Starting phenix.real_space_refine on Thu Jul 2 02:27:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jbh_61314/07_2026/9jbh_61314.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jbh_61314/07_2026/9jbh_61314.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.73 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9jbh_61314/07_2026/9jbh_61314.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jbh_61314/07_2026/9jbh_61314.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9jbh_61314/07_2026/9jbh_61314.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jbh_61314/07_2026/9jbh_61314.map" } resolution = 2.73 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= 0.040 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 10 5.49 5 S 30 5.16 5 C 3898 2.51 5 N 812 2.21 5 O 974 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 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: 5724 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2609 Classifications: {'peptide': 334} Link IDs: {'PTRANS': 15, 'TRANS': 318} Chain: "B" Number of atoms: 2609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2609 Classifications: {'peptide': 334} Link IDs: {'PTRANS': 15, 'TRANS': 318} Chain: "A" Number of atoms: 253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 253 Unusual residues: {'3PE': 3, 'CDL': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 253 Unusual residues: {'3PE': 3, 'CDL': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 1.45, per 1000 atoms: 0.25 Number of scatterers: 5724 At special positions: 0 Unit cell: (75.952, 105.848, 71.912, 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 30 16.00 P 10 15.00 O 974 8.00 N 812 7.00 C 3898 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: 0.50 Conformation dependent library (CDL) restraints added in 181.3 milliseconds 1328 Ramachandran restraints generated. 664 Oldfield, 0 Emsley, 664 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1256 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 0 sheets defined 84.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.13 Creating SS restraints... Processing helix chain 'A' and resid 38 through 62 removed outlier: 4.043A pdb=" N PHE A 43 " --> pdb=" O ILE A 39 " (cutoff:3.500A) Proline residue: A 44 - end of helix Processing helix chain 'A' and resid 66 through 80 removed outlier: 3.808A pdb=" N LYS A 71 " --> pdb=" O SER A 67 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N GLY A 72 " --> pdb=" O THR A 68 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LEU A 73 " --> pdb=" O GLN A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 93 removed outlier: 3.506A pdb=" N VAL A 92 " --> pdb=" O LYS A 88 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU A 93 " --> pdb=" O ASN A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 125 removed outlier: 3.828A pdb=" N LEU A 103 " --> pdb=" O ASP A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 141 Proline residue: A 138 - end of helix Processing helix chain 'A' and resid 149 through 158 removed outlier: 3.736A pdb=" N ILE A 153 " --> pdb=" O LEU A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 167 Processing helix chain 'A' and resid 168 through 196 removed outlier: 3.636A pdb=" N ALA A 173 " --> pdb=" O ILE A 169 " (cutoff:3.500A) Proline residue: A 174 - end of helix removed outlier: 3.941A pdb=" N ASN A 181 " --> pdb=" O LEU A 177 " (cutoff:3.500A) Proline residue: A 182 - end of helix Processing helix chain 'A' and resid 202 through 217 removed outlier: 3.713A pdb=" N VAL A 214 " --> pdb=" O GLY A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 233 removed outlier: 3.556A pdb=" N PHE A 221 " --> pdb=" O ASN A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 250 removed outlier: 4.194A pdb=" N ASN A 243 " --> pdb=" O VAL A 239 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N PHE A 244 " --> pdb=" O TYR A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 264 Processing helix chain 'A' and resid 272 through 288 Processing helix chain 'A' and resid 288 through 302 Processing helix chain 'A' and resid 306 through 320 removed outlier: 3.659A pdb=" N HIS A 310 " --> pdb=" O SER A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 337 removed outlier: 4.001A pdb=" N ALA A 330 " --> pdb=" O ALA A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 367 removed outlier: 3.696A pdb=" N ALA A 355 " --> pdb=" O THR A 351 " (cutoff:3.500A) Proline residue: A 356 - end of helix Processing helix chain 'B' and resid 41 through 62 Processing helix chain 'B' and resid 66 through 80 removed outlier: 3.786A pdb=" N LYS B 71 " --> pdb=" O SER B 67 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N GLY B 72 " --> pdb=" O THR B 68 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N LEU B 73 " --> pdb=" O GLN B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 93 removed outlier: 3.506A pdb=" N LEU B 93 " --> pdb=" O ASN B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 125 removed outlier: 3.847A pdb=" N LEU B 103 " --> pdb=" O ASP B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 128 No H-bonds generated for 'chain 'B' and resid 126 through 128' Processing helix chain 'B' and resid 129 through 141 Proline residue: B 138 - end of helix Processing helix chain 'B' and resid 149 through 158 removed outlier: 3.708A pdb=" N ILE B 153 " --> pdb=" O LEU B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 