Starting phenix.real_space_refine on Wed Feb 4 11:29:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9hgn_52152/02_2026/9hgn_52152.cif Found real_map, /net/cci-nas-00/data/ceres_data/9hgn_52152/02_2026/9hgn_52152.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9hgn_52152/02_2026/9hgn_52152.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9hgn_52152/02_2026/9hgn_52152.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9hgn_52152/02_2026/9hgn_52152.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9hgn_52152/02_2026/9hgn_52152.map" } resolution = 2.94 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= 0.057 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 63 5.16 5 C 6449 2.51 5 N 1685 2.21 5 O 1922 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10119 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3374 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 426, 3364 Classifications: {'peptide': 426} Link IDs: {'PTRANS': 26, 'TRANS': 399} Conformer: "B" Number of residues, atoms: 426, 3364 Classifications: {'peptide': 426} Link IDs: {'PTRANS': 26, 'TRANS': 399} bond proxies already assigned to first conformer: 3455 Chain: "B" Number of atoms: 3374 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 426, 3364 Classifications: {'peptide': 426} Link IDs: {'PTRANS': 26, 'TRANS': 399} Conformer: "B" Number of residues, atoms: 426, 3364 Classifications: {'peptide': 426} Link IDs: {'PTRANS': 26, 'TRANS': 399} bond proxies already assigned to first conformer: 3455 Chain: "C" Number of atoms: 3371 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 426, 3364 Classifications: {'peptide': 426} Link IDs: {'PTRANS': 26, 'TRANS': 399} Conformer: "B" Number of residues, atoms: 426, 3364 Classifications: {'peptide': 426} Link IDs: {'PTRANS': 26, 'TRANS': 399} bond proxies already assigned to first conformer: 3458 Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N AHIS A 8 " occ=0.58 ... (18 atoms not shown) pdb=" NE2BHIS A 8 " occ=0.42 residue: pdb=" N AHIS B 33 " occ=0.32 ... (18 atoms not shown) pdb=" NE2BHIS B 33 " occ=0.68 Time building chain proxies: 4.10, per 1000 atoms: 0.41 Number of scatterers: 10119 At special positions: 0 Unit cell: (86.1, 84, 145.95, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 63 16.00 O 1922 8.00 N 1685 7.00 C 6449 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 24 " - pdb=" SG CYS A 284 " distance=2.03 Simple disulfide: pdb=" SG CYS A 59 " - pdb=" SG CYS A 92 " distance=2.03 Simple disulfide: pdb=" SG CYS A 68 " - pdb=" SG CYS A 114 " distance=2.03 Simple disulfide: pdb=" SG CYS A 153 " - pdb=" SG CYS A 158 " distance=2.03 Simple disulfide: pdb=" SG CYS A 177 " - pdb=" SG CYS A 224 " distance=2.03 Simple disulfide: pdb=" SG CYS A 219 " - pdb=" SG CYS A 253 " distance=2.03 Simple disulfide: pdb=" SG CYS B 24 " - pdb=" SG CYS B 284 " distance=2.03 Simple disulfide: pdb=" SG CYS B 59 " - pdb=" SG CYS B 92 " distance=2.03 Simple disulfide: pdb=" SG CYS B 68 " - pdb=" SG CYS B 114 " distance=2.03 Simple disulfide: pdb=" SG CYS B 153 " - pdb=" SG CYS B 158 " distance=2.03 Simple disulfide: pdb=" SG CYS B 177 " - pdb=" SG CYS B 224 " distance=2.03 Simple disulfide: pdb=" SG CYS B 219 " - pdb=" SG CYS B 253 " distance=2.03 Simple disulfide: pdb=" SG CYS C 24 " - pdb=" SG CYS C 284 " distance=2.03 Simple disulfide: pdb=" SG CYS C 59 " - pdb=" SG CYS C 92 " distance=2.03 Simple disulfide: pdb=" SG CYS C 68 " - pdb=" SG CYS C 114 " distance=2.03 Simple disulfide: pdb=" SG CYS C 153 " - pdb=" SG CYS C 158 " distance=2.03 Simple disulfide: pdb=" SG CYS C 177 " - pdb=" SG CYS C 224 " distance=2.03 Simple disulfide: pdb=" SG CYS C 219 " - pdb=" SG CYS C 253 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.80 Conformation dependent library (CDL) restraints added in 880.6 milliseconds 2558 Ramachandran restraints generated. 1279 Oldfield, 0 Emsley, 1279 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2376 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 22 sheets defined 24.3% alpha, 33.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain 'A' and resid 24 through 29 removed outlier: 3.643A pdb=" N SER A 28 " --> pdb=" O PRO A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 101 Processing helix chain 'A' and resid 148 through 150 No H-bonds generated for 'chain 'A' and resid 148 through 150' Processing helix chain 'A' and resid 172 through 179 Processing helix chain 'A' and resid 194 through 198 Processing helix chain 'A' and resid 241 through 249 removed outlier: 3.910A pdb=" N ARG A 249 " --> pdb=" O PHE A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 293 Processing helix chain 'A' and resid 298 through 306 Processing helix chain 'A' and resid 370 through 372 No H-bonds generated for 'chain 'A' and resid 370 through 372' Processing helix chain 'A' and resid 383 through 400 removed outlier: 3.607A pdb=" N LEU A 398 " --> pdb=" O SER A 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 29 Processing helix chain 'B' and resid 88 through 101 Processing helix chain 'B' and resid 148 through 150 No H-bonds generated for 'chain 'B' and resid 148 through 150' Processing helix chain 'B' and resid 172 through 179 Processing helix chain 'B' and resid 194 through 198 removed outlier: 3.602A pdb=" N LEU B 198 " --> pdb=" O LEU B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 248 Processing helix chain 'B' and resid 265 through 294 removed outlier: 3.534A pdb=" N ILE B 278 " --> pdb=" O ASP B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 306 removed outlier: 3.585A pdb=" N LEU B 305 " --> pdb=" O ASP B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 372 No H-bonds generated for 'chain 'B' and resid 370 through 372' Processing helix chain 'B' and resid 383 through 400 Processing helix chain 'C' and resid 24 through 29 Processing helix chain 'C' and resid 88 through 101 Processing helix chain 'C' and resid 148 through 150 No H-bonds generated for 'chain 'C' and resid 148 through 150' Processing helix chain 'C' and resid 172 through 179 Processing helix chain 'C' and resid 194 through 198 Processing helix chain 'C' and resid 241 through 249 removed outlier: 3.791A pdb=" N ARG C 249 " --> pdb=" O PHE C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 266 through 293 removed outlier: 3.871A pdb=" N ILE C 278 " --> pdb=" O ASP C 274 