Starting phenix.real_space_refine on Fri Sep 11 14:56:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ofj_20047/09_2026/6ofj_20047.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ofj_20047/09_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_20047/09_2026/6ofj_20047.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ofj_20047/09_2026/6ofj_20047.map" model { file = "/net/cci-nas-00/data/ceres_data/6ofj_20047/09_2026/6ofj_20047.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ofj_20047/09_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-2.2.1-6174/lib/python3.11/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: 1.89, 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: 1.20 Conformation dependent library (CDL) restraints added in 272.7 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: 0.21 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: 2.35 Time building geometry restraints manager: 1.65 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: 0.010 Normalize map: mean=0, sd=1: 0.670 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: 0.070 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.970 Find NCS groups from input model: 0.070 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:1.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3306 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/Z covalent geometry : bond 0.00671 / 0.28 ( 5332) covalent geometry : angle 0.96046 / 0.49 ( 7264) SS BOND : bond 0.00331 / 0.16 ( 2) SS BOND : angle 0.47379 / 0.24 ( 4) hydrogen bonds : bond 0.15683 / 10.05 ( 286) hydrogen bonds : angle 7.39055 / 5.26 ( 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 : 0.134 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: 0.1299 time to fit residues: 10.7183 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 : 0.110 ------------------------------------------------------------------------------- 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... A 184 GLN A 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 = 0.155415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4468 r_free = 0.4468 target = 0.127112 restraints weight = 45788.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4505 r_free = 0.4505 target = 0.130410 restraints weight = 33763.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4532 r_free = 0.4532 target = 0.132977 restraints weight = 26941.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4551 r_free = 0.4551 target = 0.134902 restraints weight = 22374.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4566 r_free = 0.4566 target = 0.136455 restraints weight = 19184.369| |-----------------------------------------------------------------------------| r_work (final): 0.4350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5191 moved from start: 0.2680 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/Z covalent geometry : bond 0.00272 / 0.13 ( 5332) covalent geometry : angle 0.63583 / 0.33 ( 7264) SS BOND : bond 0.00179 / 0.09 ( 2) SS BOND : angle 0.66460 / 0.34 ( 4) hydrogen bonds : bond 0.05178 / 3.26 ( 286) hydrogen bonds : angle 5.64135 / 4.00 ( 834) *********************** REFINEMENT MACRO_CYCLE 2 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 62 residues out of total 277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 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: B 87 VAL cc_start: 0.9244 (p) cc_final: 0.8721 (p) REVERT: B 181 GLU cc_start: 0.7293 (mp0) cc_final: 0.6842 (mp0) REVERT: B 253 MET cc_start: 0.8021 (ttm) cc_final: 0.7708 (tpp) outliers start: 0 outliers final: 0 residues processed: 62 average time/residue: 0.0861 time to fit residues: 6.7555 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 : 0.081 ------------------------------------------------------------------------------- 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: 9.9990 chunk 16 optimal weight: 0.9990 chunk 50 optimal weight: 3.9990 chunk 49 optimal weight: 9.9990 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: 8.9990 chunk 36 optimal weight: 5.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 73 ASN ** B 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 184 GLN ** B 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4427 r_free = 0.4427 target = 0.137084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.117549 restraints weight = 54754.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.119773 restraints weight = 43913.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.121544 restraints weight = 36592.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.122982 restraints weight = 31556.