Starting phenix.real_space_refine on Thu Jul 2 04:39:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8pvv_17973/07_2026/8pvv_17973.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pvv_17973/07_2026/8pvv_17973.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.81 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8pvv_17973/07_2026/8pvv_17973.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pvv_17973/07_2026/8pvv_17973.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8pvv_17973/07_2026/8pvv_17973.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8pvv_17973/07_2026/8pvv_17973.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8pvv_17973/07_2026/8pvv_17973.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pvv_17973/07_2026/8pvv_17973.map" } resolution = 2.81 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= 1.000 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: 6 Type Number sf(0) Gaussians P 50 5.49 5 Mg 1 5.21 5 S 13 5.16 5 C 3979 2.51 5 N 1079 2.21 5 O 1355 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 39 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6477 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 3478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3478 Classifications: {'peptide': 427} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 23, 'TRANS': 403} Chain: "C" Number of atoms: 1913 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 229, 1894 Classifications: {'peptide': 229} Link IDs: {'PTRANS': 8, 'TRANS': 220} Conformer: "B" Number of residues, atoms: 229, 1894 Classifications: {'peptide': 229} Link IDs: {'PTRANS': 8, 'TRANS': 220} bond proxies already assigned to first conformer: 1916 Chain: "R" Number of atoms: 549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 549 Classifications: {'RNA': 25} Modifications used: {'p5*END': 1, 'rna2p_pur': 1, 'rna3p_pur': 18, 'rna3p_pyr': 6} Link IDs: {'rna2p': 1, 'rna3p': 23} Chain: "S" Number of atoms: 500 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 500 Classifications: {'DNA': 25} Link IDs: {'rna3p': 24} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "C" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "R" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "S" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N ALYS C 52 " occ=0.50 ... (16 atoms not shown) pdb=" NZ BLYS C 52 " occ=0.50 residue: pdb=" N AHIS C 137 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS C 137 " occ=0.50 Time building chain proxies: 1.71, per 1000 atoms: 0.26 Number of scatterers: 6477 At special positions: 0 Unit cell: (75.9, 83.6, 99, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 13 16.00 P 50 15.00 Mg 1 11.99 O 1355 8.00 N 1079 7.00 C 3979 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: 0.47 Conformation dependent library (CDL) restraints added in 409.8 milliseconds 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1240 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 7 sheets defined 36.0% alpha, 30.8% beta 22 base pairs and 37 stacking pairs defined. Time for finding SS restraints: 0.53 Creating SS restraints... Processing helix chain 'A' and resid 25 through 37 Processing helix chain 'A' and resid 58 through 74 Processing helix chain 'A' and resid 92 through 107 Processing helix chain 'A' and resid 119 through 132 removed outlier: 3.961A pdb=" N TYR A 129 " --> pdb=" O LYS A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 147 Processing helix chain 'A' and resid 148 through 164 Processing helix chain 'A' and resid 221 through 241 Processing helix chain 'A' and resid 263 through 278 Processing helix chain 'A' and resid 303 through 307 Processing helix chain 'A' and resid 359 through 376 removed outlier: 3.705A pdb=" N LYS A 376 " --> pdb=" O TYR A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 407 Proline residue: A 394 - end of helix Processing helix chain 'A' and resid 417 through 423 removed outlier: 3.674A pdb=" N GLN A 421 " --> pdb=" O ASN A 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 66 removed outlier: 3.601A pdb=" N ILE C 66 " --> pdb=" O GLY C 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 63 through 66' Processing helix chain 'C' and resid 77 through 93 removed outlier: 4.174A pdb=" N GLY C 81 " --> pdb=" O ASN C 77 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N LYS C 82 " --> pdb=" O ALA C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 163 through 172 Processing helix chain 'C' and resid 172 through 187 Processing helix chain 'C' and resid 199 through 216 Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 213 removed outlier: 5.566A pdb=" N TRP A 210 " --> pdb=" O PHE A 202 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N PHE A 202 " --> pdb=" O TRP A 210 