Starting phenix.real_space_refine on Mon Jul 28 03:07:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ofj_20047/07_2025/6ofj_20047.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ofj_20047/07_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_20047/07_2025/6ofj_20047.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ofj_20047/07_2025/6ofj_20047.map" model { file = "/net/cci-nas-00/data/ceres_data/6ofj_20047/07_2025/6ofj_20047.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ofj_20047/07_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/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: 5.01, per 1000 atoms: 0.49 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: 2.45 Conformation dependent library (CDL) restraints added in 649.7 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: 0.66 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: 3.14 Time building geometry restraints manager: 3.02 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: 0.500 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: 0.160 Extract box with map and model: 0.420 Check model and map are aligned: 0.070 Set scattering table: 0.110 Process input model: 23.310 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3698 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.081 5334 Z= 0.278 Angle : 0.960 9.412 7268 Z= 0.491 Chirality : 0.046 0.165 808 Planarity : 0.006 0.045 904 Dihedral : 15.744 79.861 1846 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.12 % Favored : 92.88 % Rotamer: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 Details of bonding type rmsd hydrogen bonds : bond 0.15683 ( 286) hydrogen bonds : angle 7.39055 ( 834) SS BOND : bond 0.00331 ( 2) SS BOND : angle 0.47379 ( 4) covalent geometry : bond 0.00671 ( 5332) covalent geometry : angle 0.96046 ( 7264) *********************** 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 : 0.432 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: 0.3039 time to fit residues: 24.8292 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 : 0.422 ------------------------------------------------------------------------------- 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 = 0.122360 restraints weight = 53109.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.124868 restraints weight = 40932.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.126768 restraints weight = 32935.369| |-----------------------------------------------------------------------------| r_work (final): 0.4242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5417 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 5334 Z= 0.158 Angle : 0.665 10.286 7268 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 A 177 Details of bonding type rmsd hydrogen bonds : bond 0.05264 ( 286) hydrogen bonds : angle 5.76371 ( 834) SS BOND : bond 0.00363 ( 2) SS BOND : angle 0.80294 ( 4) covalent geometry : bond 0.00350 ( 5332) covalent geometry : angle 0.66501 ( 7264) *********************** 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 : 0.361 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: 0.7138 (mp0) cc_final: 0.6756 (mp0) REVERT: B 256 ILE cc_start: 0.9236 (mm) cc_final: 0.8929 (tt) outliers start: 0 outliers final: 0 residues processed: 58 average time/residue: 0.2534 time to fit residues: 18.0113 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 : 0.373 ------------------------------------------------------------------------------- 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: 0.7980 chunk 39 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 59 optimal weight: 1.9990 chunk 16 optimal weight: 0.3980 chunk 29 optimal weight: 20.0000 chunk 33 optimal weight: 7.9990 chunk 62 optimal weight: 7.9990 chunk 19 optimal weight: 10.0000 chunk 42 optimal weight: 0.0570 overall best weight: 0.8300 ------------------------------------------------------------------------------- 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 = 0.4453 r_free = 0.4453 target = 0.141774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.111996 restraints weight = 46420.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.115822 restraints weight = 33660.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.118796 restraints weight = 26422.172| |-----------------------------------------------------------------------------| r_work (final): 0.4183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5550 moved from start: 0.3990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 5334 Z= 0.113 Angle : 0.578 7.854 7268 Z= 0.302 Chirality : 0.037 0.141 808 Planarity : 0.004 0.027 904 Dihedral : 5.122 16.150 698 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.67 % Favored : 91.33 % 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: -2.94 (0.29), residues: 646 helix: -1.27 (0.23), residues: 394 sheet: None (None), residues: 0 loop : -3.00 (0.35), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 35 HIS 0.005 0.001 HIS A 278 PHE 0.022 0.001 PHE A 276 TYR 0.008 0.001 TYR B 74 ARG 0.001 0.000 ARG A 21 Details of bonding type rmsd hydrogen bonds : bond 0.04319 ( 286) hydrogen bonds : angle 5.22340 ( 834) SS BOND : bond 0.00014 ( 2) SS BOND : angle 0.78769 ( 4) covalent geometry : bond 0.00250 ( 5332) covalent geometry : angle 0.57812 ( 7264) *********************** 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 61 residues out of total 277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.399 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: 0.9329 (mtp) cc_final: 0.8908 (ttm) REVERT: B 253 MET cc_start: 0.8204 (tpp) cc_final: 0.7857 (tpp) REVERT: B 256 ILE cc_start: 0.9252 (mm) cc_final: 0.8938 (tt) outliers start: 0 outliers final: 0 residues processed: 61 average time/residue: 0.3327 time to fit residues: 24.0631 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 : 0.401 ------------------------------------------------------------------------------- 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: 9.9990 chunk 16 optimal weight: 5.9990 chunk 40 optimal weight: 20.0000 chunk 43 optimal weight: 8.9990 chunk 22 optimal weight: 9.9990 chunk 36 optimal weight: 9.9990 chunk 21 optimal weight: 0.9990 chunk 12 optimal weight: 5.9990 chunk 62 optimal weight: 9.9990 chunk 48 optimal weight: 5.9990 chunk 44 optimal weight: 5.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 73 ASN ** B 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.132142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.113636 restraints weight = 57062.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.115847 restraints weight = 44774.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.117476 restraints weight = 37295.186| |-----------------------------------------------------------------------------| r_work (final): 0.4084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5699 moved from start: 0.5587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 5334 Z= 0.236 Angle : 0.722 6.039 7268 Z= 0.411 Chirality : 0.041 0.128 808 Planarity : 0.007 0.071 904 Dihedral : 5.721 17.818 698 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 17.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.15 % Favored : 88.85 % Rotamer: Outliers : 0.36 % Allowed : 1.81 % 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 (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: -4.08 (0.26), residues: 646 helix: -2.13 (0.20), residues: 384 sheet: None (None), residues: 0 loop : -3.55 (0.31), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 175 HIS 0.013 0.002 HIS A 278 PHE 0.021 0.002 PHE A 273 TYR 0.024 0.003 TYR B 274 ARG 0.007 0.001 ARG B 252 Details of bonding type rmsd hydrogen bonds : bond 0.04940 ( 286) hydrogen bonds : angle 5.80695 ( 834) SS BOND : bond 0.00280 ( 2) SS BOND : angle 0.45571 ( 4) covalent geometry : bond 0.00502 ( 5332) covalent geometry : angle 0.72185 ( 7264) *********************** 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: 1 poor density : 53 time to evaluate : 0.396 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 4 THR cc_start: 0.9397 (OUTLIER) cc_final: 0.9144 (m) REVERT: B 253 MET cc_start: 0.7834 (tpp) cc_final: 0.7482 (tpp) outliers start: 1 outliers final: 0 residues processed: 54 average time/residue: 0.2507 time to fit residues: 16.7060 Evaluate side-chains 48 residues out of total 277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 47 time to evaluate : 0.381 ------------------------------------------------------------------------------- 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: 0.0170 chunk 12 optimal weight: 0.7980 chunk 56 optimal weight: 7.9990 chunk 16 optimal weight: 7.9990 chunk 47 optimal weight: 9.9990 chunk 43 optimal weight: 9.9990 chunk 46 optimal weight: 0.0070 chunk 17 optimal weight: 0.0970 chunk 34 optimal weight: 0.0030 chunk 3 optimal weight: 0.0000 chunk 38 optimal weight: 10.0000 overall best weight: 0.0248 ------------------------------------------------------------------------------- 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 = 0.4414 r_free = 0.4414 target = 0.138653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.118920 restraints weight = 53472.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.121615 restraints weight = 41201.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.123656 restraints weight = 33296.803| |-----------------------------------------------------------------------------| r_work (final): 0.4194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5468 moved from start: 0.5327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 5334 Z= 0.107 Angle : 0.537 4.457 7268 Z= 0.285 Chirality : 0.037 0.144 808 Planarity : 0.004 0.030 904 Dihedral : 4.987 16.501 698 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.91 % Favored : 90.09 % 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 (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: -2.65 (0.30), residues: 646 helix: -1.03 (0.24), residues: 394 sheet: None (None), residues: 0 loop : -2.90 (0.35), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 35 HIS 0.002 0.001 HIS A 100 PHE 0.016 0.001 PHE A 37 TYR 0.009 0.001 TYR B 29 ARG 0.002 0.001 ARG B 135 Details of bonding type rmsd hydrogen bonds : bond 0.03904 ( 286) hydrogen bonds : angle 5.01738 ( 834) SS BOND : bond 0.00065 ( 2) SS BOND : angle 0.82987 ( 4) covalent geometry : bond 0.00233 ( 5332) covalent geometry : angle 0.53661 ( 7264) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 646 Ramachandran restraints generated. 