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.123725 restraints weight = 27758.571| |-----------------------------------------------------------------------------| r_work (final): 0.4176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5465 moved from start: 0.4598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 5334 Z= 0.188 Angle : 0.655 5.697 7268 Z= 0.365 Chirality : 0.039 0.129 808 Planarity : 0.006 0.043 904 Dihedral : 5.403 17.238 698 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.36 % Favored : 91.64 % 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: -2.88 (0.28), residues: 646 helix: -1.19 (0.22), residues: 388 sheet: None (None), residues: 0 loop : -3.00 (0.34), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 252 TYR 0.016 0.002 TYR B 274 PHE 0.019 0.002 PHE B 273 TRP 0.009 0.001 TRP B 175 HIS 0.012 0.002 HIS B 278 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.19 ( 5332) covalent geometry : angle 0.65539 / 0.37 ( 7264) SS BOND : bond 0.00201 / 0.10 ( 2) SS BOND : angle 0.72341 / 0.37 ( 4) hydrogen bonds : bond 0.04931 / 3.13 ( 286) hydrogen bonds : angle 5.50502 / 3.89 ( 834) *********************** REFINEMENT MACRO_CYCLE 3 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 56 residues out of total 277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.142 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 87 VAL cc_start: 0.9143 (p) cc_final: 0.8845 (p) outliers start: 0 outliers final: 0 residues processed: 56 average time/residue: 0.0823 time to fit residues: 5.9410 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 : 0.087 ------------------------------------------------------------------------------- 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: 0.5980 chunk 52 optimal weight: 2.9990 chunk 40 optimal weight: 9.9990 chunk 13 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 30 optimal weight: 7.9990 chunk 10 optimal weight: 0.0070 chunk 22 optimal weight: 9.9990 chunk 62 optimal weight: 7.9990 chunk 11 optimal weight: 10.0000 chunk 55 optimal weight: 6.9990 overall best weight: 1.9204 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 200 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 = 0.4422 r_free = 0.4422 target = 0.138088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.118173 restraints weight = 54035.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.120576 restraints weight = 42251.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.122479 restraints weight = 34490.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.123850 restraints weight = 29302.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.124961 restraints weight = 25799.956| |-----------------------------------------------------------------------------| r_work (final): 0.4196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5375 moved from start: 0.4975 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= 0.124 Angle : 0.569 5.226 7268 Z= 0.308 Chirality : 0.038 0.134 808 Planarity : 0.004 0.038 904 Dihedral : 5.162 17.023 698 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.05 % Favored : 91.95 % 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: -2.23 (0.31), residues: 646 helix: -0.73 (0.24), residues: 398 sheet: None (None), residues: 0 loop : -2.69 (0.37), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 135 TYR 0.010 0.001 TYR A 30 PHE 0.015 0.001 PHE B 159 TRP 0.004 0.001 TRP A 35 HIS 0.006 0.001 HIS B 278 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 ( 5332) covalent geometry : angle 0.56877 / 0.31 ( 7264) SS BOND : bond 0.00090 / 0.04 ( 2) SS BOND : angle 0.74457 / 0.37 ( 4) hydrogen bonds : bond 0.04329 / 2.76 ( 286) hydrogen bonds : angle 5.24842 / 3.73 ( 834) *********************** REFINEMENT MACRO_CYCLE 4 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 53 residues out of total 277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 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: B 87 VAL cc_start: 0.9238 (p) cc_final: 0.8840 (p) outliers start: 0 outliers final: 0 residues processed: 53 average time/residue: 0.0919 time to fit residues: 6.2732 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 : 0.131 ------------------------------------------------------------------------------- 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: 0.3980 chunk 52 optimal weight: 10.0000 chunk 41 optimal weight: 20.0000 chunk 33 optimal weight: 0.5980 chunk 56 optimal weight: 7.9990 chunk 45 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 43 optimal weight: 8.9990 chunk 49 optimal weight: 0.0970 chunk 25 optimal weight: 9.9990 chunk 47 optimal weight: 8.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 200 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 = 0.4446 r_free = 0.4446 target = 0.138625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.118875 restraints weight = 54611.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.121307 restraints weight = 42737.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.123261 restraints weight = 34694.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.124671 restraints weight = 29168.