Starting phenix.real_space_refine on Thu Sep 10 22:33:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6nt7_0504/09_2026/6nt7_0504.cif Found real_map, /net/cci-nas-00/data/ceres_data/6nt7_0504/09_2026/6nt7_0504.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6nt7_0504/09_2026/6nt7_0504.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6nt7_0504/09_2026/6nt7_0504.map" model { file = "/net/cci-nas-00/data/ceres_data/6nt7_0504/09_2026/6nt7_0504.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6nt7_0504/09_2026/6nt7_0504.cif" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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 P 2 5.49 5 S 36 5.16 5 C 3040 2.51 5 N 834 2.21 5 O 817 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 4729 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2342 Classifications: {'peptide': 294} Link IDs: {'PTRANS': 11, 'TRANS': 282} Chain breaks: 6 Chain: "B" Number of atoms: 2342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2342 Classifications: {'peptide': 294} Link IDs: {'PTRANS': 11, 'TRANS': 282} Chain breaks: 6 Chain: "A" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 45 Unusual residues: {'1SY': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.24, per 1000 atoms: 0.26 Number of scatterers: 4729 At special positions: 0 Unit cell: (79.8, 57.96, 103.32, 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 36 16.00 P 2 15.00 O 817 8.00 N 834 7.00 C 3040 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.28 Conformation dependent library (CDL) restraints added in 131.0 milliseconds 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1124 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 4 sheets defined 59.9% alpha, 10.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.08 Creating SS restraints... Processing helix chain 'A' and resid 23 through 41 Processing helix chain 'A' and resid 49 through 76 removed outlier: 4.547A pdb=" N ALA A 59 " --> pdb=" O THR A 55 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N GLY A 63 " --> pdb=" O ALA A 59 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU A 65 " --> pdb=" O GLN A 61 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ALA A 73 " --> pdb=" O CYS A 69 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N GLU A 74 " --> pdb=" O CYS A 70 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLU A 75 " --> pdb=" O CYS A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 83 Processing helix chain 'A' and resid 88 through 95 removed outlier: 4.259A pdb=" N PHE A 95 " --> pdb=" O LEU A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 108 removed outlier: 3.741A pdb=" N LEU A 103 " --> pdb=" O TRP A 99 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLY A 108 " --> pdb=" O LEU A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 140 removed outlier: 3.633A pdb=" N LEU A 139 " --> pdb=" O LEU A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 156 removed outlier: 3.567A pdb=" N SER A 156 " --> pdb=" O LEU A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 172 removed outlier: 3.765A pdb=" N GLY A 163 " --> pdb=" O ASN A 159 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N TYR A 172 " --> pdb=" O TYR A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 177 removed outlier: 3.728A pdb=" N LEU A 177 " --> pdb=" O LEU A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 189 removed outlier: 3.823A pdb=" N CYS A 183 " --> pdb=" O ARG A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 201 removed outlier: 3.711A pdb=" N TRP A 201 " --> pdb=" O ARG A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 276 Processing helix chain 'A' and resid 285 through 306 Processing helix chain 'A' and resid 329 through 341 removed outlier: 3.807A pdb=" N GLN A 341 " --> pdb=" O HIS A 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 4.547A pdb=" N ALA B 59 " --> pdb=" O THR B 55 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N GLY B 63 " --> pdb=" O ALA B 59 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU B 65 " --> pdb=" O GLN B 61 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ALA B 73 " --> pdb=" O CYS B 69 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N GLU B 74 " --> pdb=" O CYS B 70 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLU B 75 " --> pdb=" O CYS B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 83 Processing helix chain 'B' and resid 88 through 95 removed outlier: 4.258A pdb=" N PHE B 95 " --> pdb=" O LEU B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 108 removed outlier: 3.741A pdb=" N LEU B 103 " --> pdb=" O TRP B 99 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLY B 108 " --> pdb=" O LEU B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 140 removed outlier: 3.632A pdb=" N LEU B 139 " --> pdb=" O LEU B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 156 removed outlier: 3.567A pdb=" N SER B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 172 removed outlier: 3.765A pdb=" N GLY B 163 " --> pdb=" O ASN B 159 