167 Processing helix chain 'B' and resid 168 through 195 removed outlier: 3.591A pdb=" N ALA B 173 " --> pdb=" O ILE B 169 " (cutoff:3.500A) Proline residue: B 174 - end of helix removed outlier: 4.062A pdb=" N ASN B 181 " --> pdb=" O LEU B 177 " (cutoff:3.500A) Proline residue: B 182 - end of helix Processing helix chain 'B' and resid 202 through 217 removed outlier: 3.685A pdb=" N VAL B 214 " --> pdb=" O GLY B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 233 removed outlier: 3.843A pdb=" N VAL B 223 " --> pdb=" O ILE B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 249 removed outlier: 4.142A pdb=" N ASN B 243 " --> pdb=" O VAL B 239 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N PHE B 244 " --> pdb=" O TYR B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 264 removed outlier: 3.643A pdb=" N SER B 255 " --> pdb=" O SER B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 288 Processing helix chain 'B' and resid 288 through 301 Processing helix chain 'B' and resid 306 through 320 removed outlier: 3.716A pdb=" N HIS B 310 " --> pdb=" O SER B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 337 removed outlier: 3.916A pdb=" N ALA B 330 " --> pdb=" O ALA B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 341 through 367 removed outlier: 3.590A pdb=" N SER B 345 " --> pdb=" O GLU B 341 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA B 355 " --> pdb=" O THR B 351 " (cutoff:3.500A) Proline residue: B 356 - end of helix 368 hydrogen bonds defined for protein. 1086 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: 0.79 Time building geometry restraints manager: 0.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 806 1.31 - 1.44: 1489 1.44 - 1.56: 3477 1.56 - 1.68: 22 1.68 - 1.81: 50 Bond restraints: 5844 Sorted by residual: bond pdb=" C PRO B 138 " pdb=" O PRO B 138 " ideal model delta sigma weight residual 1.237 1.186 0.051 1.16e-02 7.43e+03 1.94e+01 bond pdb=" C PRO A 138 " pdb=" O PRO A 138 " ideal model delta sigma weight residual 1.238 1.187 0.050 1.24e-02 6.50e+03 1.64e+01 bond pdb=" OB5 CDL A 402 " pdb=" PB2 CDL A 402 " ideal model delta sigma weight residual 1.657 1.579 0.078 2.00e-02 2.50e+03 1.52e+01 bond pdb=" OB5 CDL B 402 " pdb=" PB2 CDL B 402 " ideal model delta sigma weight residual 1.657 1.579 0.078 2.00e-02 2.50e+03 1.50e+01 bond pdb=" OA5 CDL A 402 " pdb=" PA1 CDL A 402 " ideal model delta sigma weight residual 1.651 1.579 0.072 2.00e-02 2.50e+03 1.30e+01 ... (remaining 5839 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.99: 7594 1.99 - 3.97: 185 3.97 - 5.96: 35 5.96 - 7.94: 9 7.94 - 9.93: 1 Bond angle restraints: 7824 Sorted by residual: angle pdb=" CA ASN A 202 " pdb=" C ASN A 202 " pdb=" O ASN A 202 " ideal model delta sigma weight residual 121.65 116.07 5.58 1.17e+00 7.31e-01 2.27e+01 angle pdb=" CA PRO B 127 " pdb=" N PRO B 127 " pdb=" CD PRO B 127 " ideal model delta sigma weight residual 112.00 106.20 5.80 1.40e+00 5.10e-01 1.72e+01 angle pdb=" CA SER A 200 " pdb=" C SER A 200 " pdb=" O SER A 200 " ideal model delta sigma weight residual 121.66 117.00 4.66 1.17e+00 7.31e-01 1.59e+01 angle pdb=" CA ASN A 202 " pdb=" C ASN A 202 " pdb=" N LYS A 203 " ideal model delta sigma weight residual 115.67 120.32 -4.65 1.23e+00 6.61e-01 1.43e+01 angle pdb=" CA LYS B 303 " pdb=" CB LYS B 303 " pdb=" CG LYS B 303 " ideal model delta sigma weight residual 114.10 121.04 -6.94 2.00e+00 2.50e-01 1.20e+01 ... (remaining 7819 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 36.00: 3456 36.00 - 71.99: 193 71.99 - 107.99: 5 107.99 - 143.99: 0 143.99 - 179.98: 4 Dihedral angle restraints: 3658 sinusoidal: 1710 harmonic: 1948 Sorted by residual: dihedral pdb=" CB5 CDL B 402 " pdb=" CB4 CDL B 402 " pdb=" OB6 CDL B 402 " pdb=" CB6 CDL B 402 " ideal model delta sinusoidal sigma weight residual 144.75 -35.27 -179.98 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" CB5 CDL A 402 " pdb=" CB4 CDL A 402 " pdb=" OB6 CDL A 402 " pdb=" CB6 CDL A 402 " ideal model delta sinusoidal sigma weight residual 144.75 -36.16 -179.09 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" O21 3PE A 404 " pdb=" C2 3PE A 404 " pdb=" C3 3PE A 404 " pdb=" O31 3PE A 404 " ideal model delta sinusoidal sigma weight residual 60.47 -103.24 163.71 1 3.00e+01 1.11e-03 2.09e+01 ... (remaining 3655 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 628 0.042 - 0.083: 194 0.083 - 0.124: 52 0.124 - 0.166: 5 0.166 - 0.207: 3 Chirality restraints: 882 Sorted by residual: chirality pdb=" CA ILE A 139 " pdb=" N ILE A 139 " pdb=" C ILE A 139 " pdb=" CB ILE A 139 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CA ILE B 139 " pdb=" N ILE B 139 " pdb=" C ILE B 139 " pdb=" CB ILE B 139 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.20 2.00e-01 2.50e+01 9.60e-01 chirality pdb=" CA LEU B 107 " pdb=" N LEU B 107 " pdb=" C LEU B 107 " pdb=" CB LEU B 107 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 6.97e-01 ... (remaining 879 not shown) Planarity restraints: 908 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER B 126 " 0.082 5.00e-02 4.00e+02 1.21e-01 2.35e+01 pdb=" N PRO B 127 " -0.209 5.00e-02 4.00e+02 pdb=" CA PRO B 127 " 0.064 5.00e-02 4.00e+02 pdb=" CD PRO B 127 " 0.064 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 126 " 0.042 5.00e-02 4.00e+02 6.39e-02 6.52e+00 pdb=" N PRO A 127 " -0.110 5.00e-02 4.00e+02 pdb=" CA PRO A 127 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 