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 208 through 213 removed outlier: 5.566A pdb=" N TRP A 210 " --> pdb=" O PHE A 202 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N PHE A 202 " --> pdb=" O TRP A 210 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N ILE A 181 " --> pdb=" O THR A 250 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N HIS A 252 " --> pdb=" O ILE A 181 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N ILE A 183 " --> pdb=" O HIS A 252 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N GLU A 247 " --> pdb=" O LYS A 286 " (cutoff:3.500A) removed outlier: 8.385A pdb=" N ALA A 288 " --> pdb=" O GLU A 247 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N LEU A 249 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N LEU A 290 " --> pdb=" O LEU A 249 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N LEU A 251 " --> pdb=" O LEU A 290 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N LEU A 292 " --> pdb=" O LEU A 251 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N VAL A 253 " --> pdb=" O LEU A 292 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N TYR A 287 " --> pdb=" O ASP A 353 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N ASP A 353 " --> pdb=" O TYR A 287 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ILE A 289 " --> pdb=" O VAL A 351 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N GLU A 3 " --> pdb=" O LYS A 317 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N MET A 2 " --> pdb=" O VAL C 242 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 20 through 22 removed outlier: 3.769A pdb=" N ILE A 170 " --> pdb=" O ARG A 14 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 83 through 87 removed outlier: 7.040A pdb=" N ILE A 49 " --> pdb=" O SER A 84 " (cutoff:3.500A) removed outlier: 8.053A pdb=" N PHE A 86 " --> pdb=" O ILE A 49 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N LEU A 51 " --> pdb=" O PHE A 86 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N ALA A 50 " --> pdb=" O MET A 112 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N VAL A 114 " --> pdb=" O ALA A 50 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N ILE A 52 " --> pdb=" O VAL A 114 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 101 through 105 removed outlier: 6.707A pdb=" N ARG C 110 " --> pdb=" O LYS C 103 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 101 through 105 removed outlier: 6.707A pdb=" N ARG C 110 " --> pdb=" O LYS C 103 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N PHE C 143 " --> pdb=" O ILE C 28 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASN C 30 " --> pdb=" O LYS C 233 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 52 through 55 removed outlier: 3.551A pdb=" N ILE C 73 " --> pdb=" O ILE C 35 " (cutoff:3.500A) 271 hydrogen bonds defined for protein. 762 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 54 hydrogen bonds 104 hydrogen bond angles 0 basepair planarities 22 basepair parallelities 37 stacking parallelities Total time for adding SS restraints: 0.91 Time building geometry restraints manager: 0.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 1563 1.33 - 1.45: 1532 1.45 - 1.57: 3480 1.57 - 1.69: 98 1.69 - 1.80: 25 Bond restraints: 6698 Sorted by residual: bond pdb=" C1' DT S 16 " pdb=" N1 DT S 16 " ideal model delta sigma weight residual 1.468 1.519 -0.051 1.40e-02 5.10e+03 1.31e+01 bond pdb=" O3' C R 14 " pdb=" P U R 15 " ideal model delta sigma weight residual 1.607 1.652 -0.045 1.50e-02 4.44e+03 9.12e+00 bond pdb=" C3' DG S 26 " pdb=" C2' DG S 26 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.02e+00 bond pdb=" C3' DC S 37 " pdb=" C2' DC S 37 " ideal model delta sigma weight residual 1.516 1.536 -0.020 8.00e-03 1.56e+04 6.14e+00 bond pdb=" C3' DC S 35 " pdb=" C2' DC S 35 " ideal model delta sigma weight residual 1.516 1.536 -0.020 8.00e-03 1.56e+04 6.04e+00 ... (remaining 6693 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.83: 9056 1.83 - 3.67: 226 3.67 - 5.50: 18 5.50 - 7.34: 7 7.34 - 9.17: 1 Bond angle restraints: 9308 Sorted by residual: angle pdb=" N3 DT S 39 " pdb=" C4 DT S 39 " pdb=" O4 DT S 39 " ideal model delta sigma weight residual 119.90 122.42 -2.52 6.00e-01 2.78e+00 1.77e+01 angle pdb=" N3 DT S 17 " pdb=" C4 DT S 17 " pdb=" O4 DT S 17 " ideal model delta sigma weight residual 119.90 122.42 -2.52 6.00e-01 2.78e+00 1.76e+01 angle pdb=" N3 DT S 36 " pdb=" C4 DT S 36 " pdb=" O4 DT S 36 " ideal model delta sigma weight residual 119.90 122.38 -2.48 6.00e-01 2.78e+00 1.71e+01 angle pdb=" N3 DT S 24 " pdb=" C4 DT S 24 " pdb=" O4 DT S 24 " ideal model delta sigma weight residual 119.90 122.37 -2.47 6.00e-01 2.78e+00 1.69e+01 angle pdb=" N3 DT S 20 " pdb=" C4 DT S 20 " pdb=" O4 DT S 20 " ideal model delta