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 306 Processing helix chain 'C' and resid 370 through 372 No H-bonds generated for 'chain 'C' and resid 370 through 372' Processing helix chain 'C' and resid 383 through 400 Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 7 Processing sheet with id=AA2, first strand: chain 'A' and resid 15 through 16 Processing sheet with id=AA3, first strand: chain 'A' and resid 213 through 214 removed outlier: 7.812A pdb=" N TRP A 236 " --> pdb=" O PRO A 46 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N MET A 239 " --> pdb=" O TRP A 227 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N TRP A 227 " --> pdb=" O MET A 239 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 120 through 122 removed outlier: 4.069A pdb=" N THR A 120 " --> pdb=" O CYS A 68 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 152 through 153 removed outlier: 3.502A pdb=" N GLU A 142 " --> pdb=" O ASP A 137 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N HIS A 80 " --> pdb=" O PHE A 425 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N PHE A 425 " --> pdb=" O HIS A 80 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 339 through 340 Processing sheet with id=AA7, first strand: chain 'B' and resid 2 through 7 Processing sheet with id=AA8, first strand: chain 'B' and resid 15 through 16 Processing sheet with id=AA9, first strand: chain 'B' and resid 210 through 214 removed outlier: 4.438A pdb=" N ALA B 211 " --> pdb=" O SER B 207 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N SER B 207 " --> pdb=" O ALA B 211 " (cutoff:3.500A) removed outlier: 8.077A pdb=" N TRP B 236 " --> pdb=" O PRO B 46 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N MET B 239 " --> pdb=" O TRP B 227 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N TRP B 227 " --> pdb=" O MET B 239 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N CYS B 219 " --> pdb=" O ARG B 230 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 53 through 54 Processing sheet with id=AB2, first strand: chain 'B' and resid 76 through 85 removed outlier: 3.948A pdb=" N ALA B 61 " --> pdb=" O PHE B 85 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 115 through 116 removed outlier: 5.748A pdb=" N GLY B 115 " --> pdb=" O PHE B 70 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 260 through 261 Processing sheet with id=AB5, first strand: chain 'B' and resid 339 through 340 removed outlier: 3.590A pdb=" N GLU B 367 " --> pdb=" O ARG B 375 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 2 through 7 Processing sheet with id=AB7, first strand: chain 'C' and resid 15 through 16 Processing sheet with id=AB8, first strand: chain 'C' and resid 213 through 214 removed outlier: 4.450A pdb=" N MET C 239 " --> pdb=" O TRP C 227 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N TRP C 227 " --> pdb=" O MET C 239 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AC1, first strand: chain 'C' and resid 81 through 83 removed outlier: 3.507A pdb=" N THR C 130 " --> pdb=" O MET C 58 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 81 through 83 Processing sheet with id=AC3, first strand: chain 'C' and resid 260 through 261 removed outlier: 3.784A pdb=" N GLN C 403 " --> pdb=" O ALA C 261 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 339 through 340 466 hydrogen bonds defined for protein. 1218 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.85 Time building geometry restraints manager: 1.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1661 1.31 - 1.44: 3038 1.44 - 1.56: 5643 1.56 - 1.69: 2 1.69 - 1.82: 90 Bond restraints: 10434 Sorted by residual: bond pdb=" N PRO B 159 " pdb=" CA PRO B 159 " ideal model delta sigma weight residual 1.465 1.406 0.059 1.19e-02 7.06e+03 2.47e+01 bond pdb=" C PRO B 159 " pdb=" O PRO B 159 " ideal model delta sigma weight residual 1.233 1.180 0.053 1.18e-02 7.18e+03 1.98e+01 bond pdb=" C THR B 166 " pdb=" O THR B 166 " ideal model delta sigma weight residual 1.235 1.202 0.033 1.14e-02 7.69e+03 8.62e+00 bond pdb=" N VAL B 161 " pdb=" CA VAL B 161 " ideal model delta sigma weight residual 1.462 1.492 -0.030 1.14e-02 7.69e+03 6.94e+00 bond pdb=" CB PRO C 159 " pdb=" CG PRO C 159 " ideal model delta sigma weight residual 1.492 1.619 -0.127 5.00e-02 4.00e+02 6.46e+00 ... (remaining 10429 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.74: 13828 1.74 - 3.48: 309 3.48 - 5.22: 62 5.22 - 6.97: 9 6.97 - 8.71: 5 Bond angle restraints: 14213 Sorted by residual: angle pdb=" C GLN C 416 " pdb=" CA GLN C 416 " pdb=" CB GLN C 416 " ideal model delta sigma weight residual 116.54 109.67 6.87 1.15e+00 7.56e-01 3.57e+01 angle pdb=" N PRO B 159 " pdb=" CA PRO B 159 " pdb=" C PRO B 159 " ideal model delta sigma weight residual 111.41 103.82 7.59 1.50e+00 4.44e-01 2.56e+01 angle pdb=" CA VAL B 161 " pdb=" C VAL B 161 " pdb=" O VAL B 161 " ideal model delta sigma weight residual 121.27 116.27 5.00 1.04e+00 9.25e-01 2.31e+01 angle pdb=" CA PRO C 159 " pdb=" N PRO C 159 " pdb=" CD PRO C 159 " ideal model delta sigma weight residual 112.00 105.60 6.40 1.40e+00 5.10e-01 2.09e+01 angle pdb=" CA GLN C 416 " pdb=" C GLN C 416 " pdb=" N LEU C 417 " ideal model delta sigma weight residual 119.52 116.38 3.14 7.90e-01 1.60e+00 1.58e+01 ... (remaining 14208 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.68: 5351 17.68 - 35.36: 555 35.36 - 53.04: 195 53.04 - 70.71: 40 70.71 - 88.39: 9 Dihedral angle restraints: 6150 sinusoidal: 2439 harmonic: 3711 Sorted by residual: dihedral pdb=" CB CYS B 59 " pdb=" SG CYS B 59 " pdb=" SG CYS B 92 " pdb=" CB CYS B 92 " ideal model delta sinusoidal sigma weight residual 93.00 169.48 -76.48 1 1.00e+01 1.00e-02 7.36e+01 dihedral pdb=" CB CYS C 68 " pdb=" SG CYS C 68 " pdb=" SG CYS C 114 " pdb=" CB CYS C 114 " ideal model delta sinusoidal sigma weight residual 93.00 23.10 69.90 1 1.00e+01 1.00e-02 6.30e+01 dihedral pdb=" CB CYS C 24 " pdb=" SG CYS C 24 " pdb=" SG CYS C 284 " pdb=" CB CYS C 284 " ideal model delta sinusoidal sigma weight residual -86.00 -142.07 56.07 1 1.00e+01 1.00e-02 4.24e+01 ... (remaining 6147 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 1171 0.048 - 0.096: 256 0.096 - 0.144: 66 0.144 - 0.192: 7 0.192 - 0.240: 3 Chirality restraints: 1503 Sorted by residual: chirality pdb=" CA THR B 165 " pdb=" N THR B 165 " pdb=" C THR