Starting phenix.real_space_refine on Wed Mar 4 01:47:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ofj_20047/03_2026/6ofj_20047.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ofj_20047/03_2026/6ofj_20047.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6ofj_20047/03_2026/6ofj_20047.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ofj_20047/03_2026/6ofj_20047.map" model { file = "/net/cci-nas-00/data/ceres_data/6ofj_20047/03_2026/6ofj_20047.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ofj_20047/03_2026/6ofj_20047.cif" } resolution = 4.5 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= 0.002 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 S 52 5.16 5 C 3442 2.51 5 N 796 2.21 5 O 878 1.98 5 H 5142 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 34 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10310 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 5155 Classifications: {'peptide': 325} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 18, 'TRANS': 306} Chain: "B" Number of atoms: 5155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 5155 Classifications: {'peptide': 325} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 18, 'TRANS': 306} Time building chain proxies: 1.87, per 1000 atoms: 0.18 Number of scatterers: 10310 At special positions: 0 Unit cell: (93.96, 52.65, 85.86, 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 52 16.00 O 878 8.00 N 796 7.00 C 3442 6.00 H 5142 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 110 " - pdb=" SG CYS A 187 " distance=2.03 Simple disulfide: pdb=" SG CYS B 110 " - pdb=" SG CYS B 187 " 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: 0.78 Conformation dependent library (CDL) restraints added in 331.8 milliseconds 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1212 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 2 sheets defined 71.4% alpha, 1.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.16 Creating SS restraints... Processing helix chain 'A' and resid 14 through 18 removed outlier: 3.573A pdb=" N THR A 17 " --> pdb=" O SER A 14 " (cutoff:3.500A) Processing helix chain 'A' and resid 33 through 65 removed outlier: 3.815A pdb=" N PHE A 37 " --> pdb=" O GLU A 33 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LEU A 47 " --> pdb=" O TYR A 43 " (cutoff:3.500A) Proline residue: A 53 - end of helix Processing helix chain 'A' and resid 70 through 90 removed outlier: 4.020A pdb=" N TYR A 74 " --> pdb=" O THR A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 101 removed outlier: 3.797A pdb=" N THR A 94 " --> pdb=" O GLY A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 141 removed outlier: 3.631A pdb=" N GLY A 114 " --> pdb=" O CYS A 110 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N PHE A 115 " --> pdb=" O ASN A 111 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N PHE A 116 " --> pdb=" O LEU A 112 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ALA A 117 " --> pdb=" O GLU A 113 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N THR A 118 " --> pdb=" O GLY A 114 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N LEU A 119 " --> pdb=" O PHE A 115 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N LEU A 128 " --> pdb=" O ALA A 124 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N VAL A 129 " --> pdb=" O LEU A 125 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N VAL A 130 " --> pdb=" O TRP A 126 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU A 131 " --> pdb=" O SER A 127 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLU A 134 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 168 Processing helix chain 'A' and resid 169 through 173 Processing helix chain 'A' and resid 200 through 212 removed outlier: 3.574A pdb=" N VAL A 210 " --> pdb=" O TYR A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 224 removed outlier: 3.580A pdb=" N LEU A 216 " --> pdb=" O PHE A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 278 Proline residue: A 267 - end of helix removed outlier: 4.156A pdb=" N ALA A 272 " --> pdb=" O TYR A 268 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N TYR A 274 " --> pdb=" O GLY A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 295 removed outlier: 3.809A pdb=" N MET A 288 " --> pdb=" O GLY A 284 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ILE A 290 " --> pdb=" O ILE A 286 " (cutoff:3.500A) Proline residue: A 291 - end of helix removed outlier: 3.999A pdb=" N ALA A 295 " --> pdb=" O PRO A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 300 removed outlier: 5.672A pdb=" N ALA A 299 " --> pdb=" O LYS A 296 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL A 300 " --> pdb=" O THR A 297 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 296 through 300' Processing helix chain 'A' and resid 301 through 310 removed outlier: 3.825A pdb=" N ILE A 305 " --> pdb=" O TYR A 301 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N TYR A 306 " --> pdb=" O ASN A 302 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N MET A 309 " --> pdb=" O ILE A 305 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ASN A 310 " --> pdb=" O TYR A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 322 removed outlier: 4.792A pdb=" N CYS A 322 " --> pdb=" O