sigma weight residual 119.90 122.33 -2.43 6.00e-01 2.78e+00 1.64e+01 ... (remaining 9303 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.05: 3375 17.05 - 34.09: 356 34.09 - 51.14: 138 51.14 - 68.18: 72 68.18 - 85.23: 9 Dihedral angle restraints: 3950 sinusoidal: 2012 harmonic: 1938 Sorted by residual: dihedral pdb=" CA ASP C 155 " pdb=" C ASP C 155 " pdb=" N ARG C 156 " pdb=" CA ARG C 156 " ideal model delta harmonic sigma weight residual -180.00 -160.87 -19.13 0 5.00e+00 4.00e-02 1.46e+01 dihedral pdb=" CA TYR C 22 " pdb=" C TYR C 22 " pdb=" N ILE C 23 " pdb=" CA ILE C 23 " ideal model delta harmonic sigma weight residual 180.00 -163.36 -16.64 0 5.00e+00 4.00e-02 1.11e+01 dihedral pdb=" CB MET C 201 " pdb=" CG MET C 201 " pdb=" SD MET C 201 " pdb=" CE MET C 201 " ideal model delta sinusoidal sigma weight residual -60.00 -117.17 57.17 3 1.50e+01 4.44e-03 9.43e+00 ... (remaining 3947 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 779 0.050 - 0.099: 199 0.099 - 0.149: 58 0.149 - 0.199: 9 0.199 - 0.249: 2 Chirality restraints: 1047 Sorted by residual: chirality pdb=" C2' G R 12 " pdb=" C3' G R 12 " pdb=" O2' G R 12 " pdb=" C1' G R 12 " both_signs ideal model delta sigma weight residual False -2.75 -2.50 -0.25 2.00e-01 2.50e+01 1.55e+00 chirality pdb=" C3' G R 12 " pdb=" C4' G R 12 " pdb=" O3' G R 12 " pdb=" C2' G R 12 " both_signs ideal model delta sigma weight residual False -2.48 -2.70 0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" CA ASN C 68 " pdb=" N ASN C 68 " pdb=" C ASN C 68 " pdb=" CB ASN C 68 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.83e-01 ... (remaining 1044 not shown) Planarity restraints: 995 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 423 " 0.051 5.00e-02 4.00e+02 7.84e-02 9.84e+00 pdb=" N PRO A 424 " -0.136 5.00e-02 4.00e+02 pdb=" CA PRO A 424 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO A 424 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 341 " 0.035 5.00e-02 4.00e+02 5.33e-02 4.55e+00 pdb=" N PRO A 342 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO A 342 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 342 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 134 " 0.032 5.00e-02 4.00e+02 4.85e-02 3.77e+00 pdb=" N PRO A 135 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO A 135 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 135 " 0.027 5.00e-02 4.00e+02 ... (remaining 992 not shown) Histogram of nonbonded interaction distances: 1.71 - 2.35: 12 2.35 - 2.98: 3172 2.98 - 3.62: 10221 3.62 - 4.26: 17559 4.26 - 4.90: 27536 Nonbonded interactions: 58500 Sorted by model distance: nonbonded pdb=" OP1 A R 1 " pdb="MG MG R 101 " model vdw 1.707 2.170 nonbonded pdb=" NE2 GLN A 159 " pdb="MG MG R 101 " model vdw 2.033 2.250 nonbonded pdb=" O THR C 191 " pdb=" O HOH C 301 " model vdw 2.242 3.040 nonbonded pdb=" O LEU A 427 " pdb="MG MG R 101 " model vdw 2.264 2.170 nonbonded pdb=" OD1 ASP C 57 " pdb=" O2' G R 18 " model vdw 2.268 3.040 ... (remaining 58495 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 0.010 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.410 Find NCS groups from input model: 0.020 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:5.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 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 : 0.004 0.051 6698 Z= 0.274 Angle : 0.662 9.169 9308 Z= 0.438 Chirality : 0.051 0.249 1047 Planarity : 0.005 0.078 995 Dihedral : 18.006 85.227 2710 Min Nonbonded Distance : 1.707 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 0.33 % Allowed : 0.00 % Favored : 99.67 % 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: 0.55 (0.32), residues: 658 helix: 1.38 (0.35), residues: 216 sheet: 0.36 (0.44), residues: 157 loop : -0.33 (0.34), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 334 TYR 0.019 0.002 TYR C 197 PHE 0.027 0.002 PHE C 205 TRP 0.008 0.001 TRP C 180 HIS 0.005 0.001 HIS C 187 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.27 ( 6698) covalent geometry : angle 0.66209 / 0.44 ( 9308) hydrogen bonds : bond 0.18685 / 12.82 ( 300) hydrogen bonds : angle 7.52433 / 5.21 ( 866) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.155 Fit side-chains REVERT: C 229 ASP cc_start: 0.7901 (m-30) cc_final: 0.7633 (m-30) outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.4295 time to fit residues: 37.1159 Evaluate side-chains 59 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 49 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 8.