127 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 337 " -0.010 2.00e-02 2.50e+03 1.93e-02 3.71e+00 pdb=" C ASN A 337 " 0.033 2.00e-02 2.50e+03 pdb=" O ASN A 337 " -0.013 2.00e-02 2.50e+03 pdb=" N MET A 338 " -0.011 2.00e-02 2.50e+03 ... (remaining 905 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1159 2.78 - 3.31: 5629 3.31 - 3.84: 9757 3.84 - 4.37: 12022 4.37 - 4.90: 20189 Nonbonded interactions: 48756 Sorted by model distance: nonbonded pdb=" O VAL B 172 " pdb=" OG SER B 176 " model vdw 2.248 3.040 nonbonded pdb=" O VAL B 91 " pdb=" ND2 ASN B 230 " model vdw 2.321 3.120 nonbonded pdb=" O VAL A 91 " pdb=" ND2 ASN A 230 " model vdw 2.348 3.120 nonbonded pdb=" O VAL A 340 " pdb=" OG1 THR A 344 " model vdw 2.362 3.040 nonbonded pdb=" O SER A 101 " pdb=" OG SER A 105 " model vdw 2.366 3.040 ... (remaining 48751 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints 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 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: 4.320 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: 6.700 Find NCS groups from input model: 0.090 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:6.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 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 : 0.005 0.094 5844 Z= 0.271 Angle : 0.757 9.929 7824 Z= 0.415 Chirality : 0.043 0.207 882 Planarity : 0.007 0.121 908 Dihedral : 20.329 179.983 2402 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 1.56 % Allowed : 20.93 % Favored : 77.51 % 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: 0.77 (0.33), residues: 664 helix: 0.93 (0.24), residues: 500 sheet: None (None), residues: 0 loop : -0.59 (0.50), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 79 TYR 0.009 0.001 TYR B 316 PHE 0.018 0.001 PHE B 102 TRP 0.009 0.001 TRP A 363 HIS 0.007 0.003 HIS A 310 Details of bonding type rmsd/Z covalent geometry : bond 0.00506 / 0.27 ( 5844) covalent geometry : angle 0.75738 / 0.42 ( 7824) hydrogen bonds : bond 0.15565 / 10.36 ( 368) hydrogen bonds : angle 6.22503 / 4.47 ( 1086) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1328 Ramachandran restraints generated. 664 Oldfield, 0 Emsley, 664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1328 Ramachandran restraints generated. 664 Oldfield, 0 Emsley, 664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 94 time to evaluate : 0.209 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 293 LEU cc_start: 0.8168 (mp) cc_final: 0.7927 (mt) REVERT: B 293 LEU cc_start: 0.8205 (mp) cc_final: 0.7885 (mt) outliers start: 9 outliers final: 7 residues processed: 102 average time/residue: 0.4260 time to fit residues: 46.0846 Evaluate side-chains 92 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 85 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 351 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 49 optimal weight: 5.9990 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 0.6980 chunk 27 optimal weight: 5.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 230 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.189469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.161069 restraints weight = 5983.914| |-----------------------------------------------------------------------------| r_work (start): 0.3889 rms_B_bonded: 1.36 r_work: 0.3686 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3541 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.1342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 5844 Z= 0.180 Angle : 0.654 7.808 7824 Z= 0.319 Chirality : 0.045 0.181 882 Planarity : 0.006 0.070 908 Dihedral : 19.327 173.996 1231 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 3.29 % Allowed : 18.17 % Favored : 78.55 % 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 (0.33), residues: 664 helix: 0.79 (0.23), residues: 512 sheet: None (None), residues: 0 loop : -0.06 (0.53), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 79 TYR 0.011 0.002 TYR A 170 PHE 0.031 0.002 PHE B 221 TRP 0.007 0.001 TRP A 363 HIS 0.004 0.002 HIS A 310 Details of bonding type rmsd/Z covalent geometry : bond 0.00438 / 0.18 ( 5844) covalent geometry : angle 0.65413 / 0.32 ( 7824) hydrogen bonds : bond 0.04956 / 3.45 ( 368) hydrogen bonds : angle 5.11956 / 3.64 ( 1086) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1328 Ramachandran restraints generated. 664 Oldfield, 0 Emsley, 664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1328 Ramachandran restraints generated. 664 Oldfield, 0 Emsley, 664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 83 time to evaluate : 0.188 Fit side-chains revert: symmetry clash REVERT: A 194 LYS cc_start: 0.8001 (mtpt) cc_final: 0.7501 (ptpp) REVERT: A 295 ARG cc_start: 0.7574 (mtp180) cc_final: 0.7359 (ttm-80) REVERT: B 338 MET cc_start: 0.6612 (OUTLIER) cc_final: 0.5931 (ptp) outliers start: 19 outliers final: 9 residues processed: 93 average time/residue: 0.5279 time to fit residues: 51.4831 Evaluate side-chains 86 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 76 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 129 SER Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 338 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 33 optimal weight: 2.9990 chunk 62 optimal weight: 5.9990 chunk 0 optimal weight: 2.9990 chunk 57 optimal weight: 0.8980 chunk 20 optimal weight: 0.7980 chunk 31 optimal weight: 