Starting phenix.real_space_refine on Fri Oct 23 19:16:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9hbs_52028/10_2026/9hbs_52028.cif Found real_map, /net/cci-nas-00/data/ceres_data/9hbs_52028/10_2026/9hbs_52028.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.68 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9hbs_52028/10_2026/9hbs_52028.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9hbs_52028/10_2026/9hbs_52028.map" model { file = "/net/cci-nas-00/data/ceres_data/9hbs_52028/10_2026/9hbs_52028.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9hbs_52028/10_2026/9hbs_52028.cif" } resolution = 3.68 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= -0.000 sd= 0.008 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: 5 Type Number sf(0) Gaussians P 74 5.49 5 S 68 5.16 5 C 6737 2.51 5 N 1962 2.21 5 O 2203 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11044 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2387 Classifications: {'peptide': 311} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 300} Chain breaks: 1 Chain: "B" Number of atoms: 2422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2422 Classifications: {'peptide': 316} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 305} Chain: "C" Number of atoms: 2391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 2391 Classifications: {'peptide': 312} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 301} Chain breaks: 1 Chain: "D" Number of atoms: 2398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2398 Classifications: {'peptide': 313} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 302} Chain breaks: 1 Chain: "G" Number of atoms: 744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 744 Classifications: {'RNA': 38} Modifications used: {'rna2p': 5, 'rna3p': 33} Link IDs: {'rna2p': 5, 'rna3p': 32} Chain breaks: 1 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 114 Unresolved non-hydrogen dihedrals: 38 Chain: "H" Number of atoms: 702 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 702 Classifications: {'RNA': 36} Modifications used: {'rna2p': 4, 'rna3p': 32} Link IDs: {'rna2p': 3, 'rna3p': 32} Chain breaks: 2 Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 108 Unresolved non-hydrogen dihedrals: 36 Time building chain proxies: 2.71, per 1000 atoms: 0.25 Number of scatterers: 11044 At special positions: 0 Unit cell: (129.876, 113.436, 86.31, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 68 16.00 P 74 15.00 O 2203 8.00 N 1962 7.00 C 6737 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: 0.98 Conformation dependent library (CDL) restraints added in 344.4 milliseconds 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2290 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 11 sheets defined 51.3% alpha, 4.7% beta 0 base pairs and 35 stacking pairs defined. Time for finding SS restraints: 1.13 Creating SS restraints... Processing helix chain 'A' and resid 36 through 51 removed outlier: 3.580A pdb=" N PHE A 42 " --> pdb=" O ASN A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 54 No H-bonds generated for 'chain 'A' and resid 52 through 54' Processing helix chain 'A' and resid 58 through 74 Processing helix chain 'A' and resid 88 through 101 Processing helix chain 'A' and resid 119 through 128 Processing helix chain 'A' and resid 134 through 142 Processing helix chain 'A' and resid 143 through 172 Processing helix chain 'A' and resid 182 through 187 Processing helix chain 'A' and resid 193 through 200 removed outlier: 3.604A pdb=" N TYR A 197 " --> pdb=" O SER A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 214 Processing helix chain 'A' and resid 232 through 237 Processing helix chain 'A' and resid 249 through 258 Processing helix chain 'A' and resid 263 through 268 Processing helix chain 'A' and resid 340 through 349 Processing helix chain 'B' and resid 36 through 51 Processing helix chain 'B' and resid 58 through 74 Processing helix chain 'B' and resid 88 through 101 Processing helix chain 'B' and resid 119 through 128 removed outlier: 3.520A pdb=" N VAL B 128 " --> pdb=" O CYS B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 142 Processing helix chain 'B' and resid 143 through 173 Processing helix chain 'B' and resid 182 through 187 Processing helix chain 'B' and resid 193 through 200 Processing helix chain 'B' and resid 206 through 215 Processing helix chain 'B' and resid 232 through 237 Processing helix chain 'B' and resid 249 through 258 Processing helix chain 'B' and resid 263 through 268 removed outlier: 3.620A pdb=" N LEU B 266 " --> pdb=" O ASP B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 312 Processing helix chain 'B' and resid 315 through 320 Processing helix chain 'B' and resid 340 through 349 Processing helix chain 'C' and resid 36 through 51 removed outlier: 3.972A pdb=" N PHE C 42 " --> pdb=" O ASN C 38 " (cutoff:3.500A) Processing helix chain 'C' and resid 52 through 54 No H-bonds generated for 'chain 'C' and resid 52 through 54' Processing helix chain 'C' and resid 58 through 74 Processing helix chain 'C' and resid 88 through 101 Processing helix chain 'C' and resid 118 through 127 removed outlier: 4.458A pdb=" N GLU C 122 " --> pdb=" O SER C 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 134 through 142 Processing helix chain 'C' and resid 143 through 173 Processing helix chain 'C' and resid 182 through 187 Processing helix chain 'C' and resid 193 through 200 Processing helix chain 'C' and resid 205 through 216 removed outlier: 3.558A pdb=" N ALA C 209 " --> pdb=" O GLY C 205 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N GLU C 216 " --> pdb=" O ALA C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 237 Processing helix chain 'C' and resid 249 through 258 Processing helix chain 'C' and resid 263 through 268 Processing helix chain 'C' and resid 317 through 320 Processing helix chain 'C' and resid 340 through 350 Processing helix chain 'D' and resid 36 through 51 Processing helix chain 'D' and resid 58 through 74 Processing helix chain 'D' and resid 88 through 101 Processing helix chain 'D' and resid 119 through 128 removed outlier: 3.557A pdb=" N VAL D 128 " --> pdb=" O CYS D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 134 through 142 Processing helix chain 'D' and resid 143 through 173 Processing helix chain 'D' and resid 182 through 187 Processing helix chain 'D' and resid 193 through 200 Processing helix chain 'D' and resid 206 through 215 Processing helix chain 'D' and resid 232 through 237 Processing helix chain 'D' and