VAL A 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 14 through 18 removed outlier: 3.572A pdb=" N THR B 17 " --> pdb=" O SER B 14 " (cutoff:3.500A) Processing helix chain 'B' and resid 33 through 65 removed outlier: 3.815A pdb=" N PHE B 37 " --> pdb=" O GLU B 33 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LEU B 47 " --> pdb=" O TYR B 43 " (cutoff:3.500A) Proline residue: B 53 - end of helix Processing helix chain 'B' and resid 70 through 90 removed outlier: 4.020A pdb=" N TYR B 74 " --> pdb=" O THR B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 101 removed outlier: 3.797A pdb=" N THR B 94 " --> pdb=" O GLY B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 141 removed outlier: 3.631A pdb=" N GLY B 114 " --> pdb=" O CYS B 110 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N PHE B 115 " --> pdb=" O ASN B 111 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N PHE B 116 " --> pdb=" O LEU B 112 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ALA B 117 " --> pdb=" O GLU B 113 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N THR B 118 " --> pdb=" O GLY B 114 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N LEU B 119 " --> pdb=" O PHE B 115 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N LEU B 128 " --> pdb=" O ALA B 124 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N VAL B 129 " --> pdb=" O LEU B 125 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N VAL B 130 " --> pdb=" O TRP B 126 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LEU B 131 " --> pdb=" O SER B 127 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLU B 134 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 168 Processing helix chain 'B' and resid 169 through 173 Processing helix chain 'B' and resid 200 through 212 removed outlier: 3.574A pdb=" N VAL B 210 " --> pdb=" O TYR B 206 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 224 removed outlier: 3.579A pdb=" N LEU B 216 " --> pdb=" O PHE B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 278 Proline residue: B 267 - end of helix removed outlier: 4.156A pdb=" N ALA B 272 " --> pdb=" O TYR B 268 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N TYR B 274 " --> pdb=" O GLY B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 295 removed outlier: 3.808A pdb=" N MET B 288 " --> pdb=" O GLY B 284 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ILE B 290 " --> pdb=" O ILE B 286 " (cutoff:3.500A) Proline residue: B 291 - end of helix removed outlier: 3.999A pdb=" N ALA B 295 " --> pdb=" O PRO B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 300 removed outlier: 5.671A pdb=" N ALA B 299 " --> pdb=" O LYS B 296 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL B 300 " --> pdb=" O THR B 297 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 296 through 300' Processing helix chain 'B' and resid 301 through 310 removed outlier: 3.824A pdb=" N ILE B 305 " --> pdb=" O TYR B 301 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N TYR B 306 " --> pdb=" O ASN B 302 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N MET B 309 " --> pdb=" O ILE B 305 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ASN B 310 " --> pdb=" O TYR B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 322 removed outlier: 4.791A pdb=" N CYS B 322 " --> pdb=" O VAL B 318 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 179 through 181 removed outlier: 3.589A pdb=" N ILE A 179 " --> pdb=" O GLY A 188 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 179 through 181 removed outlier: 3.589A pdb=" N ILE B 179 " --> pdb=" O GLY B 188 " (cutoff:3.500A) 286 hydrogen bonds defined for protein. 834 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: 2.05 Time building geometry restraints manager: 1.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 5126 1.03 - 1.23: 18 1.23 - 1.42: 2308 1.42 - 1.62: 2938 1.62 - 1.81: 84 Bond restraints: 10474 Sorted by residual: bond pdb=" N MET B 1 " pdb=" H3 MET B 1 " ideal model delta sigma weight residual 0.890 0.961 -0.071 2.00e-02 2.50e+03 1.25e+01 bond pdb=" N MET A 1 " pdb=" H2 MET A 1 " ideal model delta sigma weight residual 0.890 0.961 -0.071 2.00e-02 2.50e+03 1.25e+01 bond pdb=" N MET B 1 " pdb=" H2 MET B 1 " ideal model delta sigma weight residual 0.890 0.960 -0.070 2.00e-02 2.50e+03 1.22e+01 bond pdb=" N MET A 1 " pdb=" H3 MET A 1 " ideal model delta sigma weight residual 0.890 0.959 -0.069 2.00e-02 2.50e+03 1.20e+01 bond pdb=" CB LYS A 325 " pdb=" CG LYS A 325 " ideal model delta sigma weight residual 1.520 1.601 -0.081 3.00e-02 1.11e+03 7.33e+00 ... (remaining 10469 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.10: 18177 2.10 - 4.20: 602 4.20 - 6.29: 94 6.29 - 8.39: 16 8.39 - 10.49: 5 Bond angle restraints: 18894 Sorted by residual: angle pdb=" N ALA A 169 " pdb=" CA ALA A 169 " pdb=" C ALA A 169 " ideal model delta sigma weight residual 109.81 118.10 -8.29 2.21e+00 2.05e-01 1.41e+01 angle pdb=" N ALA B 169 " pdb=" CA ALA B 169 " pdb=" C ALA B 169 " ideal model delta sigma weight residual 109.81 118.08 -8.27 2.21e+00 2.05e-01 1.40e+01 angle pdb=" N PRO A 170 " pdb=" CA PRO A 170 " pdb=" C PRO A 170 " ideal model delta sigma weight residual 110.70 114.99 -4.29 1.22e+00 6.72e-01 1.24e+01 angle pdb=" H1 MET A 1 " pdb=" N MET A 1 " pdb=" H3 MET A 1 " ideal model delta sigma weight residual 109.47 98.98 10.49 3.00e+00 1.11e-01 1.22e+01 angle pdb=" N PRO B 170 " pdb=" CA PRO B 170 " pdb=" C PRO B 170 " ideal model delta sigma weight residual 110.70 114.93 -4.23 1.22e+00 6.72e-01 1.20e+01 ... (remaining 18889 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.97: 4349 15.97 - 31.94: 501 31.94 - 47.92: 130 47.92 - 63.89: 50 63.89 - 79.86: 8 Dihedral angle restraints: 5038 sinusoidal: 2580 harmonic: 2458 Sorted by residual: dihedral pdb=" CB CYS B 110 " pdb=" SG CYS B 110 " pdb=" SG CYS B 187 " pdb=" CB CYS B 187 " ideal model delta sinusoidal sigma weight residual -86.00 -120.97 34.97 1 1.00e+01 1.00e-02 1.73e+01 dihedral pdb=" CB CYS A 110 " pdb=" SG CYS A 110 " pdb=" SG CYS A 187 " pdb=" CB CYS A 187 " ideal model delta sinusoidal sigma weight residual -86.00 -120.96 34.96 1 1.00e+01 1.00e-02 1.73e+01 dihedral pdb=" CA PHE A 221 " pdb=" C PHE A 221 " pdb=" N CYS A 222 " pdb=" CA CYS A 222 " ideal model delta harmonic sigma weight residual 180.00 159.24 20.76 0 5.00e+00 4.00e-02 1.72e+01 ... (remaining 5035 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 468 0.033 - 0.066: 220 0.066 - 0.099: 85 0.099 - 0.132: 26 0.132 - 0.165: 9 Chirality restraints: 808 Sorted by residual: chirality pdb=" CA ILE A 179 " pdb=" N ILE A 179 " pdb=" C ILE A 179 " pdb=" CB ILE A 179 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 6.82e-01 chirality pdb=" CA ILE B 179 " pdb=" N ILE B 179 " pdb=" C ILE B 179 " pdb=" CB ILE B 179 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 6.81e-01 chirality pdb=" CA PRO B 71 " pdb=" N PRO B 71 " pdb=" C PRO B 71 " pdb=" CB PRO B 71 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.16 2.00e-01 2.50e+01 6.25e-01 ... (remaining 805 not shown) Planarity restraints: 1516 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 70 " 0.030 5.00e-02 4.00e+02 4.54e-02 3.30e+00 pdb=" N PRO A 71 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO A 71 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 71 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 70 " -0.030 5.00e-02 4.00e+02 4.52e-02 3.26e+00 pdb=" N PRO B 71 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO B 71 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 71 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 302 " 0.030 5.00e-02 4.00e+02 4.51e-02 3.25e+00 pdb=" N PRO A 303 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO A 303 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 303 " 0.026 5.00e-02 4.00e+02 ... (remaining 1513 not shown) Histogram of nonbonded interaction distances: 1.77 - 2.34: 2817 2.34 - 2.90: 22232 2.90 - 3.47: 25912 3.47 - 4.03: 32708 4.03 - 4.60: 48833 Nonbonded interactions: 132502 Sorted by model distance: nonbonded pdb=" OG1 THR A 198 " pdb="HD21 ASN A 200 " model vdw 1.773 2.450 nonbonded pdb=" OG1 THR B 198 " pdb="HD21 ASN B 200 " model vdw 1.774 2.450 nonbonded pdb=" HZ3 LYS A 245 " pdb=" OE1 GLU A 249 " model vdw 1.797 2.450 nonbonded pdb=" HZ3 LYS B 245 " pdb=" OE1 GLU B 249 " model vdw 1.797 2.450 nonbonded pdb=" OE1 GLU B 196 " pdb=" H GLU B 196 " model vdw 1.800 2.450 ... (remaining 132497 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints Number of NCS constrained groups: 1 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'B' } Set refine NCS operators NCS operators will be refined. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=0.98 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: 0.490 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: 0.030 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.020 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3698 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 : 0.007 0.081 5334 Z= 0.278 Angle : 0.960 9.412 7268 Z= 0.491 Chirality : 0.046 0.165 808 Planarity : 0.006 0.045 904 Dihedral : 15.744 79.861 1846 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.12 % Favored : 92.88 % Rotamer: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % 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: -4.36 (0.26), residues: 646 helix: -2.60 (0.20), residues: 382 sheet: None (None), residues: 0 loop : -3.23 (0.33), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 252 TYR 0.020 0.002 TYR A 301 PHE 0.018 0.002 PHE B 159 TRP 0.004 0.001 TRP A 265 HIS 0.004 0.001 HIS B 152 Details of bonding type rmsd covalent geometry : bond 0.00671 ( 5332) covalent geometry : angle 0.96046 ( 7264) SS BOND : bond 0.00331 ( 2) SS BOND : angle 0.47379 ( 4) hydrogen bonds : bond 0.15683 ( 286) hydrogen bonds : angle 7.39055 ( 834) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 0.128 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 LEU cc_start: 0.7454 (mm) cc_final: 0.7166 (mm) REVERT: A 126 TRP cc_start: 0.3005 (m100) cc_final: 0.2313 (m100) outliers start: 0 outliers final: 0 residues processed: 69 average time/residue: 0.1250 time to fit residues: 10.2791 Evaluate side-chains 51 residues out of total 277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 49 optimal weight: 0.0050 chunk 53 optimal weight: 0.0970 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 0.4980 chunk 62 optimal weight: 10.0000 chunk 51 optimal weight: 5.9990 chunk 38 optimal weight: 9.9990 chunk 61 optimal weight: 20.0000 chunk 45 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 17 optimal weight: 0.0670 overall best weight: 0.7332 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 184 GLN B 200 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4756 r_free = 0.4756 target = 0.155409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4466 r_free = 0.4466 target = 0.127051 restraints weight = 45776.