0.3980 chunk 44 optimal weight: 0.5980 chunk 29 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 48 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.4192 r_free = 0.4192 target = 0.189664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.160694 restraints weight = 5951.904| |-----------------------------------------------------------------------------| r_work (start): 0.3879 rms_B_bonded: 1.50 r_work: 0.3677 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3532 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.1542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 5844 Z= 0.163 Angle : 0.626 6.603 7824 Z= 0.304 Chirality : 0.043 0.169 882 Planarity : 0.005 0.059 908 Dihedral : 18.688 174.233 1225 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % Rotamer: Outliers : 3.11 % Allowed : 19.03 % Favored : 77.85 % 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: 0.76 (0.32), residues: 664 helix: 0.79 (0.23), residues: 512 sheet: None (None), residues: 0 loop : -0.14 (0.51), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 79 TYR 0.011 0.002 TYR A 170 PHE 0.029 0.002 PHE B 221 TRP 0.006 0.001 TRP A 363 HIS 0.004 0.002 HIS A 310 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.16 ( 5844) covalent geometry : angle 0.62617 / 0.30 ( 7824) hydrogen bonds : bond 0.04600 / 3.21 ( 368) hydrogen bonds : angle 4.98672 / 3.53 ( 1086) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1328 Ramachandran restraints generated. 664 Oldfield, 0 Emsley, 664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1328 Ramachandran restraints generated. 664 Oldfield, 0 Emsley, 664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 87 time to evaluate : 0.205 Fit side-chains revert: symmetry clash REVERT: A 194 LYS cc_start: 0.7915 (mtpt) cc_final: 0.7684 (ptpp) REVERT: A 217 ASN cc_start: 0.7278 (OUTLIER) cc_final: 0.6980 (t0) REVERT: B 129 SER cc_start: 0.8444 (OUTLIER) cc_final: 0.8108 (m) REVERT: B 194 LYS cc_start: 0.8241 (ptmt) cc_final: 0.7955 (ptmm) REVERT: B 205 LYS cc_start: 0.7205 (OUTLIER) cc_final: 0.6875 (ttmm) REVERT: B 295 ARG cc_start: 0.7418 (mtp180) cc_final: 0.7171 (ttm-80) REVERT: B 338 MET cc_start: 0.6501 (OUTLIER) cc_final: 0.6042 (ptp) outliers start: 18 outliers final: 10 residues processed: 99 average time/residue: 0.4766 time to fit residues: 49.7077 Evaluate side-chains 93 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 79 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 217 ASN Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 338 MET Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 129 SER Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 205 LYS Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 338 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 48 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 57 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 34 optimal weight: 0.5980 chunk 20 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 63 optimal weight: 0.7980 chunk 30 optimal weight: 0.8980 chunk 27 optimal weight: 6.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.4189 r_free = 0.4189 target = 0.189295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.159307 restraints weight = 6008.085| |-----------------------------------------------------------------------------| r_work (start): 0.3856 rms_B_bonded: 1.45 r_work: 0.3673 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3528 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.1741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 5844 Z= 0.166 Angle : 0.638 6.699 7824 Z= 0.309 Chirality : 0.044 0.165 882 Planarity : 0.005 0.055 908 Dihedral : 18.635 173.552 1224 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 3.63 % Allowed : 18.69 % Favored : 77.68 % 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: 0.76 (0.32), residues: 664 helix: 0.78 (0.23), residues: 512 sheet: None (None), residues: 0 loop : -0.10 (0.51), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 130 TYR 0.011 0.002 TYR B 170 PHE 0.031 0.002 PHE B 221 TRP 0.006 0.001 TRP A 363 HIS 0.001 0.000 HIS A 310 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.17 ( 5844) covalent geometry : angle 0.63818 / 0.31 ( 7824) hydrogen bonds : bond 0.04552 / 3.17 ( 368) hydrogen bonds : angle 4.97681 / 3.54 ( 1086) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1328 Ramachandran restraints generated. 664 Oldfield, 0 Emsley, 664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1328 Ramachandran restraints generated. 664 Oldfield, 0 Emsley, 664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 83 time to evaluate : 0.168 Fit side-chains revert: symmetry clash REVERT: A 264 MET cc_start: 0.8062 (mtm) cc_final: 0.7710 (mtt) REVERT: B 129 SER cc_start: 0.8417 (OUTLIER) cc_final: 0.8094 (m) REVERT: B 194 LYS cc_start: 0.8277 (ptmt) cc_final: 0.8017 (ptmm) REVERT: B 205 LYS cc_start: 0.7307 (OUTLIER) cc_final: 0.6944 (ttmm) REVERT: B 272 LYS cc_start: 0.8110 (OUTLIER) cc_final: 0.7717 (mttt) REVERT: B 338 MET cc_start: 0.6423 (OUTLIER) cc_final: 0.5712 (ptp) outliers start: 21 outliers final: 13 residues processed: 94 average time/residue: 0.5238 time to fit residues: 51.6451 Evaluate side-chains 96 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 79 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 129 SER Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 205 LYS Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 272 LYS Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 338 MET Chi-restraints excluded: chain B residue 358 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 53 optimal weight: 0.0980 chunk 25 optimal weight: 0.9980 chunk 65 optimal weight: 4.9990 chunk 57 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 11 optimal weight: 0.5980 chunk 20 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 chunk 31 optimal weight: 0.4980 chunk 39 optimal weight: 3.