Starting phenix.real_space_refine on Wed Sep 17 06:10:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jbh_61314/09_2025/9jbh_61314.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jbh_61314/09_2025/9jbh_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9jbh_61314/09_2025/9jbh_61314.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jbh_61314/09_2025/9jbh_61314.map" model { file = "/net/cci-nas-00/data/ceres_data/9jbh_61314/09_2025/9jbh_61314.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jbh_61314/09_2025/9jbh_61314.cif" } 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-2.0-5805/lib/python3.9/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: 1.77, per 1000 atoms: 0.31 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: 0.56 Conformation dependent library (CDL) restraints added in 385.7 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.18 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: 0.91 Time building geometry restraints manager: 0.72 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=" N PHE A 137 " pdb=" CA PHE A 137 " ideal model delta sigma weight residual 1.459 1.490 -0.031 1.04e-02 9.25e+03 8.86e+00 bond pdb=" C ASN A 202 " pdb=" O ASN A 202 " ideal model delta sigma weight residual 1.233 1.196 0.037 1.30e-02 5.92e+03 8.02e+00 bond pdb=" N ILE A 139 " pdb=" CA ILE A 139 " ideal model delta sigma weight residual 1.460 1.493 -0.033 1.19e-02 7.06e+03 7.59e+00 ... (remaining 5839 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.99: 7641 1.99 - 3.97: 150 3.97 - 5.96: 29 5.96 - 7.94: 3 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 - 32.74: 3393 32.74 - 65.48: 220 65.48 - 98.23: 11 98.23 - 130.97: 0 130.97 - 163.71: 2 Dihedral angle restraints: 3626 sinusoidal: 1678 harmonic: 1948 Sorted by residual: 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 dihedral pdb=" O21 3PE B 404 " pdb=" C2 3PE B 404 " pdb=" C3 3PE B 404 " pdb=" O31 3PE B 404 " ideal model delta sinusoidal sigma weight residual 60.47 -102.81 163.28 1 3.00e+01 1.11e-03 2.09e+01 dihedral pdb=" CB GLU B 339 " pdb=" CG GLU B 339 " pdb=" CD GLU B 339 " pdb=" OE1 GLU B 339 " ideal model delta sinusoidal sigma weight residual 0.00 -88.31 88.31 1 3.00e+01 1.11e-03 1.04e+01 ... (remaining 3623 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 628 0.042 - 0.083: 196 0.083 - 0.124: 50 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: 5.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.710 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 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 0.094 5844 Z= 0.205 Angle : 0.684 9.929 7824 Z= 0.401 Chirality : 0.043 0.207 882 Planarity : 0.007 0.121 908 Dihedral : 19.284 163.710 2370 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 aren 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 covalent geometry : bond 0.00362 ( 5844) covalent geometry : angle 0.68450 ( 7824) hydrogen bonds : bond 0.15565 ( 368) hydrogen bonds : angle 6.22503 ( 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 : 0.231 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: 0.4719 time to fit residues: 50.9029 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 : 0.206 ------------------------------------------------------------------------------- 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: 0.9980 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 0.6980 chunk 27 optimal weight: 5.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 230 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.189126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.159305 restraints weight = 5985.117| |-----------------------------------------------------------------------------| r_work (start): 0.3861 rms_B_bonded: 1.42 r_work: 0.3675 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3530 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.1363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 5844 Z= 0.187 Angle : 0.657 7.921 7824 Z= 0.322 Chirality : 0.045 0.180 882 Planarity : 0.006 0.070 908 Dihedral : 18.403 135.655 1199 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 3.63 % Allowed : 17.99 % Favored : 78.37 % 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 aren not related in a simple way. whole: 0.74 (0.33), residues: 664 helix: 0.75 (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 0.030 0.002 PHE B 221 TRP 0.007 0.001 TRP A 363 HIS 0.003 0.002 HIS A 310 Details of bonding type rmsd covalent geometry : bond 0.00460 ( 5844) covalent geometry : angle 0.65712 ( 7824) hydrogen bonds : bond 0.05102 ( 368) hydrogen bonds : angle 5.17256 ( 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 