Starting phenix.real_space_refine on Thu Jul 2 01:53:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b4f_44179/07_2026/9b4f_44179.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b4f_44179/07_2026/9b4f_44179.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.27 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9b4f_44179/07_2026/9b4f_44179.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b4f_44179/07_2026/9b4f_44179.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9b4f_44179/07_2026/9b4f_44179.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b4f_44179/07_2026/9b4f_44179.map" } resolution = 3.27 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= 0.001 sd= 0.023 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 Ca 2 9.91 5 S 40 5.16 5 C 3802 2.51 5 N 876 2.21 5 O 892 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 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: 5612 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2805 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 9, 'TRANS': 325} Chain breaks: 1 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' CA': 1} Chain breaks: 1 Restraints were copied for chains: B Time building chain proxies: 1.61, per 1000 atoms: 0.29 Number of scatterers: 5612 At special positions: 0 Unit cell: (64.206, 127.674, 72.324, 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) Ca 2 19.99 S 40 16.00 O 892 8.00 N 876 7.00 C 3802 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 153 " - pdb=" SG CYS A 213 " distance=2.03 Simple disulfide: pdb=" SG CYS B 153 " - pdb=" SG CYS B 213 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.33 Conformation dependent library (CDL) restraints added in 153.1 milliseconds 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1264 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 0 sheets defined 77.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.14 Creating SS restraints... Processing helix chain 'A' and resid 40 through 46 Processing helix chain 'A' and resid 47 through 60 removed outlier: 3.544A pdb=" N ARG A 60 " --> pdb=" O PHE A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 87 Processing helix chain 'A' and resid 99 through 119 removed outlier: 3.944A pdb=" N PHE A 105 " --> pdb=" O TRP A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 134 Processing helix chain 'A' and resid 135 through 139 Processing helix chain 'A' and resid 157 through 162 removed outlier: 4.046A pdb=" N ILE A 161 " --> pdb=" O THR A 157 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ILE A 162 " --> pdb=" O TRP A 158 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 157 through 162' Processing helix chain 'A' and resid 167 through 184 Processing helix chain 'A' and resid 185 through 203 removed outlier: 3.573A pdb=" N CYS A 189 " --> pdb=" O SER A 185 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLU A 197 " --> pdb=" O SER A 193 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU A 198 " --> pdb=" O ILE A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 218 removed outlier: 3.569A pdb=" N VAL A 218 " --> pdb=" O TRP A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 224 Processing helix chain 'A' and resid 226 through 240 Processing helix chain 'A' and resid 285 through 311 removed outlier: 3.876A pdb=" N TYR A 291 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N THR A 304 " --> pdb=" O THR A 300 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N PHE A 305 " --> pdb=" O GLU A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 342 removed outlier: 3.815A pdb=" N TRP A 321 " --> pdb=" O HIS A 317 " (cutoff:3.500A) Proline residue: A 333 - end of helix removed outlier: 3.936A pdb=" N ARG A 336 " --> pdb=" O ALA A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 373 removed outlier: 4.061A pdb=" N TRP A 355 " --> pdb=" O GLY A 351 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLN A 373 " --> pdb=" O ILE A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 379 removed outlier: 3.540A pdb=" N THR A 379 " --> pdb=" O PHE A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 409 Processing helix chain 'B' and resid 41 through 46 Processing helix