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.4197 r_free = 0.4197 target = 0.190094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.159652 restraints weight = 6131.741| |-----------------------------------------------------------------------------| r_work (start): 0.3865 rms_B_bonded: 1.48 r_work: 0.3681 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3535 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.1810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 5844 Z= 0.148 Angle : 0.613 6.215 7824 Z= 0.298 Chirality : 0.043 0.164 882 Planarity : 0.005 0.054 908 Dihedral : 18.429 174.310 1224 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Rotamer: Outliers : 4.50 % Allowed : 18.51 % Favored : 76.99 % 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: 0.90 (0.32), residues: 664 helix: 0.90 (0.23), residues: 512 sheet: None (None), residues: 0 loop : -0.12 (0.51), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 130 TYR 0.009 0.002 TYR A 170 PHE 0.030 0.002 PHE B 221 TRP 0.006 0.001 TRP A 363 HIS 0.001 0.000 HIS A 310 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.15 ( 5844) covalent geometry : angle 0.61325 / 0.30 ( 7824) hydrogen bonds : bond 0.04333 / 3.01 ( 368) hydrogen bonds : angle 4.84717 / 3.44 ( 1086) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1328 Ramachandran restraints generated. 664 Oldfield, 0 Emsley, 664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1328 Ramachandran restraints generated. 664 Oldfield, 0 Emsley, 664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 83 time to evaluate : 0.195 Fit side-chains revert: symmetry clash REVERT: A 194 LYS cc_start: 0.7878 (ptpp) cc_final: 0.7439 (ptmm) REVERT: A 217 ASN cc_start: 0.7265 (OUTLIER) cc_final: 0.6992 (t0) REVERT: A 264 MET cc_start: 0.8059 (mtm) cc_final: 0.7678 (mtt) REVERT: A 337 ASN cc_start: 0.8377 (t0) cc_final: 0.8060 (t0) REVERT: B 129 SER cc_start: 0.8397 (OUTLIER) cc_final: 0.8068 (m) REVERT: B 194 LYS cc_start: 0.8275 (ptmt) cc_final: 0.8043 (ptmm) REVERT: B 205 LYS cc_start: 0.7331 (OUTLIER) cc_final: 0.6980 (ttmm) REVERT: B 272 LYS cc_start: 0.8128 (OUTLIER) cc_final: 0.7731 (mttt) REVERT: B 338 MET cc_start: 0.6274 (OUTLIER) cc_final: 0.5655 (ptp) outliers start: 26 outliers final: 14 residues processed: 97 average time/residue: 0.4910 time to fit residues: 49.9350 Evaluate side-chains 100 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 81 time to evaluate : 0.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 217 ASN Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 338 MET Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 129 SER Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 205 LYS Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 272 LYS Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 295 ARG Chi-restraints excluded: chain B residue 338 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 52 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 chunk 23 optimal weight: 0.0370 chunk 20 optimal weight: 0.9990 chunk 50 optimal weight: 0.6980 chunk 27 optimal weight: 5.9990 chunk 21 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 10 optimal weight: 0.4980 chunk 61 optimal weight: 0.5980 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 143 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.190821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.160849 restraints weight = 6010.494| |-----------------------------------------------------------------------------| r_work (start): 0.3878 rms_B_bonded: 1.46 r_work: 0.3696 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3551 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.1911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 5844 Z= 0.141 Angle : 0.610 8.399 7824 Z= 0.295 Chirality : 0.043 0.163 882 Planarity : 0.005 0.054 908 Dihedral : 18.268 174.363 1224 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 4.33 % Allowed : 19.38 % Favored : 76.30 % 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: 0.97 (0.32), residues: 664 helix: 0.95 (0.23), residues: 512 sheet: None (None), residues: 0 loop : -0.09 (0.50), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 79 TYR 0.009 0.001 TYR B 170 PHE 0.030 0.002 PHE B 221 TRP 0.005 0.001 TRP B 193 HIS 0.001 0.000 HIS A 310 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.14 ( 5844) covalent geometry : angle 0.61019 / 0.29 ( 7824) hydrogen bonds : bond 0.04197 / 2.91 ( 368) hydrogen bonds : angle 4.80949 / 3.44 ( 1086) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1328 Ramachandran restraints generated. 664 Oldfield, 0 Emsley, 664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1328 Ramachandran restraints generated. 