resid 249 through 258 Processing helix chain 'D' and resid 263 through 268 removed outlier: 3.690A pdb=" N LEU D 266 " --> pdb=" O ASP D 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 315 through 320 Processing helix chain 'D' and resid 340 through 350 Processing sheet with id=AA1, first strand: chain 'A' and resid 247 through 248 Processing sheet with id=AA2, first strand: chain 'A' and resid 285 through 286 Processing sheet with id=AA3, first strand: chain 'B' and resid 109 through 110 Processing sheet with id=AA4, first strand: chain 'B' and resid 247 through 248 Processing sheet with id=AA5, first strand: chain 'B' and resid 284 through 286 Processing sheet with id=AA6, first strand: chain 'C' and resid 109 through 110 Processing sheet with id=AA7, first strand: chain 'C' and resid 270 through 272 Processing sheet with id=AA8, first strand: chain 'C' and resid 284 through 286 Processing sheet with id=AA9, first strand: chain 'D' and resid 109 through 110 Processing sheet with id=AB1, first strand: chain 'D' and resid 270 through 271 Processing sheet with id=AB2, first strand: chain 'D' and resid 284 through 286 449 hydrogen bonds defined for protein. 1287 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 35 stacking parallelities Total time for adding SS restraints: 1.56 Time building geometry restraints manager: 1.29 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: 3369 1.34 - 1.46: 2817 1.46 - 1.58: 4969 1.58 - 1.69: 143 1.69 - 1.81: 92 Bond restraints: 11390 Sorted by residual: bond pdb=" N3 Y5P G 16 " pdb=" C4 Y5P G 16 " ideal model delta sigma weight residual 1.458 1.332 0.126 2.00e-02 2.50e+03 3.95e+01 bond pdb=" N3 Y5P H 40 " pdb=" C4 Y5P H 40 " ideal model delta sigma weight residual 1.458 1.332 0.126 2.00e-02 2.50e+03 3.94e+01 bond pdb=" N3 Y5P G 40 " pdb=" C4 Y5P G 40 " ideal model delta sigma weight residual 1.458 1.333 0.125 2.00e-02 2.50e+03 3.93e+01 bond pdb=" N3 Y5P H 16 " pdb=" C4 Y5P H 16 " ideal model delta sigma weight residual 1.458 1.333 0.125 2.00e-02 2.50e+03 3.91e+01 bond pdb=" N3 Y5P H 20 " pdb=" C4 Y5P H 20 " ideal model delta sigma weight residual 1.458 1.333 0.125 2.00e-02 2.50e+03 3.91e+01 ... (remaining 11385 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.39: 15046 2.39 - 4.79: 378 4.79 - 7.18: 107 7.18 - 9.58: 55 9.58 - 11.97: 27 Bond angle restraints: 15613 Sorted by residual: angle pdb=" N1 Y5P G 8 " pdb=" C2 Y5P G 8 " pdb=" N3 Y5P G 8 " ideal model delta sigma weight residual 126.68 114.71 11.97 3.00e+00 1.11e-01 1.59e+01 angle pdb=" N1 Y5P G 6 " pdb=" C2 Y5P G 6 " pdb=" N3 Y5P G 6 " ideal model delta sigma weight residual 126.68 114.76 11.92 3.00e+00 1.11e-01 1.58e+01 angle pdb=" N1 Y5P H 39 " pdb=" C2 Y5P H 39 " pdb=" N3 Y5P H 39 " ideal model delta sigma weight residual 126.68 114.76 11.92 3.00e+00 1.11e-01 1.58e+01 angle pdb=" N1 Y5P H 6 " pdb=" C2 Y5P H 6 " pdb=" N3 Y5P H 6 " ideal model delta sigma weight residual 126.68 114.76 11.92 3.00e+00 1.11e-01 1.58e+01 angle pdb=" N1 Y5P G 39 " pdb=" C2 Y5P G 39 " pdb=" N3 Y5P G 39 " ideal model delta sigma weight residual 126.68 114.82 11.86 3.00e+00 1.11e-01 1.56e+01 ... (remaining 15608 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.41: 7598 35.41 - 70.82: 389 70.82 - 106.22: 177 106.22 - 141.63: 1 141.63 - 177.04: 3 Dihedral angle restraints: 8168 sinusoidal: 4605 harmonic: 3563 Sorted by residual: dihedral pdb=" P Y5P G 37 " pdb=" O5' Y5P G 37 " pdb=" C5' Y5P G 37 " pdb=" C4' Y5P G 37 " ideal model delta sinusoidal sigma weight residual -111.10 65.94 -177.04 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" P Y5P H 37 " pdb=" O5' Y5P H 37 " pdb=" C5' Y5P H 37 " pdb=" C4' Y5P H 37 " ideal model delta sinusoidal sigma weight residual -111.10 64.13 -175.23 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" P Y5P H 6 " pdb=" O5' Y5P H 6 " pdb=" C5' Y5P H 6 " pdb=" C4' Y5P H 6 " ideal model delta sinusoidal sigma weight residual 248.90 77.12 171.78 1 3.00e+01 1.11e-03 2.12e+01 ... (remaining 8165 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 1275 0.031 - 0.061: 358 0.061 - 0.092: 57 0.092 - 0.122: 54 0.122 - 0.153: 15 Chirality restraints: 1759 Sorted by residual: chirality pdb=" C1' P5P G 34 " pdb=" O4' P5P G 34 " pdb=" C2' P5P G 34 " pdb=" N9 P5P G 34 " both_signs ideal model delta sigma weight residual False 2.46 2.31 0.15 2.00e-01 2.50e+01 5.83e-01 chirality pdb=" CA ILE A 230 " pdb=" N ILE A 230 " pdb=" C ILE A 230 " pdb=" CB ILE A 230 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.02e-01 chirality pdb=" CA ILE D 230 " pdb=" N ILE D 230 " pdb=" C ILE D 230 " pdb=" CB ILE D 230 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.97e-01 ... (remaining 1756 not shown) Planarity restraints: 1762 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' P5P G 35 " 0.021 2.00e-02 2.50e+03 1.12e-02 3.13e+00 pdb=" N9 P5P G 35 " -0.027 2.00e-02 2.50e+03 pdb=" C8 P5P G 35 " 0.000 2.00e-02 2.50e+03 pdb=" N7 P5P G 35 " 0.004 2.00e-02 2.50e+03 pdb=" C5 P5P G 35 " 0.003 2.00e-02 2.50e+03 pdb=" C6 P5P G 35 " 0.002 2.00e-02 2.50e+03 pdb=" N1 P5P G 35 " 0.005 2.00e-02 2.50e+03 pdb=" C2 P5P G 35 " -0.000 2.00e-02 2.50e+03 pdb=" N3 P5P G 35 " -0.004 2.00e-02 2.50e+03 pdb=" C4 P5P G 35 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' P5P G 34 " 0.019 2.00e-02 2.50e+03 9.94e-03 2.47e+00 pdb=" N9 P5P G 34 " -0.024 2.00e-02 2.50e+03 pdb=" C8 P5P G 34 " -0.002 2.00e-02 2.50e+03 pdb=" N7 P5P G 34 " 0.001 2.00e-02 2.50e+03 pdb=" C5 P5P G 34 " 0.004 2.00e-02 2.50e+03 pdb=" C6 P5P G 34 " 0.007 2.00e-02 2.50e+03 pdb=" N1 P5P G 34 " 0.001 2.00e-02 2.50e+03 pdb=" C2 P5P G 34 " -0.003 2.00e-02 2.50e+03 pdb=" N3 P5P G 34 " -0.004 2.00e-02 2.50e+03 pdb=" C4 P5P G 34 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' P5P G 4 " 0.018 2.00e-02 2.50e+03 9.30e-03 2.16e+00 pdb=" N9 P5P G 4 " -0.022 2.00e-02 2.50e+03 pdb=" C8 P5P G 4 " -0.001 2.00e-02 2.50e+03 pdb=" N7 P5P G 4 " 0.004 2.00e-02 2.50e+03 pdb=" C5 P5P G 4 " 0.000 2.00e-02 2.50e+03 pdb=" C6 P5P G 4 " 0.005 2.00e-02 2.50e+03 pdb=" N1 P5P G 4 " 0.003 2.00e-02 2.50e+03 pdb=" C2 P5P G 4 " -0.001 2.00e-02 2.50e+03 pdb=" N3 P5P G 4 " -0.004 2.00e-02 2.50e+03 pdb=" C4 P5P G 4 " -0.002 2.00e-02 2.50e+03 ... (remaining 1759 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 416 2.71 - 3.26: 10929 3.26 - 3.80: 17578 3.80 - 4.35: 21341 4.35 - 4.90: 35587 Nonbonded interactions: 85851 Sorted by model distance: nonbonded pdb=" ND2 ASN A 59 " pdb=" OE2 GLU A 252 " model vdw 2.160 3.120 nonbonded pdb=" O SER C 113 " pdb=" OG SER C 113 " model vdw 2.171 3.040 nonbonded pdb=" O SER A 113 " pdb=" OG SER A 113 " model vdw 2.181 3.040 nonbonded pdb=" O2' P5P H 4 " pdb=" O5' P5P H 5 " model vdw 2.193 3.040 nonbonded pdb=" OD1 ASN B 38 " pdb=" OG SER B 155 " model vdw 2.194 3.040 ... (remaining 85846 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' and (resid 35 through 309 or resid 317 through 349)) selection = (chain 'B' and (resid 35 through 309 or resid 317 through 349)) selection = (chain 'C' and (resid 35 through 309 or resid 317 through 349)) selection = (chain 'D' and (resid 35 through 309 or resid 315 or resid 318 through 349)) } ncs_group { reference = (chain 'G' and (resid 3 through 5 or resid 8 or resid 10 through 14 or resid 19 \ through 20 or resid 25 or resid 30 through 36 or resid 38 through 40)) selection = (chain 'H' and (resid 1 through 3 or resid 6 or resid 8 through 13 or resid 18 t \ hrough 19 or resid 24 or resid 29 through 35 or resid 37 through 39)) } 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 group one per residue 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: 2.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.980 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6537 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 : 0.012 0.126 11390 Z= 0.578 Angle : 1.106 11.974 15613 Z= 0.427 Chirality : 0.035 0.153 1759 Planarity : 0.003 0.025 1762 Dihedral : 22.706 177.038 5878 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.47 % Favored : 96.45 % Rotamer: Outliers : 1.57 % Allowed : 18.09 % Favored : 80.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 1.22 (0.25), residues: 1238 helix: 1.74 (0.22), residues: 605 sheet: -1.49 (0.64), residues: 54 loop : 0.13 (0.28), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 251 TYR 0.007 0.001 TYR D 342 PHE 0.007 0.001 PHE D 42 TRP 0.010 0.001 TRP D 259 HIS 0.004 0.001 HIS C 153 Details of bonding type rmsd/Z covalent geometry : bond 0.01162 / 0.58 (11390) covalent geometry : angle 1.10580 / 0.43 (15613) hydrogen bonds : bond 0.14567 / 10.20 ( 449) hydrogen bonds : angle 5.00032 / 3.61 ( 1287) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 320 time to evaluate : 0.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 PHE cc_start: 0.7022 (t80) cc_final: 0.6818 (t80) REVERT: A 153 HIS cc_start: 0.7286 (OUTLIER) cc_final: 0.6706 (t70) REVERT: A 170 TYR cc_start: 0.7833 (t80) cc_final: 0.7255 (t80) REVERT: A 179 ARG cc_start: 0.6098 (mtm180) cc_final: 0.5863 (ttm110) REVERT: B 127 CYS cc_start: 0.7336 (m) cc_final: 0.7096 (m) REVERT: B 167 LYS cc_start: 0.7713 (tptm) cc_final: 0.7452 (tppt) REVERT: B 187 GLN cc_start: 0.7468 (tt0) cc_final: 0.7177 (tm-30) REVERT: B 297 VAL cc_start: 0.8518 (t) cc_final: 0.8262 (m) REVERT: C 84 VAL cc_start: 0.6068 (t) cc_final: 0.5700 (m) REVERT: C 295 LEU cc_start: 0.8182 (mt) cc_final: 0.7980 (mp) outliers start: 16 outliers final: 6 residues processed: 333 average time/residue: 0.1240 time to fit residues: 54.9276 Evaluate side-chains 188 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 181 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 153 HIS Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 340 SER Chi-restraints excluded: chain B residue 252 GLU Chi-restraints excluded: chain D residue 153 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: [98, 107, 10, 66, 124, 103, 77, 122, 91, 55, 129] chunk 98 optimal weight: 7.9990 chunk 107 optimal weight: 0.0970 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 7.9990 chunk 91 optimal weight: 0.9990 chunk 55 optimal weight: 0.0000 chunk 129 optimal weight: 5.9990 overall best weight: 0.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 148 GLN A 243 GLN B 48 HIS B 240 HIS ** D 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4793 r_free = 0.4793 target = 0.257418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4538 r_free = 0.4538 target = 0.228366 restraints weight = 15322.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4551 r_free = 0.4551 target = 0.230776 restraints weight = 25663.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4544 r_free = 0.4544 target = 0.230329 restraints weight = 17462.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4542 r_free = 0.4542 target = 0.230199 restraints weight = 14749.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4545 r_free = 0.4545 target = 0.230694 restraints weight = 12934.704| |-----------------------------------------------------------------------------| r_work (final): 0.4527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6281 moved from start: 0.2684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 11390 Z= 0.138 Angle : 0.687 7.843 15613 Z= 0.330 Chirality : 0.039 0.155 1759 Planarity : 0.004 0.048 1762 Dihedral : 23.765 173.442 3601 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.58 % Favored : 97.33 % Rotamer: Outliers : 3.24 % Allowed : 21.53 % Favored : 75.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 1.12 (0.25), residues: 1238 helix: 1.46 (0.22), residues: 625 sheet: -1.21 (0.67), residues: 54 loop : 0.25 (0.29), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 109 TYR 0.016 0.002 TYR C 123 PHE 0.022 0.002 PHE D 208 TRP 0.021 0.001 TRP D 270 HIS 0.007 0.001 HIS C 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 (11390) covalent geometry : angle 0.68663 / 0.33 (15613) hydrogen bonds : bond 0.04052 / 2.78 ( 449) hydrogen bonds : angle 4.44972 / 3.24 ( 1287) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 206 time to evaluate : 0.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 TYR cc_start: 0.7699 (t80) cc_final: 0.7238 (t80) REVERT: B 167 LYS cc_start: 0.8029 (tptm) cc_final: 0.7741 (tppt) REVERT: B 297 VAL cc_start: 0.8543 (t) cc_final: 0.8273 (m) REVERT: C 37 ARG cc_start: 0.4529 (ppt170) cc_final: 0.4284 (pmt-80) outliers start: 33 outliers final: 19 residues processed: 226 average time/residue: 0.1109 time to fit residues: 34.5408 Evaluate side-chains 187 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 168 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 124 CYS Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain C residue 127 CYS Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 340 SER Chi-restraints excluded: chain D residue 72 MET Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 119 ARG Chi-restraints excluded: chain D residue 143 ASP Chi-restraints excluded: chain D residue 171 VAL Chi-restraints excluded: chain D residue 173 LEU Chi-restraints excluded: chain D residue 234 ARG Chi-restraints excluded: chain D residue 303 SER Chi-restraints excluded: chain D residue 345 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: [74, 28, 64, 110, 13, 27, 96, 53, 95, 38, 117] chunk 74 optimal weight: 0.5980 chunk 28 optimal weight: 0.9990 chunk 64 optimal weight: 2.9990 chunk 110 optimal weight: 4.9990 chunk 13 optimal weight: 0.9980 chunk 27 optimal weight: 10.0000 chunk 96 optimal weight: 0.9990 chunk 53 optimal weight: 0.6980 chunk 95 optimal weight: 0.9990 chunk 38 optimal weight: 7.9990 chunk 117 optimal weight: 6.