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4506 r_free = 0.4506 target = 0.130457 restraints weight = 33828.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4532 r_free = 0.4532 target = 0.132987 restraints weight = 26815.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4550 r_free = 0.4550 target = 0.134892 restraints weight = 22304.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4565 r_free = 0.4565 target = 0.136403 restraints weight = 19166.248| |-----------------------------------------------------------------------------| r_work (final): 0.4332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5308 moved from start: 0.2718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5334 Z= 0.128 Angle : 0.636 9.689 7268 Z= 0.334 Chirality : 0.040 0.127 808 Planarity : 0.005 0.031 904 Dihedral : 5.583 16.760 698 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % 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: -3.19 (0.28), residues: 646 helix: -1.55 (0.22), residues: 394 sheet: None (None), residues: 0 loop : -2.94 (0.35), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG A 21 TYR 0.025 0.002 TYR A 191 PHE 0.037 0.001 PHE A 276 TRP 0.006 0.001 TRP A 35 HIS 0.003 0.001 HIS B 278 Details of bonding type rmsd covalent geometry : bond 0.00272 ( 5332) covalent geometry : angle 0.63583 ( 7264) SS BOND : bond 0.00179 ( 2) SS BOND : angle 0.66460 ( 4) hydrogen bonds : bond 0.05178 ( 286) hydrogen bonds : angle 5.64135 ( 834) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 646 Ramachandran restraints generated. 323 Oldfield, 0 Emsley, 323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 646 Ramachandran restraints generated. 323 Oldfield, 0 Emsley, 323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.103 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 87 VAL cc_start: 0.9244 (p) cc_final: 0.8724 (p) REVERT: B 181 GLU cc_start: 0.7298 (mp0) cc_final: 0.6793 (mp0) REVERT: B 256 ILE cc_start: 0.9230 (mm) cc_final: 0.8951 (tt) outliers start: 0 outliers final: 0 residues processed: 61 average time/residue: 0.1038 time to fit residues: 7.7459 Evaluate side-chains 52 residues out of total 277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 11 optimal weight: 10.0000 chunk 16 optimal weight: 0.9990 chunk 50 optimal weight: 0.3980 chunk 49 optimal weight: 0.8980 chunk 22 optimal weight: 10.0000 chunk 28 optimal weight: 5.9990 chunk 13 optimal weight: 1.9990 chunk 3 optimal weight: 10.0000 chunk 5 optimal weight: 3.9990 chunk 51 optimal weight: 10.0000 chunk 36 optimal weight: 9.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4449 r_free = 0.4449 target = 0.139508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.107264 restraints weight = 42293.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.110136 restraints weight = 32143.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.112496 restraints weight = 26696.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.114379 restraints weight = 22989.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.115862 restraints weight = 20360.142| |-----------------------------------------------------------------------------| r_work (final): 0.4208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5556 moved from start: 0.3936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5334 Z= 0.120 Angle : 0.573 6.380 7268 Z= 0.303 Chirality : 0.037 0.131 808 Planarity : 0.004 0.028 904 Dihedral : 5.078 15.637 698 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.91 % Favored : 90.09 % Rotamer: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % 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: -3.11 (0.28), residues: 646 helix: -1.41 (0.22), residues: 396 sheet: None (None), residues: 0 loop : -3.08 (0.34), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 135 TYR 0.009 0.001 TYR B 74 PHE 0.020 0.001 PHE B 276 TRP 0.007 0.001 TRP B 35 HIS 0.005 0.001 HIS A 278 Details of bonding type rmsd covalent geometry : bond 0.00264 ( 5332) covalent geometry : angle 0.57267 ( 7264) SS BOND : bond 0.00058 ( 2) SS BOND : angle 0.61957 ( 4) hydrogen bonds : bond 0.04329 ( 286) hydrogen bonds : angle 5.17973 ( 834) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 646 Ramachandran restraints generated. 323 Oldfield, 0 Emsley, 323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 646 Ramachandran restraints generated. 323 Oldfield, 0 Emsley, 323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 0.127 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: symmetry clash revert: symmetry clash REVERT: B 44 MET cc_start: 0.9345 (mtp) cc_final: 0.8937 (ttm) REVERT: B 87 VAL cc_start: 0.9012 (p) cc_final: 0.8753 (p) REVERT: B 135 ARG cc_start: 0.9379 (mmp-170) cc_final: 0.9029 (mmp80) REVERT: B 253 MET cc_start: 0.8194 (tpp) cc_final: 0.7851 (tpp) REVERT: B 256 ILE cc_start: 0.9251 (mm) cc_final: 0.8930 (tt) outliers start: 0 outliers final: 0 residues processed: 60 average time/residue: 0.1256 time to fit residues: 8.9819 Evaluate side-chains 48 residues out of total 277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 0.