B 165 " pdb=" CB THR B 165 " both_signs ideal model delta sigma weight residual False 2.53 2.29 0.24 2.00e-01 2.50e+01 1.45e+00 chirality pdb=" CA THR B 166 " pdb=" N THR B 166 " pdb=" C THR B 166 " pdb=" CB THR B 166 " both_signs ideal model delta sigma weight residual False 2.53 2.75 -0.22 2.00e-01 2.50e+01 1.22e+00 chirality pdb=" CB THR C 67 " pdb=" CA THR C 67 " pdb=" OG1 THR C 67 " pdb=" CG2 THR C 67 " both_signs ideal model delta sigma weight residual False 2.55 2.36 0.19 2.00e-01 2.50e+01 9.46e-01 ... (remaining 1500 not shown) Planarity restraints: 1829 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN C 106 " 0.047 5.00e-02 4.00e+02 7.19e-02 8.27e+00 pdb=" N PRO C 107 " -0.124 5.00e-02 4.00e+02 pdb=" CA PRO C 107 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO C 107 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA SER B 164 " 0.012 2.00e-02 2.50e+03 2.43e-02 5.91e+00 pdb=" C SER B 164 " -0.042 2.00e-02 2.50e+03 pdb=" O SER B 164 " 0.015 2.00e-02 2.50e+03 pdb=" N THR B 165 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER C 298 " 0.035 5.00e-02 4.00e+02 5.29e-02 4.48e+00 pdb=" N PRO C 299 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO C 299 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO C 299 " 0.029 5.00e-02 4.00e+02 ... (remaining 1826 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1132 2.75 - 3.29: 9780 3.29 - 3.83: 17449 3.83 - 4.36: 20951 4.36 - 4.90: 36489 Nonbonded interactions: 85801 Sorted by model distance: nonbonded pdb=" OD1 ASP B 280 " pdb=" OH TYR B 385 " model vdw 2.213 3.040 nonbonded pdb=" OH TYR A 139 " pdb=" O PHE A 405 " model vdw 2.252 3.040 nonbonded pdb=" NE1 TRP C 357 " pdb=" O ASP C 359 " model vdw 2.256 3.120 nonbonded pdb=" OD1 ASP A 274 " pdb=" NH1 ARG A 277 " model vdw 2.263 3.120 nonbonded pdb=" OD2 ASP A 192 " pdb=" OG SER A 197 " model vdw 2.286 3.040 ... (remaining 85796 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 1 through 7 or resid 9 through 32 or resid 34 through 426) \ ) selection = (chain 'B' and (resid 1 through 7 or resid 9 through 32 or resid 34 through 426) \ ) selection = (chain 'C' and (resid 1 through 7 or resid 9 through 32 or resid 34 through 426) \ ) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.13 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.570 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 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 : 0.004 0.127 10452 Z= 0.176 Angle : 0.668 8.706 14249 Z= 0.384 Chirality : 0.045 0.240 1503 Planarity : 0.006 0.072 1829 Dihedral : 16.323 88.392 3720 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.48 % Favored : 95.44 % Rotamer: Outliers : 2.06 % Allowed : 21.81 % Favored : 76.14 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.87 (0.24), residues: 1279 helix: 0.17 (0.30), residues: 283 sheet: -1.90 (0.31), residues: 229 loop : -0.34 (0.24), residues: 767 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 83 TYR 0.028 0.001 TYR C 380 PHE 0.012 0.001 PHE B 326 TRP 0.018 0.001 TRP B 227 HIS 0.005 0.001 HIS B 49 Details of bonding type rmsd covalent geometry : bond 0.00354 (10434) covalent geometry : angle 0.66388 (14213) SS BOND : bond 0.00270 ( 18) SS BOND : angle 1.63016 ( 36) hydrogen bonds : bond 0.14705 ( 462) hydrogen bonds : angle 7.01685 ( 1218) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2558 Ramachandran restraints generated. 1279 Oldfield, 0 Emsley, 1279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2558 Ramachandran restraints generated. 1279 Oldfield, 0 Emsley, 1279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 126 time to evaluate : 0.399 Fit side-chains REVERT: B 184 MET cc_start: 0.8271 (ptp) cc_final: 0.8050 (ptp) REVERT: C 255 GLU cc_start: 0.7597 (tp30) cc_final: 0.7330 (tt0) outliers start: 22 outliers final: 16 residues processed: 143 average time/residue: 0.4958 time to fit residues: 77.3022 Evaluate side-chains 127 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 111 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 260 SER Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 20 ASN Chi-restraints excluded: chain B residue 35 ASP Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 208 ASN Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain C residue 24 CYS Chi-restraints excluded: chain C residue 404 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 108 optimal weight: 2.9990 chunk 49 optimal weight: 8.9990 chunk 97 optimal weight: 1.9990 chunk 113 optimal weight: 0.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 123 optimal weight: 3.9990 chunk 65 optimal weight: 0.1980 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.5980 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 163 ASN ** B 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 22 HIS ** C 80 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 = 0.3702 r_free = 0.3702 target = 0.152300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.120422 restraints weight = 22552.878| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 2.57 r_work: 0.3136 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2966 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2966 r_free = 0.2966 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2966 r_free = 0.2966 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2966 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.0904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 10452 Z= 0.234 Angle : 0.647 7.478 14249 Z= 0.336 Chirality : 0.046 0.216 1503 Planarity : 0.006 0.063 1829 Dihedral : 5.682 43.753 1396 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.80 % Favored : 95.13 % Rotamer: Outliers : 3.75 % Allowed : 19.21 % Favored : 77.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.24), residues: 1279 helix: 0.60 (0.31), residues: 289 sheet: -1.67 (0.31), residues: 240 loop : -0.28 (0.24), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 83 TYR 0.025 0.002 TYR C 380 PHE 0.014 0.002 PHE A 2 TRP 0.019 0.002 TRP B 227 HIS 0.005 0.001 HIS C 49 Details of bonding type rmsd covalent geometry : bond 0.00558 (10434) covalent geometry : angle 0.63910 (14213) SS BOND : bond 0.00285 ( 18) SS BOND : angle 2.10169 ( 36) hydrogen bonds : bond 0.04746 ( 462) hydrogen bonds : angle 5.92861 ( 1218) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2558 Ramachandran restraints generated. 