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4916 r_free = 0.4916 target = 0.264468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4655 r_free = 0.4655 target = 0.233826 restraints weight = 15279.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4661 r_free = 0.4661 target = 0.235983 restraints weight = 25658.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4665 r_free = 0.4665 target = 0.236847 restraints weight = 16627.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4665 r_free = 0.4665 target = 0.237043 restraints weight = 13198.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4668 r_free = 0.4668 target = 0.237595 restraints weight = 12793.011| |-----------------------------------------------------------------------------| r_work (final): 0.4725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6320 moved from start: 0.3265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11390 Z= 0.141 Angle : 0.670 8.042 15613 Z= 0.321 Chirality : 0.038 0.168 1759 Planarity : 0.004 0.039 1762 Dihedral : 23.588 172.965 3591 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.75 % Favored : 97.09 % Rotamer: Outliers : 3.74 % Allowed : 21.53 % Favored : 74.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 0.99 (0.25), residues: 1238 helix: 1.27 (0.21), residues: 627 sheet: -1.07 (0.67), residues: 54 loop : 0.28 (0.29), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 86 TYR 0.018 0.002 TYR A 197 PHE 0.024 0.002 PHE D 50 TRP 0.037 0.002 TRP D 270 HIS 0.008 0.001 HIS D 300 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 (11390) covalent geometry : angle 0.66960 / 0.32 (15613) hydrogen bonds : bond 0.03633 / 2.46 ( 449) hydrogen bonds : angle 4.44590 / 3.26 ( 1287) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 182 time to evaluate : 0.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 TYR cc_start: 0.7663 (t80) cc_final: 0.7228 (t80) REVERT: B 41 VAL cc_start: 0.8380 (p) cc_final: 0.8004 (m) REVERT: B 297 VAL cc_start: 0.8532 (t) cc_final: 0.8254 (m) outliers start: 38 outliers final: 22 residues processed: 209 average time/residue: 0.1048 time to fit residues: 30.5969 Evaluate side-chains 187 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 165 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 TRP Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 124 CYS Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 348 THR Chi-restraints excluded: chain C residue 127 CYS Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 292 SER Chi-restraints excluded: chain C residue 345 LEU Chi-restraints excluded: chain D residue 72 MET Chi-restraints excluded: chain D residue 119 ARG Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 171 VAL Chi-restraints excluded: chain D residue 173 LEU Chi-restraints excluded: chain D residue 234 ARG Chi-restraints excluded: chain D residue 345 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: [69, 85, 14, 63, 22, 44, 97, 98, 120, 46, 8] chunk 69 optimal weight: 0.6980 chunk 85 optimal weight: 0.5980 chunk 14 optimal weight: 0.1980 chunk 63 optimal weight: 6.9990 chunk 22 optimal weight: 0.9980 chunk 44 optimal weight: 0.4980 chunk 97 optimal weight: 0.6980 chunk 98 optimal weight: 0.2980 chunk 120 optimal weight: 0.0570 chunk 46 optimal weight: 0.5980 chunk 8 optimal weight: 0.9990 overall best weight: 0.3298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 59 ASN ** C 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 326 GLN ** D 343 HIS ** 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 = 0.4792 r_free = 0.4792 target = 0.256927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4479 r_free = 0.4479 target = 0.221176 restraints weight = 15185.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4482 r_free = 0.4482 target = 0.222055 restraints weight = 23836.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4488 r_free = 0.4488 target = 0.223179 restraints weight = 21139.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4488 r_free = 0.4488 target = 0.223257 restraints weight = 14437.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4494 r_free = 0.4494 target = 0.224129 restraints weight = 12820.739| |-----------------------------------------------------------------------------| r_work (final): 0.4480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6421 moved from start: 0.3729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 11390 Z= 0.111 Angle : 0.657 7.411 15613 Z= 0.314 Chirality : 0.038 0.181 1759 Planarity : 0.004 0.032 1762 Dihedral : 23.403 171.899 3591 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.50 % Favored : 97.42 % Rotamer: Outliers : 3.15 % Allowed : 22.12 % Favored : 74.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 0.88 (0.25), residues: 1238 helix: 1.10 (0.21), residues: 633 sheet: -0.80 (0.69), residues: 54 loop : 0.27 (0.29), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 158 TYR 0.021 0.002 TYR A 197 PHE 0.019 0.002 PHE D 50 TRP 0.023 0.001 TRP D 270 HIS 0.008 0.001 HIS D 300 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 (11390) covalent geometry : angle 0.65738 / 0.31 (15613) hydrogen bonds : bond 0.03362 / 2.26 ( 449) hydrogen bonds : angle 4.36818 / 3.20 ( 1287) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 183 time to evaluate : 0.285 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 ARG cc_start: 0.6685 (ttm-80) cc_final: 0.5988 (mmt180) REVERT: A 170 TYR cc_start: 0.7636 (t80) cc_final: 0.7180 (t80) REVERT: B 187 GLN cc_start: 0.7498 (tm-30) cc_final: 0.7193 (tm-30) REVERT: B 297 VAL cc_start: 0.8468 (t) cc_final: 0.8185 (m) REVERT: D 149 MET cc_start: 0.6321 (tpt) cc_final: 0.5998 (tpt) REVERT: D 251 ARG cc_start: 0.6893 (mtp180) cc_final: 0.6672 (mtp85) outliers start: 32 outliers final: 17 residues processed: 205 average time/residue: 0.1003 time to fit residues: 28.5947 Evaluate side-chains 182 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 165 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 TRP Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain B residue 303 SER Chi-restraints excluded: chain C