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 10.0000 chunk 51 optimal weight: 0.7980 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 17 ASN A 99 GLN A 102 ASN A 354 ASN C 136 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.133247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.110729 restraints weight = 25003.487| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 3.02 r_work: 0.3374 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3349 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3349 r_free = 0.3349 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3349 r_free = 0.3349 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3349 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.1108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 6698 Z= 0.231 Angle : 0.670 7.185 9308 Z= 0.367 Chirality : 0.049 0.197 1047 Planarity : 0.006 0.052 995 Dihedral : 19.362 84.358 1357 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.32 % Allowed : 9.59 % Favored : 89.09 % 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: 0.49 (0.32), residues: 658 helix: 1.39 (0.34), residues: 217 sheet: 0.32 (0.43), residues: 156 loop : -0.43 (0.33), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 156 TYR 0.019 0.002 TYR C 197 PHE 0.017 0.002 PHE C 205 TRP 0.009 0.001 TRP C 180 HIS 0.005 0.001 HIS C 187 Details of bonding type rmsd/Z covalent geometry : bond 0.00500 / 0.23 ( 6698) covalent geometry : angle 0.67008 / 0.37 ( 9308) hydrogen bonds : bond 0.06660 / 4.41 ( 300) hydrogen bonds : angle 5.40961 / 3.74 ( 866) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 62 time to evaluate : 0.211 Fit side-chains REVERT: A 260 MET cc_start: 0.7694 (OUTLIER) cc_final: 0.7084 (ppp) outliers start: 6 outliers final: 2 residues processed: 65 average time/residue: 0.4118 time to fit residues: 28.3040 Evaluate side-chains 54 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 51 time to evaluate : 0.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 MET Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain C residue 74 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 21 optimal weight: 5.9990 chunk 4 optimal weight: 7.9990 chunk 1 optimal weight: 9.9990 chunk 66 optimal weight: 20.0000 chunk 51 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 11 optimal weight: 0.5980 chunk 40 optimal weight: 1.9990 chunk 3 optimal weight: 5.9990 chunk 59 optimal weight: 0.5980 chunk 65 optimal weight: 4.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 99 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.133019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.110854 restraints weight = 17410.492| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 2.24 r_work: 0.3400 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3298 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3268 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3268 r_free = 0.3268 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3268 r_free = 0.3268 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3268 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.1354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 6698 Z= 0.216 Angle : 0.624 6.243 9308 Z= 0.345 Chirality : 0.048 0.198 1047 Planarity : 0.005 0.052 995 Dihedral : 19.257 88.562 1357 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.82 % Allowed : 12.89 % Favored : 85.29 % 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: 0.43 (0.32), residues: 658 helix: 1.41 (0.34), residues: 218 sheet: 0.08 (0.42), residues: 159 loop : -0.39 (0.34), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 110 TYR 0.021 0.002 TYR A 124 PHE 0.016 0.002 PHE C 205 TRP 0.010 0.001 TRP C 180 HIS 0.004 0.001 HIS C 187 Details of bonding type rmsd/Z covalent geometry : bond 0.00470 / 0.22 ( 6698) covalent geometry : angle 0.62390 / 0.35 ( 9308) hydrogen bonds : bond 0.06019 / 3.99 ( 300) hydrogen bonds : angle 5.02972 / 3.47 ( 866) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 58 time to evaluate : 0.241 Fit side-chains REVERT: A 421 GLN cc_start: 0.7909 (mp10) cc_final: 0.7660 (mp10) REVERT: C 104 GLU cc_start: 0.7581 (mm-30) cc_final: 0.7298 (pt0) REVERT: C 155 ASP cc_start: 0.8226 (t0) cc_final: 0.7157 (t0) outliers start: 9 outliers final: 2 residues processed: 60 average time/residue: 0.4329 time to fit residues: 27.5425 Evaluate side-chains 57 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 55 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 365 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 4 optimal weight: 6.9990 chunk 12 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 36 optimal weight: 4.9990 chunk 41 optimal weight: 6.9990 chunk 13 optimal weight: 0.7980 chunk 8 optimal weight: 0.8980 chunk 50 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 2 optimal weight: 5.