664 Oldfield, 0 Emsley, 664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 84 time to evaluate : 0.213 Fit side-chains revert: symmetry clash REVERT: A 194 LYS cc_start: 0.7844 (ptpp) cc_final: 0.7516 (ptmm) REVERT: A 217 ASN cc_start: 0.7309 (OUTLIER) cc_final: 0.7060 (t0) REVERT: A 264 MET cc_start: 0.8043 (mtm) cc_final: 0.7667 (mtt) REVERT: A 337 ASN cc_start: 0.8408 (t0) cc_final: 0.8091 (t0) REVERT: B 129 SER cc_start: 0.8365 (OUTLIER) cc_final: 0.8022 (m) REVERT: B 143 GLN cc_start: 0.6891 (OUTLIER) cc_final: 0.6061 (tp-100) REVERT: B 194 LYS cc_start: 0.8290 (ptmt) cc_final: 0.8078 (ptmm) REVERT: B 205 LYS cc_start: 0.7307 (OUTLIER) cc_final: 0.6964 (ttmm) REVERT: B 272 LYS cc_start: 0.8125 (OUTLIER) cc_final: 0.7714 (mttt) REVERT: B 338 MET cc_start: 0.6200 (OUTLIER) cc_final: 0.5610 (ptp) outliers start: 25 outliers final: 14 residues processed: 97 average time/residue: 0.5080 time to fit residues: 51.8150 Evaluate side-chains 100 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 80 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 217 ASN Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 338 MET Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 129 SER Chi-restraints excluded: chain B residue 143 GLN Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 205 LYS Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 272 LYS Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 295 ARG Chi-restraints excluded: chain B residue 338 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 53 optimal weight: 0.0570 chunk 25 optimal weight: 0.7980 chunk 14 optimal weight: 0.6980 chunk 40 optimal weight: 0.5980 chunk 46 optimal weight: 0.8980 chunk 7 optimal weight: 0.9980 chunk 63 optimal weight: 0.7980 chunk 28 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 143 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.190739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.160664 restraints weight = 6104.246| |-----------------------------------------------------------------------------| r_work (start): 0.3876 rms_B_bonded: 1.47 r_work: 0.3692 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3544 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.1934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 5844 Z= 0.146 Angle : 0.621 8.789 7824 Z= 0.301 Chirality : 0.043 0.171 882 Planarity : 0.005 0.054 908 Dihedral : 18.206 173.753 1224 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 4.84 % Allowed : 18.69 % Favored : 76.47 % 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: 0.96 (0.32), residues: 664 helix: 0.94 (0.23), residues: 512 sheet: None (None), residues: 0 loop : -0.09 (0.50), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 79 TYR 0.009 0.001 TYR B 170 PHE 0.030 0.002 PHE B 221 TRP 0.005 0.001 TRP A 363 HIS 0.001 0.001 HIS A 310 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.15 ( 5844) covalent geometry : angle 0.62109 / 0.30 ( 7824) hydrogen bonds : bond 0.04212 / 2.93 ( 368) hydrogen bonds : angle 4.79698 / 3.42 ( 1086) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1328 Ramachandran restraints generated. 664 Oldfield, 0 Emsley, 664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1328 Ramachandran restraints generated. 664 Oldfield, 0 Emsley, 664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 84 time to evaluate : 0.208 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 194 LYS cc_start: 0.7873 (ptpp) cc_final: 0.7532 (ptmm) REVERT: A 217 ASN cc_start: 0.7336 (OUTLIER) cc_final: 0.7065 (t0) REVERT: A 264 MET cc_start: 0.8021 (mtm) cc_final: 0.7679 (mtt) REVERT: A 337 ASN cc_start: 0.8476 (t0) cc_final: 0.8157 (t0) REVERT: B 129 SER cc_start: 0.8367 (OUTLIER) cc_final: 0.8023 (m) REVERT: B 143 GLN cc_start: 0.7140 (OUTLIER) cc_final: 0.6272 (tp-100) REVERT: B 205 LYS cc_start: 0.7291 (OUTLIER) cc_final: 0.6950 (ttmm) REVERT: B 272 LYS cc_start: 0.8104 (OUTLIER) cc_final: 0.7703 (mttt) REVERT: B 338 MET cc_start: 0.6217 (OUTLIER) cc_final: 0.5563 (ptp) outliers start: 28 outliers final: 16 residues processed: 99 average time/residue: 0.5180 time to fit residues: 53.7577 Evaluate side-chains 104 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 82 time to evaluate : 0.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 217 ASN Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 338 MET Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 129 SER Chi-restraints excluded: chain B residue 143 GLN Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 205 LYS Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 272 LYS Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 295 ARG Chi-restraints excluded: chain B residue 338 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 36 optimal weight: 0.7980 chunk 62 optimal weight: 0.5980 chunk 56 optimal weight: 0.0270 chunk 26 optimal weight: 0.8980 chunk 13 optimal weight: 0.9990 chunk 35 optimal weight: 0.3980 chunk 40 optimal weight: 0.3980 chunk 20 optimal weight: 1.9990 chunk 21 optimal weight: 0.5980 chunk 2 optimal weight: 1.9990 chunk 55 optimal weight: 0.5980 overall best weight: 0.4038 ------------------------------------------------------------------------------- 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 = 0.4220 r_free = 0.4220 target = 0.192247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.162801 restraints weight = 6022.834| |-----------------------------------------------------------------------------| r_work (start): 0.3899 rms_B_bonded: 1.44 r_work: 0.3715 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3568 