residue 127 CYS Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 292 SER Chi-restraints excluded: chain C residue 340 SER Chi-restraints excluded: chain C residue 345 LEU Chi-restraints excluded: chain D residue 72 MET Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 119 ARG Chi-restraints excluded: chain D residue 171 VAL Chi-restraints excluded: chain D residue 173 LEU Chi-restraints excluded: chain D residue 303 SER Chi-restraints excluded: chain D residue 345 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: [85, 115, 34, 40, 118, 87, 12, 89, 110, 53, 43] chunk 85 optimal weight: 6.9990 chunk 115 optimal weight: 0.7980 chunk 34 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 118 optimal weight: 3.9990 chunk 87 optimal weight: 0.9980 chunk 12 optimal weight: 0.4980 chunk 89 optimal weight: 0.0970 chunk 110 optimal weight: 4.9990 chunk 53 optimal weight: 0.5980 chunk 43 optimal weight: 0.6980 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 96 ASN C 240 HIS ** D 343 HIS ** 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 = 0.4785 r_free = 0.4785 target = 0.255938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4516 r_free = 0.4516 target = 0.225527 restraints weight = 15168.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4522 r_free = 0.4522 target = 0.227201 restraints weight = 27221.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4523 r_free = 0.4523 target = 0.227771 restraints weight = 20115.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4521 r_free = 0.4521 target = 0.227490 restraints weight = 15652.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4526 r_free = 0.4526 target = 0.228275 restraints weight = 12982.340| |-----------------------------------------------------------------------------| r_work (final): 0.4516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6311 moved from start: 0.3950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11390 Z= 0.114 Angle : 0.641 9.451 15613 Z= 0.305 Chirality : 0.037 0.164 1759 Planarity : 0.003 0.031 1762 Dihedral : 23.242 172.534 3591 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.26 % Favored : 97.66 % Rotamer: Outliers : 3.64 % Allowed : 22.03 % Favored : 74.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 0.88 (0.25), residues: 1238 helix: 1.10 (0.22), residues: 630 sheet: -0.58 (0.69), residues: 54 loop : 0.26 (0.28), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 92 TYR 0.015 0.001 TYR A 207 PHE 0.023 0.002 PHE C 54 TRP 0.022 0.001 TRP A 270 HIS 0.006 0.001 HIS C 48 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 (11390) covalent geometry : angle 0.64146 / 0.31 (15613) hydrogen bonds : bond 0.03346 / 2.26 ( 449) hydrogen bonds : angle 4.35890 / 3.18 ( 1287) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 176 time to evaluate : 0.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 ARG cc_start: 0.6659 (ttm-80) cc_final: 0.6062 (mmt180) REVERT: A 170 TYR cc_start: 0.7661 (t80) cc_final: 0.7164 (t80) REVERT: B 187 GLN cc_start: 0.7554 (tm-30) cc_final: 0.7193 (tm-30) REVERT: B 297 VAL cc_start: 0.8547 (t) cc_final: 0.8294 (m) REVERT: C 150 MET cc_start: 0.4958 (mmp) cc_final: 0.4456 (mmp) outliers start: 37 outliers final: 27 residues processed: 199 average time/residue: 0.0945 time to fit residues: 27.2613 Evaluate side-chains 188 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 161 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 TRP Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 268 GLU Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 127 CYS Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 226 GLN Chi-restraints excluded: chain C residue 240 HIS Chi-restraints excluded: chain C residue 292 SER Chi-restraints excluded: chain C residue 345 LEU Chi-restraints excluded: chain D residue 43 ASN Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 72 MET Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 119 ARG Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 171 VAL Chi-restraints excluded: chain D residue 173 LEU Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 303 SER Chi-restraints excluded: chain D residue 345 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: [39, 23, 101, 9, 122, 52, 80, 78, 51, 89, 55] chunk 39 optimal weight: 0.9980 chunk 23 optimal weight: 0.8980 chunk 101 optimal weight: 9.9990 chunk 9 optimal weight: 1.9990 chunk 122 optimal weight: 9.9990 chunk 52 optimal weight: 2.9990 chunk 80 optimal weight: 4.9990 chunk 78 optimal weight: 6.9990 chunk 51 optimal weight: 0.7980 chunk 89 optimal weight: 2.9990 chunk 55 optimal weight: 6.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 243 GLN ** D 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4749 r_free = 0.4749 target = 0.251041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4474 r_free = 0.4474 target = 0.220186 restraints weight = 15215.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4487 r_free = 0.4487 target = 0.222555 restraints weight = 27692.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4480 r_free = 0.4480 target = 0.222266 restraints weight = 20275.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4480 r_free = 0.4480 target = 0.222284 restraints weight = 15147.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4484 r_free = 0.4484 target = 0.222918 restraints weight = 13843.639| |-----------------------------------------------------------------------------| r_work (final): 0.4473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6427 moved from start: 0.4187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 11390 Z= 0.190 Angle : 0.702 8.016 15613 Z= 0.337 Chirality : 0.040 0.170 1759 Planarity : 0.004 0.032 1762 Dihedral : 23.115 173.960 3590 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.15 % Favored : 96.77 % Rotamer: Outliers : 3.83 % Allowed : 22.52 % Favored : 73.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 0.64 (0.25), residues: 1238 helix: 0.90 (0.21), residues: 623 sheet: -0.53 (0.70), residues: 54 loop : 0.13 (0.28), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 241 TYR 0.012 0.002 TYR A 207 PHE 0.020 0.002 PHE C 54 TRP 0.045 0.002 TRP D 270 HIS 0.026 0.002 HIS C 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00450 / 0.19 (11390) covalent geometry : angle 0.70214 / 0.34 (15613) hydrogen bonds : bond 0.03723 / 2.53 ( 449) hydrogen bonds : angle 4.57968 / 3.35 ( 1287) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 170 time to evaluate : 0.