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 99 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.132147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.110036 restraints weight = 16754.797| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 2.18 r_work: 0.3392 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3291 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3266 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3266 r_free = 0.3266 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3266 r_free = 0.3266 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3266 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.1493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 6698 Z= 0.239 Angle : 0.633 6.211 9308 Z= 0.349 Chirality : 0.048 0.196 1047 Planarity : 0.005 0.051 995 Dihedral : 19.188 88.587 1357 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.15 % Allowed : 14.38 % Favored : 83.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.37 (0.32), residues: 658 helix: 1.35 (0.34), residues: 218 sheet: 0.01 (0.42), residues: 159 loop : -0.39 (0.34), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 110 TYR 0.023 0.002 TYR A 124 PHE 0.013 0.002 PHE A 138 TRP 0.010 0.002 TRP C 180 HIS 0.004 0.001 HIS C 136 Details of bonding type rmsd/Z covalent geometry : bond 0.00526 / 0.24 ( 6698) covalent geometry : angle 0.63347 / 0.35 ( 9308) hydrogen bonds : bond 0.05962 / 3.95 ( 300) hydrogen bonds : angle 4.95722 / 3.42 ( 866) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 56 time to evaluate : 0.204 Fit side-chains REVERT: A 260 MET cc_start: 0.7970 (OUTLIER) cc_final: 0.7331 (ppp) REVERT: A 421 GLN cc_start: 0.8027 (mp10) cc_final: 0.7777 (mp10) REVERT: C 104 GLU cc_start: 0.7567 (mm-30) cc_final: 0.7339 (pt0) outliers start: 11 outliers final: 5 residues processed: 61 average time/residue: 0.4156 time to fit residues: 26.8770 Evaluate side-chains 59 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 53 time to evaluate : 0.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 MET Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 365 HIS Chi-restraints excluded: chain C residue 57 ASP Chi-restraints excluded: chain C residue 74 ASP Chi-restraints excluded: chain C residue 107 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 48 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 64 optimal weight: 4.9990 chunk 25 optimal weight: 0.9990 chunk 35 optimal weight: 0.9990 chunk 66 optimal weight: 20.0000 chunk 53 optimal weight: 0.9980 chunk 62 optimal weight: 6.9990 chunk 55 optimal weight: 0.8980 chunk 10 optimal weight: 0.0980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 99 GLN A 211 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.135518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.113192 restraints weight = 18798.298| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 2.30 r_work: 0.3442 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3337 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3308 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3308 r_free = 0.3308 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3308 r_free = 0.3308 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3308 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.1617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6698 Z= 0.145 Angle : 0.563 5.986 9308 Z= 0.317 Chirality : 0.045 0.192 1047 Planarity : 0.005 0.052 995 Dihedral : 19.152 91.785 1357 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.15 % Allowed : 14.71 % Favored : 83.14 % 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: 0.67 (0.32), residues: 658 helix: 1.58 (0.35), residues: 218 sheet: 0.32 (0.43), residues: 159 loop : -0.30 (0.35), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 110 TYR 0.012 0.002 TYR A 152 PHE 0.011 0.001 PHE A 426 TRP 0.007 0.001 TRP C 180 HIS 0.002 0.001 HIS C 187 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.15 ( 6698) covalent geometry : angle 0.56328 / 0.32 ( 9308) hydrogen bonds : bond 0.05284 / 3.42 ( 300) hydrogen bonds : angle 4.69335 / 3.23 ( 866) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 65 time to evaluate : 0.229 Fit side-chains REVERT: A 260 MET cc_start: 0.7799 (OUTLIER) cc_final: 0.7188 (ppp) REVERT: A 278 GLN cc_start: 0.7238 (mp10) cc_final: 0.6940 (mp10) REVERT: A 421 GLN cc_start: 0.8030 (mp10) cc_final: 0.7809 (mp10) REVERT: C 104 GLU cc_start: 0.7550 (mm-30) cc_final: 0.7249 (pt0) outliers start: 11 outliers final: 3 residues processed: 70 average time/residue: 0.3824 time to fit residues: 28.3672 Evaluate side-chains 62 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 58 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 260 MET Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain C residue 57 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 41 optimal weight: 0.8980 chunk 57 optimal weight: 0.7980 chunk 60 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 chunk 24 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 chunk 16 optimal weight: 0.8980 chunk 6 optimal weight: 4.9990 chunk 54 optimal weight: 0.9980 chunk 35 optimal weight: 5.9990 chunk 30 optimal weight: 0.