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 50 optimal weight: 7.9990 chunk 52 optimal weight: 8.9990 chunk 40 optimal weight: 9.9990 chunk 13 optimal weight: 0.2980 chunk 12 optimal weight: 0.2980 chunk 30 optimal weight: 9.9990 chunk 10 optimal weight: 0.7980 chunk 22 optimal weight: 9.9990 chunk 62 optimal weight: 9.9990 chunk 11 optimal weight: 5.9990 chunk 55 optimal weight: 10.0000 overall best weight: 3.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 73 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4404 r_free = 0.4404 target = 0.136537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.116936 restraints weight = 55397.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.119417 restraints weight = 43575.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.121347 restraints weight = 35822.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.122872 restraints weight = 30326.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.124053 restraints weight = 26450.953| |-----------------------------------------------------------------------------| r_work (final): 0.4175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5479 moved from start: 0.4887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5334 Z= 0.152 Angle : 0.603 5.037 7268 Z= 0.332 Chirality : 0.039 0.142 808 Planarity : 0.005 0.044 904 Dihedral : 5.192 15.637 698 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.60 % Favored : 90.40 % Rotamer: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % 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: -3.25 (0.27), residues: 646 helix: -1.46 (0.22), residues: 394 sheet: None (None), residues: 0 loop : -3.24 (0.32), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 135 TYR 0.016 0.002 TYR B 274 PHE 0.020 0.002 PHE B 261 TRP 0.006 0.001 TRP A 175 HIS 0.008 0.001 HIS A 278 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 5332) covalent geometry : angle 0.60264 ( 7264) SS BOND : bond 0.00109 ( 2) SS BOND : angle 0.57490 ( 4) hydrogen bonds : bond 0.04358 ( 286) hydrogen bonds : angle 5.28115 ( 834) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 646 Ramachandran restraints generated. 323 Oldfield, 0 Emsley, 323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 646 Ramachandran restraints generated. 323 Oldfield, 0 Emsley, 323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.132 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 44 MET cc_start: 0.9368 (mtp) cc_final: 0.8898 (ttm) REVERT: B 87 VAL cc_start: 0.9103 (p) cc_final: 0.8808 (p) outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.0984 time to fit residues: 6.8136 Evaluate side-chains 50 residues out of total 277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 51 optimal weight: 10.0000 chunk 52 optimal weight: 8.9990 chunk 41 optimal weight: 9.9990 chunk 33 optimal weight: 0.1980 chunk 56 optimal weight: 5.9990 chunk 45 optimal weight: 4.9990 chunk 14 optimal weight: 3.9990 chunk 43 optimal weight: 10.0000 chunk 49 optimal weight: 0.6980 chunk 25 optimal weight: 7.9990 chunk 47 optimal weight: 10.0000 overall best weight: 3.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.133576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.115135 restraints weight = 55277.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.117569 restraints weight = 42506.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.119375 restraints weight = 34579.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.120689 restraints weight = 29267.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.121713 restraints weight = 25685.759| |-----------------------------------------------------------------------------| r_work (final): 0.4148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5484 moved from start: 0.5512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5334 Z= 0.157 Angle : 0.601 5.277 7268 Z= 0.331 Chirality : 0.038 0.131 808 Planarity : 0.005 0.037 904 Dihedral : 5.246 18.635 698 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.91 % Favored : 90.09 % Rotamer: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % 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: -3.15 (0.28), residues: 646 helix: -1.36 (0.22), residues: 394 sheet: None (None), residues: 0 loop : -3.25 (0.33), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 135 TYR 0.014 0.002 TYR A 274 PHE 0.014 0.001 PHE A 273 TRP 0.007 0.001 TRP B 175 HIS 0.008 0.002 HIS A 278 Details of bonding type rmsd covalent geometry : bond 0.00342 ( 5332) covalent geometry : angle 0.60115 ( 7264) SS BOND : bond 0.00042 ( 2) SS BOND : angle 0.61356 ( 4) hydrogen bonds : bond 0.04051 ( 286) hydrogen bonds : angle 5.17444 ( 834) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 646 Ramachandran restraints generated. 323 Oldfield, 0 Emsley, 323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 646 Ramachandran restraints generated. 