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 PHE cc_start: 0.5858 (t80) cc_final: 0.5579 (t80) REVERT: A 112 ARG cc_start: 0.6807 (ttm-80) cc_final: 0.6543 (ttm-80) REVERT: A 151 LYS cc_start: 0.7472 (OUTLIER) cc_final: 0.7241 (mtpp) REVERT: A 170 TYR cc_start: 0.7743 (t80) cc_final: 0.7278 (t80) REVERT: B 162 ARG cc_start: 0.7807 (OUTLIER) cc_final: 0.6745 (mtp85) REVERT: B 187 GLN cc_start: 0.7568 (tm-30) cc_final: 0.7141 (tm-30) REVERT: B 297 VAL cc_start: 0.8685 (t) cc_final: 0.8440 (m) REVERT: D 138 ILE cc_start: 0.4504 (mm) cc_final: 0.4164 (mm) outliers start: 39 outliers final: 33 residues processed: 199 average time/residue: 0.1022 time to fit residues: 28.6289 Evaluate side-chains 197 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 162 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 TRP Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 151 LYS Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 162 ARG Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 348 THR Chi-restraints excluded: chain C residue 37 ARG Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 92 ARG Chi-restraints excluded: chain C residue 127 CYS Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 240 HIS Chi-restraints excluded: chain C residue 292 SER Chi-restraints excluded: chain C residue 340 SER Chi-restraints excluded: chain C residue 345 LEU Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 119 ARG Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 171 VAL Chi-restraints excluded: chain D residue 173 LEU Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 303 SER Chi-restraints excluded: chain D residue 345 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: [110, 113, 42, 14, 8, 68, 111, 89, 120, 61, 28] chunk 110 optimal weight: 3.9990 chunk 113 optimal weight: 0.8980 chunk 42 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 68 optimal weight: 8.9990 chunk 111 optimal weight: 3.9990 chunk 89 optimal weight: 4.9990 chunk 120 optimal weight: 0.3980 chunk 61 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 243 GLN C 240 HIS ** D 343 HIS ** 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 = 0.4776 r_free = 0.4776 target = 0.254483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4453 r_free = 0.4453 target = 0.217845 restraints weight = 15003.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4452 r_free = 0.4452 target = 0.218632 restraints weight = 25819.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4460 r_free = 0.4460 target = 0.219949 restraints weight = 20533.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4473 r_free = 0.4473 target = 0.221782 restraints weight = 13575.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4474 r_free = 0.4474 target = 0.222106 restraints weight = 12229.553| |-----------------------------------------------------------------------------| r_work (final): 0.4447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6518 moved from start: 0.4371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11390 Z= 0.139 Angle : 0.668 8.721 15613 Z= 0.316 Chirality : 0.038 0.180 1759 Planarity : 0.004 0.062 1762 Dihedral : 22.985 174.598 3590 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.83 % Favored : 97.09 % Rotamer: Outliers : 3.54 % Allowed : 23.40 % Favored : 73.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 0.65 (0.25), residues: 1238 helix: 0.92 (0.21), residues: 625 sheet: -0.41 (0.71), residues: 54 loop : 0.11 (0.28), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 336 TYR 0.012 0.001 TYR A 123 PHE 0.020 0.002 PHE C 54 TRP 0.032 0.002 TRP A 270 HIS 0.005 0.001 HIS C 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 (11390) covalent geometry : angle 0.66757 / 0.32 (15613) hydrogen bonds : bond 0.03461 / 2.36 ( 449) hydrogen bonds : angle 4.46441 / 3.26 ( 1287) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 167 time to evaluate : 0.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 PHE cc_start: 0.5987 (t80) cc_final: 0.5723 (t80) REVERT: A 112 ARG cc_start: 0.6946 (ttm-80) cc_final: 0.6184 (mmt180) REVERT: A 170 TYR cc_start: 0.7836 (t80) cc_final: 0.7316 (t80) REVERT: B 162 ARG cc_start: 0.7690 (OUTLIER) cc_final: 0.6602 (mtp85) REVERT: B 297 VAL cc_start: 0.8692 (t) cc_final: 0.8444 (m) REVERT: B 311 GLU cc_start: 0.6825 (mm-30) cc_final: 0.6343 (tm-30) REVERT: C 150 MET cc_start: 0.5010 (mmp) cc_final: 0.4404 (mmp) outliers start: 36 outliers final: 30 residues processed: 189 average time/residue: 0.0963 time to fit residues: 25.8171 Evaluate side-chains 189 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 158 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 TRP Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 162 ARG Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 273 SER Chi-restraints excluded: chain C residue 37 ARG Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 92 ARG Chi-restraints excluded: chain C residue 127 CYS Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 226 GLN Chi-restraints excluded: chain C residue 240 HIS Chi-restraints excluded: chain C residue 292 SER Chi-restraints excluded: chain C residue 310 ILE Chi-restraints excluded: chain C residue 340 SER Chi-restraints excluded: chain C residue 345 LEU Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 119 ARG Chi-restraints excluded: chain D residue 171 VAL Chi-restraints excluded: chain D residue 173 LEU Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 303 SER Chi-restraints excluded: chain D residue 345 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: [56, 53, 43, 113, 22, 73, 90, 103, 77, 16, 52] chunk 56 optimal weight: 0.9990 chunk 53 optimal weight: 0.6980 chunk 43 optimal weight: 0.9990 chunk 113 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 chunk 73 optimal weight: 5.9990 chunk 90 optimal weight: 2.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 0.9990 chunk 16 optimal weight: 0.6980 chunk 52 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 243 GLN C 240 HIS ** D 343 HIS ** 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 = 0.4762 r_free = 0.4762 target = 0.252895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4485 r_free = 0.4485 target = 0.221564 restraints weight = 15058.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4499 r_free = 0.4499 target = 0.223881 restraints weight = 27151.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4502 r_free = 0.4502 target = 0.224441 restraints weight = 20223.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4507 r_free = 0.4507 target = 0.225359 restraints weight = 14116.