chain 'B' and resid 47 through 60 removed outlier: 3.544A pdb=" N ARG B 60 " --> pdb=" O PHE B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 87 Processing helix chain 'B' and resid 99 through 119 removed outlier: 3.944A pdb=" N PHE B 105 " --> pdb=" O TRP B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 134 Processing helix chain 'B' and resid 135 through 139 Processing helix chain 'B' and resid 157 through 162 removed outlier: 4.045A pdb=" N ILE B 161 " --> pdb=" O THR B 157 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ILE B 162 " --> pdb=" O TRP B 158 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 157 through 162' Processing helix chain 'B' and resid 167 through 184 Processing helix chain 'B' and resid 185 through 203 removed outlier: 3.573A pdb=" N CYS B 189 " --> pdb=" O SER B 185 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLU B 197 " --> pdb=" O SER B 193 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU B 198 " --> pdb=" O ILE B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 218 removed outlier: 3.570A pdb=" N VAL B 218 " --> pdb=" O TRP B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 219 through 224 Processing helix chain 'B' and resid 226 through 240 Processing helix chain 'B' and resid 285 through 311 removed outlier: 3.876A pdb=" N TYR B 291 " --> pdb=" O VAL B 287 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N THR B 304 " --> pdb=" O THR B 300 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N PHE B 305 " --> pdb=" O GLU B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 342 removed outlier: 3.815A pdb=" N TRP B 321 " --> pdb=" O HIS B 317 " (cutoff:3.500A) Proline residue: B 333 - end of helix removed outlier: 3.936A pdb=" N ARG B 336 " --> pdb=" O ALA B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 373 removed outlier: 4.061A pdb=" N TRP B 355 " --> pdb=" O GLY B 351 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLN B 373 " --> pdb=" O ILE B 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 375 through 379 removed outlier: 3.539A pdb=" N THR B 379 " --> pdb=" O PHE B 376 " (cutoff:3.500A) Processing helix chain 'B' and resid 386 through 409 347 hydrogen bonds defined for protein. 1023 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: 0.86 Time building geometry restraints manager: 0.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1258 1.33 - 1.45: 1497 1.45 - 1.57: 2999 1.57 - 1.69: 0 1.69 - 1.81: 60 Bond restraints: 5814 Sorted by residual: bond pdb=" C ARG A 95 " pdb=" O ARG A 95 " ideal model delta sigma weight residual 1.238 1.215 0.023 1.28e-02 6.10e+03 3.21e+00 bond pdb=" C ARG B 95 " pdb=" O ARG B 95 " ideal model delta sigma weight residual 1.238 1.215 0.023 1.28e-02 6.10e+03 3.21e+00 bond pdb=" CA ARG A 95 " pdb=" C ARG A 95 " ideal model delta sigma weight residual 1.524 1.501 0.022 1.26e-02 6.30e+03 3.16e+00 bond pdb=" CA ARG B 95 " pdb=" C ARG B 95 " ideal model delta sigma weight residual 1.524 1.502 0.022 1.26e-02 6.30e+03 3.05e+00 bond pdb=" C ALA A 332 " pdb=" N PRO A 333 " ideal model delta sigma weight residual 1.337 1.352 -0.015 1.24e-02 6.50e+03 1.39e+00 ... (remaining 5809 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.77: 7769 1.77 - 3.53: 141 3.53 - 5.30: 14 5.30 - 7.06: 4 7.06 - 8.83: 2 Bond angle restraints: 7930 Sorted by residual: angle pdb=" N GLU A 241 " pdb=" CA GLU A 241 " pdb=" C GLU A 241 " ideal model delta sigma weight residual 108.58 117.41 -8.83 1.82e+00 3.02e-01 2.35e+01 angle pdb=" N GLU B 241 " pdb=" CA GLU B 241 " pdb=" C GLU B 241 " ideal model delta sigma weight residual 108.58 117.39 -8.81 1.82e+00 3.02e-01 2.34e+01 angle pdb=" N ASP B 344 " pdb=" CA ASP B 344 " pdb=" C ASP B 344 " ideal model delta sigma weight residual 114.75 109.57 5.18 1.26e+00 6.30e-01 1.69e+01 angle pdb=" N ASP A 344 " pdb=" CA ASP A 344 " pdb=" C ASP A 344 " ideal model delta sigma weight residual 114.75 109.59 5.16 1.26e+00 6.30e-01 1.68e+01 angle pdb=" N HIS B 164 " pdb=" CA HIS B 164 " pdb=" C HIS B 164 " ideal model delta sigma weight residual 114.56 110.39 4.17 1.27e+00 6.20e-01 1.08e+01 ... (remaining 7925 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.82: 2906 14.82 - 29.64: 228 29.64 - 44.47: 62 44.47 - 59.29: 10 59.29 - 74.11: 6 Dihedral angle restraints: 3212 sinusoidal: 1252 harmonic: 1960 Sorted by residual: dihedral pdb=" C ARG A 95 " pdb=" N ARG A 95 " pdb=" CA ARG A 95 " pdb=" CB ARG A 95 " ideal model delta harmonic sigma weight residual -122.60 -134.78 12.18 0 2.50e+00 1.60e-01 2.38e+01 dihedral pdb=" C ARG B 95 " pdb=" N ARG B 95 " pdb=" CA ARG B 95 " pdb=" CB ARG B 95 " ideal model delta harmonic sigma weight residual -122.60 -134.75 12.15 0 2.50e+00 1.60e-01 2.36e+01 dihedral pdb=" N ARG A 95 " pdb=" C ARG A 95 " pdb=" CA ARG A 95 " pdb=" CB ARG A 95 " ideal model delta harmonic sigma weight residual 122.80 132.58 -9.78 0 2.50e+00 1.60e-01 1.53e+01 ... (remaining 3209 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.102: 862 0.102 - 0.203: 4 0.203 - 0.305: 0 0.305 - 0.406: 0 0.406 - 0.508: 2 Chirality restraints: 868 Sorted by residual: chirality pdb=" CA ARG A 95 " pdb=" N ARG A 95 " pdb=" C ARG A 95 " pdb=" CB ARG A 95 " both_signs ideal model delta sigma weight residual False 2.51 2.00 0.51 2.00e-01 2.50e+01 6.45e+00 chirality pdb=" CA ARG B 95 " pdb=" N ARG B 95 " pdb=" C ARG B 95 " pdb=" CB ARG B 95 " both_signs ideal model delta sigma weight residual False 2.51 2.00 0.51 2.00e-01 2.50e+01 6.39e+00 chirality pdb=" CA GLU A 241 " pdb=" N GLU A 241 " pdb=" C GLU A 241 " pdb=" CB GLU A 241 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.87e-01 ... (remaining 865 not shown) Planarity restraints: 946 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS A 97 " -0.028 5.00e-02 4.00e+02 4.31e-02 2.98e+00 pdb=" N PRO A 98 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO A 98 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 98 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS B 97 " 0.028 5.00e-02 4.00e+02 4.31e-02 2.97e+00 pdb=" N PRO B 98 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO B 98 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 98 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 220 " -0.008 2.00e-02 2.50e+03 1.62e-02 2.64e+00 pdb=" C LEU B 220 " 0.028 2.00e-02 2.50e+03 pdb=" O LEU B 220 " -0.011 2.00e-02 2.50e+03 pdb=" N ASP B 221 " -0.009 2.00e-02 2.50e+03 ... (remaining 943 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.78: 1377 2.78 - 3.31: 5355 3.31 - 3.84: 9065 3.84 - 4.37: 9926 4.37 - 4.90: 18231 Nonbonded interactions: 43954 Sorted by model distance: nonbonded pdb=" OG SER A 84 " pdb=" O ARG A 102 " model vdw 2.255 3.040 nonbonded pdb=" OG SER B 84 " pdb=" O ARG B 102 " model vdw 2.256 3.040 nonbonded pdb=" O ILE B 327 " pdb=" OG1 THR B 331 " model vdw 2.275 3.040 nonbonded pdb=" O ILE A 327 " pdb=" OG1 THR A 331 " model vdw 2.275 3.040 nonbonded pdb=" NH1 ARG B 95 " pdb=" O GLU B 241 " model vdw 2.302 3.120 ... (remaining 43949 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: 3.120 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: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 6.300 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 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 : 0.003 0.023 5816 Z= 0.153 Angle : 0.569 8.829 7934 Z= 0.352 Chirality : 0.043 0.508 868 Planarity : 0.004 0.043 946 Dihedral : 12.087 74.110 1942 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.06 % Favored : 90.94 % Rotamer: Outliers : 1.68 % Allowed : 6.04 % Favored : 92.28 % Cbeta Deviations : 0.32 % 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: -2.07 (0.30), residues: 662 helix: -0.36 (0.22), residues: 478 sheet: None (None), residues: 0 loop : -4.04 (0.37), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 102 TYR 0.008 0.001 TYR B 111 PHE 0.016 0.001 PHE A 313 TRP 0.011 0.001 TRP A 176 HIS 0.002 0.001 HIS B 164 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.15 ( 5814) covalent geometry : angle 0.56920 / 0.35 ( 7930) SS BOND : bond 0.00118 / 0.08 ( 2) SS BOND : angle 0.66843 / 0.53 ( 4) hydrogen bonds : bond 0.09275 / 5.96 ( 347) hydrogen bonds : angle 5.42184 / 3.90 ( 1023) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 54 time to evaluate : 0.203 Fit side-chains REVERT: A 88 PHE cc_start: 0.7901 (OUTLIER) cc_final: 0.7674 (m-10) REVERT: A 95 ARG cc_start: 