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N TYR B 172 " --> pdb=" O TYR B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 177 removed outlier: 3.728A pdb=" N LEU B 177 " --> pdb=" O LEU B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 189 removed outlier: 3.823A pdb=" N CYS B 183 " --> pdb=" O ARG B 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 201 removed outlier: 3.711A pdb=" N TRP B 201 " --> pdb=" O ARG B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 276 Processing helix chain 'B' and resid 285 through 306 Processing helix chain 'B' and resid 329 through 341 removed outlier: 3.807A pdb=" N GLN B 341 " --> pdb=" O HIS B 337 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 224 through 228 removed outlier: 5.571A pdb=" N TYR A 226 " --> pdb=" O VAL A 251 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N VAL A 251 " --> pdb=" O TYR A 226 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ALA A 228 " --> pdb=" O LEU A 249 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N HIS A 204 " --> pdb=" O VAL A 263 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 233 through 237 removed outlier: 6.599A pdb=" N ARG A 237 " --> pdb=" O LYS A 241 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N LYS A 241 " --> pdb=" O ARG A 237 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 224 through 228 removed outlier: 5.572A pdb=" N TYR B 226 " --> pdb=" O VAL B 251 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N VAL B 251 " --> pdb=" O TYR B 226 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ALA B 228 " --> pdb=" O LEU B 249 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N HIS B 204 " --> pdb=" O VAL B 263 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 233 through 237 removed outlier: 6.598A pdb=" N ARG B 237 " --> pdb=" O LYS B 241 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N LYS B 241 " --> pdb=" O ARG B 237 " (cutoff:3.500A) 240 hydrogen bonds defined for protein. 696 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: 0.56 Time building geometry restraints manager: 0.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 744 1.32 - 1.44: 1271 1.44 - 1.56: 2767 1.56 - 1.69: 5 1.69 - 1.81: 40 Bond restraints: 4827 Sorted by residual: bond pdb=" C40 1SY A 401 " pdb=" N39 1SY A 401 " ideal model delta sigma weight residual 1.304 1.424 -0.120 2.00e-02 2.50e+03 3.57e+01 bond pdb=" C3' 1SY A 401 " pdb=" C4' 1SY A 401 " ideal model delta sigma weight residual 1.531 1.421 0.110 2.00e-02 2.50e+03 3.00e+01 bond pdb=" C36 1SY A 401 " pdb=" N42 1SY A 401 " ideal model delta sigma weight residual 1.357 1.460 -0.103 2.00e-02 2.50e+03 2.63e+01 bond pdb=" C1' 1SY A 401 " pdb=" N9 1SY A 401 " ideal model delta sigma weight residual 1.458 1.362 0.096 2.00e-02 2.50e+03 2.29e+01 bond pdb=" C2' 1SY A 401 " pdb=" C3' 1SY A 401 " ideal model delta sigma weight residual 1.530 1.442 0.088 2.00e-02 2.50e+03 1.92e+01 ... (remaining 4822 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.72: 6458 3.72 - 7.45: 65 7.45 - 11.17: 11 11.17 - 14.89: 2 14.89 - 18.62: 4 Bond angle restraints: 6540 Sorted by residual: angle pdb=" O19 1SY A 401 " pdb=" P18 1SY A 401 " pdb=" O44 1SY A 401 " ideal model delta sigma weight residual 123.21 104.59 18.62 3.00e+00 1.11e-01 3.85e+01 angle pdb=" O29 1SY A 401 " pdb=" P27 1SY A 401 " pdb=" O30 1SY A 401 " ideal model delta sigma weight residual 123.47 106.08 17.39 3.00e+00 1.11e-01 3.36e+01 angle pdb=" C25 1SY A 401 " pdb=" O26 1SY A 401 " pdb=" P27 1SY A 401 " ideal model delta sigma weight residual 123.41 107.13 16.28 3.00e+00 1.11e-01 2.94e+01 angle pdb=" O17 1SY A 401 " pdb=" P18 1SY A 401 " pdb=" O20 1SY A 401 " ideal model delta sigma weight residual 100.83 115.85 -15.02 3.00e+00 1.11e-01 2.51e+01 angle pdb=" C VAL A 176 " pdb=" N LEU A 177 " pdb=" CA LEU A 177 " ideal model delta sigma weight residual 120.58 125.95 -5.37 1.32e+00 5.74e-01 1.66e+01 ... (remaining 6535 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.92: 2603 15.92 - 31.85: 256 31.85 - 47.77: 61 47.77 - 63.70: 15 63.70 - 79.62: 8 Dihedral angle restraints: 2943 sinusoidal: 1225 harmonic: 1718 Sorted by residual: dihedral pdb=" CA GLN B 56 " pdb=" C GLN B 56 " pdb=" N LEU B 57 " pdb=" CA LEU B 57 " ideal model delta harmonic sigma weight residual -180.00 -160.40 -19.60 0 5.00e+00 4.00e-02 1.54e+01 dihedral pdb=" CA GLN A 56 " pdb=" C GLN A 56 " pdb=" N LEU A 57 " pdb=" CA LEU A 57 " ideal model delta harmonic sigma weight residual -180.00 -160.45 -19.55 0 5.00e+00 4.00e-02 1.53e+01 dihedral pdb=" CA PRO A 96 " pdb=" C PRO A 96 " pdb=" N PRO A 97 " pdb=" CA PRO A 97 " ideal model delta harmonic sigma weight residual -180.00 -162.69 -17.31 0 5.00e+00 4.00e-02 1.20e+01 ... (remaining 2940 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 461 0.035 - 0.071: 218 0.071 - 0.106: 53 0.106 - 0.141: 22 0.141 - 0.176: 8 Chirality restraints: 762 Sorted by residual: chirality pdb=" CA LEU B 177 " pdb=" N LEU B 177 " pdb=" C LEU B 177 " pdb=" CB LEU B 177 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.76e-01 