Starting phenix.real_space_refine on Fri Feb 14 07:50:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ofj_20047/02_2025/6ofj_20047.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ofj_20047/02_2025/6ofj_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_20047/02_2025/6ofj_20047.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ofj_20047/02_2025/6ofj_20047.map" model { file = "/net/cci-nas-00/data/ceres_data/6ofj_20047/02_2025/6ofj_20047.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ofj_20047/02_2025/6ofj_20047.cif" } resolution = 4.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 5.24, per 1000 atoms: 0.51 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: 2.58 Conformation dependent library (CDL) restraints added in 706.0 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: 0.74 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: 3.53 Time building geometry restraints manager: 3.13 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: 0.03 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: 0.170 Extract box with map and model: 0.410 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 24.090 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.010 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.460 ------------------------------------------------------------------------------- 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 5332 Z= 0.445 Angle : 0.960 9.412 7264 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.004 0.001 TRP A 265 HIS 0.004 0.001 HIS B 152 PHE 0.018 0.002 PHE B 159 TYR 0.020 0.002 TYR A 301 ARG 0.003 0.001 ARG A 252 *********************** 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 : 0.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 LEU cc_start: 0.7455 (mm) cc_final: 0.7166 (mm) REVERT: A 126 TRP cc_start: 0.3004 (m100) cc_final: 0.2347 (m100) REVERT: A 179 ILE cc_start: 0.4059 (tt) cc_final: 0.3853 (tt) outliers start: 0 outliers final: 0 residues processed: 69 average time/residue: 0.3001 time to fit residues: 24.4540 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 : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 54 optimal weight: 9.9990 chunk 48 optimal weight: 6.9990 chunk 26 optimal weight: 9.9990 chunk 16 optimal weight: 0.0070 chunk 32 optimal weight: 10.0000 chunk 25 optimal weight: 0.0170 chunk 50 optimal weight: 0.0570 chunk 19 optimal weight: 10.0000 chunk 30 optimal weight: 10.0000 chunk 37 optimal weight: 4.9990 chunk 58 optimal weight: 9.9990 overall best weight: 2.4158 ------------------------------------------------------------------------------- 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 = 0.4482 r_free = 0.4482 target = 0.140905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.122361 restraints weight = 53109.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.124850 restraints weight = 40940.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.126847 restraints weight = 32968.573| |-----------------------------------------------------------------------------| r_work (final): 0.4238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5412 moved from start: 0.3050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 5332 Z= 0.220 Angle : 0.665 10.286 7264 Z= 0.355 Chirality : 0.039 0.119 808 Planarity : 0.005 0.036 904 Dihedral : 5.641 17.416 698 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.24 (0.28), residues: 646 helix: -1.58 (0.22), residues: 390 sheet: None (None), residues: 0 loop : -2.99 (0.36), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 35 HIS 0.005 0.001 HIS B 278 PHE 0.038 0.002 PHE A 276 TYR 0.018 0.002 TYR B 191 ARG 0.002 0.000 ARG B 177 *********************** 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 58 residues out of total 277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.398 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 181 GLU cc_start: 0.7111 (mp0) cc_final: 0.6732 (mp0) REVERT: B 256 ILE cc_start: 0.9230 (mm) cc_final: 0.8918 (tt) outliers start: 0 outliers final: 0 residues processed: 58 average time/residue: 0.2606 time to fit residues: 18.4925 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 : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 35 optimal weight: 7.9990 chunk 45 optimal weight: 0.0470 chunk 39 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 59 optimal weight: 0.6980 chunk 16 optimal weight: 8.9990 chunk 29 optimal weight: 20.0000 chunk 33 optimal weight: 7.9990 chunk 62 optimal weight: 6.9990 chunk 19 optimal weight: 9.9990 chunk 42 optimal weight: 3.9990 overall best weight: 2.5482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4431 r_free = 0.4431 target = 0.138931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.119300 restraints weight = 53715.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.122080 restraints weight = 41446.