323 Oldfield, 0 Emsley, 323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 646 Ramachandran restraints generated. 323 Oldfield, 0 Emsley, 323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 0.358 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 1 MET cc_start: 0.6846 (pmm) cc_final: 0.6544 (ptm) REVERT: B 44 MET cc_start: 0.9259 (mtp) cc_final: 0.8650 (ttm) REVERT: B 87 VAL cc_start: 0.9281 (p) cc_final: 0.8743 (p) outliers start: 0 outliers final: 0 residues processed: 53 average time/residue: 0.2289 time to fit residues: 15.1245 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 : 0.363 ------------------------------------------------------------------------------- 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: 0.8980 chunk 15 optimal weight: 9.9990 chunk 19 optimal weight: 0.8980 chunk 6 optimal weight: 10.0000 chunk 22 optimal weight: 9.9990 chunk 60 optimal weight: 0.0270 chunk 49 optimal weight: 0.6980 chunk 43 optimal weight: 8.9990 chunk 62 optimal weight: 7.9990 chunk 4 optimal weight: 8.9990 chunk 7 optimal weight: 3.9990 overall best weight: 1.3040 ------------------------------------------------------------------------------- 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 = 0.4400 r_free = 0.4400 target = 0.137135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.117858 restraints weight = 53771.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.120420 restraints weight = 41388.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.122267 restraints weight = 33789.931| |-----------------------------------------------------------------------------| r_work (final): 0.4174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5504 moved from start: 0.5784 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= 0.105 Angle : 0.524 4.540 7268 Z= 0.281 Chirality : 0.037 0.134 808 Planarity : 0.004 0.032 904 Dihedral : 4.748 15.459 698 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.67 % Favored : 91.33 % Rotamer: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.47 (0.30), residues: 646 helix: -0.91 (0.24), residues: 394 sheet: None (None), residues: 0 loop : -2.79 (0.36), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 175 HIS 0.004 0.001 HIS A 278 PHE 0.013 0.001 PHE B 37 TYR 0.008 0.001 TYR A 30 ARG 0.003 0.000 ARG A 135 Details of bonding type rmsd hydrogen bonds : bond 0.03772 ( 286) hydrogen bonds : angle 4.91225 ( 834) SS BOND : bond 0.00036 ( 2) SS BOND : angle 0.44935 ( 4) covalent geometry : bond 0.00222 ( 5332) covalent geometry : angle 0.52422 ( 7264) *********************** 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 52 residues out of total 277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.364 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: B 1 MET cc_start: 0.7206 (pmm) cc_final: 0.6902 (ptm) REVERT: B 44 MET cc_start: 0.9236 (mtp) cc_final: 0.8615 (ttm) REVERT: B 87 VAL cc_start: 0.9119 (p) cc_final: 0.8719 (p) outliers start: 0 outliers final: 0 residues processed: 52 average time/residue: 0.2401 time to fit residues: 15.4969 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 : 0.394 ------------------------------------------------------------------------------- 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: 1.9990 chunk 53 optimal weight: 5.9990 chunk 6 optimal weight: 7.9990 chunk 21 optimal weight: 5.9990 chunk 15 optimal weight: 8.9990 chunk 4 optimal weight: 7.9990 chunk 34 optimal weight: 1.9990 chunk 1 optimal weight: 0.2980 chunk 46 optimal weight: 5.9990 chunk 57 optimal weight: 7.9990 chunk 18 optimal weight: 8.9990 overall best weight: 3.2588 ------------------------------------------------------------------------------- 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** ** 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 = 0.4358 r_free = 0.4358 target = 0.131841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.113180 restraints weight = 54009.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.115681 restraints weight = 41032.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.117556 restraints weight = 32948.410| |-----------------------------------------------------------------------------| r_work (final): 0.4126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5592 moved from start: 0.6420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5334 Z= 0.165 Angle : 0.592 4.874 7268 Z= 0.331 Chirality : 0.038 0.121 808 Planarity : 0.005 0.038 904 Dihedral : 5.153 19.476 698 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.60 % Favored : 90.40 % 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: -3.01 (0.28), residues: 646 helix: -1.27 (0.22), residues: 386 sheet: None (None), residues: 0 loop : -3.09 (0.35), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 175 HIS 0.008 0.003 HIS