105 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 84 time to evaluate : 0.208 Fit side-chains revert: symmetry clash REVERT: A 194 LYS cc_start: 0.8009 (mtpt) cc_final: 0.7513 (ptpp) REVERT: A 295 ARG cc_start: 0.7575 (mtp180) cc_final: 0.7348 (ttm-80) REVERT: B 338 MET cc_start: 0.6628 (OUTLIER) cc_final: 0.6214 (ptp) outliers start: 21 outliers final: 11 residues processed: 93 average time/residue: 0.5664 time to fit residues: 55.1864 Evaluate side-chains 88 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 76 time to evaluate : 0.221 ------------------------------------------------------------------------------- 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 37 MET 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 246 ASP 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: 0.7980 chunk 20 optimal weight: 0.9990 chunk 31 optimal weight: 0.5980 chunk 44 optimal weight: 0.9980 chunk 29 optimal weight: 0.5980 chunk 14 optimal weight: 0.7980 chunk 6 optimal weight: 3.9990 chunk 48 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.189167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.158949 restraints weight = 5942.135| |-----------------------------------------------------------------------------| r_work (start): 0.3857 rms_B_bonded: 1.44 r_work: 0.3669 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3523 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.1566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 5844 Z= 0.171 Angle : 0.630 6.739 7824 Z= 0.308 Chirality : 0.044 0.169 882 Planarity : 0.006 0.058 908 Dihedral : 18.053 119.322 1193 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % Rotamer: Outliers : 3.63 % Allowed : 19.03 % Favored : 77.34 % 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 aren not related in a simple way. whole: 0.69 (0.32), residues: 664 helix: 0.73 (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 0.030 0.002 PHE B 221 TRP 0.006 0.001 TRP A 363 HIS 0.002 0.001 HIS B 310 Details of bonding type rmsd covalent geometry : bond 0.00419 ( 5844) covalent geometry : angle 0.63040 ( 7824) hydrogen bonds : bond 0.04690 ( 368) hydrogen bonds : angle 5.03174 ( 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 106 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 85 time to evaluate : 0.224 Fit side-chains revert: symmetry clash REVERT: A 194 LYS cc_start: 0.7917 (mtpt) cc_final: 0.7686 (ptpp) REVERT: A 217 ASN cc_start: 0.7291 (OUTLIER) cc_final: 0.6969 (t0) REVERT: B 129 SER cc_start: 0.8461 (OUTLIER) cc_final: 0.8126 (m) REVERT: B 194 LYS cc_start: 0.8239 (ptmt) cc_final: 0.7955 (ptmm) REVERT: B 205 LYS cc_start: 0.7202 (OUTLIER) cc_final: 0.6868 (ttmm) REVERT: B 272 LYS cc_start: 0.8128 (OUTLIER) cc_final: 0.7735 (mttt) outliers start: 21 outliers final: 12 residues processed: 99 average time/residue: 0.5430 time to fit residues: 56.4238 Evaluate side-chains 94 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 78 time to evaluate : 0.212 ------------------------------------------------------------------------------- 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 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 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 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: 0.7980 chunk 57 optimal weight: 0.9990 chunk 11 optimal weight: 0.9980 chunk 1 optimal weight: 0.6980 chunk 34 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 27 optimal weight: 6.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.188657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.158374 restraints weight = 6001.541| |-----------------------------------------------------------------------------| r_work (start): 0.3847 rms_B_bonded: 1.45 r_work: 0.3662 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3515 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.1751 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= 0.176 Angle : 0.646 6.862 7824 Z= 0.314 Chirality : 0.045 0.168 882 Planarity : 0.005 0.056 908 Dihedral : 17.981 117.439 1192 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 4.15 % Allowed : 18.51 % Favored : 77.34 % 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 aren not related in a simple way. whole: 0.67 (0.32), residues: 664 helix: 0.71 (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 79 TYR 0.011 0.002 TYR B 170 PHE 0.032 0.002 PHE B 221 TRP 0.006 0.001 TRP A 363 HIS 0.001 0.000 HIS B 310 Details of bonding type rmsd covalent geometry : bond 0.00432 ( 5844) covalent geometry : angle 0.64573 ( 7824) hydrogen bonds : bond 0.04665 ( 368) hydrogen bonds : angle 5.04019 ( 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 