0.7635 (OUTLIER) cc_final: 0.5737 (mpp80) REVERT: A 243 ARG cc_start: 0.7602 (mtp180) cc_final: 0.6434 (mmt180) REVERT: B 95 ARG cc_start: 0.7586 (OUTLIER) cc_final: 0.5652 (mpp80) REVERT: B 243 ARG cc_start: 0.7579 (mtp180) cc_final: 0.6371 (mmt180) outliers start: 10 outliers final: 6 residues processed: 63 average time/residue: 0.0971 time to fit residues: 7.8454 Evaluate side-chains 53 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 44 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 PHE Chi-restraints excluded: chain A residue 95 ARG Chi-restraints excluded: chain A residue 172 HIS Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 226 ASN Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain B residue 172 HIS Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 226 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 49 optimal weight: 0.0980 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 0.1980 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.0970 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 chunk 27 optimal weight: 0.5980 overall best weight: 0.3578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 97 HIS A 309 HIS B 41 HIS B 97 HIS B 309 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.180030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.131114 restraints weight = 5865.222| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 2.23 r_work: 0.3268 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.1086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 5816 Z= 0.098 Angle : 0.466 6.650 7934 Z= 0.247 Chirality : 0.036 0.113 868 Planarity : 0.004 0.038 946 Dihedral : 7.117 58.416 746 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.16 % Favored : 91.84 % Rotamer: Outliers : 2.52 % Allowed : 8.72 % Favored : 88.76 % 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: -0.21 (0.34), residues: 662 helix: 1.02 (0.25), residues: 480 sheet: None (None), residues: 0 loop : -3.41 (0.42), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 95 TYR 0.014 0.001 TYR A 55 PHE 0.011 0.001 PHE A 313 TRP 0.012 0.001 TRP A 176 HIS 0.002 0.001 HIS B 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00209 / 0.10 ( 5814) covalent geometry : angle 0.46650 / 0.25 ( 7930) SS BOND : bond 0.00179 / 0.12 ( 2) SS BOND : angle 0.27094 / 0.14 ( 4) hydrogen bonds : bond 0.03027 / 2.01 ( 347) hydrogen bonds : angle 4.15475 / 2.94 ( 1023) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 52 time to evaluate : 0.181 Fit side-chains REVERT: A 95 ARG cc_start: 0.6888 (OUTLIER) cc_final: 0.5131 (mpp80) REVERT: B 95 ARG cc_start: 0.6883 (OUTLIER) cc_final: 0.5108 (mpp80) outliers start: 15 outliers final: 6 residues processed: 64 average time/residue: 0.0645 time to fit residues: 5.7291 Evaluate side-chains 52 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 44 time to evaluate : 0.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 ARG Chi-restraints excluded: chain A residue 172 HIS Chi-restraints excluded: chain A residue 226 ASN Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain B residue 172 HIS Chi-restraints excluded: chain B residue 226 ASN Chi-restraints excluded: chain B residue 397 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 65 optimal weight: 0.9990 chunk 34 optimal weight: 4.9990 chunk 57 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 39 optimal weight: 0.5980 chunk 41 optimal weight: 0.7980 chunk 9 optimal weight: 0.6980 chunk 55 optimal weight: 1.9990 chunk 43 optimal weight: 4.9990 chunk 0 optimal weight: 8.9990 chunk 42 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- 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 = 0.3874 r_free = 0.3874 target = 0.171439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.125022 restraints weight = 5932.980| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 2.11 r_work: 0.3217 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.1198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 5816 Z= 0.162 Angle : 0.512 7.341 7934 Z= 0.267 Chirality : 0.038 0.148 868 Planarity : 0.005 0.043 946 Dihedral : 6.731 57.442 740 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.46 % Favored : 91.54 % Rotamer: Outliers : 3.02 % Allowed : 10.57 % Favored : 86.41 % 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: -0.09 (0.35), residues: 662 helix: 1.06 (0.25), residues: 490 sheet: None (None), residues: 0 loop : -3.46 (0.45), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 95 TYR 0.014 0.001 TYR A 55 PHE 0.014 0.001 PHE B 313 TRP 0.015 0.001 TRP A 176 HIS 0.001 0.000 HIS B 246 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.16 ( 5814) covalent geometry : angle 0.51188 / 0.27 ( 7930) SS BOND : bond 0.00157 / 0.11 ( 2) SS BOND : angle 0.34700 / 0.20 ( 4) hydrogen bonds : bond 0.03857 / 2.56 ( 347) hydrogen bonds : angle 4.17151 / 2.98 ( 1023) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 49 time to evaluate : 0.196 Fit side-chains REVERT: A 88 PHE cc_start: 0.7956 (OUTLIER) cc_final: 0.7575 (m-10) REVERT: A 95 ARG cc_start: 0.7085 (OUTLIER) cc_final: 0.5243 (mpp80) REVERT: A 243 ARG cc_start: 0.7699 (mtp180) cc_final: 0.5882 (mmt180) REVERT: B 88 PHE cc_start: 0.7997 (OUTLIER) cc_final: 0.7498 (m-10) REVERT: B 95 ARG cc_start: 0.7068 (OUTLIER) cc_final: 0.5196 (mpp80) outliers start: 18 outliers final: 9 residues processed: 62 average time/residue: 0.0732 time to fit residues: 6.1518 Evaluate side-chains 56 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 43 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 PHE Chi-restraints excluded: chain A residue 95 ARG Chi-restraints excluded: chain A residue 172 HIS Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 226 ASN Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain B residue 88 PHE Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain B residue 172 HIS Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 225 CYS Chi-restraints excluded: chain B residue 226 ASN Chi-restraints excluded: chain B residue 397 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 24 optimal weight: 3.9990 chunk 2 optimal weight: 0.9980 chunk 53 optimal weight: 0.3980 chunk 41 optimal weight: 0.5980 chunk 22 optimal weight: 1.9990 chunk 14 optimal weight: 0.0980 chunk 30 optimal weight: 0.9980 chunk 40 optimal weight: 0.5980 chunk 50 optimal weight: 0.2980 chunk 23 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 overall best weight: 0.3980 ------------------------------------------------------------------------------- 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 = 0.3944 r_free = 0.3944 target = 0.179368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.131944 restraints weight = 5893.212| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 2.17 r_work: 0.3273 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.1448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 5816 Z= 0.095 Angle : 0.453 7.299 7934 Z= 0.236 Chirality : 0.036 0.115 868 Planarity : 0.004 0.042 946 Dihedral : 6.361 59.025 740 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.85 % Favored : 92.15 % Rotamer: Outliers : 2.68 % Allowed : 12.75 % Favored : 84.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.35), residues: 662 helix: 1.55 (0.25), residues: 488 sheet: None (None), residues: 0 loop : -3.22 (0.45), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 95 TYR 0.015 0.001 TYR A 55 PHE 0.011 0.001 PHE B 313 TRP 0.012 0.001 TRP A 321 HIS 0.001 0.000 HIS B 164 Details of bonding type rmsd/Z covalent geometry : bond 0.00206 / 0.09 ( 5814) covalent geometry : angle 0.45311 / 0.24 ( 7930) SS BOND : bond 0.00099 / 0.07 ( 2) SS BOND : angle 0.27923 / 0.20 ( 4) hydrogen bonds : bond 0.03028 / 2.02 ( 347) hydrogen bonds : angle 3.94989 / 2.80 ( 1023) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 47 time to evaluate : 0.224 Fit side-chains REVERT: A 88 PHE cc_start: 0.7814 (OUTLIER) cc_final: 0.7549 (m-10) REVERT: A 95 ARG cc_start: 0.6935 (OUTLIER) cc_final: 0.5172 (mpp80) REVERT: A 172 HIS cc_start: 0.6992 (OUTLIER) cc_final: 0.6763 (t70) REVERT: A 243 ARG cc_start: 0.7660 (mtp180) cc_final: 0.5862 (mmt180) REVERT: B 95 ARG cc_start: 0.7015 (OUTLIER) cc_final: 0.5211 (mpp80) outliers start: 16 outliers final: 6 residues processed: 56 average time/residue: 0.0770 time to fit residues: 5.7945 Evaluate side-chains 51 