chirality pdb=" CA LEU A 177 " pdb=" N LEU A 177 " pdb=" C LEU A 177 " pdb=" CB LEU A 177 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.18 2.00e-01 2.50e+01 7.67e-01 chirality pdb=" C22 1SY A 401 " pdb=" C21 1SY A 401 " pdb=" C24 1SY A 401 " pdb=" O23 1SY A 401 " both_signs ideal model delta sigma weight residual False -2.70 -2.52 -0.17 2.00e-01 2.50e+01 7.63e-01 ... (remaining 759 not shown) Planarity restraints: 797 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 95 " 0.042 5.00e-02 4.00e+02 6.36e-02 6.47e+00 pdb=" N PRO B 96 " -0.110 5.00e-02 4.00e+02 pdb=" CA PRO B 96 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 96 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 95 " 0.042 5.00e-02 4.00e+02 6.34e-02 6.42e+00 pdb=" N PRO A 96 " -0.110 5.00e-02 4.00e+02 pdb=" CA PRO A 96 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 96 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 230 " 0.030 5.00e-02 4.00e+02 4.51e-02 3.25e+00 pdb=" N PRO A 231 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO A 231 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 231 " 0.025 5.00e-02 4.00e+02 ... (remaining 794 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 928 2.77 - 3.30: 4184 3.30 - 3.84: 7177 3.84 - 4.37: 7909 4.37 - 4.90: 13645 Nonbonded interactions: 33843 Sorted by model distance: nonbonded pdb=" OG SER B 268 " pdb=" O2' 1SY A 401 " model vdw 2.238 3.040 nonbonded pdb=" O SER A 52 " pdb=" OG1 THR A 55 " model vdw 2.281 3.040 nonbonded pdb=" O SER B 52 " pdb=" OG1 THR B 55 " model vdw 2.281 3.040 nonbonded pdb=" O LEU B 187 " pdb=" OG1 THR B 190 " model vdw 2.313 3.040 nonbonded pdb=" O LEU A 187 " pdb=" OG1 THR A 190 " model vdw 2.314 3.040 ... (remaining 33838 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 11 through 342) selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 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: 0.450 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: 0.000 Extract box with map and model: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 5.700 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 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 : 0.009 0.120 4827 Z= 0.417 Angle : 1.087 18.616 6540 Z= 0.526 Chirality : 0.046 0.176 762 Planarity : 0.007 0.064 797 Dihedral : 14.421 79.619 1819 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.29 (0.28), residues: 560 helix: -2.00 (0.22), residues: 308 sheet: -1.47 (0.65), residues: 74 loop : -2.45 (0.36), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 289 TYR 0.008 0.001 TYR A 100 PHE 0.012 0.002 PHE B 329 TRP 0.006 0.002 TRP B 88 HIS 0.008 0.002 HIS B 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00877 / 0.42 ( 4827) covalent geometry : angle 1.08676 / 0.53 ( 6540) hydrogen bonds : bond 0.19029 / 13.05 ( 240) hydrogen bonds : angle 8.61611 / 6.13 ( 696) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.114 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 303 ILE cc_start: 0.9436 (mt) cc_final: 0.9222 (mm) REVERT: B 303 ILE cc_start: 0.9381 (mt) cc_final: 0.9158 (mm) outliers start: 0 outliers final: 0 residues processed: 81 average time/residue: 0.0859 time to fit residues: 8.5910 Evaluate side-chains 35 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 0.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 54 optimal weight: 0.8980 chunk 24 optimal weight: 6.9990 chunk 48 optimal weight: 4.9990 chunk 56 optimal weight: 0.8980 chunk 26 optimal weight: 7.9990 chunk 2 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 31 optimal weight: 6.9990 chunk 25 optimal weight: 0.9980 chunk 50 optimal weight: 5.9990 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 78 HIS A 337 HIS B 78 HIS B 337 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.083468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.067451 restraints weight = 17035.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.069213 restraints weight = 10886.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.070453 restraints weight = 8056.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.071189 restraints weight = 6522.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.071867 restraints weight = 5693.104| |-----------------------------------------------------------------------------| r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.2504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4827 Z= 0.151 Angle : 0.664 9.860 6540 Z= 0.316 Chirality : 0.041 0.154 762 Planarity : 0.005 0.053 797 Dihedral : 7.303 35.489 701 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.93 % Allowed : 8.98 % Favored : 88.