105 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 81 time to evaluate : 0.209 Fit side-chains revert: symmetry clash REVERT: A 217 ASN cc_start: 0.7311 (OUTLIER) cc_final: 0.6984 (t0) REVERT: B 129 SER cc_start: 0.8443 (OUTLIER) cc_final: 0.8119 (m) REVERT: B 194 LYS cc_start: 0.8275 (ptmt) cc_final: 0.8011 (ptmm) REVERT: B 205 LYS cc_start: 0.7301 (OUTLIER) cc_final: 0.6950 (ttmm) REVERT: B 272 LYS cc_start: 0.8094 (OUTLIER) cc_final: 0.7719 (mttt) REVERT: B 338 MET cc_start: 0.6413 (OUTLIER) cc_final: 0.5716 (ptp) outliers start: 24 outliers final: 15 residues processed: 94 average time/residue: 0.5268 time to fit residues: 51.8916 Evaluate side-chains 97 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 77 time to evaluate : 0.187 ------------------------------------------------------------------------------- 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 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 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: 0.8980 chunk 25 optimal weight: 0.9990 chunk 65 optimal weight: 0.6980 chunk 57 optimal weight: 0.5980 chunk 13 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 45 optimal weight: 0.9980 chunk 31 optimal weight: 0.3980 chunk 39 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 143 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.189669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.159108 restraints weight = 6109.549| |-----------------------------------------------------------------------------| r_work (start): 0.3856 rms_B_bonded: 1.48 r_work: 0.3671 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3523 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.1859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 5844 Z= 0.160 Angle : 0.622 6.539 7824 Z= 0.305 Chirality : 0.044 0.168 882 Planarity : 0.005 0.055 908 Dihedral : 17.731 113.367 1192 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Rotamer: Outliers : 5.02 % Allowed : 18.17 % Favored : 76.82 % 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 aren not related in a simple way. whole: 0.78 (0.32), residues: 664 helix: 0.80 (0.23), residues: 512 sheet: None (None), residues: 0 loop : -0.11 (0.51), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 79 TYR 0.010 0.002 TYR A 170 PHE 0.031 0.002 PHE B 221 TRP 0.006 0.001 TRP A 363 HIS 0.001 0.001 HIS B 310 Details of bonding type rmsd covalent geometry : bond 0.00389 ( 5844) covalent geometry : angle 0.62173 ( 7824) hydrogen bonds : bond 0.04475 ( 368) hydrogen bonds : angle 4.91913 ( 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 118 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 89 time to evaluate : 0.215 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 194 LYS cc_start: 0.7910 (OUTLIER) cc_final: 0.7520 (ptmm) REVERT: A 217 ASN cc_start: 0.7347 (OUTLIER) cc_final: 0.7055 (t0) REVERT: A 264 MET cc_start: 0.8096 (mtm) cc_final: 0.7777 (mtt) REVERT: A 288 LEU cc_start: 0.6906 (OUTLIER) cc_final: 0.6522 (mm) REVERT: A 337 ASN cc_start: 0.8455 (t0) cc_final: 0.8146 (t0) REVERT: B 129 SER cc_start: 0.8415 (OUTLIER) cc_final: 0.8083 (m) REVERT: B 143 GLN cc_start: 0.7005 (OUTLIER) cc_final: 0.6176 (tp-100) REVERT: B 194 LYS cc_start: 0.8291 (ptmt) cc_final: 0.8057 (ptmm) REVERT: B 205 LYS cc_start: 0.7329 (OUTLIER) cc_final: 0.6981 (ttmm) REVERT: B 272 LYS cc_start: 0.8093 (OUTLIER) cc_final: 0.7707 (mttt) REVERT: B 338 MET cc_start: 0.6293 (OUTLIER) cc_final: 0.5667 (ptp) outliers start: 29 outliers final: 14 residues processed: 103 average time/residue: 0.4874 time to fit residues: 52.6419 Evaluate side-chains 108 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 86 time to evaluate : 0.216 ------------------------------------------------------------------------------- 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 194 LYS Chi-restraints excluded: chain A residue 217 ASN Chi-restraints excluded: chain A residue 239 VAL 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 52 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 23 optimal weight: 0.0050 chunk 20 optimal weight: 0.0670 chunk 50 optimal weight: 0.7980 chunk 27 optimal weight: 4.9990 chunk 21 optimal weight: 0.5980 chunk 59 optimal weight: 0.5980 chunk 10 optimal weight: 0.7980 chunk 61 optimal weight: 0.6980 overall best weight: 0.3932 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 143 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.191835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.161879 restraints weight = 5987.534| |-----------------------------------------------------------------------------| r_work (start): 0.3888 