1279 Oldfield, 0 Emsley, 1279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2558 Ramachandran restraints generated. 1279 Oldfield, 0 Emsley, 1279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 118 time to evaluate : 0.399 Fit side-chains REVERT: B 42 GLN cc_start: 0.8563 (OUTLIER) cc_final: 0.7502 (tm-30) REVERT: B 239 MET cc_start: 0.8262 (mtp) cc_final: 0.7922 (mtp) REVERT: B 242 LYS cc_start: 0.8028 (OUTLIER) cc_final: 0.7711 (mmmt) REVERT: C 85 PHE cc_start: 0.7545 (t80) cc_final: 0.7124 (t80) REVERT: C 255 GLU cc_start: 0.7909 (tp30) cc_final: 0.7530 (tt0) outliers start: 40 outliers final: 17 residues processed: 146 average time/residue: 0.5162 time to fit residues: 81.7378 Evaluate side-chains 134 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 115 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 375 ARG Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 42 GLN Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 180 ASN Chi-restraints excluded: chain B residue 242 LYS Chi-restraints excluded: chain B residue 350 THR Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain C residue 24 CYS Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 386 MET Chi-restraints excluded: chain C residue 404 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 78 optimal weight: 0.9990 chunk 20 optimal weight: 0.8980 chunk 45 optimal weight: 0.0040 chunk 22 optimal weight: 0.6980 chunk 101 optimal weight: 1.9990 chunk 123 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 37 optimal weight: 0.4980 chunk 61 optimal weight: 0.5980 chunk 83 optimal weight: 4.9990 chunk 91 optimal weight: 10.0000 overall best weight: 0.5392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 22 HIS ** C 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 162 HIS ** C 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.153962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.120536 restraints weight = 29219.024| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 4.04 r_work: 0.3093 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3093 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3093 r_free = 0.3093 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3092 r_free = 0.3092 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3092 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.1056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10452 Z= 0.146 Angle : 0.585 6.818 14249 Z= 0.303 Chirality : 0.044 0.188 1503 Planarity : 0.005 0.059 1829 Dihedral : 5.342 53.593 1380 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.87 % Favored : 95.05 % Rotamer: Outliers : 3.22 % Allowed : 19.57 % Favored : 77.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.24), residues: 1279 helix: 0.83 (0.31), residues: 289 sheet: -1.81 (0.30), residues: 258 loop : -0.30 (0.25), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 375 TYR 0.019 0.001 TYR C 380 PHE 0.011 0.001 PHE C 210 TRP 0.017 0.001 TRP B 227 HIS 0.004 0.001 HIS C 162 Details of bonding type rmsd covalent geometry : bond 0.00345 (10434) covalent geometry : angle 0.57816 (14213) SS BOND : bond 0.00277 ( 18) SS BOND : angle 1.89638 ( 36) hydrogen bonds : bond 0.03908 ( 462) hydrogen bonds : angle 5.62642 ( 1218) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2558 Ramachandran restraints generated. 1279 Oldfield, 0 Emsley, 1279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2558 Ramachandran restraints generated. 1279 Oldfield, 0 Emsley, 1279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 118 time to evaluate : 0.240 Fit side-chains REVERT: A 342 ARG cc_start: 0.7738 (OUTLIER) cc_final: 0.7495 (mtm110) REVERT: B 239 MET cc_start: 0.8198 (mtp) cc_final: 0.7559 (mtp) REVERT: B 242 LYS cc_start: 0.7946 (OUTLIER) cc_final: 0.7730 (mmmt) REVERT: C 47 LYS cc_start: 0.7384 (ttmt) cc_final: 0.7179 (tmmm) REVERT: C 255 GLU cc_start: 0.7938 (tp30) cc_final: 0.7511 (tt0) outliers start: 34 outliers final: 14 residues processed: 141 average time/residue: 0.4645 time to fit residues: 71.0348 Evaluate side-chains 129 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 113 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 114 CYS Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 342 ARG Chi-restraints excluded: chain A residue 375 ARG Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 242 LYS Chi-restraints excluded: chain B residue 350 THR Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 146 SER Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 258 SER Chi-restraints excluded: chain C residue 404 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 13 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 1 optimal weight: 0.7980 chunk 75 optimal weight: 0.5980 chunk 123 optimal weight: 0.3980 chunk 94 optimal weight: 0.5980 chunk 60 optimal weight: 0.7980 chunk 43 optimal weight: 2.9990 chunk 6 optimal weight: 4.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 22 HIS ** C 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 162 HIS ** C 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.154197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.121416 restraints weight = 22915.270| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 2.93 r_work: 0.3158 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3163 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3163 r_free = 0.3163 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3162 r_free = 0.3162 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3162 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.1194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 10452 Z= 0.157 Angle : 0.577 7.852 14249 Z= 0.299 Chirality : 0.043 0.193 1503 Planarity : 0.005 0.058 1829 Dihedral : 4.960 44.146 1377 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.64 % Favored : 95.28 % Rotamer: Outliers : 3.13 % Allowed : 19.93 % Favored : 76.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.24), residues: 1279 helix: 0.90 (0.31), residues: 289 sheet: -1.89 (0.32), residues: 216 loop : -0.31 (0.24), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 375 TYR 0.017 0.001 TYR A 380 PHE 0.011 0.001 PHE C 210 TRP 0.018 0.001 TRP B 227 HIS 0.003 0.001 HIS C 60 Details of bonding type rmsd covalent geometry : bond 0.00370 (10434) covalent geometry : angle 0.57075 (14213) SS BOND : bond 0.00270 ( 18) SS BOND : angle 1.82084 ( 36) hydrogen bonds : bond 0.03747 ( 462) hydrogen bonds : angle 5.52234 ( 1218) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2558 Ramachandran restraints generated. 