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.34 (0.34), residues: 560 helix: 0.06 (0.28), residues: 322 sheet: -1.89 (0.62), residues: 82 loop : -2.10 (0.39), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 294 TYR 0.003 0.001 TYR B 169 PHE 0.015 0.002 PHE B 266 TRP 0.025 0.002 TRP A 99 HIS 0.004 0.001 HIS A 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.15 ( 4827) covalent geometry : angle 0.66448 / 0.32 ( 6540) hydrogen bonds : bond 0.05193 / 3.75 ( 240) hydrogen bonds : angle 5.57001 / 3.91 ( 696) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 49 time to evaluate : 0.139 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 54 CYS cc_start: 0.8883 (m) cc_final: 0.8511 (t) REVERT: B 49 ILE cc_start: 0.7675 (OUTLIER) cc_final: 0.6806 (tp) REVERT: B 54 CYS cc_start: 0.8967 (m) cc_final: 0.8645 (t) outliers start: 15 outliers final: 9 residues processed: 57 average time/residue: 0.0654 time to fit residues: 4.8607 Evaluate side-chains 44 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 34 time to evaluate : 0.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 100 TYR Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 284 PHE Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 100 TYR Chi-restraints excluded: chain B residue 284 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 57 optimal weight: 3.9990 chunk 32 optimal weight: 0.0370 chunk 42 optimal weight: 7.9990 chunk 56 optimal weight: 0.8980 chunk 17 optimal weight: 10.0000 chunk 49 optimal weight: 3.9990 chunk 18 optimal weight: 9.9990 chunk 1 optimal weight: 20.0000 chunk 39 optimal weight: 0.4980 chunk 43 optimal weight: 2.9990 chunk 11 optimal weight: 20.0000 overall best weight: 1.6862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.083532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.067156 restraints weight = 16872.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.068891 restraints weight = 10884.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.070092 restraints weight = 8145.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.070903 restraints weight = 6678.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.071520 restraints weight = 5815.495| |-----------------------------------------------------------------------------| r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.2981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4827 Z= 0.131 Angle : 0.597 9.017 6540 Z= 0.279 Chirality : 0.040 0.160 762 Planarity : 0.004 0.047 797 Dihedral : 6.657 32.100 701 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.15 % Allowed : 11.52 % Favored : 86.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.36), residues: 560 helix: 1.00 (0.29), residues: 320 sheet: -1.99 (0.63), residues: 82 loop : -1.62 (0.43), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 286 TYR 0.004 0.001 TYR A 169 PHE 0.010 0.001 PHE B 95 TRP 0.025 0.002 TRP B 99 HIS 0.002 0.001 HIS A 78 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.13 ( 4827) covalent geometry : angle 0.59690 / 0.28 ( 6540) hydrogen bonds : bond 0.04491 / 3.17 ( 240) hydrogen bonds : angle 5.03307 / 3.51 ( 696) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 41 time to evaluate : 0.203 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 70 CYS cc_start: 0.8545 (m) cc_final: 0.8303 (p) REVERT: A 284 PHE cc_start: 0.7719 (OUTLIER) cc_final: 0.7048 (m-80) REVERT: B 54 CYS cc_start: 0.8914 (m) cc_final: 0.8477 (t) outliers start: 11 outliers final: 5 residues processed: 48 average time/residue: 0.0542 time to fit residues: 3.7237 Evaluate side-chains 39 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 33 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 284 PHE Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 284 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 33 optimal weight: 9.9990 chunk 10 optimal weight: 5.9990 chunk 5 optimal weight: 7.9990 chunk 31 optimal weight: 5.9990 chunk 48 optimal weight: 10.0000 chunk 38 optimal weight: 10.0000 chunk 25 optimal weight: 0.9980 chunk 11 optimal weight: 6.9990 chunk 1 optimal weight: 10.0000 chunk 3 optimal weight: 6.9990 chunk 4 optimal weight: 2.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.081745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.065430 restraints weight = 17341.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.066994 restraints weight = 11643.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.068117 restraints weight = 8957.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.068827 restraints weight = 7448.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.069373 restraints weight = 6578.007| |-----------------------------------------------------------------------------| r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.3207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 4827 Z= 0.252 Angle : 0.698 8.941 6540 Z= 0.329 Chirality : 0.042 0.161 762 Planarity : 0.004 0.045 797 Dihedral : 6.551 30.990 701 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 4.30 % Allowed : 12.89 % Favored : 82.