323 Oldfield, 0 Emsley, 323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 0.138 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 87 VAL cc_start: 0.9279 (p) cc_final: 0.8902 (p) REVERT: B 256 ILE cc_start: 0.8546 (mt) cc_final: 0.8298 (tt) outliers start: 0 outliers final: 0 residues processed: 53 average time/residue: 0.0953 time to fit residues: 6.3748 Evaluate side-chains 46 residues out of total 277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 27 optimal weight: 0.6980 chunk 7 optimal weight: 0.9990 chunk 48 optimal weight: 4.9990 chunk 60 optimal weight: 7.9990 chunk 36 optimal weight: 20.0000 chunk 6 optimal weight: 8.9990 chunk 14 optimal weight: 0.9990 chunk 63 optimal weight: 0.0010 chunk 5 optimal weight: 0.5980 chunk 21 optimal weight: 4.9990 chunk 15 optimal weight: 9.9990 overall best weight: 0.6590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4376 r_free = 0.4376 target = 0.135983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.116630 restraints weight = 52276.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.119256 restraints weight = 40132.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.121221 restraints weight = 32309.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.122723 restraints weight = 27004.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.123851 restraints weight = 23240.699| |-----------------------------------------------------------------------------| r_work (final): 0.4176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5386 moved from start: 0.5670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 5334 Z= 0.100 Angle : 0.525 4.862 7268 Z= 0.279 Chirality : 0.037 0.134 808 Planarity : 0.004 0.032 904 Dihedral : 4.855 16.846 698 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.98 % Favored : 91.02 % Rotamer: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % 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: -2.63 (0.30), residues: 646 helix: -0.90 (0.24), residues: 394 sheet: None (None), residues: 0 loop : -3.10 (0.35), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 135 TYR 0.006 0.001 TYR B 74 PHE 0.012 0.001 PHE A 37 TRP 0.005 0.000 TRP A 35 HIS 0.005 0.001 HIS A 211 Details of bonding type rmsd covalent geometry : bond 0.00215 ( 5332) covalent geometry : angle 0.52538 ( 7264) SS BOND : bond 0.00009 ( 2) SS BOND : angle 0.51766 ( 4) hydrogen bonds : bond 0.03675 ( 286) hydrogen bonds : angle 4.84201 ( 834) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 646 Ramachandran restraints generated. 323 Oldfield, 0 Emsley, 323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 646 Ramachandran restraints generated. 323 Oldfield, 0 Emsley, 323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 0.080 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 87 VAL cc_start: 0.9228 (p) cc_final: 0.8841 (p) outliers start: 0 outliers final: 0 residues processed: 53 average time/residue: 0.1120 time to fit residues: 7.3282 Evaluate side-chains 48 residues out of total 277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 0.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 55 optimal weight: 0.0270 chunk 63 optimal weight: 5.9990 chunk 8 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 chunk 61 optimal weight: 10.0000 chunk 51 optimal weight: 1.9990 chunk 32 optimal weight: 9.9990 chunk 35 optimal weight: 2.9990 chunk 38 optimal weight: 10.0000 chunk 45 optimal weight: 2.9990 chunk 58 optimal weight: 10.0000 overall best weight: 1.7844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.134808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.116074 restraints weight = 54376.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.118460 restraints weight = 42461.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.120165 restraints weight = 34834.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.121482 restraints weight = 29720.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.122504 restraints weight = 26035.587| |-----------------------------------------------------------------------------| r_work (final): 0.4154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5430 moved from start: 0.5937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 5334 Z= 0.113 Angle : 0.527 4.594 7268 Z= 0.285 Chirality : 0.037 0.125 808 Planarity : 0.004 0.033 904 Dihedral : 4.776 16.854 698 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.91 % Favored : 90.09 % Rotamer: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % 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: -2.62 (0.30), residues: 646 helix: -0.99 (0.23), residues: 398 sheet: None (None), residues: 0 loop : -2.95 (0.36), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 135 TYR 0.008 0.001 TYR A 30 PHE 0.012 0.001 PHE A 294 TRP 0.003 0.001 TRP A 35 HIS 0.005 0.001 HIS A 278 Details of bonding type rmsd covalent geometry : bond 0.00242 ( 5332) covalent geometry : angle 0.52679 ( 7264) SS BOND : bond 0.00030 ( 2) SS BOND : angle 0.35225 ( 4) hydrogen bonds : bond 0.03626 ( 286) hydrogen bonds : angle 4.82529 ( 834) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 646 Ramachandran restraints generated. 323 Oldfield, 0 Emsley, 323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 646 Ramachandran restraints generated. 