1279 Oldfield, 0 Emsley, 1279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2558 Ramachandran restraints generated. 1279 Oldfield, 0 Emsley, 1279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 125 time to evaluate : 0.396 Fit side-chains REVERT: B 42 GLN cc_start: 0.8337 (OUTLIER) cc_final: 0.7145 (tm-30) REVERT: B 194 GLU cc_start: 0.7181 (OUTLIER) cc_final: 0.6888 (tp30) REVERT: C 221 MET cc_start: 0.8560 (ptp) cc_final: 0.8185 (ptm) REVERT: C 255 GLU cc_start: 0.7776 (tp30) cc_final: 0.7375 (tp30) outliers start: 33 outliers final: 17 residues processed: 148 average time/residue: 0.5708 time to fit residues: 90.6093 Evaluate side-chains 130 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 111 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 114 CYS Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 375 ARG Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 42 GLN Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 194 GLU Chi-restraints excluded: chain B residue 350 THR Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain C residue 24 CYS Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 404 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 20 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 18 optimal weight: 0.6980 chunk 121 optimal weight: 0.8980 chunk 118 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 chunk 51 optimal weight: 0.9990 chunk 67 optimal weight: 0.5980 chunk 43 optimal weight: 0.0030 chunk 94 optimal weight: 0.0570 chunk 25 optimal weight: 0.7980 overall best weight: 0.4308 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 HIS A ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 162 HIS ** C 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 403 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.155936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.123202 restraints weight = 26068.832| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 3.49 r_work: 0.3162 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3151 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3151 r_free = 0.3151 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3151 r_free = 0.3151 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3151 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.1345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10452 Z= 0.130 Angle : 0.559 6.344 14249 Z= 0.289 Chirality : 0.043 0.181 1503 Planarity : 0.005 0.057 1829 Dihedral : 4.815 47.744 1376 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.48 % Favored : 95.44 % Rotamer: Outliers : 2.86 % Allowed : 20.29 % Favored : 76.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.47 (0.24), residues: 1279 helix: 1.01 (0.31), residues: 289 sheet: -1.82 (0.33), residues: 210 loop : -0.30 (0.23), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 375 TYR 0.017 0.001 TYR C 325 PHE 0.010 0.001 PHE C 210 TRP 0.016 0.001 TRP B 227 HIS 0.003 0.001 HIS B 407 Details of bonding type rmsd covalent geometry : bond 0.00304 (10434) covalent geometry : angle 0.55269 (14213) SS BOND : bond 0.00313 ( 18) SS BOND : angle 1.77935 ( 36) hydrogen bonds : bond 0.03501 ( 462) hydrogen bonds : angle 5.41064 ( 1218) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2558 Ramachandran restraints generated. 1279 Oldfield, 0 Emsley, 1279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2558 Ramachandran restraints generated. 1279 Oldfield, 0 Emsley, 1279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 127 time to evaluate : 0.375 Fit side-chains REVERT: B 42 GLN cc_start: 0.8369 (OUTLIER) cc_final: 0.7160 (tm-30) REVERT: B 180 ASN cc_start: 0.7916 (OUTLIER) cc_final: 0.7667 (t0) REVERT: B 194 GLU cc_start: 0.7207 (OUTLIER) cc_final: 0.6935 (tp30) REVERT: B 239 MET cc_start: 0.8150 (mtp) cc_final: 0.7942 (mtp) REVERT: C 221 MET cc_start: 0.8528 (ptp) cc_final: 0.8182 (ptm) REVERT: C 255 GLU cc_start: 0.7703 (tp30) cc_final: 0.7308 (tp30) outliers start: 30 outliers final: 18 residues processed: 150 average time/residue: 0.3860 time to fit residues: 63.5469 Evaluate side-chains 138 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 117 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 114 CYS Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 375 ARG Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 42 GLN Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 180 ASN Chi-restraints excluded: chain B residue 194 GLU Chi-restraints excluded: chain B residue 350 THR Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain C residue 24 CYS Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 146 SER Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 258 SER Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 404 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 42 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 chunk 76 optimal weight: 0.9980 chunk 70 optimal weight: 0.7980 chunk 111 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 116 optimal weight: 0.5980 chunk 32 optimal weight: 0.5980 chunk 83 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 22 HIS C 162 HIS ** C 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.153697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.119763 restraints weight = 33296.794| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 4.47 r_work: 0.3050 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3048 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3048 r_free = 0.3048 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3049 r_free = 0.3049 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3049 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.1450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 10452 Z= 0.178 Angle : 0.587 7.179 14249 Z= 0.302 Chirality : 0.044 0.194 1503 Planarity : 0.005 0.055 1829 Dihedral : 4.689 26.116 1374 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.17 % Favored : 95.75 % Rotamer: Outliers : 3.04 % Allowed : 20.82 % Favored : 76.