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.37), residues: 560 helix: 1.39 (0.30), residues: 308 sheet: -1.94 (0.63), residues: 80 loop : -0.94 (0.49), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 289 TYR 0.005 0.001 TYR A 172 PHE 0.018 0.002 PHE B 95 TRP 0.025 0.002 TRP B 99 HIS 0.004 0.001 HIS A 78 Details of bonding type rmsd/Z covalent geometry : bond 0.00558 / 0.25 ( 4827) covalent geometry : angle 0.69765 / 0.33 ( 6540) hydrogen bonds : bond 0.04543 / 3.13 ( 240) hydrogen bonds : angle 5.22911 / 3.65 ( 696) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 34 time to evaluate : 0.151 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 284 PHE cc_start: 0.7774 (OUTLIER) cc_final: 0.7155 (m-80) REVERT: B 54 CYS cc_start: 0.8920 (m) cc_final: 0.8380 (t) REVERT: B 284 PHE cc_start: 0.7778 (OUTLIER) cc_final: 0.7136 (m-80) outliers start: 22 outliers final: 10 residues processed: 49 average time/residue: 0.0556 time to fit residues: 3.8185 Evaluate side-chains 44 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 32 time to evaluate : 0.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 284 PHE Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 284 PHE Chi-restraints excluded: chain B residue 316 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 26 optimal weight: 1.9990 chunk 35 optimal weight: 10.0000 chunk 27 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 24 optimal weight: 5.9990 chunk 11 optimal weight: 9.9990 chunk 25 optimal weight: 0.9980 chunk 4 optimal weight: 7.9990 chunk 20 optimal weight: 8.9990 chunk 37 optimal weight: 6.9990 chunk 9 optimal weight: 9.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.082475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.066249 restraints weight = 17056.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.067982 restraints weight = 10850.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.069191 restraints weight = 8094.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.069821 restraints weight = 6627.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.070546 restraints weight = 5878.455| |-----------------------------------------------------------------------------| r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.3479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4827 Z= 0.145 Angle : 0.632 10.787 6540 Z= 0.284 Chirality : 0.041 0.176 762 Planarity : 0.004 0.042 797 Dihedral : 6.027 26.372 701 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.54 % Allowed : 16.02 % Favored : 81.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.37), residues: 560 helix: 1.78 (0.30), residues: 306 sheet: -1.93 (0.64), residues: 80 loop : -0.94 (0.48), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 301 TYR 0.004 0.001 TYR B 314 PHE 0.011 0.001 PHE B 95 TRP 0.027 0.002 TRP A 99 HIS 0.002 0.001 HIS A 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 ( 4827) covalent geometry : angle 0.63160 / 0.28 ( 6540) hydrogen bonds : bond 0.03890 / 2.72 ( 240) hydrogen bonds : angle 4.82735 / 3.36 ( 696) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 37 time to evaluate : 0.165 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 284 PHE cc_start: 0.7790 (OUTLIER) cc_final: 0.7213 (m-80) REVERT: B 54 CYS cc_start: 0.8850 (m) cc_final: 0.8308 (t) REVERT: B 128 LEU cc_start: 0.8501 (pp) cc_final: 0.8041 (tt) REVERT: B 284 PHE cc_start: 0.7779 (OUTLIER) cc_final: 0.7122 (m-80) outliers start: 13 outliers final: 7 residues processed: 45 average time/residue: 0.0532 time to fit residues: 3.4321 Evaluate side-chains 43 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 34 time to evaluate : 0.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 100 TYR Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 279 ASP Chi-restraints excluded: chain A residue 284 PHE Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 284 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 50 optimal weight: 5.9990 chunk 14 optimal weight: 0.8980 chunk 49 optimal weight: 3.9990 chunk 34 optimal weight: 6.9990 chunk 2 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 43 optimal weight: 6.9990 chunk 11 optimal weight: 8.9990 chunk 16 optimal weight: 0.9980 chunk 22 optimal weight: 4.9990 chunk 32 optimal weight: 8.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.083457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.067027 restraints weight = 17603.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.068789 restraints weight = 11350.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.069959 restraints weight = 8491.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.070788 restraints weight = 6998.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.071336 restraints weight = 6096.889| |-----------------------------------------------------------------------------| r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.3661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4827 Z= 0.120 Angle : 0.597 10.115 6540 Z= 0.273 Chirality : 0.040 0.178 762 Planarity : 0.003 0.040 797 Dihedral : 5.699 26.480 701 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 3.91 % Allowed : 16.02 % Favored : 80.