rms_B_bonded: 1.45 r_work: 0.3706 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3559 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.1871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 5844 Z= 0.129 Angle : 0.597 8.649 7824 Z= 0.290 Chirality : 0.043 0.166 882 Planarity : 0.005 0.054 908 Dihedral : 17.283 110.219 1192 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 9.86 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 aren not related in a simple way. whole: 1.04 (0.32), residues: 664 helix: 1.00 (0.23), residues: 512 sheet: None (None), residues: 0 loop : -0.06 (0.50), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 79 TYR 0.008 0.001 TYR B 170 PHE 0.027 0.002 PHE B 221 TRP 0.005 0.001 TRP A 363 HIS 0.001 0.000 HIS A 310 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 5844) covalent geometry : angle 0.59696 ( 7824) hydrogen bonds : bond 0.04067 ( 368) hydrogen bonds : angle 4.77409 ( 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: 20 poor density : 89 time to evaluate : 0.243 Fit side-chains REVERT: A 194 LYS cc_start: 0.7850 (ptpp) cc_final: 0.7501 (ptmm) REVERT: A 264 MET cc_start: 0.8098 (mtm) cc_final: 0.7748 (mtt) REVERT: A 338 MET cc_start: 0.6811 (OUTLIER) cc_final: 0.6157 (ptp) REVERT: B 129 SER cc_start: 0.8355 (OUTLIER) cc_final: 0.8002 (m) REVERT: B 143 GLN cc_start: 0.6982 (OUTLIER) cc_final: 0.6177 (tp-100) REVERT: B 194 LYS cc_start: 0.8266 (ptmt) cc_final: 0.8055 (ptmm) REVERT: B 205 LYS cc_start: 0.7294 (OUTLIER) cc_final: 0.6952 (ttmm) REVERT: B 272 LYS cc_start: 0.8100 (OUTLIER) cc_final: 0.7825 (mttt) outliers start: 20 outliers final: 11 residues processed: 100 average time/residue: 0.5069 time to fit residues: 53.2496 Evaluate side-chains 98 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 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 144 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 A residue 338 MET 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 53 optimal weight: 0.0870 chunk 25 optimal weight: 0.5980 chunk 14 optimal weight: 0.6980 chunk 40 optimal weight: 0.5980 chunk 46 optimal weight: 0.5980 chunk 7 optimal weight: 1.9990 chunk 63 optimal weight: 0.8980 chunk 28 optimal weight: 0.8980 chunk 21 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.191368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.161174 restraints weight = 6086.371| |-----------------------------------------------------------------------------| r_work (start): 0.3881 rms_B_bonded: 1.47 r_work: 0.3695 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3546 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.1958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 5844 Z= 0.142 Angle : 0.617 8.518 7824 Z= 0.301 Chirality : 0.044 0.166 882 Planarity : 0.005 0.054 908 Dihedral : 17.091 108.684 1190 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Rotamer: Outliers : 4.33 % Allowed : 20.24 % Favored : 75.43 % 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 aren not related in a simple way. whole: 1.03 (0.32), residues: 664 helix: 1.01 (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 0.005 0.000 ARG B 79 TYR 0.008 0.001 TYR A 170 PHE 0.028 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 covalent geometry : bond 0.00342 ( 5844) covalent geometry : angle 0.61659 ( 7824) hydrogen bonds : bond 0.04160 ( 368) hydrogen bonds : angle 4.76363 ( 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 115 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 90 time to evaluate : 0.209 Fit side-chains revert: symmetry clash REVERT: A 194 LYS cc_start: 0.7808 (ptpp) cc_final: 0.7477 (ptmm) REVERT: A 264 MET cc_start: 0.8089 (mtm) cc_final: 0.7758 (mtt) REVERT: A 337 ASN cc_start: 0.8449 (t0) cc_final: 0.8152 (t0) REVERT: B 129 SER cc_start: 0.8372 (OUTLIER) cc_final: 0.8018 (m) REVERT: B 205 LYS cc_start: 0.7275 (OUTLIER) cc_final: 0.6927 (ttmm) REVERT: B 272 LYS cc_start: 0.8154 (OUTLIER) cc_final: 0.7854 (mttt) REVERT: B 338 MET cc_start: 0.6181 (OUTLIER) cc_final: 0.5598 (ptp) outliers start: 25 outliers final: 14 residues processed: 103 average time/residue: 0.5002 time to fit residues: 53.9658 Evaluate side-chains 102 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 84 time to evaluate : 0.146 ------------------------------------------------------------------------------- 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 36 optimal weight: 0.6980 chunk 62 optimal weight: 0.5980 chunk 56 optimal weight: 0.0170 chunk 26 optimal weight: 1.9990 chunk 13 optimal weight: 0.3980 chunk 35 optimal weight: 0.5980 chunk 40 optimal weight: 0.5980 chunk 20 optimal weight: 1.9990 chunk 21 optimal