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.125830 restraints weight = 25545.166| |-----------------------------------------------------------------------------| r_work (final): 0.4229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5307 moved from start: 0.5145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 5334 Z= 0.107 Angle : 0.547 5.130 7268 Z= 0.293 Chirality : 0.037 0.148 808 Planarity : 0.004 0.036 904 Dihedral : 5.030 17.823 698 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.05 % Favored : 91.95 % 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: -1.81 (0.32), residues: 646 helix: -0.43 (0.25), residues: 398 sheet: None (None), residues: 0 loop : -2.45 (0.38), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 135 TYR 0.007 0.001 TYR B 30 PHE 0.014 0.001 PHE A 37 TRP 0.004 0.000 TRP B 35 HIS 0.003 0.001 HIS B 65 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.11 ( 5332) covalent geometry : angle 0.54662 / 0.29 ( 7264) SS BOND : bond 0.00069 / 0.03 ( 2) SS BOND : angle 0.71104 / 0.35 ( 4) hydrogen bonds : bond 0.04107 / 2.62 ( 286) hydrogen bonds : angle 5.06303 / 3.59 ( 834) *********************** REFINEMENT MACRO_CYCLE 5 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 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 87 VAL cc_start: 0.9242 (p) cc_final: 0.8850 (p) REVERT: B 253 MET cc_start: 0.7176 (tpp) cc_final: 0.6940 (tpp) outliers start: 0 outliers final: 0 residues processed: 53 average time/residue: 0.0897 time to fit residues: 6.1100 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 : 0.129 ------------------------------------------------------------------------------- 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: 2.9990 chunk 7 optimal weight: 0.8980 chunk 48 optimal weight: 9.9990 chunk 60 optimal weight: 0.0770 chunk 36 optimal weight: 9.9990 chunk 6 optimal weight: 10.0000 chunk 14 optimal weight: 0.2980 chunk 63 optimal weight: 0.2980 chunk 5 optimal weight: 5.9990 chunk 21 optimal weight: 0.7980 chunk 15 optimal weight: 9.9990 overall best weight: 0.4738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 200 ASN B 302 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 = 0.4470 r_free = 0.4470 target = 0.144316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.111215 restraints weight = 42045.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.114855 restraints weight = 31155.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.117689 restraints weight = 24651.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.119930 restraints weight = 20415.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.121644 restraints weight = 17553.409| |-----------------------------------------------------------------------------| r_work (final): 0.4214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5388 moved from start: 0.5408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 5334 Z= 0.098 Angle : 0.517 5.060 7268 Z= 0.273 Chirality : 0.037 0.141 808 Planarity : 0.004 0.033 904 Dihedral : 4.684 15.468 698 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % 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: -1.47 (0.32), residues: 646 helix: -0.17 (0.25), residues: 402 sheet: None (None), residues: 0 loop : -2.31 (0.39), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 135 TYR 0.008 0.001 TYR A 301 PHE 0.028 0.001 PHE A 261 TRP 0.004 0.000 TRP B 35 HIS 0.003 0.001 HIS B 278 Details of bonding type rmsd/Z covalent geometry : bond 0.00214 / 0.10 ( 5332) covalent geometry : angle 0.51660 / 0.27 ( 7264) SS BOND : bond 0.00038 / 0.02 ( 2) SS BOND : angle 0.56627 / 0.28 ( 4) hydrogen bonds : bond 0.03881 / 2.47 ( 286) hydrogen bonds : angle 4.77127 / 3.38 ( 834) *********************** REFINEMENT MACRO_CYCLE 6 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 54 residues out of total 277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.149 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 76 LEU cc_start: 0.8170 (mp) cc_final: 0.7894 (pp) REVERT: B 87 VAL cc_start: 0.9245 (p) cc_final: 0.8904 (p) REVERT: B 253 MET cc_start: 0.7242 (tpp) cc_final: 0.7019 (tpp) outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.1059 time to fit residues: 7.0950 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 : 0.115 ------------------------------------------------------------------------------- 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: 10.0000 chunk 63 optimal weight: 10.0000 chunk 8 optimal weight: 9.9990 chunk 34 optimal weight: 0.9980 chunk 61 optimal weight: 9.9990 chunk 51 optimal weight: 3.9990 chunk 32 optimal weight: 9.9990 chunk 35 optimal weight: 2.9990 chunk 38 optimal weight: 8.9990 chunk 45 optimal weight: 0.6980 chunk 58 optimal weight: 7.9990 overall best weight: 3.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4344 r_free = 0.4344 target = 0.133112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.115094 restraints weight = 54839.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.117339 restraints weight = 42751.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.119055 restraints weight = 35122.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.120372 restraints weight = 29979.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.121369 restraints weight = 26263.895| |-----------------------------------------------------------------------------| r_work (final): 0.4141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5468 moved from start: 0.6079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 5334 Z= 0.169 Angle : 0.625 5.272 7268 Z= 0.345 Chirality : 0.038 0.123 808 Planarity : 0.006 0.047 904 Dihedral : 4.993 16.344 698 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.98 % Favored : 91.02 % 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: -1.94 (0.31), residues: 646 helix: -0.41 (0.24), residues: 390 sheet: None (None), residues: 0 loop : -2.67 (0.36), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 135 TYR 0.018 0.002 TYR A 274 PHE 0.016 0.002 PHE A 273 TRP 0.010 0.001 TRP A 175 HIS 0.010 0.002 