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.38), residues: 560 helix: 2.13 (0.30), residues: 306 sheet: -1.84 (0.64), residues: 80 loop : -0.85 (0.47), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 289 TYR 0.005 0.001 TYR A 314 PHE 0.008 0.001 PHE B 95 TRP 0.028 0.002 TRP A 99 HIS 0.002 0.000 HIS A 78 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 ( 4827) covalent geometry : angle 0.59714 / 0.27 ( 6540) hydrogen bonds : bond 0.03673 / 2.56 ( 240) hydrogen bonds : angle 4.56144 / 3.17 ( 696) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 41 time to evaluate : 0.189 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 128 LEU cc_start: 0.8425 (pp) cc_final: 0.7976 (tp) REVERT: A 284 PHE cc_start: 0.7847 (OUTLIER) cc_final: 0.7370 (m-80) REVERT: B 54 CYS cc_start: 0.8816 (m) cc_final: 0.8377 (t) REVERT: B 128 LEU cc_start: 0.8460 (pp) cc_final: 0.8040 (tp) REVERT: B 284 PHE cc_start: 0.7799 (OUTLIER) cc_final: 0.7247 (m-80) outliers start: 20 outliers final: 12 residues processed: 55 average time/residue: 0.0504 time to fit residues: 4.0522 Evaluate side-chains 48 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 34 time to evaluate : 0.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 100 TYR Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 279 ASP Chi-restraints excluded: chain A residue 284 PHE Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 95 PHE Chi-restraints excluded: chain B residue 100 TYR Chi-restraints excluded: chain B residue 284 PHE Chi-restraints excluded: chain B residue 316 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 39 optimal weight: 3.9990 chunk 52 optimal weight: 7.9990 chunk 54 optimal weight: 0.9980 chunk 16 optimal weight: 6.9990 chunk 26 optimal weight: 5.9990 chunk 46 optimal weight: 7.9990 chunk 55 optimal weight: 0.0040 chunk 0 optimal weight: 10.0000 chunk 1 optimal weight: 9.9990 chunk 18 optimal weight: 9.9990 chunk 41 optimal weight: 7.9990 overall best weight: 3.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.082008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.065992 restraints weight = 17665.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.067628 restraints weight = 11672.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.068709 restraints weight = 8878.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.069467 restraints weight = 7402.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.069974 restraints weight = 6513.162| |-----------------------------------------------------------------------------| r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.3790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 4827 Z= 0.202 Angle : 0.655 9.280 6540 Z= 0.305 Chirality : 0.042 0.179 762 Planarity : 0.004 0.041 797 Dihedral : 5.835 28.501 701 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 4.10 % Allowed : 16.99 % Favored : 78.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.01 (0.38), residues: 560 helix: 2.17 (0.30), residues: 306 sheet: -1.85 (0.64), residues: 80 loop : -0.75 (0.49), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 198 TYR 0.004 0.001 TYR B 245 PHE 0.014 0.001 PHE B 95 TRP 0.029 0.002 TRP A 99 HIS 0.003 0.001 HIS A 78 Details of bonding type rmsd/Z covalent geometry : bond 0.00450 / 0.20 ( 4827) covalent geometry : angle 0.65467 / 0.30 ( 6540) hydrogen bonds : bond 0.03943 / 2.70 ( 240) hydrogen bonds : angle 4.83371 / 3.38 ( 696) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 33 time to evaluate : 0.191 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 128 LEU cc_start: 0.8441 (pp) cc_final: 0.7969 (tp) REVERT: A 284 PHE cc_start: 0.7803 (OUTLIER) cc_final: 0.7312 (m-80) REVERT: B 54 CYS cc_start: 0.8786 (m) cc_final: 0.8352 (t) REVERT: B 128 LEU cc_start: 0.8435 (pp) cc_final: 0.8006 (tp) REVERT: B 279 ASP cc_start: 0.6194 (OUTLIER) cc_final: 0.5693 (p0) REVERT: B 284 PHE cc_start: 0.7788 (OUTLIER) cc_final: 0.7191 (m-80) REVERT: B 328 HIS cc_start: 0.7042 (OUTLIER) cc_final: 0.6590 (t-90) outliers start: 21 outliers final: 13 residues processed: 47 average time/residue: 0.0544 time to fit residues: 3.6848 Evaluate side-chains 50 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 33 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 95 PHE Chi-restraints excluded: chain A residue 100 TYR Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 279 ASP Chi-restraints excluded: chain A residue 284 PHE Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 95 PHE Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 279 ASP Chi-restraints excluded: chain B residue 284 PHE Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 328 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 47 optimal weight: 6.9990 chunk 1 optimal weight: 5.9990 chunk 54 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 chunk 6 optimal weight: 4.9990 chunk 3 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 35 optimal weight: 0.0770 chunk 53 optimal weight: 2.9990 chunk 12 optimal weight: 5.9990 chunk 14 optimal weight: 0.9980 overall best weight: 1.4142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.083826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.067633 restraints weight = 17457.