B 278 PHE 0.023 0.002 PHE B 203 TYR 0.015 0.002 TYR B 274 ARG 0.004 0.001 ARG A 135 Details of bonding type rmsd hydrogen bonds : bond 0.03970 ( 286) hydrogen bonds : angle 5.18147 ( 834) SS BOND : bond 0.00047 ( 2) SS BOND : angle 0.38506 ( 4) covalent geometry : bond 0.00348 ( 5332) covalent geometry : angle 0.59187 ( 7264) *********************** 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 : 0.359 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 1 MET cc_start: 0.7487 (pmm) cc_final: 0.7134 (ptm) REVERT: B 44 MET cc_start: 0.9278 (mtp) cc_final: 0.8676 (ttm) outliers start: 0 outliers final: 0 residues processed: 51 average time/residue: 0.2349 time to fit residues: 14.8486 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 : 0.366 ------------------------------------------------------------------------------- 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: 0.5980 chunk 53 optimal weight: 2.9990 chunk 62 optimal weight: 10.0000 chunk 17 optimal weight: 0.0770 chunk 2 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 44 optimal weight: 0.9980 chunk 24 optimal weight: 3.9990 chunk 20 optimal weight: 9.9990 chunk 15 optimal weight: 10.0000 chunk 29 optimal weight: 10.0000 overall best weight: 1.7342 ------------------------------------------------------------------------------- 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 = 0.4383 r_free = 0.4383 target = 0.133919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.116204 restraints weight = 55359.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.118552 restraints weight = 42945.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.120255 restraints weight = 34895.584| |-----------------------------------------------------------------------------| r_work (final): 0.4161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5526 moved from start: 0.6566 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= 0.110 Angle : 0.535 4.688 7268 Z= 0.289 Chirality : 0.037 0.132 808 Planarity : 0.004 0.038 904 Dihedral : 4.948 18.062 698 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.91 % Favored : 90.09 % 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: -2.58 (0.30), residues: 646 helix: -0.93 (0.23), residues: 394 sheet: None (None), residues: 0 loop : -2.95 (0.36), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 126 HIS 0.004 0.001 HIS B 278 PHE 0.013 0.001 PHE A 294 TYR 0.008 0.001 TYR B 43 ARG 0.003 0.001 ARG A 135 Details of bonding type rmsd hydrogen bonds : bond 0.03744 ( 286) hydrogen bonds : angle 5.03622 ( 834) SS BOND : bond 0.00068 ( 2) SS BOND : angle 0.36867 ( 4) covalent geometry : bond 0.00238 ( 5332) covalent geometry : angle 0.53527 ( 7264) *********************** 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 53 residues out of total 277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 0.358 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: 0.9265 (mtp) cc_final: 0.8666 (ttm) outliers start: 0 outliers final: 0 residues processed: 53 average time/residue: 0.2442 time to fit residues: 16.0462 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 : 0.363 ------------------------------------------------------------------------------- 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: 6.9990 chunk 11 optimal weight: 7.9990 chunk 13 optimal weight: 0.3980 chunk 10 optimal weight: 0.0070 chunk 2 optimal weight: 0.4980 chunk 37 optimal weight: 3.9990 chunk 59 optimal weight: 4.9990 chunk 22 optimal weight: 10.0000 chunk 48 optimal weight: 8.9990 chunk 8 optimal weight: 8.9990 chunk 7 optimal weight: 1.9990 overall best weight: 1.3802 ------------------------------------------------------------------------------- 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** 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 = 0.4391 r_free = 0.4391 target = 0.135003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.117039 restraints weight = 53584.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.119375 restraints weight = 41675.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.121129 restraints weight = 33917.761| |-----------------------------------------------------------------------------| r_work (final): 0.4175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5516 moved from start: 0.6785 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= 0.106 Angle : 0.521 4.516 7268 Z= 0.280 Chirality : 0.036 0.122 808 Planarity : 0.004 0.038 904 Dihedral : 4.751 16.168 698 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 6.80 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 (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: -2.42 (0.30), residues: 646 helix: -0.82 (0.23), residues: 406 sheet: None (None), residues: 0 loop : -2.94 (0.38), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 126 HIS 0.003 0.001 HIS B 278 PHE 0.017 0.001 PHE A 313 TYR 0.008 0.001 TYR A 43 ARG 0.005 0.001 ARG B 314 Details of bonding type rmsd hydrogen bonds : bond 0.03610 ( 286) hydrogen bonds : angle 4.90886 ( 834) SS BOND : bond 0.00066 ( 2) SS BOND : angle 0.32119 ( 4) covalent geometry : bond 0.00229 ( 5332) covalent geometry : angle 0.52107 ( 7264) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 646 Ramachandran restraints generated. 