HIS A 278 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.17 ( 5332) covalent geometry : angle 0.62472 / 0.35 ( 7264) SS BOND : bond 0.00185 / 0.09 ( 2) SS BOND : angle 0.49206 / 0.25 ( 4) hydrogen bonds : bond 0.04165 / 2.68 ( 286) hydrogen bonds : angle 5.18209 / 3.66 ( 834) *********************** REFINEMENT MACRO_CYCLE 7 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 53 residues out of total 277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 0.142 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 87 VAL cc_start: 0.9281 (p) cc_final: 0.8926 (p) outliers start: 0 outliers final: 0 residues processed: 53 average time/residue: 0.0962 time to fit residues: 6.5562 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 : 0.134 ------------------------------------------------------------------------------- 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: 0.9990 chunk 35 optimal weight: 5.9990 chunk 63 optimal weight: 4.9990 chunk 52 optimal weight: 8.9990 chunk 31 optimal weight: 0.9980 chunk 51 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 chunk 14 optimal weight: 2.9990 chunk 56 optimal weight: 6.9990 chunk 42 optimal weight: 0.0010 overall best weight: 0.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4456 r_free = 0.4456 target = 0.135465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.102184 restraints weight = 38757.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.105252 restraints weight = 28917.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.107351 restraints weight = 23473.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.109002 restraints weight = 20232.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.110204 restraints weight = 18007.858| |-----------------------------------------------------------------------------| r_work (final): 0.4600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5465 moved from start: 0.6072 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= 0.102 Angle : 0.536 5.124 7268 Z= 0.284 Chirality : 0.037 0.137 808 Planarity : 0.004 0.040 904 Dihedral : 4.707 16.120 698 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % 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: -1.30 (0.32), residues: 646 helix: 0.01 (0.25), residues: 400 sheet: None (None), residues: 0 loop : -2.31 (0.39), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 135 TYR 0.007 0.001 TYR B 43 PHE 0.015 0.001 PHE B 37 TRP 0.004 0.000 TRP B 35 HIS 0.002 0.001 HIS A 278 Details of bonding type rmsd/Z covalent geometry : bond 0.00219 / 0.10 ( 5332) covalent geometry : angle 0.53636 / 0.28 ( 7264) SS BOND : bond 0.00009 / 0.00 ( 2) SS BOND : angle 0.64918 / 0.32 ( 4) hydrogen bonds : bond 0.03806 / 2.44 ( 286) hydrogen bonds : angle 4.77784 / 3.37 ( 834) *********************** REFINEMENT MACRO_CYCLE 8 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 54 residues out of total 277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 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: 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: 0.9191 (p) cc_final: 0.8830 (p) outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.0998 time to fit residues: 6.8673 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 : 0.135 ------------------------------------------------------------------------------- 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: 0.0980 chunk 17 optimal weight: 7.9990 chunk 16 optimal weight: 10.0000 chunk 19 optimal weight: 5.9990 chunk 15 optimal weight: 9.9990 chunk 31 optimal weight: 7.9990 chunk 14 optimal weight: 0.6980 chunk 32 optimal weight: 9.9990 chunk 28 optimal weight: 0.6980 chunk 5 optimal weight: 0.3980 chunk 18 optimal weight: 7.9990 overall best weight: 1.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4408 r_free = 0.4408 target = 0.135749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.117002 restraints weight = 53637.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.119512 restraints weight = 40496.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.121479 restraints weight = 32224.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.122923 restraints weight = 26788.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.124003 restraints weight = 23055.284| |-----------------------------------------------------------------------------| r_work (final): 0.4213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5338 moved from start: 0.6326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 5334 Z= 0.113 Angle : 0.540 5.273 7268 Z= 0.290 Chirality : 0.037 0.134 808 Planarity : 0.004 0.044 904 Dihedral : 4.653 18.326 698 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.74 % Favored : 92.26 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.16 (0.32), residues: 646 helix: 0.12 (0.25), residues: 406 sheet: None (None), residues: 0 loop : -2.32 (0.40), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 135 TYR 0.009 0.001 TYR A 30 PHE 0.013 0.001 PHE B 37 TRP 0.003 0.001 TRP A 35 HIS 0.004 0.001 HIS A 278 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 ( 5332) covalent geometry : angle 0.54008 / 0.29 ( 7264) SS BOND : bond 0.00001 / 0.00 ( 2) SS BOND : angle 0.36735 / 0.18 ( 4) hydrogen bonds : bond 0.03694 / 2.37 ( 286) hydrogen bonds : angle 4.80261 / 3.39 ( 834) *********************** REFINEMENT MACRO_CYCLE 9 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 53 residues out of total 277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 0.134 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: 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: 0.9280 (p) cc_final: 0.8936 (p) outliers start: 0 outliers final: 0 residues processed: 53 average time/residue: 0.0929 time to fit residues: 6.3281 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 : 0.093 ------------------------------------------------------------------------------- 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: 8.9990 chunk 3 optimal weight: 0.0050 chunk 7 optimal weight: 0.7980 chunk 44 optimal weight: 1.9990 chunk 56 optimal weight: 0.0270 chunk 34 optimal weight: 0.7980 chunk 2 optimal weight: 0.0980 chunk 40 optimal weight: 5.9990 chunk 15 optimal weight: 10.0000 chunk 62 optimal weight: 7.9990 chunk 33 optimal weight: 2.9990 overall best weight: 0.3452 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4440 r_free = 0.4440 target = 0.138972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.119693 restraints weight = 51687.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.122475 restraints weight = 38223.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.124585 restraints weight = 29888.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.126071 restraints weight = 24597.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.127252 restraints weight = 21103.888| |-----------------------------------------------------------------------------| r_work (final): 0.4260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5203 moved from start: 0.6445 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= 0.094 Angle : 0.505 4.387 7268 Z= 0.265 Chirality : 0.037 0.134 808 Planarity : 0.004 0.040 904 Dihedral : 4.430 18.495 698 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.79 (0.33), residues: 646 helix: 0.46 (0.25), residues: 406 sheet: None (None), residues: 0 loop : -2.26 (0.41), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG A 135 TYR 0.007 0.001 TYR B 43 PHE 0.015 0.001 PHE A 37 TRP 0.005 0.000 TRP B 35 HIS 0.002 0.001 HIS A 278 Details of bonding type rmsd/Z covalent geometry : bond 0.00205 / 0.09 ( 5332) covalent geometry : angle 0.50483 / 0.26 ( 7264) SS BOND : bond 0.00060 / 0.03 ( 2) SS BOND : angle 0.48677 / 0.23 ( 4) hydrogen bonds : bond 0.03567 / 2.27 ( 286) hydrogen bonds : angle 4.52499 / 3.19 ( 834) ********************** REFINEMENT MACRO_CYCLE 10 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 54 residues out of total 277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.140 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: 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: 0.9254 (p) cc_final: 0.8913 (p) REVERT: B 238 GLN cc_start: 0.6841 (tp40) cc_final: 0.6172 (tm-30) outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.1103 time to fit residues: 7.4268 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 : 0.153 ------------------------------------------------------------------------------- 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: 8.9990 chunk 47 optimal weight: 9.9990 chunk 44 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 32 optimal weight: 10.0000 chunk 23 optimal weight: 0.8980 chunk 53 optimal weight: 5.9990 chunk 24 optimal weight: 3.9990 chunk 8 optimal weight: 9.9990 chunk 39 optimal weight: 0.9980 chunk 49 optimal weight: 5.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 2 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 = 0.4408 r_free = 0.4408 target = 0.135748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.116771 restraints weight = 53859.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.119524 restraints weight = 40123.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.121512 restraints weight = 31693.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.122942 restraints weight = 26247.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.124066 restraints weight = 22555.874| |-----------------------------------------------------------------------------| r_work (final): 0.4229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5333 moved from start: 0.6730 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= 0.114 Angle : 0.519 4.478 7268 Z= 0.280 Chirality : 0.037 0.119 808 Planarity : 0.005 0.045 904 Dihedral : 4.455 17.446 698 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.67 % Favored : 91.33 % 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: -0.94 (0.33), residues: 646 helix: 0.42 (0.25), residues: 408 sheet: None (None), residues: 0 loop : -2.52 (0.40), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 135 TYR 0.011 0.001 TYR B 30 PHE 0.012 0.001 PHE A 37 TRP 0.004 0.001 TRP B 175 HIS 0.004 0.001 HIS B 195 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.11 ( 5332) covalent geometry : angle 0.51885 / 0.28 ( 7264) SS BOND : bond 0.00023 / 0.01 ( 2) SS BOND : angle 0.26872 / 0.13 ( 4) hydrogen bonds : bond 0.03508 / 2.25 ( 286) hydrogen bonds : angle 4.67425 / 3.30 ( 834) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1393.47 seconds wall clock time: 24 minutes 30.42 seconds (1470.42 seconds total)