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 99 GLN C 137 HIS B Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.135418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.112730 restraints weight = 21293.645| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 2.48 r_work: 0.3421 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3318 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3291 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3291 r_free = 0.3291 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3291 r_free = 0.3291 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3291 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.1743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6698 Z= 0.154 Angle : 0.567 6.388 9308 Z= 0.316 Chirality : 0.045 0.191 1047 Planarity : 0.005 0.050 995 Dihedral : 19.103 92.099 1357 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.15 % Allowed : 15.87 % Favored : 81.98 % 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: 0.78 (0.32), residues: 658 helix: 1.64 (0.35), residues: 218 sheet: 0.55 (0.43), residues: 157 loop : -0.33 (0.34), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 110 TYR 0.012 0.002 TYR C 87 PHE 0.010 0.001 PHE A 426 TRP 0.007 0.001 TRP C 180 HIS 0.002 0.001 HIS C 187 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.15 ( 6698) covalent geometry : angle 0.56742 / 0.32 ( 9308) hydrogen bonds : bond 0.05243 / 3.41 ( 300) hydrogen bonds : angle 4.61742 / 3.18 ( 866) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 70 time to evaluate : 0.134 Fit side-chains REVERT: A 260 MET cc_start: 0.7898 (OUTLIER) cc_final: 0.7269 (ppp) REVERT: A 278 GLN cc_start: 0.7278 (mp10) cc_final: 0.7034 (mp10) REVERT: A 421 GLN cc_start: 0.8031 (mp10) cc_final: 0.7783 (mp10) REVERT: C 104 GLU cc_start: 0.7569 (mm-30) cc_final: 0.7262 (pt0) outliers start: 11 outliers final: 5 residues processed: 75 average time/residue: 0.3737 time to fit residues: 29.7317 Evaluate side-chains 69 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 63 time to evaluate : 0.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 260 MET Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 365 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 34 optimal weight: 5.9990 chunk 67 optimal weight: 10.0000 chunk 33 optimal weight: 4.9990 chunk 44 optimal weight: 4.9990 chunk 55 optimal weight: 0.7980 chunk 40 optimal weight: 3.9990 chunk 18 optimal weight: 6.9990 chunk 53 optimal weight: 0.7980 chunk 21 optimal weight: 4.9990 chunk 6 optimal weight: 5.9990 chunk 14 optimal weight: 3.9990 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 82 ASN A 99 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.131510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.108642 restraints weight = 17039.133| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 2.26 r_work: 0.3380 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3274 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3248 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3248 r_free = 0.3248 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3248 r_free = 0.3248 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3248 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.1778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.059 6698 Z= 0.300 Angle : 0.667 6.122 9308 Z= 0.363 Chirality : 0.049 0.193 1047 Planarity : 0.006 0.051 995 Dihedral : 19.063 88.596 1357 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.64 % Allowed : 15.54 % Favored : 81.82 % 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: 0.45 (0.31), residues: 658 helix: 1.38 (0.34), residues: 218 sheet: 0.31 (0.42), residues: 157 loop : -0.50 (0.33), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 54 TYR 0.021 0.003 TYR A 124 PHE 0.019 0.002 PHE A 138 TRP 0.013 0.002 TRP C 180 HIS 0.003 0.001 HIS A 252 Details of bonding type rmsd/Z covalent geometry : bond 0.00670 / 0.30 ( 6698) covalent geometry : angle 0.66739 / 0.36 ( 9308) hydrogen bonds : bond 0.06125 / 4.09 ( 300) hydrogen bonds : angle 4.85831 / 3.34 ( 866) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 58 time to evaluate : 0.140 Fit side-chains REVERT: A 99 GLN cc_start: 0.8399 (OUTLIER) cc_final: 0.7685 (mp-120) REVERT: A 260 MET cc_start: 0.7892 (OUTLIER) cc_final: 0.7254 (ppp) REVERT: A 278 GLN cc_start: 0.7443 (mp10) cc_final: 0.7196 (mp10) REVERT: A 421 GLN cc_start: 0.8182 (mp10) cc_final: 0.7976 (mp10) REVERT: C 104 GLU cc_start: 0.7591 (mm-30) cc_final: 0.7332 (pt0) outliers start: 14 outliers final: 9 residues processed: 68 average time/residue: 0.3848 time to fit residues: 27.7376 Evaluate side-chains 67 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 56 time to evaluate : 0.