : 0.077 0.926 2319 Planarity : 0.004 0.040 1697 Dihedral : 21.832 178.513 3743 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 4.90 % Allowed : 23.46 % Favored : 71.64 % 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 are not related in a simple way. whole: 0.52 (0.26), residues: 1054 helix: 1.18 (0.22), residues: 570 sheet: 1.45 (0.55), residues: 94 loop : -1.19 (0.29), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 49 TYR 0.013 0.001 TYR B 179 PHE 0.010 0.001 PHE J 205 TRP 0.004 0.001 TRP B 78 HIS 0.005 0.001 HIS B 280 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.15 (13862) covalent geometry : angle 0.86725 / 0.38 (19665) hydrogen bonds : bond 0.04672 / 2.97 ( 607) hydrogen bonds : angle 3.57657 / 2.47 ( 1589) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 174 time to evaluate : 0.450 Fit side-chains REVERT: B 62 MET cc_start: 0.5077 (mpp) cc_final: 0.4851 (mpp) REVERT: B 139 LEU cc_start: 0.7981 (OUTLIER) cc_final: 0.7692 (mp) REVERT: J 30 ILE cc_start: 0.7160 (OUTLIER) cc_final: 0.6906 (pt) REVERT: J 298 ASN cc_start: 0.8625 (t0) cc_final: 0.8396 (t0) outliers start: 47 outliers final: 32 residues processed: 204 average time/residue: 0.6094 time to fit residues: 135.7186 Evaluate side-chains 208 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 174 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 151 LYS Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 242 LYS Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain C residue 14 ILE Chi-restraints excluded: chain C residue 256 MET Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain J residue 6 THR Chi-restraints excluded: chain J residue 30 ILE Chi-restraints excluded: chain J residue 39 VAL Chi-restraints excluded: chain J residue 49 LEU Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain J residue 115 ASN Chi-restraints excluded: chain J residue 119 LYS Chi-restraints excluded: chain J residue 145 LYS Chi-restraints excluded: chain J residue 179 LEU Chi-restraints excluded: chain J residue 184 LYS Chi-restraints excluded: chain J residue 192 VAL Chi-restraints excluded: chain J residue 194 LYS Chi-restraints excluded: chain J residue 196 ILE Chi-restraints excluded: chain J residue 205 PHE Chi-restraints excluded: chain J residue 207 LEU Chi-restraints excluded: chain J residue 216 VAL Chi-restraints excluded: chain J residue 239 ILE Chi-restraints excluded: chain J residue 261 GLN Chi-restraints excluded: chain J residue 262 VAL Chi-restraints excluded: chain J residue 273 VAL Chi-restraints excluded: chain J residue 277 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 47 optimal weight: 5.9990 chunk 6 optimal weight: 0.5980 chunk 13 optimal weight: 0.3980 chunk 105 optimal weight: 4.9990 chunk 1 optimal weight: 0.4980 chunk 16 optimal weight: 0.4980 chunk 73 optimal weight: 0.9990 chunk 45 optimal weight: 6.9990 chunk 56 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 overall best weight: 0.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 157 ASN ** J 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 136 ASN J 198 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.189716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.154471 restraints weight = 16048.999| |-----------------------------------------------------------------------------| r_work (start): 0.3792 rms_B_bonded: 1.30 r_work: 0.3594 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3436 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.1706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13862 Z= 0.158 Angle : 0.866 12.766 19665 Z= 0.381 Chirality : 0.076 0.946 2319 Planarity : 0.004 0.039 1697 Dihedral : 21.762 178.514 3738 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 4.17 % Allowed : 23.98 % Favored : 71.85 % 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 are not related in a simple way. whole: 0.59 (0.26), residues: 1054 helix: 1.24 (0.22), residues: 568 sheet: 1.86 (0.54), residues: 90 loop : -1.24 (0.29), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 49 TYR 0.015 0.001 TYR B 179 PHE 0.012 0.001 PHE B 96 TRP 0.005 0.001 TRP B 78 HIS 0.006 0.001 HIS B 280 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.16 (13862) covalent geometry : angle 0.86594 / 0.38 (19665) hydrogen bonds : bond 0.04760 / 3.06 ( 607) hydrogen bonds : angle 3.55875 / 2.46 ( 1589) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 178 time to evaluate : 0.400 Fit side-chains REVERT: B 62 MET cc_start: 0.5135 (mpp) cc_final: 0.4905 (mpp) REVERT: B 139 LEU cc_start: 0.8010 (OUTLIER) cc_final: 0.7720 (mp) REVERT: J 30 ILE cc_start: 0.7145 (OUTLIER) cc_final: 0.6744 (pp) REVERT: J 298 ASN cc_start: 0.8640 (t0) cc_final: 0.8406 (t0) outliers start: 40 outliers final: 27 residues processed: 202 average time/residue: 0.6234 time to fit residues: 137.3422 Evaluate side-chains 201 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 172 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 151 LYS Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 242 LYS Chi-restraints excluded: chain C residue 14 ILE Chi-restraints excluded: chain C residue 256 MET Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain J residue 6 THR Chi-restraints excluded: chain J residue 30 ILE Chi-restraints excluded: chain J residue 39 VAL Chi-restraints excluded: chain J residue 49 LEU Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain J residue 179 LEU Chi-restraints excluded: chain J residue 184 LYS Chi-restraints excluded: chain J residue 189 GLU Chi-restraints excluded: chain J residue 194 LYS Chi-restraints excluded: chain J residue 196 ILE Chi-restraints excluded: chain J residue 205 PHE Chi-restraints excluded: chain J residue 207 LEU Chi-restraints excluded: chain J residue 216 VAL Chi-restraints excluded: chain J residue 234 VAL Chi-restraints excluded: chain J residue 261 GLN Chi-restraints excluded: chain J residue 262 VAL Chi-restraints excluded: chain J residue 273 VAL Chi-restraints excluded: chain J residue 277 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 87 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 104 optimal weight: 3.9990 chunk 59 optimal weight: 0.8980 chunk 38 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 70 optimal weight: 0.9990 chunk 106 optimal weight: 2.9990 chunk 43 optimal weight: 5.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 261 GLN B 157 ASN B 240 GLN ** J 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 136 ASN J 198 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.186602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.150799 restraints weight = 16095.289| |-----------------------------------------------------------------------------| r_work (start): 0.3737 rms_B_bonded: 1.24 r_work: 0.3536 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3380 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.1600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 13862 Z= 0.272 Angle : 0.972 14.003 19665 Z= 0.435 Chirality : 0.086 1.025 2319 Planarity : 0.005 0.060 1697 Dihedral : 21.874 179.986 3736 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 4.59 % Allowed : 24.40 % Favored : 71.01 % 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 are not related in a simple way. whole: 0.18 (0.25), residues: 1054 helix: 0.87 (0.22), residues: 565 sheet: 1.76 (0.53), residues: 90 loop : -1.37 (0.29), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 213 TYR 0.023 0.002 TYR A 179 PHE 0.021 0.003 PHE B 10 TRP 0.008 0.003 TRP B 78 HIS 0.008 0.002 HIS B 280 Details of bonding type rmsd/Z covalent geometry : bond 0.00616 / 0.27 (13862) covalent geometry : angle 0.97234 / 0.44 (19665) hydrogen bonds : bond 0.06271 / 4.06 ( 607) hydrogen bonds : angle 3.81632 / 2.66 ( 1589) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 175 time to evaluate : 0.384 Fit side-chains REVERT: C 279 LEU cc_start: 0.7167 (mt) cc_final: 0.6949 (mt) REVERT: C 292 ARG cc_start: 0.7938 (mtp-110) cc_final: 0.7536 (mtm180) REVERT: B 62 MET cc_start: 0.5170 (mpp) cc_final: 0.4926 (mpp) REVERT: B 139 LEU cc_start: 0.8030 (OUTLIER) cc_final: 0.7739 (mp) REVERT: J 30 ILE cc_start: 0.7145 (OUTLIER) cc_final: 0.6869 (pt) REVERT: J 298 ASN cc_start: 0.8653 (t0) cc_final: 0.8422 (t0) outliers start: 44 outliers final: 37 residues processed: 203 average time/residue: 0.6151 time to fit residues: 136.1096 Evaluate side-chains 214 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 175 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 151 LYS Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain C residue 14 ILE Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain C residue 256 MET Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain J residue 6 THR Chi-restraints excluded: chain J residue 30 ILE Chi-restraints excluded: chain J residue 39 VAL Chi-restraints excluded: chain J residue 49 LEU Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain J residue 115 ASN Chi-restraints excluded: chain J residue 119 LYS Chi-restraints excluded: chain J residue 179 LEU Chi-restraints excluded: chain J residue 184 LYS Chi-restraints excluded: chain J residue 189 GLU Chi-restraints excluded: chain J