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4509 r_free = 0.4509 target = 0.225629 restraints weight = 13934.262| |-----------------------------------------------------------------------------| r_work (final): 0.4499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6367 moved from start: 0.4552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11390 Z= 0.131 Angle : 0.678 9.465 15613 Z= 0.320 Chirality : 0.038 0.183 1759 Planarity : 0.004 0.055 1762 Dihedral : 22.915 174.228 3590 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 3.44 % Allowed : 24.19 % Favored : 72.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 0.66 (0.25), residues: 1238 helix: 0.97 (0.21), residues: 623 sheet: -0.38 (0.70), residues: 54 loop : 0.06 (0.28), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 251 TYR 0.013 0.002 TYR A 123 PHE 0.023 0.002 PHE A 50 TRP 0.028 0.002 TRP D 270 HIS 0.022 0.001 HIS C 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 (11390) covalent geometry : angle 0.67770 / 0.32 (15613) hydrogen bonds : bond 0.03440 / 2.31 ( 449) hydrogen bonds : angle 4.42215 / 3.23 ( 1287) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 165 time to evaluate : 0.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 ARG cc_start: 0.6859 (ttm-80) cc_final: 0.6293 (mmt180) REVERT: A 141 SER cc_start: 0.7513 (OUTLIER) cc_final: 0.6972 (m) REVERT: A 170 TYR cc_start: 0.7710 (t80) cc_final: 0.7220 (t80) REVERT: B 155 SER cc_start: 0.7930 (OUTLIER) cc_final: 0.7503 (p) REVERT: B 162 ARG cc_start: 0.7776 (OUTLIER) cc_final: 0.6701 (mtp85) REVERT: B 297 VAL cc_start: 0.8701 (t) cc_final: 0.8469 (m) REVERT: B 311 GLU cc_start: 0.6778 (mm-30) cc_final: 0.6397 (tm-30) REVERT: C 150 MET cc_start: 0.4786 (mmp) cc_final: 0.4047 (mmp) outliers start: 35 outliers final: 28 residues processed: 189 average time/residue: 0.0992 time to fit residues: 26.3551 Evaluate side-chains 191 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 160 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 TRP Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 162 ARG Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 273 SER Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain C residue 37 ARG Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 127 CYS Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 226 GLN Chi-restraints excluded: chain C residue 240 HIS Chi-restraints excluded: chain C residue 292 SER Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 119 ARG Chi-restraints excluded: chain D residue 150 MET Chi-restraints excluded: chain D residue 171 VAL Chi-restraints excluded: chain D residue 173 LEU Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 303 SER Chi-restraints excluded: chain D residue 345 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: [88, 78, 24, 32, 45, 12, 105, 59, 47, 5, 19] chunk 88 optimal weight: 0.7980 chunk 78 optimal weight: 6.9990 chunk 24 optimal weight: 3.9990 chunk 32 optimal weight: 0.0870 chunk 45 optimal weight: 0.8980 chunk 12 optimal weight: 0.6980 chunk 105 optimal weight: 0.9990 chunk 59 optimal weight: 3.9990 chunk 47 optimal weight: 0.4980 chunk 5 optimal weight: 4.9990 chunk 19 optimal weight: 0.1980 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 240 HIS ** D 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4768 r_free = 0.4768 target = 0.253684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4425 r_free = 0.4425 target = 0.215735 restraints weight = 14939.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4409 r_free = 0.4409 target = 0.214865 restraints weight = 22900.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4417 r_free = 0.4417 target = 0.216177 restraints weight = 20986.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4441 r_free = 0.4441 target = 0.219748 restraints weight = 13634.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4440 r_free = 0.4440 target = 0.219669 restraints weight = 10329.277| |-----------------------------------------------------------------------------| r_work (final): 0.4426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6556 moved from start: 0.4646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 11390 Z= 0.113 Angle : 0.674 9.811 15613 Z= 0.317 Chirality : 0.037 0.184 1759 Planarity : 0.004 0.046 1762 Dihedral : 22.843 174.313 3590 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 3.34 % Allowed : 24.29 % Favored : 72.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 0.70 (0.25), residues: 1238 helix: 1.01 (0.21), residues: 629 sheet: -0.35 (0.69), residues: 54 loop : 0.05 (0.28), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 251 TYR 0.014 0.001 TYR A 123 PHE 0.024 0.001 PHE A 54 TRP 0.029 0.002 TRP A 270 HIS 0.010 0.001 HIS C 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 (11390) covalent geometry : angle 0.67382 / 0.32 (15613) hydrogen bonds : bond 0.03320 / 2.22 ( 449) hydrogen bonds : angle 4.35754 / 3.18 ( 1287) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 161 time to evaluate : 0.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 LYS cc_start: 0.7463 (OUTLIER) cc_final: 0.7248 (mtpp) REVERT: A 170 TYR cc_start: 0.7883 (t80) cc_final: 0.7335 (t80) REVERT: B 162 ARG cc_start: 0.7847 (OUTLIER) cc_final: 0.6743 (mtp85) REVERT: B 217 ARG cc_start: 0.8073 (mmm-85) cc_final: 0.7747 (mmt90) REVERT: B 297 VAL cc_start: 0.8702 (t) cc_final: 0.8459 (m) REVERT: B 311 GLU cc_start: 0.6922 (mm-30) cc_final: 0.6433 (tm-30) REVERT: C 150 MET cc_start: 0.4950 (mmp) cc_final: 0.4132 (mmp) REVERT: D 150 MET cc_start: 0.6366 (OUTLIER) cc_final: 0.5998 (ppp) REVERT: D 251 ARG cc_start: 0.7106 (ttt180) cc_final: 0.6867 (mtp180) outliers start: 34 outliers final: 28 residues processed: 184 average time/residue: 0.1075 time to fit residues: 27.6618 Evaluate side-chains 187 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 156 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 TRP Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 151 LYS Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 162 ARG Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 268 GLU Chi-restraints excluded: chain B residue 273 SER Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain C residue 37 ARG Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 127 CYS Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 226 GLN Chi-restraints excluded: chain C residue 240 HIS Chi-restraints excluded: chain C residue 292 SER Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 119 ARG Chi-restraints excluded: chain D residue 150 MET Chi-restraints excluded: chain D residue 171 VAL Chi-restraints excluded: chain D residue 173 LEU Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 303 SER Chi-restraints excluded: chain D residue 345 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: [36, 124, 100, 1, 38, 58, 121, 89, 102, 116, 71] chunk 36 optimal weight: 0.7980 chunk 124 optimal weight: 9.9990 chunk 100 optimal weight: 0.7980 chunk 1 optimal weight: 4.9990 chunk 38 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 121 optimal weight: 6.9990 chunk 89 optimal weight: 0.9990 chunk 102 optimal weight: 8.9990 chunk 116 optimal weight: 0.9980 chunk 71 optimal weight: 0.0980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 243 GLN D 300 HIS ** D 343 HIS ** 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 = 0.4765 r_free = 0.4765 target = 0.253251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4452 r_free = 0.4452 target = 0.217395 restraints weight = 15035.