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 99 GLN Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 260 MET Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 365 HIS Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain C residue 107 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 35 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 47 optimal weight: 7.9990 chunk 48 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 4 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 159 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.134224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.110403 restraints weight = 23796.925| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 2.72 r_work: 0.3397 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3382 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3382 r_free = 0.3382 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3382 r_free = 0.3382 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3382 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.1839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 6698 Z= 0.166 Angle : 0.586 5.966 9308 Z= 0.326 Chirality : 0.046 0.233 1047 Planarity : 0.005 0.050 995 Dihedral : 19.103 91.516 1357 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.48 % Allowed : 16.53 % Favored : 80.99 % 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: 0.54 (0.32), residues: 658 helix: 1.41 (0.34), residues: 218 sheet: 0.45 (0.43), residues: 157 loop : -0.45 (0.34), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 110 TYR 0.025 0.002 TYR A 124 PHE 0.011 0.001 PHE A 426 TRP 0.008 0.001 TRP C 180 HIS 0.003 0.001 HIS C 136 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.17 ( 6698) covalent geometry : angle 0.58604 / 0.33 ( 9308) hydrogen bonds : bond 0.05483 / 3.57 ( 300) hydrogen bonds : angle 4.71133 / 3.25 ( 866) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 63 time to evaluate : 0.173 Fit side-chains REVERT: A 260 MET cc_start: 0.7731 (OUTLIER) cc_final: 0.7037 (ppp) REVERT: A 278 GLN cc_start: 0.7274 (mp10) cc_final: 0.6998 (mp10) REVERT: A 421 GLN cc_start: 0.8305 (mt0) cc_final: 0.8097 (mp10) REVERT: C 159 ASN cc_start: 0.7227 (t0) cc_final: 0.7010 (t0) outliers start: 13 outliers final: 7 residues processed: 73 average time/residue: 0.3742 time to fit residues: 29.1027 Evaluate side-chains 66 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 58 time to evaluate : 0.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 260 MET Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 365 HIS Chi-restraints excluded: chain C residue 107 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 53 optimal weight: 4.9990 chunk 13 optimal weight: 0.5980 chunk 45 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 50 optimal weight: 0.0980 chunk 33 optimal weight: 3.9990 chunk 40 optimal weight: 0.9980 chunk 0 optimal weight: 8.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 99 GLN A 102 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.134427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.111920 restraints weight = 21996.602| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 2.87 r_work: 0.3394 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3377 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3377 r_free = 0.3377 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3377 r_free = 0.3377 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3377 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.1928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6698 Z= 0.167 Angle : 0.582 5.974 9308 Z= 0.323 Chirality : 0.046 0.293 1047 Planarity : 0.005 0.050 995 Dihedral : 19.080 92.004 1357 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.31 % Allowed : 16.86 % Favored : 80.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.32), residues: 658 helix: 1.51 (0.34), residues: 218 sheet: 0.59 (0.43), residues: 157 loop : -0.42 (0.34), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 110 TYR 0.015 0.002 TYR A 225 PHE 0.010 0.001 PHE A 138 TRP 0.007 0.001 TRP C 180 HIS 0.002 0.001 HIS C 187 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.17 ( 6698) covalent geometry : angle 0.58219 / 0.32 ( 9308) hydrogen bonds : bond 0.05403 / 3.53 ( 300) hydrogen bonds : angle 4.66050 / 3.21 ( 866) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 62 time to evaluate : 0.172 Fit side-chains REVERT: A 260 MET cc_start: 0.7683 (OUTLIER) cc_final: 0.6992 (ppp) REVERT: A 278 GLN cc_start: 0.7145 (mp10) cc_final: 0.6886 (mp10) REVERT: A 421 GLN cc_start: 0.8288 (mt0) cc_final: 0.8046 (mp10) outliers start: 12 outliers final: 8 residues processed: 70 average time/residue: 0.3981 time to fit residues: 29.4886 Evaluate side-chains 63 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 54 time to evaluate : 0.