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.124149 restraints weight = 33272.764| |-----------------------------------------------------------------------------| r_work (final): 0.4173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5516 moved from start: 0.4315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5332 Z= 0.202 Angle : 0.619 7.404 7264 Z= 0.330 Chirality : 0.038 0.138 808 Planarity : 0.005 0.035 904 Dihedral : 5.265 17.046 698 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 5.54 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.28 (0.28), residues: 646 helix: -1.52 (0.22), residues: 392 sheet: None (None), residues: 0 loop : -3.17 (0.34), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 35 HIS 0.008 0.001 HIS B 278 PHE 0.019 0.001 PHE B 276 TYR 0.011 0.002 TYR B 274 ARG 0.003 0.000 ARG B 135 *********************** 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 59 residues out of total 277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 0.426 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: 0.9367 (mtp) cc_final: 0.8935 (ttm) REVERT: B 253 MET cc_start: 0.8145 (tpp) cc_final: 0.6559 (tpp) REVERT: B 256 ILE cc_start: 0.9240 (mm) cc_final: 0.8855 (tt) outliers start: 0 outliers final: 0 residues processed: 59 average time/residue: 0.3471 time to fit residues: 23.9606 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 : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 20 optimal weight: 4.9990 chunk 16 optimal weight: 0.9990 chunk 40 optimal weight: 6.9990 chunk 43 optimal weight: 9.9990 chunk 22 optimal weight: 9.9990 chunk 36 optimal weight: 5.9990 chunk 21 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 62 optimal weight: 10.0000 chunk 48 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- 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 = 0.4423 r_free = 0.4423 target = 0.139261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.119540 restraints weight = 52830.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.122068 restraints weight = 41067.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.124324 restraints weight = 33163.937| |-----------------------------------------------------------------------------| r_work (final): 0.4203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5465 moved from start: 0.4807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 5332 Z= 0.148 Angle : 0.529 4.798 7264 Z= 0.287 Chirality : 0.037 0.138 808 Planarity : 0.004 0.033 904 Dihedral : 4.882 15.850 698 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.98 % Favored : 91.02 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.71 (0.29), residues: 646 helix: -1.07 (0.23), residues: 400 sheet: None (None), residues: 0 loop : -2.98 (0.35), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 35 HIS 0.004 0.001 HIS B 278 PHE 0.015 0.001 PHE A 37 TYR 0.008 0.001 TYR B 74 ARG 0.004 0.000 ARG B 135 *********************** 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 54 residues out of total 277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.388 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 outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.2947 time to fit residues: 18.9459 Evaluate side-chains 49 residues out of total 277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 10 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 56 optimal weight: 6.9990 chunk 16 optimal weight: 7.9990 chunk 47 optimal weight: 9.9990 chunk 43 optimal weight: 7.9990 chunk 46 optimal weight: 0.2980 chunk 17 optimal weight: 0.0980 chunk 34 optimal weight: 0.4980 chunk 3 optimal weight: 0.9980 chunk 38 optimal weight: 9.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 = 0.4441 r_free = 0.4441 target = 0.139278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.120019 restraints weight = 52569.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.122765 restraints weight = 40495.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.124790 restraints weight = 32564.909| |-----------------------------------------------------------------------------| r_work (final): 0.4221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5404 moved from start: 0.5055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 5332 Z= 0.130 Angle : 0.519 4.452 7264 Z= 0.276 Chirality : 0.037 0.137 808 Planarity : 0.004 0.036 904 Dihedral : 4.741 15.385 698 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 4.56 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.43 (0.30), residues: 646 helix: -0.88 (0.24), residues: 400 sheet: None (None), residues: 0 loop : -2.80 (0.37), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP B 161 HIS 0.004 0.001 HIS A 211 PHE 0.015 0.001 PHE B 37 TYR 0.006 0.001 TYR A 30 ARG 0.005 0.001 ARG A 177 *********************** 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 54 residues out of total 277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.388 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: B 44 MET cc_start: 0.9387 (mtp) cc_final: 0.8923 (ttm) REVERT: B 87 VAL cc_start: 0.9262 (p) cc_final: 0.8710 (p) REVERT: B 253 MET cc_start: 0.8149 (tpp) cc_final: 0.7437 (tpp) REVERT: B 256 ILE cc_start: 0.9230 (mm) cc_final: 0.8876 (tt) outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.3102 time to fit residues: 20.1394 Evaluate side-chains 49 residues out of total 277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 44 optimal weight: 0.9980 chunk 15 optimal weight: 10.0000 chunk 19 optimal weight: 7.9990 chunk 6 optimal weight: 9.9990 chunk 22 optimal weight: 9.9990 chunk 60 optimal weight: 3.9990 chunk 49 optimal weight: 0.9980 chunk 43 optimal weight: 6.9990 chunk 62 optimal weight: 7.9990 chunk 4 optimal weight: 20.0000 chunk 7 optimal weight: 0.7980 overall best weight: 2.7584 ------------------------------------------------------------------------------- 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 = 0.4371 r_free = 0.4371 target = 0.134520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.115774 restraints weight = 55368.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.118136 restraints weight = 43324.