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.1986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 5844 Z= 0.129 Angle : 0.600 8.658 7824 Z= 0.292 Chirality : 0.042 0.172 882 Planarity : 0.005 0.054 908 Dihedral : 17.912 174.127 1224 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 3.98 % Allowed : 20.07 % Favored : 75.95 % 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: 1.15 (0.32), residues: 664 helix: 1.08 (0.23), residues: 518 sheet: None (None), residues: 0 loop : -0.08 (0.52), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 130 TYR 0.008 0.001 TYR A 170 PHE 0.027 0.002 PHE B 221 TRP 0.005 0.001 TRP A 363 HIS 0.001 0.001 HIS A 310 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.13 ( 5844) covalent geometry : angle 0.59989 / 0.29 ( 7824) hydrogen bonds : bond 0.03984 / 2.77 ( 368) hydrogen bonds : angle 4.68135 / 3.34 ( 1086) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1328 Ramachandran restraints generated. 664 Oldfield, 0 Emsley, 664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1328 Ramachandran restraints generated. 664 Oldfield, 0 Emsley, 664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 88 time to evaluate : 0.145 Fit side-chains revert: symmetry clash REVERT: A 194 LYS cc_start: 0.7854 (ptpp) cc_final: 0.7526 (ptmm) REVERT: A 217 ASN cc_start: 0.7265 (OUTLIER) cc_final: 0.7057 (t0) REVERT: A 264 MET cc_start: 0.7999 (mtm) cc_final: 0.7649 (mtt) REVERT: B 129 SER cc_start: 0.8337 (OUTLIER) cc_final: 0.7982 (m) REVERT: B 155 GLU cc_start: 0.7189 (tp30) cc_final: 0.6880 (tp30) REVERT: B 194 LYS cc_start: 0.8297 (ptmt) cc_final: 0.8079 (ptmm) REVERT: B 205 LYS cc_start: 0.7263 (OUTLIER) cc_final: 0.6932 (ttmm) REVERT: B 272 LYS cc_start: 0.8116 (OUTLIER) cc_final: 0.7829 (mttt) REVERT: B 338 MET cc_start: 0.6155 (OUTLIER) cc_final: 0.5629 (ptp) REVERT: B 347 MET cc_start: 0.7777 (OUTLIER) cc_final: 0.7393 (ttm) outliers start: 23 outliers final: 13 residues processed: 100 average time/residue: 0.4768 time to fit residues: 50.2106 Evaluate side-chains 101 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 82 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 217 ASN Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 338 MET Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 129 SER Chi-restraints excluded: chain B residue 205 LYS Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 272 LYS Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 295 ARG Chi-restraints excluded: chain B residue 338 MET Chi-restraints excluded: chain B residue 347 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 3 optimal weight: 2.9990 chunk 60 optimal weight: 5.9990 chunk 44 optimal weight: 0.6980 chunk 1 optimal weight: 0.7980 chunk 28 optimal weight: 0.9980 chunk 20 optimal weight: 0.8980 chunk 23 optimal weight: 0.0370 chunk 64 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 56 optimal weight: 0.3980 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 89 ASN ** B 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.190753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.160486 restraints weight = 6020.219| |-----------------------------------------------------------------------------| r_work (start): 0.3878 rms_B_bonded: 1.48 r_work: 0.3693 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3546 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 5844 Z= 0.145 Angle : 0.609 6.466 7824 Z= 0.300 Chirality : 0.044 0.176 882 Planarity : 0.005 0.054 908 Dihedral : 17.745 173.127 1222 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 3.46 % Allowed : 20.93 % Favored : 75.61 % 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: 1.08 (0.32), residues: 664 helix: 1.04 (0.23), residues: 510 sheet: None (None), residues: 0 loop : -0.09 (0.50), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 130 TYR 0.009 0.001 TYR B 151 PHE 0.029 0.002 PHE B 221 TRP 0.005 0.001 TRP A 363 HIS 0.002 0.001 HIS A 310 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.14 ( 5844) covalent geometry : angle 0.60890 / 0.30 ( 7824) hydrogen bonds : bond 0.04209 / 2.92 ( 368) hydrogen bonds : angle 4.71647 / 3.36 ( 1086) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1328 Ramachandran restraints generated. 664 Oldfield, 0 Emsley, 664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1328 Ramachandran restraints generated. 664 Oldfield, 0 Emsley, 664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 82 time to evaluate : 0.202 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 194 LYS cc_start: 0.7863 (ptpp) cc_final: 0.7513 (ptmm) REVERT: A 217 ASN cc_start: 0.7296 (OUTLIER) cc_final: 0.7060 (t0) REVERT: A 337 ASN cc_start: 0.8412 (t0) cc_final: 0.8103 (t0) REVERT: B 129 SER cc_start: 0.8334 (OUTLIER) cc_final: 0.7976 (m) REVERT: B 194 LYS cc_start: 0.8312 (ptmt) cc_final: 0.8105 (ptmm) REVERT: B 272 LYS cc_start: 0.8151 (OUTLIER) cc_final: 0.7752 (mttt) REVERT: B 338 MET cc_start: 0.6128 (OUTLIER) cc_final: 0.5496 (ptp) REVERT: B 347 MET cc_start: 0.7792 (OUTLIER) cc_final: 0.7347 (ttm) outliers start: 20 outliers final: 13 residues processed: 93 average time/residue: 0.5056 time to fit residues: 49.3634 Evaluate side-chains 98 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 80 time to evaluate : 0.