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.24), residues: 1279 helix: 0.96 (0.31), residues: 289 sheet: -1.90 (0.32), residues: 216 loop : -0.30 (0.23), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 375 TYR 0.018 0.002 TYR C 325 PHE 0.011 0.001 PHE C 210 TRP 0.017 0.001 TRP B 227 HIS 0.004 0.001 HIS B 133 Details of bonding type rmsd covalent geometry : bond 0.00424 (10434) covalent geometry : angle 0.57892 (14213) SS BOND : bond 0.00305 ( 18) SS BOND : angle 1.95813 ( 36) hydrogen bonds : bond 0.03742 ( 462) hydrogen bonds : angle 5.48060 ( 1218) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2558 Ramachandran restraints generated. 1279 Oldfield, 0 Emsley, 1279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2558 Ramachandran restraints generated. 1279 Oldfield, 0 Emsley, 1279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 116 time to evaluate : 0.501 Fit side-chains REVERT: A 35 ASP cc_start: 0.8362 (OUTLIER) cc_final: 0.8090 (m-30) REVERT: B 42 GLN cc_start: 0.8383 (OUTLIER) cc_final: 0.7175 (tm-30) REVERT: B 180 ASN cc_start: 0.7955 (OUTLIER) cc_final: 0.7698 (t0) REVERT: B 239 MET cc_start: 0.8307 (mtp) cc_final: 0.7975 (mtp) REVERT: C 221 MET cc_start: 0.8651 (ptp) cc_final: 0.8267 (ptm) REVERT: C 255 GLU cc_start: 0.7851 (tp30) cc_final: 0.7423 (tt0) outliers start: 32 outliers final: 20 residues processed: 142 average time/residue: 0.4538 time to fit residues: 70.7112 Evaluate side-chains 138 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 115 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 114 CYS Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 375 ARG Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 42 GLN Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 180 ASN Chi-restraints excluded: chain B residue 350 THR Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain C residue 24 CYS Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 146 SER Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 258 SER Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 404 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 32 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 80 optimal weight: 0.0980 chunk 11 optimal weight: 0.3980 chunk 88 optimal weight: 3.9990 chunk 93 optimal weight: 0.0470 chunk 56 optimal weight: 2.9990 chunk 102 optimal weight: 0.5980 chunk 24 optimal weight: 0.9990 chunk 49 optimal weight: 5.9990 chunk 59 optimal weight: 0.4980 overall best weight: 0.3278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 162 HIS ** C 208 ASN ** 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 = 0.3772 r_free = 0.3772 target = 0.156801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.123399 restraints weight = 32210.272| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 4.57 r_work: 0.3101 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3096 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3096 r_free = 0.3096 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3096 r_free = 0.3096 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3096 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.1515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10452 Z= 0.117 Angle : 0.553 7.534 14249 Z= 0.285 Chirality : 0.042 0.178 1503 Planarity : 0.005 0.055 1829 Dihedral : 4.565 25.797 1374 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.64 % Favored : 95.28 % Rotamer: Outliers : 2.23 % Allowed : 21.89 % Favored : 75.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.24), residues: 1279 helix: 1.16 (0.31), residues: 289 sheet: -1.78 (0.33), residues: 210 loop : -0.26 (0.23), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 375 TYR 0.019 0.001 TYR C 325 PHE 0.010 0.001 PHE C 210 TRP 0.016 0.001 TRP B 227 HIS 0.003 0.001 HIS B 407 Details of bonding type rmsd covalent geometry : bond 0.00272 (10434) covalent geometry : angle 0.54617 (14213) SS BOND : bond 0.00282 ( 18) SS BOND : angle 1.75090 ( 36) hydrogen bonds : bond 0.03369 ( 462) hydrogen bonds : angle 5.29020 ( 1218) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2558 Ramachandran restraints generated. 1279 Oldfield, 0 Emsley, 1279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2558 Ramachandran restraints generated. 1279 Oldfield, 0 Emsley, 1279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 128 time to evaluate : 0.411 Fit side-chains REVERT: A 35 ASP cc_start: 0.8327 (m-30) cc_final: 0.8058 (m-30) REVERT: A 156 TYR cc_start: 0.7467 (t80) cc_final: 0.7236 (t80) REVERT: B 30 LEU cc_start: 0.9005 (mt) cc_final: 0.8696 (mm) REVERT: B 42 GLN cc_start: 0.8367 (OUTLIER) cc_final: 0.7205 (tm-30) REVERT: B 45 MET cc_start: 0.8167 (mtp) cc_final: 0.7847 (mtt) REVERT: B 180 ASN cc_start: 0.7910 (OUTLIER) cc_final: 0.7660 (t0) REVERT: B 194 GLU cc_start: 0.7204 (OUTLIER) cc_final: 0.6918 (tp30) REVERT: B 239 MET cc_start: 0.8225 (mtp) cc_final: 0.7912 (mtp) REVERT: C 221 MET cc_start: 0.8594 (ptp) cc_final: 0.8216 (ptm) REVERT: C 255 GLU cc_start: 0.7819 (tp30) cc_final: 0.7490 (tp30) outliers start: 23 outliers final: 16 residues processed: 147 average time/residue: 0.4798 time to fit residues: 77.3141 Evaluate side-chains 141 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 122 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 114 CYS Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 375 ARG Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 42 GLN Chi-restraints excluded: chain B residue 180 ASN Chi-restraints excluded: chain B residue 194 GLU Chi-restraints excluded: chain B residue 350 THR Chi-restraints excluded: chain C residue 24 CYS Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 404 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 87 optimal weight: 0.5980 chunk 54 optimal weight: 0.7980 chunk 67 optimal weight: 0.0000 chunk 0 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 92 optimal weight: 5.9990 chunk 13 optimal weight: 0.6980 chunk 22 optimal weight: 0.6980 chunk 112 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 116 optimal weight: 0.9990 overall best weight: 0.