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.119899 restraints weight = 35823.313| |-----------------------------------------------------------------------------| r_work (final): 0.4124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5555 moved from start: 0.5760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 5332 Z= 0.192 Angle : 0.560 4.718 7264 Z= 0.307 Chirality : 0.037 0.121 808 Planarity : 0.005 0.035 904 Dihedral : 4.889 18.209 698 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.05 % Favored : 91.95 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.79 (0.29), residues: 646 helix: -1.03 (0.23), residues: 400 sheet: None (None), residues: 0 loop : -3.21 (0.34), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 175 HIS 0.007 0.002 HIS A 278 PHE 0.013 0.002 PHE A 273 TYR 0.013 0.002 TYR A 274 ARG 0.004 0.001 ARG B 177 *********************** 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 : 0.408 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: 0.9351 (mtp) cc_final: 0.8877 (ttm) REVERT: B 253 MET cc_start: 0.8030 (tpp) cc_final: 0.7515 (tpp) outliers start: 0 outliers final: 0 residues processed: 53 average time/residue: 0.2688 time to fit residues: 17.6233 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 : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 31 optimal weight: 6.9990 chunk 53 optimal weight: 7.9990 chunk 6 optimal weight: 6.9990 chunk 21 optimal weight: 7.9990 chunk 15 optimal weight: 10.0000 chunk 4 optimal weight: 20.0000 chunk 34 optimal weight: 0.7980 chunk 1 optimal weight: 6.9990 chunk 46 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 18 optimal weight: 10.0000 overall best weight: 4.3588 ------------------------------------------------------------------------------- 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 = 0.4283 r_free = 0.4283 target = 0.124577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.103802 restraints weight = 47143.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.105051 restraints weight = 39402.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.106098 restraints weight = 35209.439| |-----------------------------------------------------------------------------| r_work (final): 0.4048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5792 moved from start: 0.7071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 5332 Z= 0.292 Angle : 0.712 5.338 7264 Z= 0.403 Chirality : 0.041 0.123 808 Planarity : 0.007 0.060 904 Dihedral : 5.838 19.251 698 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 16.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.84 % Favored : 89.16 % Rotamer: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.00 (0.27), residues: 646 helix: -1.99 (0.20), residues: 400 sheet: None (None), residues: 0 loop : -3.70 (0.35), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 175 HIS 0.014 0.004 HIS A 278 PHE 0.024 0.002 PHE A 273 TYR 0.026 0.003 TYR A 274 ARG 0.008 0.002 ARG B 252 *********************** 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 51 residues out of total 277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 0.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 87 VAL cc_start: 0.9157 (p) cc_final: 0.8797 (p) outliers start: 0 outliers final: 0 residues processed: 51 average time/residue: 0.2341 time to fit residues: 14.9698 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 : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 14 optimal weight: 3.9990 chunk 53 optimal weight: 0.8980 chunk 62 optimal weight: 10.0000 chunk 17 optimal weight: 8.9990 chunk 2 optimal weight: 0.0170 chunk 34 optimal weight: 0.0170 chunk 44 optimal weight: 0.4980 chunk 24 optimal weight: 5.9990 chunk 20 optimal weight: 8.9990 chunk 15 optimal weight: 9.9990 chunk 29 optimal weight: 8.9990 overall best weight: 1.0858 ------------------------------------------------------------------------------- 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 = 0.4363 r_free = 0.4363 target = 0.132067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.114078 restraints weight = 55287.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.116400 restraints weight = 43418.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.118184 restraints weight = 35582.846| |-----------------------------------------------------------------------------| r_work (final): 0.4138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5581 moved from start: 0.7210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 5332 Z= 0.154 Angle : 0.550 4.316 7264 Z= 0.297 Chirality : 0.037 0.119 808 Planarity : 0.005 0.042 904 Dihedral : 5.032 17.750 698 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 8.06 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.91 (0.29), residues: 646 helix: -1.08 (0.23), residues: 398 sheet: None (None), residues: 0 loop : -3.35 (0.35), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 35 HIS 0.002 0.001 HIS A 100 PHE 0.018 0.001 PHE B 313 TYR 0.021 0.002 TYR B 192 ARG 0.004 0.001 ARG A 314 *********************** 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 : 0.406 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: 0.9278 (mtp) cc_final: 0.8732 (ttm) REVERT: B 181 GLU cc_start: 0.7741 (mp0) cc_final: 0.7493 (mp0) outliers start: 0 outliers final: 0 residues processed: 52 average time/residue: 0.2517 time to fit residues: 16.2770 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 : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 31 optimal weight: 0.0370 chunk 11 optimal weight: 7.9990 chunk 13 optimal weight: 0.0970 chunk 10 optimal weight: 0.3980 chunk 2 optimal weight: 0.8980 chunk 37 optimal weight: 0.9990 chunk 59 optimal weight: 0.9990 chunk 22 optimal weight: 9.9990 chunk 48 optimal weight: 6.9990 chunk 8 optimal weight: 4.9990 chunk 7 optimal weight: 0.3980 overall best weight: 0.3656 ------------------------------------------------------------------------------- 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 B 302 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4390 r_free = 0.4390 target = 0.133956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.115933 restraints weight = 53758.