residue 194 LYS Chi-restraints excluded: chain J residue 196 ILE Chi-restraints excluded: chain J residue 205 PHE Chi-restraints excluded: chain J residue 207 LEU Chi-restraints excluded: chain J residue 216 VAL Chi-restraints excluded: chain J residue 220 THR Chi-restraints excluded: chain J residue 229 ILE Chi-restraints excluded: chain J residue 239 ILE Chi-restraints excluded: chain J residue 261 GLN Chi-restraints excluded: chain J residue 262 VAL Chi-restraints excluded: chain J residue 273 VAL Chi-restraints excluded: chain J residue 277 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 114 optimal weight: 0.9980 chunk 53 optimal weight: 0.9980 chunk 50 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 83 optimal weight: 0.9980 chunk 100 optimal weight: 7.9990 chunk 46 optimal weight: 30.0000 chunk 86 optimal weight: 9.9990 chunk 78 optimal weight: 0.5980 chunk 116 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 228 ASN C 261 GLN B 157 ASN ** J 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 136 ASN J 198 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.188159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.152680 restraints weight = 16023.097| |-----------------------------------------------------------------------------| r_work (start): 0.3764 rms_B_bonded: 1.22 r_work: 0.3566 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3412 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.1638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 13862 Z= 0.189 Angle : 0.902 13.110 19665 Z= 0.400 Chirality : 0.080 0.986 2319 Planarity : 0.004 0.042 1697 Dihedral : 21.879 179.317 3736 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 4.07 % Allowed : 25.23 % Favored : 70.70 % 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 are not related in a simple way. whole: 0.30 (0.25), residues: 1054 helix: 1.00 (0.22), residues: 567 sheet: 1.78 (0.53), residues: 90 loop : -1.37 (0.29), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 49 TYR 0.017 0.001 TYR B 179 PHE 0.014 0.002 PHE B 96 TRP 0.006 0.002 TRP B 78 HIS 0.007 0.001 HIS B 280 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.19 (13862) covalent geometry : angle 0.90180 / 0.40 (19665) hydrogen bonds : bond 0.05286 / 3.42 ( 607) hydrogen bonds : angle 3.69339 / 2.57 ( 1589) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 176 time to evaluate : 0.414 Fit side-chains REVERT: C 279 LEU cc_start: 0.7109 (mt) cc_final: 0.6890 (mt) REVERT: C 292 ARG cc_start: 0.7915 (mtp-110) cc_final: 0.7542 (mtm180) REVERT: B 62 MET cc_start: 0.5130 (mpp) cc_final: 0.4886 (mpp) REVERT: B 139 LEU cc_start: 0.7996 (OUTLIER) cc_final: 0.7696 (mp) REVERT: J 30 ILE cc_start: 0.7120 (OUTLIER) cc_final: 0.6838 (pt) REVERT: J 298 ASN cc_start: 0.8634 (t0) cc_final: 0.8390 (t0) outliers start: 39 outliers final: 33 residues processed: 205 average time/residue: 0.6129 time to fit residues: 136.9671 Evaluate side-chains 213 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 178 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 151 LYS Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain C residue 14 ILE Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 256 MET Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain J residue 6 THR Chi-restraints excluded: chain J residue 30 ILE Chi-restraints excluded: chain J residue 39 VAL Chi-restraints excluded: chain J residue 49 LEU Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain J residue 115 ASN Chi-restraints excluded: chain J residue 169 VAL Chi-restraints excluded: chain J residue 179 LEU Chi-restraints excluded: chain J residue 184 LYS Chi-restraints excluded: chain J residue 189 GLU Chi-restraints excluded: chain J residue 192 VAL Chi-restraints excluded: chain J residue 194 LYS Chi-restraints excluded: chain J residue 196 ILE Chi-restraints excluded: chain J residue 205 PHE Chi-restraints excluded: chain J residue 207 LEU Chi-restraints excluded: chain J residue 216 VAL Chi-restraints excluded: chain J residue 220 THR Chi-restraints excluded: chain J residue 229 ILE Chi-restraints excluded: chain J residue 234 VAL Chi-restraints excluded: chain J residue 239 ILE Chi-restraints excluded: chain J residue 261 GLN Chi-restraints excluded: chain J residue 262 VAL Chi-restraints excluded: chain J residue 273 VAL Chi-restraints excluded: chain J residue 277 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 36 optimal weight: 4.9990 chunk 94 optimal weight: 0.9980 chunk 7 optimal weight: 0.9990 chunk 6 optimal weight: 0.8980 chunk 88 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 