323 Oldfield, 0 Emsley, 323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 0.137 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 44 MET cc_start: 0.9376 (mtp) cc_final: 0.8947 (ttm) REVERT: B 87 VAL cc_start: 0.9226 (p) cc_final: 0.8843 (p) outliers start: 0 outliers final: 0 residues processed: 53 average time/residue: 0.0951 time to fit residues: 6.3874 Evaluate side-chains 47 residues out of total 277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 1 optimal weight: 6.9990 chunk 35 optimal weight: 7.9990 chunk 63 optimal weight: 5.9990 chunk 52 optimal weight: 6.9990 chunk 31 optimal weight: 5.9990 chunk 51 optimal weight: 0.0020 chunk 18 optimal weight: 7.9990 chunk 16 optimal weight: 8.9990 chunk 14 optimal weight: 2.9990 chunk 56 optimal weight: 6.9990 chunk 42 optimal weight: 3.9990 overall best weight: 3.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 302 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.129270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.111429 restraints weight = 57137.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.113563 restraints weight = 44748.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.115189 restraints weight = 36921.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.116388 restraints weight = 31616.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.117327 restraints weight = 27946.399| |-----------------------------------------------------------------------------| r_work (final): 0.4097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5587 moved from start: 0.6854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 5334 Z= 0.186 Angle : 0.636 5.008 7268 Z= 0.359 Chirality : 0.039 0.126 808 Planarity : 0.006 0.054 904 Dihedral : 5.432 16.637 698 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.53 % Favored : 89.47 % Rotamer: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.60 (0.27), residues: 646 helix: -1.63 (0.22), residues: 392 sheet: None (None), residues: 0 loop : -3.58 (0.32), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 252 TYR 0.018 0.002 TYR B 274 PHE 0.021 0.002 PHE B 273 TRP 0.009 0.001 TRP B 126 HIS 0.010 0.002 HIS B 278 Details of bonding type rmsd covalent geometry : bond 0.00379 ( 5332) covalent geometry : angle 0.63639 ( 7264) SS BOND : bond 0.00031 ( 2) SS BOND : angle 0.21174 ( 4) hydrogen bonds : bond 0.04197 ( 286) hydrogen bonds : angle 5.18706 ( 834) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 646 Ramachandran restraints generated. 323 Oldfield, 0 Emsley, 323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 646 Ramachandran restraints generated. 323 Oldfield, 0 Emsley, 323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.127 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 44 MET cc_start: 0.9355 (mtp) cc_final: 0.8773 (ttm) REVERT: B 87 VAL cc_start: 0.9256 (p) cc_final: 0.8883 (p) REVERT: B 126 TRP cc_start: 0.5638 (m100) cc_final: 0.5359 (m100) REVERT: B 253 MET cc_start: 0.7894 (mmm) cc_final: 0.7316 (tpp) outliers start: 0 outliers final: 0 residues processed: 52 average time/residue: 0.0967 time to fit residues: 6.2579 Evaluate side-chains 46 residues out of total 277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 2 optimal weight: 1.9990 chunk 17 optimal weight: 6.9990 chunk 16 optimal weight: 10.0000 chunk 19 optimal weight: 0.9990 chunk 15 optimal weight: 8.9990 chunk 31 optimal weight: 6.9990 chunk 14 optimal weight: 2.9990 chunk 32 optimal weight: 9.9990 chunk 28 optimal weight: 7.9990 chunk 5 optimal weight: 0.0770 chunk 18 optimal weight: 9.9990 overall best weight: 2.6146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.124025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.095089 restraints weight = 36528.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.098823 restraints weight = 24871.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.101301 restraints weight = 19067.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.102934 restraints weight = 15660.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.103922 restraints weight = 13629.936| |-----------------------------------------------------------------------------| r_work (final): 0.4276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5605 moved from start: 0.7032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 5334 Z= 0.130 Angle : 0.553 4.757 7268 Z= 0.304 Chirality : 0.037 0.121 808 Planarity : 0.005 0.040 904 Dihedral : 5.124 17.456 698 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.53 % Favored : 89.47 % Rotamer: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.21 (0.28), residues: 646 helix: -1.32 (0.23), residues: 392 sheet: None (None), residues: 0 loop : -3.41 (0.33), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 135 TYR 0.008 0.001 TYR B 74 PHE 0.023 0.001 PHE A 159 TRP 0.006 0.001 TRP B 126 HIS 0.005 0.002 HIS A 278 Details of bonding type rmsd covalent geometry : bond 0.00275 ( 5332) covalent geometry : angle 0.55270 ( 7264) SS BOND : bond 0.00023 ( 2) SS BOND : angle 0.31385 ( 4) hydrogen bonds : bond 0.03869 ( 286) hydrogen bonds : angle 4.96839 ( 834) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 646 Ramachandran restraints generated. 323 Oldfield, 0 Emsley, 323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 646 Ramachandran restraints generated. 