323 Oldfield, 0 Emsley, 323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 646 Ramachandran restraints generated. 323 Oldfield, 0 Emsley, 323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 44 MET cc_start: 0.9266 (mtp) cc_final: 0.8647 (ttm) REVERT: B 207 MET cc_start: 0.1370 (mmt) cc_final: 0.1155 (mmt) outliers start: 0 outliers final: 0 residues processed: 52 average time/residue: 0.2710 time to fit residues: 17.5795 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 : 0.613 ------------------------------------------------------------------------------- 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: 0.2980 chunk 27 optimal weight: 0.9980 chunk 29 optimal weight: 5.9990 chunk 40 optimal weight: 7.9990 chunk 38 optimal weight: 9.9990 chunk 24 optimal weight: 6.9990 chunk 10 optimal weight: 0.0570 chunk 8 optimal weight: 7.9990 chunk 32 optimal weight: 6.9990 chunk 23 optimal weight: 0.2980 chunk 7 optimal weight: 0.6980 overall best weight: 0.4698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4447 r_free = 0.4447 target = 0.137333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.119493 restraints weight = 55162.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.121860 restraints weight = 42866.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.123646 restraints weight = 34872.420| |-----------------------------------------------------------------------------| r_work (final): 0.4263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5012 moved from start: 0.6955 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= 0.093 Angle : 0.501 4.279 7268 Z= 0.265 Chirality : 0.037 0.123 808 Planarity : 0.004 0.035 904 Dihedral : 4.386 15.860 698 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.67 % Favored : 91.33 % Rotamer: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.99 (0.31), residues: 646 helix: -0.46 (0.24), residues: 408 sheet: None (None), residues: 0 loop : -2.83 (0.38), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 35 HIS 0.002 0.001 HIS A 100 PHE 0.013 0.001 PHE B 37 TYR 0.007 0.001 TYR B 43 ARG 0.002 0.001 ARG B 314 Details of bonding type rmsd hydrogen bonds : bond 0.03482 ( 286) hydrogen bonds : angle 4.63145 ( 834) SS BOND : bond 0.00088 ( 2) SS BOND : angle 0.39157 ( 4) covalent geometry : bond 0.00201 ( 5332) covalent geometry : angle 0.50080 ( 7264) ********************** 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 53 residues out of total 277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 0.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 44 MET cc_start: 0.9124 (mtp) cc_final: 0.8496 (ttm) REVERT: B 183 MET cc_start: 0.9199 (tpt) cc_final: 0.8799 (tpt) REVERT: B 238 GLN cc_start: 0.6640 (tp40) cc_final: 0.6415 (tm-30) outliers start: 0 outliers final: 0 residues processed: 53 average time/residue: 0.2224 time to fit residues: 14.7159 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 : 0.363 ------------------------------------------------------------------------------- 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: 1.9990 chunk 29 optimal weight: 9.9990 chunk 57 optimal weight: 6.9990 chunk 21 optimal weight: 0.9980 chunk 24 optimal weight: 7.9990 chunk 47 optimal weight: 0.7980 chunk 46 optimal weight: 3.9990 chunk 27 optimal weight: 0.3980 chunk 62 optimal weight: 5.9990 chunk 42 optimal weight: 8.9990 chunk 17 optimal weight: 9.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- 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 = 0.4417 r_free = 0.4417 target = 0.135096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.117496 restraints weight = 56683.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.119828 restraints weight = 44141.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.121537 restraints weight = 36135.364| |-----------------------------------------------------------------------------| r_work (final): 0.4205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5495 moved from start: 0.7125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 5334 Z= 0.106 Angle : 0.514 4.431 7268 Z= 0.275 Chirality : 0.036 0.121 808 Planarity : 0.004 0.040 904 Dihedral : 4.367 15.943 698 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.98 % Favored : 91.02 % 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: -2.11 (0.31), residues: 646 helix: -0.55 (0.24), residues: 408 sheet: None (None), residues: 0 loop : -2.88 (0.38), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 126 HIS 0.003 0.001 HIS A 278 PHE 0.013 0.001 PHE A 37 TYR 0.008 0.001 TYR B 74 ARG 0.003 0.001 ARG A 135 Details of bonding type rmsd hydrogen bonds : bond 0.03413 ( 286) hydrogen bonds : angle 4.68377 ( 834) SS BOND : bond 0.00063 ( 2) SS BOND : angle 0.25811 ( 4) covalent geometry : bond 0.00230 ( 5332) covalent geometry : angle 0.51441 ( 7264) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2920.64 seconds wall clock time: 52 minutes 37.40 seconds (3157.40 seconds total)