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 41 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 88 PHE Chi-restraints excluded: chain A residue 95 ARG Chi-restraints excluded: chain A residue 172 HIS Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain B residue 172 HIS Chi-restraints excluded: chain B residue 225 CYS Chi-restraints excluded: chain B residue 397 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 23 optimal weight: 0.0000 chunk 60 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 56 optimal weight: 0.0070 chunk 18 optimal weight: 0.9980 chunk 47 optimal weight: 0.7980 chunk 64 optimal weight: 0.5980 chunk 40 optimal weight: 0.7980 chunk 49 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 overall best weight: 0.4402 ------------------------------------------------------------------------------- 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 = 0.3938 r_free = 0.3938 target = 0.178443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.131624 restraints weight = 5954.903| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 2.16 r_work: 0.3276 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.1598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 5816 Z= 0.100 Angle : 0.465 8.234 7934 Z= 0.236 Chirality : 0.036 0.107 868 Planarity : 0.004 0.042 946 Dihedral : 5.958 58.447 736 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.85 % Favored : 92.15 % Rotamer: Outliers : 3.36 % Allowed : 13.09 % Favored : 83.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.82 (0.36), residues: 662 helix: 1.73 (0.25), residues: 488 sheet: None (None), residues: 0 loop : -3.08 (0.46), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 95 TYR 0.015 0.001 TYR A 55 PHE 0.010 0.001 PHE B 313 TRP 0.012 0.001 TRP A 321 HIS 0.001 0.000 HIS B 317 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.10 ( 5814) covalent geometry : angle 0.46544 / 0.24 ( 7930) SS BOND : bond 0.00103 / 0.07 ( 2) SS BOND : angle 0.30839 / 0.23 ( 4) hydrogen bonds : bond 0.03059 / 2.03 ( 347) hydrogen bonds : angle 3.85472 / 2.73 ( 1023) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 41 time to evaluate : 0.199 Fit side-chains REVERT: A 88 PHE cc_start: 0.7893 (OUTLIER) cc_final: 0.7602 (m-10) REVERT: A 95 ARG cc_start: 0.6889 (tmm-80) cc_final: 0.5218 (mpp80) REVERT: A 243 ARG cc_start: 0.7719 (mtp180) cc_final: 0.5968 (mmt180) REVERT: B 88 PHE cc_start: 0.8006 (OUTLIER) cc_final: 0.7422 (m-10) REVERT: B 95 ARG cc_start: 0.6903 (OUTLIER) cc_final: 0.5254 (mpp80) outliers start: 20 outliers final: 10 residues processed: 54 average time/residue: 0.0668 time to fit residues: 5.0038 Evaluate side-chains 55 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 42 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 88 PHE Chi-restraints excluded: chain A residue 97 HIS Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 88 PHE Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain B residue 97 HIS Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 399 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 53 optimal weight: 0.1980 chunk 30 optimal weight: 0.9980 chunk 17 optimal weight: 0.3980 chunk 42 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 chunk 13 optimal weight: 2.9990 chunk 15 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 chunk 44 optimal weight: 10.0000 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.3922 r_free = 0.3922 target = 0.176476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.128935 restraints weight = 5932.790| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 2.21 r_work: 0.3257 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.1638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 5816 Z= 0.113 Angle : 0.474 8.831 7934 Z= 0.241 Chirality : 0.036 0.109 868 Planarity : 0.004 0.043 946 Dihedral : 4.509 47.736 728 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 3.19 % Allowed : 13.76 % Favored : 83.05 % 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: 0.83 (0.35), residues: 662 helix: 1.73 (0.25), residues: 488 sheet: None (None), residues: 0 loop : -3.05 (0.46), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 95 TYR 0.015 0.001 