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 217 ASN Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 338 MET Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 129 SER Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 272 LYS Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 295 ARG Chi-restraints excluded: chain B residue 338 MET Chi-restraints excluded: chain B residue 347 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 44 optimal weight: 0.5980 chunk 4 optimal weight: 0.6980 chunk 30 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 chunk 7 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 58 optimal weight: 0.7980 chunk 27 optimal weight: 0.8980 chunk 19 optimal weight: 0.7980 chunk 64 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 143 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.189146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.158570 restraints weight = 6112.573| |-----------------------------------------------------------------------------| r_work (start): 0.3864 rms_B_bonded: 1.49 r_work: 0.3677 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3529 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.2161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 5844 Z= 0.164 Angle : 0.650 8.766 7824 Z= 0.318 Chirality : 0.044 0.210 882 Planarity : 0.005 0.053 908 Dihedral : 17.775 173.402 1222 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 3.46 % Allowed : 20.59 % Favored : 75.95 % 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: 0.96 (0.32), residues: 664 helix: 0.95 (0.23), residues: 510 sheet: None (None), residues: 0 loop : -0.12 (0.50), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 130 TYR 0.010 0.002 TYR A 151 PHE 0.033 0.002 PHE B 221 TRP 0.004 0.001 TRP A 363 HIS 0.001 0.001 HIS A 310 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.16 ( 5844) covalent geometry : angle 0.65024 / 0.32 ( 7824) hydrogen bonds : bond 0.04434 / 3.07 ( 368) hydrogen bonds : angle 4.80535 / 3.41 ( 1086) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1328 Ramachandran restraints generated. 664 Oldfield, 0 Emsley, 664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1328 Ramachandran restraints generated. 664 Oldfield, 0 Emsley, 664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 84 time to evaluate : 0.181 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 194 LYS cc_start: 0.7874 (ptpp) cc_final: 0.7535 (ptmm) REVERT: A 217 ASN cc_start: 0.7327 (OUTLIER) cc_final: 0.7038 (t0) REVERT: A 264 MET cc_start: 0.8212 (mtm) cc_final: 0.7924 (mtt) REVERT: A 337 ASN cc_start: 0.8425 (t0) cc_final: 0.8107 (t0) REVERT: B 90 MET cc_start: 0.7889 (mmp) cc_final: 0.7508 (mmp) REVERT: B 129 SER cc_start: 0.8358 (OUTLIER) cc_final: 0.8008 (m) REVERT: B 143 GLN cc_start: 0.7011 (OUTLIER) cc_final: 0.6192 (tp-100) REVERT: B 194 LYS cc_start: 0.8311 (ptmt) cc_final: 0.8103 (ptmm) REVERT: B 272 LYS cc_start: 0.8137 (OUTLIER) cc_final: 0.7841 (mttt) REVERT: B 338 MET cc_start: 0.6137 (OUTLIER) cc_final: 0.5529 (ptp) REVERT: B 347 MET cc_start: 0.7837 (OUTLIER) cc_final: 0.7365 (ttm) outliers start: 20 outliers final: 12 residues processed: 96 average time/residue: 0.4781 time to fit residues: 48.2673 Evaluate side-chains 103 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 85 time to evaluate : 0.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 217 ASN Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 338 MET Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 129 SER Chi-restraints excluded: chain B residue 143 GLN Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 272 LYS Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 338 MET Chi-restraints excluded: chain B residue 347 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 65 optimal weight: 0.6980 chunk 23 optimal weight: 0.4980 chunk 43 optimal weight: 0.5980 chunk 2 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 57 optimal weight: 0.6980 chunk 17 optimal weight: 3.9990 chunk 64 optimal weight: 0.7980 chunk 47 optimal weight: 0.9980 chunk 58 optimal weight: 0.0970 chunk 22 optimal weight: 0.6980 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 202 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.189694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.159671 restraints weight = 5978.198| |-----------------------------------------------------------------------------| r_work (start): 0.3868 rms_B_bonded: 1.46 r_work: 0.3680 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3532 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.2149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.117 5844 Z= 0.209 Angle : 1.080 59.199 7824 Z= 0.616 Chirality : 0.044 0.201 882 Planarity : 0.005 0.053 908 Dihedral : 17.774 173.405 1222 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 3.29 % Allowed : 20.76 % Favored : 75.95 % Cbeta Deviations : 0.16 % 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: 0.96 (0.32), residues: 664 helix: 0.95 (0.23), residues: 510 sheet: None (None), residues: 0 loop : -0.12 (0.50), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 130 TYR 0.009 0.002 TYR A 151 PHE 0.032 0.002 PHE B 221 TRP 0.004 0.001 TRP A 363 HIS 0.002 0.001 HIS A 310 Details of bonding type rmsd/Z covalent geometry : bond 0.00473 / 0.21 ( 5844) covalent geometry : angle 1.08011 / 0.62 ( 7824) hydrogen bonds : bond 0.04428 / 3.06 ( 368) hydrogen bonds : angle 4.80358 / 3.41 ( 1086) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2222.71 seconds wall clock time: 38 minutes 44.41 seconds (2324.41 seconds total)