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.069296 restraints weight = 11567.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.070407 restraints weight = 8801.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.071209 restraints weight = 7314.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.071665 restraints weight = 6424.755| |-----------------------------------------------------------------------------| r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.3949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4827 Z= 0.115 Angle : 0.615 11.509 6540 Z= 0.282 Chirality : 0.040 0.188 762 Planarity : 0.003 0.039 797 Dihedral : 5.463 25.493 701 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 3.32 % Allowed : 18.16 % Favored : 78.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.16 (0.38), residues: 560 helix: 2.33 (0.30), residues: 306 sheet: -1.93 (0.63), residues: 82 loop : -0.68 (0.48), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 198 TYR 0.004 0.001 TYR A 172 PHE 0.007 0.001 PHE A 95 TRP 0.031 0.002 TRP A 99 HIS 0.002 0.001 HIS A 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.12 ( 4827) covalent geometry : angle 0.61494 / 0.28 ( 6540) hydrogen bonds : bond 0.03791 / 2.61 ( 240) hydrogen bonds : angle 4.51993 / 3.17 ( 696) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 38 time to evaluate : 0.192 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 284 PHE cc_start: 0.7760 (OUTLIER) cc_final: 0.7306 (m-80) REVERT: B 54 CYS cc_start: 0.8748 (m) cc_final: 0.8319 (t) REVERT: B 284 PHE cc_start: 0.7773 (OUTLIER) cc_final: 0.7188 (m-80) REVERT: B 328 HIS cc_start: 0.6963 (OUTLIER) cc_final: 0.6557 (t-90) outliers start: 17 outliers final: 12 residues processed: 50 average time/residue: 0.0514 time to fit residues: 3.7312 Evaluate side-chains 47 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 32 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 95 PHE Chi-restraints excluded: chain A residue 100 TYR Chi-restraints excluded: chain A residue 284 PHE Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 95 PHE Chi-restraints excluded: chain B residue 100 TYR Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 279 ASP Chi-restraints excluded: chain B residue 284 PHE Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 328 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 55 optimal weight: 0.9990 chunk 8 optimal weight: 0.0770 chunk 51 optimal weight: 4.9990 chunk 1 optimal weight: 9.9990 chunk 42 optimal weight: 1.9990 chunk 46 optimal weight: 5.9990 chunk 4 optimal weight: 2.9990 chunk 36 optimal weight: 6.9990 chunk 57 optimal weight: 0.8980 chunk 21 optimal weight: 3.9990 chunk 49 optimal weight: 4.9990 overall best weight: 1.3944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.084621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.068345 restraints weight = 17298.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.069939 restraints weight = 11637.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.071067 restraints weight = 8944.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.071807 restraints weight = 7462.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.072234 restraints weight = 6603.681| |-----------------------------------------------------------------------------| r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.4141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4827 Z= 0.121 Angle : 0.582 7.709 6540 Z= 0.277 Chirality : 0.040 0.198 762 Planarity : 0.003 0.040 797 Dihedral : 5.340 26.973 701 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 3.12 % Allowed : 17.58 % Favored : 79.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.26 (0.38), residues: 560 helix: 2.35 (0.30), residues: 308 sheet: -1.65 (0.64), residues: 80 loop : -0.69 (0.48), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 198 TYR 0.003 0.001 TYR B 169 PHE 0.007 0.001 PHE B 95 TRP 0.032 0.002 TRP A 99 HIS 0.002 0.000 HIS A 162 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 ( 4827) covalent geometry : angle 0.58244 / 0.28 ( 6540) hydrogen bonds : bond 0.03793 / 2.58 ( 240) hydrogen bonds : angle 4.55750 / 3.20 ( 696) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 39 time to evaluate : 0.189 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 284 PHE cc_start: 0.7737 (OUTLIER) cc_final: 0.7327 (m-80) REVERT: B 54 CYS cc_start: 0.8666 (m) cc_final: 0.8170 (t) REVERT: B 284 PHE cc_start: 0.7698 (OUTLIER) cc_final: 0.7190 (m-80) REVERT: B 328 HIS cc_start: 0.6955 (OUTLIER) cc_final: 0.6536 (t-90) outliers start: 16 outliers final: 11 residues processed: 50 average time/residue: 0.0553 time to fit residues: 3.9835 Evaluate side-chains 50 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 36 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 95 PHE Chi-restraints excluded: chain A residue 100 TYR Chi-restraints excluded: chain A residue 284 PHE Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 95 PHE Chi-restraints excluded: chain B residue 100 TYR Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 279 ASP Chi-restraints excluded: chain B residue 284 PHE Chi-restraints excluded: chain B residue 328 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 25 optimal weight: 0.8980 chunk 5 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 chunk 1 optimal weight: 0.0470 chunk 40 optimal weight: 8.9990 chunk 24 optimal weight: 8.9990 chunk 57 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 overall best weight: 1.1884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 78 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.085093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.068748 restraints weight = 16968.