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4473 r_free = 0.4473 target = 0.220725 restraints weight = 26480.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4472 r_free = 0.4472 target = 0.221292 restraints weight = 17050.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4472 r_free = 0.4472 target = 0.221241 restraints weight = 13159.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4477 r_free = 0.4477 target = 0.221975 restraints weight = 11637.318| |-----------------------------------------------------------------------------| r_work (final): 0.4462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6463 moved from start: 0.4752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 11390 Z= 0.128 Angle : 0.691 9.878 15613 Z= 0.326 Chirality : 0.038 0.195 1759 Planarity : 0.004 0.067 1762 Dihedral : 22.805 174.520 3590 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 3.15 % Allowed : 24.48 % Favored : 72.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 0.67 (0.25), residues: 1238 helix: 0.99 (0.21), residues: 629 sheet: -0.36 (0.69), residues: 54 loop : 0.02 (0.28), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 86 TYR 0.014 0.002 TYR A 123 PHE 0.023 0.001 PHE A 54 TRP 0.032 0.002 TRP A 270 HIS 0.014 0.001 HIS C 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 (11390) covalent geometry : angle 0.69147 / 0.33 (15613) hydrogen bonds : bond 0.03347 / 2.24 ( 449) hydrogen bonds : angle 4.38180 / 3.19 ( 1287) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 157 time to evaluate : 0.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 ARG cc_start: 0.6725 (ttm-80) cc_final: 0.6158 (mmt180) REVERT: A 141 SER cc_start: 0.7619 (OUTLIER) cc_final: 0.7122 (m) REVERT: A 151 LYS cc_start: 0.7535 (OUTLIER) cc_final: 0.7304 (mtpp) REVERT: A 170 TYR cc_start: 0.7703 (t80) cc_final: 0.7173 (t80) REVERT: B 149 MET cc_start: 0.7069 (tpp) cc_final: 0.6845 (tpp) REVERT: B 162 ARG cc_start: 0.7723 (OUTLIER) cc_final: 0.6637 (mtp85) REVERT: B 297 VAL cc_start: 0.8720 (t) cc_final: 0.8468 (m) REVERT: B 311 GLU cc_start: 0.7024 (mm-30) cc_final: 0.6462 (tm-30) REVERT: D 150 MET cc_start: 0.6428 (OUTLIER) cc_final: 0.5933 (ppp) REVERT: D 251 ARG cc_start: 0.7234 (ttt180) cc_final: 0.6829 (mtp180) outliers start: 32 outliers final: 27 residues processed: 179 average time/residue: 0.0963 time to fit residues: 24.7789 Evaluate side-chains 187 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 156 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain A residue 151 LYS Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain B residue 162 ARG Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 273 SER Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain C residue 37 ARG Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 127 CYS Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 226 GLN Chi-restraints excluded: chain C residue 240 HIS Chi-restraints excluded: chain C residue 292 SER Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 119 ARG Chi-restraints excluded: chain D residue 150 MET Chi-restraints excluded: chain D residue 171 VAL Chi-restraints excluded: chain D residue 173 LEU Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 303 SER Chi-restraints excluded: chain D residue 345 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: [65, 112, 89, 128, 67, 100, 33, 63, 19, 70, 24] chunk 65 optimal weight: 5.9990 chunk 112 optimal weight: 0.0570 chunk 89 optimal weight: 0.9980 chunk 128 optimal weight: 20.0000 chunk 67 optimal weight: 7.9990 chunk 100 optimal weight: 0.0060 chunk 33 optimal weight: 0.8980 chunk 63 optimal weight: 10.0000 chunk 19 optimal weight: 0.0060 chunk 70 optimal weight: 8.9990 chunk 24 optimal weight: 4.9990 overall best weight: 0.3930 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 288 GLN C 240 HIS D 343 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4777 r_free = 0.4777 target = 0.254977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4473 r_free = 0.4473 target = 0.219809 restraints weight = 15179.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4496 r_free = 0.4496 target = 0.223494 restraints weight = 24197.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4488 r_free = 0.4488 target = 0.222972 restraints weight = 16044.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4488 r_free = 0.4488 target = 0.222960 restraints weight = 14365.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4493 r_free = 0.4493 target = 0.223658 restraints weight = 11573.136| |-----------------------------------------------------------------------------| r_work (final): 0.4469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6425 moved from start: 0.4920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 11390 Z= 0.107 Angle : 0.667 9.981 15613 Z= 0.314 Chirality : 0.037 0.180 1759 Planarity : 0.004 0.040 1762 Dihedral : 22.698 174.686 3590 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.75 % Allowed : 25.07 % Favored : 72.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 0.74 (0.25), residues: 1238 helix: 1.06 (0.21), residues: 631 sheet: -0.35 (0.68), residues: 54 loop : 0.05 (0.28), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 86 TYR 0.016 0.001 TYR A 123 PHE 0.030 0.001 PHE D 50 TRP 0.034 0.002 TRP A 270 HIS 0.005 0.001 HIS D 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.11 (11390) covalent geometry : angle 0.66691 / 0.31 (15613) hydrogen bonds : bond 0.03226 / 2.15 ( 449) hydrogen bonds : angle 4.33706 / 3.14 ( 1287) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1695.54 seconds wall clock time: 30 minutes 11.44 seconds (1811.44 seconds total)