weight: 0.5980 chunk 2 optimal weight: 0.6980 chunk 55 optimal weight: 0.6980 overall best weight: 0.4418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 89 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.192336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.162319 restraints weight = 6027.888| |-----------------------------------------------------------------------------| r_work (start): 0.3893 rms_B_bonded: 1.46 r_work: 0.3709 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3560 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.2065 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= 0.133 Angle : 0.611 8.379 7824 Z= 0.298 Chirality : 0.043 0.164 882 Planarity : 0.005 0.055 908 Dihedral : 16.675 106.041 1190 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 3.98 % Allowed : 20.76 % Favored : 75.26 % 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 aren not related in a simple way. whole: 1.16 (0.33), residues: 664 helix: 1.08 (0.23), residues: 518 sheet: None (None), residues: 0 loop : -0.06 (0.52), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 79 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 covalent geometry : bond 0.00321 ( 5844) covalent geometry : angle 0.61064 ( 7824) hydrogen bonds : bond 0.04014 ( 368) hydrogen bonds : angle 4.66746 ( 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 106 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 83 time to evaluate : 0.215 Fit side-chains revert: symmetry clash REVERT: A 194 LYS cc_start: 0.7841 (ptpp) cc_final: 0.7511 (ptmm) REVERT: B 129 SER cc_start: 0.8334 (OUTLIER) cc_final: 0.7974 (m) REVERT: B 155 GLU cc_start: 0.7165 (tp30) cc_final: 0.6910 (tp30) REVERT: B 194 LYS cc_start: 0.8321 (ptmt) cc_final: 0.8114 (ptmm) REVERT: B 272 LYS cc_start: 0.8137 (OUTLIER) cc_final: 0.7735 (mttt) REVERT: B 338 MET cc_start: 0.6118 (OUTLIER) cc_final: 0.5748 (ptp) outliers start: 23 outliers final: 14 residues processed: 95 average time/residue: 0.5268 time to fit residues: 52.5855 Evaluate side-chains 98 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 81 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 144 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 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 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 358 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: 0.8980 chunk 1 optimal weight: 0.8980 chunk 28 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 64 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 55 optimal weight: 0.8980 chunk 56 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 143 GLN ** 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 = 0.4184 r_free = 0.4184 target = 0.187928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.157345 restraints weight = 6029.955| |-----------------------------------------------------------------------------| r_work (start): 0.3838 rms_B_bonded: 1.48 r_work: 0.3654 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3505 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.2259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 5844 Z= 0.195 Angle : 0.674 8.023 7824 Z= 0.332 Chirality : 0.046 0.193 882 Planarity : 0.005 0.054 908 Dihedral : 17.093 107.860 1190 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 3.63 % Allowed : 21.28 % Favored : 75.09 % 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 aren not related in a simple way. whole: 0.62 (0.32), residues: 664 helix: 0.70 (0.22), residues: 518 sheet: None (None), residues: 0 loop : -0.30 (0.52), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 79 TYR 0.011 0.002 TYR B 158 PHE 0.035 0.002 PHE B 221 TRP 0.006 0.001 TRP A 363 HIS 0.002 0.001 HIS A 310 Details of bonding type rmsd covalent geometry : bond 0.00482 ( 5844) covalent geometry : angle 0.67441 ( 7824) hydrogen bonds : bond 0.04721 ( 368) hydrogen bonds : angle 4.95646 ( 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 106 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 85 time to evaluate : 0.215 Fit side-chains revert: symmetry clash REVERT: A 194 LYS cc_start: 0.7905 (ptpp) cc_final: 0.7531 (ptmm) REVERT: A 264 MET cc_start: 0.8253 (mtm) cc_final: 0.7968 (mtt) REVERT: A 337 ASN cc_start: 0.8523 (t0) cc_final: 0.8215 (t0) REVERT: B 129 SER cc_start: 0.8379 (OUTLIER) cc_final: 0.8037 (m) REVERT: B 143 GLN cc_start: 0.7045 (OUTLIER) cc_final: 0.6221 (tp-100) REVERT: B 194 LYS cc_start: 0.8332 (ptmt) cc_final: 0.8125 (ptmm) REVERT: B 272 LYS cc_start: 0.8128 (OUTLIER) cc_final: 0.7731 (mttt) REVERT: B 338 MET cc_start: 0.6213 (OUTLIER) cc_final: 0.5516 (ptp) REVERT: B 347 MET cc_start: 0.7879 (OUTLIER) cc_final: 0.7354 (ttm) outliers start: 21 outliers final: 13 residues processed: 96 average time/residue: 0.5337 time to fit residues: 53.6394 Evaluate side-chains 100 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 82 time to evaluate : 0.209 ------------------------------------------------------------------------------- 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 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 44 optimal weight: 0.8980 chunk 4 optimal weight: 0.1980 chunk 30 optimal weight: 0.4980 chunk 51 optimal weight: 0.6980 chunk 31 optimal weight: 0.9980 chunk 7 optimal weight: 0.9990 chunk 9 optimal weight: 0.9980 chunk 58 optimal weight: 0.7980 chunk 27 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 64 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.189636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.159361 restraints weight = 6102.659| |-----------------------------------------------------------------------------| r_work (start): 0.3858 rms_B_bonded: 1.48 r_work: 0.3674 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3527 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.2222 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= 0.152 Angle : 0.637 6.924 7824 Z= 0.315 Chirality : 0.044 0.185 882 Planarity : 0.005 0.054 908 Dihedral : 16.765 105.818 1190 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 2.77 % Allowed : 22.32 % Favored : 74.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.85 (0.32), residues: 664 helix: 0.85 (0.23), residues: 516 sheet: None (None), residues: 0 loop : -0.12 (0.51), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 79 TYR 0.009 0.001 TYR A 170 PHE 0.029 0.002 PHE B 221 TRP 0.006 0.001 TRP A 363 HIS 0.001 0.001 HIS A 310 Details of bonding type rmsd covalent geometry : bond 0.00372 ( 5844) covalent geometry : angle 0.63747 ( 7824) hydrogen bonds : bond 0.04320 ( 368) hydrogen bonds : angle 4.84053 ( 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 99 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 83 time to evaluate : 0.172 Fit side-chains revert: symmetry clash REVERT: A 194 LYS cc_start: 0.7908 (ptpp) cc_final: 0.7588 (ptmm) REVERT: A 264 MET cc_start: 0.8188 (mtm) cc_final: 0.7902 (mtt) REVERT: A 337 ASN cc_start: 0.8461 (t0) cc_final: 0.8159 (t0) REVERT: B 129 SER cc_start: 0.8326 (OUTLIER) cc_final: 0.7991 (m) REVERT: B 194 LYS cc_start: 0.8314 (ptmt) cc_final: 0.8104 (ptmm) REVERT: B 272 LYS cc_start: 0.8141 (OUTLIER) cc_final: 0.7859 (mttt) outliers start: 16 outliers final: 13 residues processed: 93 average time/residue: 0.5479 time to fit residues: 53.3902 Evaluate side-chains 96 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 81 time to evaluate : 0.192 ------------------------------------------------------------------------------- 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 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 65 optimal weight: 0.4980 chunk 23 optimal weight: 0.3980 chunk 43 optimal weight: 0.5980 chunk 2 optimal weight: 0.6980 chunk 25 optimal weight: 0.5980 chunk 57 optimal weight: 0.7980 chunk 17 optimal weight: 0.0020 chunk 64 optimal weight: 0.9990 chunk 47 optimal weight: 0.0970 chunk 58 optimal weight: 0.1980 chunk 22 optimal weight: 0.1980 overall best weight: 0.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.196648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.167187 restraints weight = 6017.997| |-----------------------------------------------------------------------------| r_work (start): 0.3952 rms_B_bonded: 1.45 r_work: 0.3770 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3620 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.2315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 5844 Z= 0.116 Angle : 0.610 8.867 7824 Z= 0.296 Chirality : 0.042 0.168 882 Planarity : 0.005 0.055 908 Dihedral : 15.638 99.421 1190 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 1.38 % Allowed : 23.36 % Favored : 75.26 % 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 aren not related in a simple way. whole: 1.54 (0.33), residues: 664 helix: 1.34 (0.23), residues: 518 sheet: None (None), residues: 0 loop : 0.12 (0.51), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 79 TYR 0.006 0.001 TYR B 162 PHE 0.021 0.001 PHE B 221 TRP 0.003 0.001 TRP A 363 HIS 0.001 0.000 HIS A 310 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 5844) covalent geometry : angle 0.61012 ( 7824) hydrogen bonds : bond 0.03645 ( 368) hydrogen bonds : angle 4.48807 ( 1086) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2355.47 seconds wall clock time: 40 minutes 57.85 seconds (2457.85 seconds total)