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.118153 restraints weight = 42152.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.119939 restraints weight = 34616.283| |-----------------------------------------------------------------------------| r_work (final): 0.4163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5516 moved from start: 0.7197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 5332 Z= 0.133 Angle : 0.512 4.376 7264 Z= 0.275 Chirality : 0.036 0.121 808 Planarity : 0.005 0.041 904 Dihedral : 4.459 15.988 698 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.05 % Favored : 91.95 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.23 (0.31), residues: 646 helix: -0.68 (0.23), residues: 408 sheet: None (None), residues: 0 loop : -2.85 (0.41), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 126 HIS 0.003 0.001 HIS A 100 PHE 0.012 0.001 PHE A 37 TYR 0.015 0.001 TYR B 192 ARG 0.003 0.001 ARG A 177 *********************** 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 53 residues out of total 277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 0.419 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 44 MET cc_start: 0.9251 (mtp) cc_final: 0.8692 (ttm) outliers start: 0 outliers final: 0 residues processed: 53 average time/residue: 0.2498 time to fit residues: 16.5358 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 : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 34 optimal weight: 0.4980 chunk 27 optimal weight: 0.9990 chunk 29 optimal weight: 3.9990 chunk 40 optimal weight: 6.9990 chunk 38 optimal weight: 6.9990 chunk 24 optimal weight: 0.7980 chunk 10 optimal weight: 4.9990 chunk 8 optimal weight: 6.9990 chunk 32 optimal weight: 10.0000 chunk 23 optimal weight: 8.9990 chunk 7 optimal weight: 0.5980 overall best weight: 1.3784 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4389 r_free = 0.4389 target = 0.131429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.099857 restraints weight = 36701.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.102701 restraints weight = 27512.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.104797 restraints weight = 22622.756| |-----------------------------------------------------------------------------| r_work (final): 0.4208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5638 moved from start: 0.7576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 5332 Z= 0.144 Angle : 0.519 4.391 7264 Z= 0.281 Chirality : 0.037 0.122 808 Planarity : 0.005 0.043 904 Dihedral : 4.513 15.443 698 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 8.16 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.16 (0.31), residues: 646 helix: -0.57 (0.23), residues: 400 sheet: None (None), residues: 0 loop : -2.89 (0.39), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP A 175 HIS 0.003 0.001 HIS A 211 PHE 0.015 0.001 PHE A 45 TYR 0.015 0.001 TYR B 192 ARG 0.003 0.001 ARG B 135 ********************** 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 : 0.397 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: 0.9228 (mtp) cc_final: 0.8581 (ttm) outliers start: 0 outliers final: 0 residues processed: 51 average time/residue: 0.2521 time to fit residues: 15.9760 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 : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 51 optimal weight: 4.9990 chunk 29 optimal weight: 10.0000 chunk 57 optimal weight: 0.7980 chunk 21 optimal weight: 5.9990 chunk 24 optimal weight: 6.9990 chunk 47 optimal weight: 4.9990 chunk 46 optimal weight: 0.6980 chunk 27 optimal weight: 0.0980 chunk 62 optimal weight: 4.9990 chunk 42 optimal weight: 4.9990 chunk 17 optimal weight: 10.0000 overall best weight: 2.3184 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4363 r_free = 0.4363 target = 0.129917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.099352 restraints weight = 38981.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.102363 restraints weight = 28863.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.104386 restraints weight = 23629.675| |-----------------------------------------------------------------------------| r_work (final): 0.4167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5697 moved from start: 0.7860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 5332 Z= 0.172 Angle : 0.548 4.628 7264 Z= 0.298 Chirality : 0.037 0.121 808 Planarity : 0.005 0.046 904 Dihedral : 4.628 16.141 698 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.60 % Favored : 90.40 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.54 (0.30), residues: 646 helix: -0.99 (0.22), residues: 410 sheet: None (None), residues: 0 loop : -2.85 (0.40), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 175 HIS 0.004 0.002 HIS B 278 PHE 0.011 0.001 PHE A 273 TYR 0.013 0.001 TYR A 192 ARG 0.004 0.001 ARG A 252 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2378.50 seconds wall clock time: 43 minutes 0.84 seconds (2580.84 seconds total)