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.070456 restraints weight = 10975.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.071626 restraints weight = 8250.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.072468 restraints weight = 6761.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.072907 restraints weight = 5898.340| |-----------------------------------------------------------------------------| r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.4287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 4827 Z= 0.110 Angle : 0.569 6.302 6540 Z= 0.270 Chirality : 0.040 0.195 762 Planarity : 0.003 0.039 797 Dihedral : 5.112 26.115 701 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.93 % Allowed : 17.97 % Favored : 79.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.41 (0.38), residues: 560 helix: 2.50 (0.30), residues: 306 sheet: -1.58 (0.64), residues: 80 loop : -0.63 (0.48), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 198 TYR 0.004 0.001 TYR A 314 PHE 0.006 0.001 PHE A 95 TRP 0.032 0.002 TRP B 99 HIS 0.001 0.000 HIS B 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.11 ( 4827) covalent geometry : angle 0.56868 / 0.27 ( 6540) hydrogen bonds : bond 0.03465 / 2.36 ( 240) hydrogen bonds : angle 4.42510 / 3.09 ( 696) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 40 time to evaluate : 0.191 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 70 CYS cc_start: 0.8552 (m) cc_final: 0.8230 (p) REVERT: A 284 PHE cc_start: 0.7709 (OUTLIER) cc_final: 0.7311 (m-80) REVERT: B 284 PHE cc_start: 0.7744 (OUTLIER) cc_final: 0.7293 (m-80) REVERT: B 328 HIS cc_start: 0.6998 (OUTLIER) cc_final: 0.6618 (t-90) outliers start: 15 outliers final: 11 residues processed: 51 average time/residue: 0.0517 time to fit residues: 3.8263 Evaluate side-chains 49 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 35 time to evaluate : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 95 PHE Chi-restraints excluded: chain A residue 100 TYR Chi-restraints excluded: chain A residue 284 PHE Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 95 PHE Chi-restraints excluded: chain B residue 100 TYR Chi-restraints excluded: chain B residue 279 ASP Chi-restraints excluded: chain B residue 284 PHE Chi-restraints excluded: chain B residue 328 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 9 optimal weight: 7.9990 chunk 7 optimal weight: 0.0170 chunk 25 optimal weight: 0.7980 chunk 3 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 30 optimal weight: 20.0000 chunk 37 optimal weight: 6.9990 chunk 29 optimal weight: 1.9990 chunk 18 optimal weight: 9.9990 chunk 35 optimal weight: 0.9980 chunk 5 optimal weight: 4.9990 overall best weight: 1.3622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 78 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.085125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.068604 restraints weight = 17464.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.070312 restraints weight = 11379.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.071495 restraints weight = 8589.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.072216 restraints weight = 7090.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.072790 restraints weight = 6258.806| |-----------------------------------------------------------------------------| r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.4406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4827 Z= 0.114 Angle : 0.571 8.185 6540 Z= 0.271 Chirality : 0.040 0.196 762 Planarity : 0.003 0.040 797 Dihedral : 5.005 26.130 701 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.93 % Allowed : 18.55 % Favored : 78.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.52 (0.38), residues: 560 helix: 2.59 (0.31), residues: 306 sheet: -1.51 (0.64), residues: 80 loop : -0.61 (0.47), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 198 TYR 0.011 0.001 TYR A 172 PHE 0.007 0.001 PHE B 95 TRP 0.030 0.002 TRP A 99 HIS 0.001 0.000 HIS A 78 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.11 ( 4827) covalent geometry : angle 0.57149 / 0.27 ( 6540) hydrogen bonds : bond 0.03420 / 2.33 ( 240) hydrogen bonds : angle 4.36656 / 3.04 ( 696) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 750.15 seconds wall clock time: 13 minutes 37.68 seconds (817.68 seconds total)