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 260 MET Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain C residue 107 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 44 optimal weight: 0.7980 chunk 52 optimal weight: 4.9990 chunk 6 optimal weight: 4.9990 chunk 8 optimal weight: 5.9990 chunk 60 optimal weight: 0.9980 chunk 66 optimal weight: 20.0000 chunk 49 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 41 optimal weight: 0.6980 chunk 57 optimal weight: 0.8980 chunk 24 optimal weight: 4.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 99 GLN C 159 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.136448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.114026 restraints weight = 28460.306| |-----------------------------------------------------------------------------| r_work (start): 0.3564 rms_B_bonded: 3.39 r_work: 0.3402 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3373 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3373 r_free = 0.3373 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3373 r_free = 0.3373 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3373 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.1974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6698 Z= 0.161 Angle : 0.575 5.963 9308 Z= 0.320 Chirality : 0.047 0.347 1047 Planarity : 0.005 0.050 995 Dihedral : 19.072 92.294 1357 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.98 % Allowed : 17.36 % Favored : 80.66 % 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: 0.71 (0.32), residues: 658 helix: 1.53 (0.34), residues: 218 sheet: 0.65 (0.44), residues: 157 loop : -0.42 (0.34), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 54 TYR 0.023 0.002 TYR A 124 PHE 0.010 0.001 PHE A 426 TRP 0.007 0.001 TRP C 180 HIS 0.002 0.001 HIS C 187 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.16 ( 6698) covalent geometry : angle 0.57482 / 0.32 ( 9308) hydrogen bonds : bond 0.05356 / 3.49 ( 300) hydrogen bonds : angle 4.63391 / 3.18 ( 866) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 60 time to evaluate : 0.136 Fit side-chains REVERT: A 260 MET cc_start: 0.7772 (OUTLIER) cc_final: 0.7086 (ppp) REVERT: A 421 GLN cc_start: 0.8291 (mt0) cc_final: 0.8054 (mp10) outliers start: 10 outliers final: 7 residues processed: 66 average time/residue: 0.4030 time to fit residues: 28.0881 Evaluate side-chains 65 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 57 time to evaluate : 0.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 260 MET Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain C residue 107 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 53 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 6 optimal weight: 4.9990 chunk 34 optimal weight: 0.1980 chunk 38 optimal weight: 0.5980 chunk 42 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 21 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 99 GLN C 159 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.137833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.115609 restraints weight = 27883.182| |-----------------------------------------------------------------------------| r_work (start): 0.3584 rms_B_bonded: 3.38 r_work: 0.3423 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3397 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3397 r_free = 0.3397 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3397 r_free = 0.3397 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3397 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.2048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6698 Z= 0.146 Angle : 0.561 5.916 9308 Z= 0.314 Chirality : 0.046 0.290 1047 Planarity : 0.005 0.050 995 Dihedral : 19.066 93.095 1357 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.98 % Allowed : 17.19 % Favored : 80.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.32), residues: 658 helix: 1.56 (0.34), residues: 217 sheet: 0.71 (0.44), residues: 157 loop : -0.43 (0.34), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 161 TYR 0.013 0.002 TYR A 225 PHE 0.011 0.001 PHE A 426 TRP 0.006 0.001 TRP C 180 HIS 0.002 0.001 HIS C 187 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.15 ( 6698) covalent geometry : angle 0.56144 / 0.31 ( 9308) hydrogen bonds : bond 0.05203 / 3.36 ( 300) hydrogen bonds : angle 4.53410 / 3.10 ( 866) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1684.55 seconds wall clock time: 29 minutes 32.39 seconds (1772.39 seconds total)