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 162 HIS C 208 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.155752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.124158 restraints weight = 23185.131| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 2.76 r_work: 0.3183 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3157 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3157 r_free = 0.3157 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3157 r_free = 0.3157 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3157 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.1592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 10452 Z= 0.144 Angle : 0.567 7.822 14249 Z= 0.292 Chirality : 0.043 0.184 1503 Planarity : 0.005 0.055 1829 Dihedral : 4.603 25.597 1374 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.17 % Favored : 95.75 % Rotamer: Outliers : 2.32 % Allowed : 22.43 % Favored : 75.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.24), residues: 1279 helix: 1.12 (0.30), residues: 289 sheet: -1.71 (0.30), residues: 258 loop : -0.21 (0.24), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 375 TYR 0.028 0.001 TYR B 209 PHE 0.010 0.001 PHE C 405 TRP 0.016 0.001 TRP B 227 HIS 0.003 0.001 HIS B 407 Details of bonding type rmsd covalent geometry : bond 0.00343 (10434) covalent geometry : angle 0.56043 (14213) SS BOND : bond 0.00284 ( 18) SS BOND : angle 1.83414 ( 36) hydrogen bonds : bond 0.03465 ( 462) hydrogen bonds : angle 5.29362 ( 1218) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2558 Ramachandran restraints generated. 1279 Oldfield, 0 Emsley, 1279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2558 Ramachandran restraints generated. 1279 Oldfield, 0 Emsley, 1279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 120 time to evaluate : 0.397 Fit side-chains REVERT: A 35 ASP cc_start: 0.8079 (m-30) cc_final: 0.7863 (m-30) REVERT: B 30 LEU cc_start: 0.9024 (mt) cc_final: 0.8776 (mm) REVERT: B 42 GLN cc_start: 0.8346 (OUTLIER) cc_final: 0.7129 (tm-30) REVERT: B 180 ASN cc_start: 0.7900 (OUTLIER) cc_final: 0.7684 (t0) REVERT: B 194 GLU cc_start: 0.7186 (OUTLIER) cc_final: 0.6974 (tp30) REVERT: B 239 MET cc_start: 0.8194 (mtp) cc_final: 0.7897 (mtp) REVERT: C 182 ILE cc_start: 0.8254 (pt) cc_final: 0.8030 (pp) REVERT: C 200 LYS cc_start: 0.7977 (mttm) cc_final: 0.7419 (mmtm) REVERT: C 221 MET cc_start: 0.8578 (ptp) cc_final: 0.8236 (ptm) outliers start: 24 outliers final: 19 residues processed: 139 average time/residue: 0.4988 time to fit residues: 75.9339 Evaluate side-chains 141 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 119 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 114 CYS Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 375 ARG Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 42 GLN Chi-restraints excluded: chain B residue 180 ASN Chi-restraints excluded: chain B residue 194 GLU Chi-restraints excluded: chain B residue 350 THR Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain C residue 24 CYS Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 146 SER Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 258 SER Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 404 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 4 optimal weight: 2.9990 chunk 120 optimal weight: 0.9980 chunk 49 optimal weight: 0.9980 chunk 118 optimal weight: 0.8980 chunk 36 optimal weight: 0.0770 chunk 13 optimal weight: 0.7980 chunk 42 optimal weight: 1.9990 chunk 79 optimal weight: 0.5980 chunk 32 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 2 optimal weight: 0.0170 overall best weight: 0.4776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 163 ASN ** B 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 162 HIS C 208 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.156317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.122917 restraints weight = 29728.464| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 4.12 r_work: 0.3114 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3106 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3106 r_free = 0.3106 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3105 r_free = 0.3105 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3105 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.1662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10452 Z= 0.134 Angle : 0.566 9.736 14249 Z= 0.291 Chirality : 0.043 0.180 1503 Planarity : 0.005 0.053 1829 Dihedral : 4.597 24.579 1374 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.32 % Favored : 95.60 % Rotamer: Outliers : 2.59 % Allowed : 22.25 % Favored : 75.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.24), residues: 1279 helix: 1.20 (0.31), residues: 289 sheet: -1.68 (0.30), residues: 258 loop : -0.19 (0.24), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 375 TYR 0.022 0.001 TYR B 209 PHE 0.010 0.001 PHE C 210 TRP 0.018 0.001 TRP B 227 HIS 0.003 0.001 HIS B 407 Details of bonding type rmsd covalent geometry : bond 0.00317 (10434) covalent geometry : angle 0.55963 (14213) SS BOND : bond 0.00274 ( 18) SS BOND : angle 1.73159 ( 36) hydrogen bonds : bond 0.03408 ( 462) hydrogen bonds : angle 5.27252 ( 1218) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2558 Ramachandran restraints generated. 1279 Oldfield, 0 Emsley, 1279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2558 Ramachandran restraints generated. 1279 Oldfield, 0 Emsley, 1279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 122 time to evaluate : 0.416 Fit side-chains REVERT: A 35 ASP cc_start: 0.8335 (m-30) cc_final: 0.8083 (m-30) REVERT: B 30 LEU cc_start: 0.9019 (mt) cc_final: 0.8726 (mm) REVERT: B 42 GLN cc_start: 0.8355 (OUTLIER) cc_final: 0.7179 (tm-30) REVERT: B 194 GLU cc_start: 0.7196 (OUTLIER) cc_final: 0.6972 (tp30) REVERT: B 239 MET cc_start: 0.8235 (mtp) cc_final: 0.7951 (mtp) REVERT: C 182 ILE cc_start: 0.8223 (pt) cc_final: 0.7984 (pp) REVERT: C 200 LYS cc_start: 0.8050 (mttm) cc_final: 0.7365 (mmtm) REVERT: C 221 MET cc_start: 0.8591 (ptp) cc_final: 0.8240 (ptm) REVERT: C 255 GLU cc_start: 0.7857 (tp30) cc_final: 0.7544 (tt0) outliers start: 27 outliers final: 24 residues processed: 144 average time/residue: 0.4739 time to fit residues: 74.7642 Evaluate side-chains 145 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 119 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 CYS Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 114 CYS Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 219 CYS Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 375 ARG Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 42 GLN Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 