115 optimal weight: 0.6980 chunk 60 optimal weight: 0.9980 chunk 16 optimal weight: 0.7980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 157 ASN ** J 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 136 ASN J 198 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.189001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.153479 restraints weight = 16131.630| |-----------------------------------------------------------------------------| r_work (start): 0.3768 rms_B_bonded: 1.24 r_work: 0.3572 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3417 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.1720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13862 Z= 0.185 Angle : 0.886 13.065 19665 Z= 0.393 Chirality : 0.078 0.976 2319 Planarity : 0.004 0.041 1697 Dihedral : 21.863 179.279 3736 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 4.17 % Allowed : 25.34 % Favored : 70.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.25), residues: 1054 helix: 1.05 (0.22), residues: 568 sheet: 1.82 (0.53), residues: 90 loop : -1.41 (0.29), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 49 TYR 0.017 0.001 TYR B 179 PHE 0.014 0.002 PHE B 96 TRP 0.006 0.002 TRP B 78 HIS 0.005 0.001 HIS B 280 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.19 (13862) covalent geometry : angle 0.88589 / 0.39 (19665) hydrogen bonds : bond 0.05197 / 3.36 ( 607) hydrogen bonds : angle 3.63236 / 2.52 ( 1589) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 175 time to evaluate : 0.426 Fit side-chains REVERT: C 279 LEU cc_start: 0.7098 (mt) cc_final: 0.6869 (mt) REVERT: C 292 ARG cc_start: 0.7917 (mtp-110) cc_final: 0.7565 (mtm180) REVERT: B 62 MET cc_start: 0.5109 (mpp) cc_final: 0.4867 (mpp) REVERT: B 139 LEU cc_start: 0.8001 (OUTLIER) cc_final: 0.7699 (mp) REVERT: J 30 ILE cc_start: 0.7104 (OUTLIER) cc_final: 0.6797 (pt) REVERT: J 298 ASN cc_start: 0.8626 (t0) cc_final: 0.8382 (t0) outliers start: 40 outliers final: 35 residues processed: 205 average time/residue: 0.6188 time to fit residues: 138.1672 Evaluate side-chains 214 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 177 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 151 LYS Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain C residue 14 ILE Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 256 MET Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain J residue 6 THR Chi-restraints excluded: chain J residue 30 ILE Chi-restraints excluded: chain J residue 39 VAL Chi-restraints excluded: chain J residue 49 LEU Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain J residue 115 ASN Chi-restraints excluded: chain J residue 169 VAL Chi-restraints excluded: chain J residue 179 LEU Chi-restraints excluded: chain J residue 184 LYS Chi-restraints excluded: chain J residue 189 GLU Chi-restraints excluded: chain J residue 192 VAL Chi-restraints excluded: chain J residue 194 LYS Chi-restraints excluded: chain J residue 196 ILE Chi-restraints excluded: chain J residue 205 PHE Chi-restraints excluded: chain J residue 207 LEU Chi-restraints excluded: chain J residue 216 VAL Chi-restraints excluded: chain J residue 220 THR Chi-restraints excluded: chain J residue 229 ILE Chi-restraints excluded: chain J residue 234 VAL Chi-restraints excluded: chain J residue 239 ILE Chi-restraints excluded: chain J residue 261 GLN Chi-restraints excluded: chain J residue 262 VAL Chi-restraints excluded: chain J residue 273 VAL Chi-restraints excluded: chain J residue 277 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 85 optimal weight: 6.9990 chunk 21 optimal weight: 0.8980 chunk 82 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 84 optimal weight: 4.9990 chunk 12 optimal weight: 0.9990 chunk 105 optimal weight: 30.0000 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 157 ASN ** J 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 136 ASN J 198 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.187848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.152708 restraints weight = 16078.994| |-----------------------------------------------------------------------------| r_work (start): 0.3755 rms_B_bonded: 1.22 r_work: 0.3556 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3411 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.1714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 13862 Z= 0.220 Angle : 0.918 13.534 19665 Z= 0.409 Chirality : 0.081 1.003 2319 Planarity : 0.005 0.045 1697 Dihedral : 21.894 179.908 3736 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 4.48 % Allowed : 25.23 % Favored : 70.28 % 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 are not related in a simple way. whole: 0.24 (0.25), residues: 1054 helix: 0.99 (0.22), residues: 559 sheet: 1.81 (0.53), residues: 90 loop : -1.42 (0.28), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 49 TYR 0.019 0.002 TYR A 179 PHE 0.018 0.002 PHE B 10 TRP 0.007 0.002 TRP B 78 HIS 0.007 0.001 HIS B 280 Details of bonding type rmsd/Z covalent geometry : bond 0.00489 / 0.22 (13862) covalent geometry : angle 0.91815 / 0.41 (19665) hydrogen bonds : bond 0.05666 / 3.68 ( 607) hydrogen bonds : angle 3.71388 / 2.58 ( 1589) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 176 time to evaluate : 0.394 Fit side-chains REVERT: C 279 LEU cc_start: 0.7167 (mt) cc_final: 0.6951 (mt) REVERT: C 292 ARG cc_start: 0.7950 (mtp-110) cc_final: 0.7599 (mtm180) REVERT: B 62 MET cc_start: 0.5055 (mpp) cc_final: 0.4832 (mpp) REVERT: B 139 LEU cc_start: 0.8016 (OUTLIER) cc_final: 0.7724 (mp) REVERT: J 30 ILE cc_start: 0.7070 (OUTLIER) cc_final: 0.6771 (pt) REVERT: J 298 ASN cc_start: 0.8633 (t0) cc_final: 0.8393 (t0) outliers start: 43 outliers final: 36 residues processed: 208 average time/residue: 0.6112 time to fit residues: 138.8691 Evaluate side-chains 215 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 177 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 151 LYS Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain C residue 14 ILE Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 256 MET Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain J residue 6 THR Chi-restraints excluded: chain J residue 30 ILE Chi-restraints excluded: chain J residue 39 VAL Chi-restraints excluded: chain J residue 49 LEU Chi-restraints excluded: chain J residue 115 ASN Chi-restraints excluded: chain J residue 169 VAL Chi-restraints excluded: chain J residue 179 LEU Chi-restraints excluded: chain J residue 184 LYS Chi-restraints excluded: chain J residue 189 GLU Chi-restraints excluded: chain J residue 192 VAL Chi-restraints excluded: chain J residue 194 LYS Chi-restraints excluded: chain J residue 196 ILE Chi-restraints excluded: chain J residue 205 PHE Chi-restraints excluded: chain J residue 207 LEU Chi-restraints excluded: chain J residue 216 VAL Chi-restraints excluded: chain J residue 220 THR Chi-restraints excluded: chain J residue 229 ILE Chi-restraints excluded: chain J residue 234 VAL Chi-restraints excluded: chain J residue 239 ILE Chi-restraints excluded: chain J residue 261 GLN Chi-restraints excluded: chain J residue 262 VAL Chi-restraints excluded: chain J residue 273 VAL Chi-restraints excluded: chain J residue 277 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 97 optimal weight: 0.9980 chunk 111 optimal weight: 0.9980 chunk 36 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 72 optimal weight: 0.6980 chunk 44 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 chunk 121 optimal weight: 1.9990 chunk 100 optimal weight: 7.9990 chunk 12 optimal weight: 0.7980 chunk 101 optimal weight: 0.0570 overall best weight: 0.7098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 228 ASN B 22 ASN B 157 ASN ** J 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 136 ASN J 198 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.188801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.154014 restraints weight = 16031.186| |-----------------------------------------------------------------------------| r_work (start): 0.3780 rms_B_bonded: 1.19 r_work: 0.3584 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3430 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.1783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13862 Z= 0.168 Angle : 0.872 12.916 19665 Z= 0.386 Chirality : 0.077 0.966 2319 Planarity : 0.004 0.042 1697 Dihedral : 21.877 179.909 3736 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 4.07 % Allowed : 26.07 % Favored : 69.86 % 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 are not related in a simple way. whole: 0.41 (0.26), residues: 1054 helix: 1.12 (0.22), residues: 567 sheet: 1.93 (0.53), residues: 90 loop : -1.39 (0.28), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 49 TYR 0.015 0.001 TYR B 179 PHE 0.012 0.001 PHE B 96 TRP 0.006 0.002 TRP B 78 HIS 0.006 0.001 HIS B 280 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.17 (13862) covalent geometry : angle 0.87169 / 0.39 (19665) hydrogen bonds : bond 0.04976 / 3.22 ( 607) hydrogen bonds : angle 3.60381 / 2.50 ( 1589) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6497.93 seconds wall clock time: 111 minutes 11.42 seconds (6671.42 seconds total)