323 Oldfield, 0 Emsley, 323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.131 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 44 MET cc_start: 0.9301 (mtp) cc_final: 0.8753 (ttm) REVERT: B 87 VAL cc_start: 0.9232 (p) cc_final: 0.8900 (p) REVERT: B 253 MET cc_start: 0.7601 (mmm) cc_final: 0.7187 (tpp) outliers start: 0 outliers final: 0 residues processed: 52 average time/residue: 0.0940 time to fit residues: 6.1843 Evaluate side-chains 44 residues out of total 277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 11 optimal weight: 9.9990 chunk 3 optimal weight: 0.1980 chunk 7 optimal weight: 2.9990 chunk 44 optimal weight: 0.5980 chunk 56 optimal weight: 0.0770 chunk 34 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 40 optimal weight: 8.9990 chunk 15 optimal weight: 1.9990 chunk 62 optimal weight: 7.9990 chunk 33 optimal weight: 0.9980 overall best weight: 0.7740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 2 ASN B 279 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4374 r_free = 0.4374 target = 0.132980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.114054 restraints weight = 55085.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.116380 restraints weight = 43156.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.118096 restraints weight = 35245.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.119398 restraints weight = 29997.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.120452 restraints weight = 26381.704| |-----------------------------------------------------------------------------| r_work (final): 0.4153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5482 moved from start: 0.7306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 5334 Z= 0.103 Angle : 0.531 4.280 7268 Z= 0.285 Chirality : 0.037 0.127 808 Planarity : 0.004 0.035 904 Dihedral : 4.778 16.737 698 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.67 % Favored : 91.33 % Rotamer: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.58 (0.30), residues: 646 helix: -1.00 (0.23), residues: 408 sheet: None (None), residues: 0 loop : -2.91 (0.38), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 135 TYR 0.021 0.002 TYR B 192 PHE 0.024 0.001 PHE B 159 TRP 0.005 0.001 TRP A 35 HIS 0.002 0.001 HIS B 278 Details of bonding type rmsd covalent geometry : bond 0.00223 ( 5332) covalent geometry : angle 0.53142 ( 7264) SS BOND : bond 0.00067 ( 2) SS BOND : angle 0.30906 ( 4) hydrogen bonds : bond 0.03671 ( 286) hydrogen bonds : angle 4.71468 ( 834) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 646 Ramachandran restraints generated. 323 Oldfield, 0 Emsley, 323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 646 Ramachandran restraints generated. 323 Oldfield, 0 Emsley, 323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 0.141 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 44 MET cc_start: 0.9259 (mtp) cc_final: 0.8743 (ttm) REVERT: B 87 VAL cc_start: 0.9236 (p) cc_final: 0.8883 (p) REVERT: B 253 MET cc_start: 0.7544 (mmm) cc_final: 0.7113 (tpp) outliers start: 0 outliers final: 0 residues processed: 51 average time/residue: 0.1003 time to fit residues: 6.3795 Evaluate side-chains 45 residues out of total 277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 31 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 chunk 44 optimal weight: 0.9980 chunk 14 optimal weight: 7.9990 chunk 32 optimal weight: 9.9990 chunk 23 optimal weight: 6.9990 chunk 53 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 8 optimal weight: 5.9990 chunk 39 optimal weight: 2.9990 chunk 49 optimal weight: 5.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.132574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.113783 restraints weight = 55669.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.116087 restraints weight = 43416.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.117826 restraints weight = 35582.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.119140 restraints weight = 30239.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.120179 restraints weight = 26512.963| |-----------------------------------------------------------------------------| r_work (final): 0.4148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5503 moved from start: 0.7454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 5334 Z= 0.103 Angle : 0.522 4.496 7268 Z= 0.278 Chirality : 0.037 0.121 808 Planarity : 0.004 0.036 904 Dihedral : 4.550 16.665 698 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.36 % Favored : 91.64 % Rotamer: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.43 (0.30), residues: 646 helix: -0.87 (0.23), residues: 412 sheet: None (None), residues: 0 loop : -2.91 (0.39), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 135 TYR 0.008 0.001 TYR B 74 PHE 0.020 0.001 PHE A 159 TRP 0.004 0.001 TRP A 35 HIS 0.002 0.001 HIS A 100 Details of bonding type rmsd covalent geometry : bond 0.00220 ( 5332) covalent geometry : angle 0.52256 ( 7264) SS BOND : bond 0.00055 ( 2) SS BOND : angle 0.18972 ( 4) hydrogen bonds : bond 0.03521 ( 286) hydrogen bonds : angle 4.61251 ( 834) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1335.11 seconds wall clock time: 23 minutes 24.26 seconds (1404.26 seconds total)