194 GLU Chi-restraints excluded: chain B residue 350 THR Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain C residue 24 CYS Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 146 SER Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 208 ASN Chi-restraints excluded: chain C residue 258 SER Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 404 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 109 optimal weight: 0.9990 chunk 14 optimal weight: 0.7980 chunk 27 optimal weight: 0.8980 chunk 63 optimal weight: 1.9990 chunk 123 optimal weight: 0.6980 chunk 104 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 101 optimal weight: 0.0980 chunk 78 optimal weight: 0.0040 chunk 66 optimal weight: 0.0170 chunk 79 optimal weight: 0.9980 overall best weight: 0.3030 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 163 ASN ** B 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 162 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.156413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.123328 restraints weight = 31148.275| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 4.38 r_work: 0.3108 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3094 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3094 r_free = 0.3094 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3094 r_free = 0.3094 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3094 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.1681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.204 10452 Z= 0.219 Angle : 0.849 58.957 14249 Z= 0.498 Chirality : 0.043 0.332 1503 Planarity : 0.005 0.053 1829 Dihedral : 4.597 24.506 1374 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.32 % Favored : 95.60 % Rotamer: Outliers : 2.59 % Allowed : 22.88 % Favored : 74.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.24), residues: 1279 helix: 1.22 (0.31), residues: 289 sheet: -1.67 (0.30), residues: 258 loop : -0.19 (0.24), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 375 TYR 0.020 0.001 TYR B 209 PHE 0.010 0.001 PHE C 210 TRP 0.017 0.001 TRP B 227 HIS 0.003 0.001 HIS B 407 Details of bonding type rmsd covalent geometry : bond 0.00443 (10434) covalent geometry : angle 0.84577 (14213) SS BOND : bond 0.00271 ( 18) SS BOND : angle 1.72207 ( 36) hydrogen bonds : bond 0.03408 ( 462) hydrogen bonds : angle 5.27175 ( 1218) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2558 Ramachandran restraints generated. 1279 Oldfield, 0 Emsley, 1279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2558 Ramachandran restraints generated. 1279 Oldfield, 0 Emsley, 1279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 119 time to evaluate : 0.407 Fit side-chains REVERT: A 35 ASP cc_start: 0.8319 (m-30) cc_final: 0.8069 (m-30) REVERT: B 30 LEU cc_start: 0.9013 (mt) cc_final: 0.8711 (mm) REVERT: B 42 GLN cc_start: 0.8347 (OUTLIER) cc_final: 0.7166 (tm-30) REVERT: B 194 GLU cc_start: 0.7201 (OUTLIER) cc_final: 0.6964 (tp30) REVERT: B 221 MET cc_start: 0.7145 (ptt) cc_final: 0.6857 (ptm) REVERT: B 239 MET cc_start: 0.8240 (mtp) cc_final: 0.7954 (mtp) REVERT: C 182 ILE cc_start: 0.8222 (pt) cc_final: 0.7968 (pp) REVERT: C 200 LYS cc_start: 0.8053 (mttm) cc_final: 0.7349 (mmtm) REVERT: C 221 MET cc_start: 0.8608 (ptp) cc_final: 0.8246 (ptm) REVERT: C 255 GLU cc_start: 0.7856 (tp30) cc_final: 0.7540 (tt0) outliers start: 27 outliers final: 23 residues processed: 141 average time/residue: 0.4914 time to fit residues: 75.5887 Evaluate side-chains 143 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 118 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 CYS Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 114 CYS Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 219 CYS Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 375 ARG Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 42 GLN Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 194 GLU Chi-restraints excluded: chain B residue 350 THR Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain C residue 24 CYS Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 146 SER Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 258 SER Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 404 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 69 optimal weight: 0.7980 chunk 28 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 81 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 67 optimal weight: 0.8980 chunk 108 optimal weight: 0.6980 chunk 93 optimal weight: 0.4980 chunk 73 optimal weight: 0.9990 chunk 6 optimal weight: 0.8980 chunk 85 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 163 ASN ** B 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 162 HIS ** C 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.156435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.122941 restraints weight = 29193.052| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 3.81 r_work: 0.3135 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3132 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3132 r_free = 0.3132 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3132 r_free = 0.3132 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3132 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.1681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.204 10452 Z= 0.219 Angle : 0.849 58.960 14249 Z= 0.498 Chirality : 0.043 0.332 1503 Planarity : 0.005 0.053 1829 Dihedral : 4.597 24.506 1374 Min Nonbonded Distance : 1.666 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.32 % Favored : 95.60 % Rotamer: Outliers : 2.50 % Allowed : 22.97 % Favored : 74.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.24), residues: 1279 helix: 1.22 (0.31), residues: 289 sheet: -1.67 (0.30), residues: 258 loop : -0.19 (0.24), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 375 TYR 0.020 0.001 TYR B 209 PHE 0.010 0.001 PHE C 210 TRP 0.017 0.001 TRP B 227 HIS 0.003 0.001 HIS B 407 Details of bonding type rmsd covalent geometry : bond 0.00443 (10434) covalent geometry : angle 0.84576 (14213) SS BOND : bond 0.00271 ( 18) SS BOND : angle 1.72205 ( 36) hydrogen bonds : bond 0.03408 ( 462) hydrogen bonds : angle 5.27175 ( 1218) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3393.81 seconds wall clock time: 58 minutes 51.87 seconds (3531.87 seconds total)