TYR B 55 PHE 0.011 0.001 PHE A 313 TRP 0.011 0.001 TRP B 321 HIS 0.001 0.000 HIS B 317 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.11 ( 5814) covalent geometry : angle 0.47437 / 0.24 ( 7930) SS BOND : bond 0.00078 / 0.05 ( 2) SS BOND : angle 0.33003 / 0.24 ( 4) hydrogen bonds : bond 0.03257 / 2.16 ( 347) hydrogen bonds : angle 3.86234 / 2.75 ( 1023) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 43 time to evaluate : 0.214 Fit side-chains REVERT: A 88 PHE cc_start: 0.7848 (OUTLIER) cc_final: 0.7559 (m-10) REVERT: A 95 ARG cc_start: 0.6889 (OUTLIER) cc_final: 0.5190 (mpp80) REVERT: A 243 ARG cc_start: 0.7738 (mtp180) cc_final: 0.5928 (mmt180) REVERT: B 88 PHE cc_start: 0.7944 (OUTLIER) cc_final: 0.7188 (m-10) REVERT: B 95 ARG cc_start: 0.6921 (tmm-80) cc_final: 0.5313 (mpp80) outliers start: 19 outliers final: 10 residues processed: 59 average time/residue: 0.0698 time to fit residues: 5.7073 Evaluate side-chains 55 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 42 time to evaluate : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 88 PHE Chi-restraints excluded: chain A residue 95 ARG Chi-restraints excluded: chain A residue 97 HIS Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 226 ASN Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 88 PHE Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 225 CYS Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 399 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 8 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 45 optimal weight: 0.5980 chunk 22 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 63 optimal weight: 0.6980 chunk 4 optimal weight: 0.8980 chunk 44 optimal weight: 9.9990 chunk 46 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 chunk 23 optimal weight: 0.4980 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 = 0.3934 r_free = 0.3934 target = 0.177805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.130015 restraints weight = 6079.039| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 2.22 r_work: 0.3241 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.1734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 5816 Z= 0.126 Angle : 0.492 9.095 7934 Z= 0.247 Chirality : 0.037 0.111 868 Planarity : 0.004 0.043 946 Dihedral : 4.071 17.068 724 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.70 % Favored : 92.30 % Rotamer: Outliers : 2.85 % Allowed : 14.93 % Favored : 82.21 % 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: 0.84 (0.35), residues: 662 helix: 1.77 (0.25), residues: 486 sheet: None (None), residues: 0 loop : -3.10 (0.46), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 95 TYR 0.016 0.001 TYR A 55 PHE 0.012 0.001 PHE B 313 TRP 0.011 0.001 TRP B 321 HIS 0.001 0.000 HIS B 317 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 ( 5814) covalent geometry : angle 0.49199 / 0.25 ( 7930) SS BOND : bond 0.00104 / 0.07 ( 2) SS BOND : angle 0.34028 / 0.25 ( 4) hydrogen bonds : bond 0.03406 / 2.27 ( 347) hydrogen bonds : angle 3.88617 / 2.77 ( 1023) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 42 time to evaluate : 0.205 Fit side-chains REVERT: A 88 PHE cc_start: 0.7986 (OUTLIER) cc_final: 0.7669 (m-10) REVERT: A 95 ARG cc_start: 0.6940 (OUTLIER) cc_final: 0.5272 (mpp80) REVERT: A 243 ARG cc_start: 0.7790 (mtp180) cc_final: 0.6049 (mmt180) REVERT: B 88 PHE cc_start: 0.8120 (OUTLIER) cc_final: 0.7434 (m-10) outliers start: 17 outliers final: 9 residues processed: 55 average time/residue: 0.0602 time to fit residues: 4.6805 Evaluate side-chains 54 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 42 time to evaluate : 0.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 88 PHE Chi-restraints excluded: chain A residue 95 ARG Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 226 ASN Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 88 PHE Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 225 CYS Chi-restraints excluded: chain B residue 226 ASN Chi-restraints excluded: chain B residue 397 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 3 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 39 optimal weight: 0.5980 chunk 20 optimal weight: 0.7980 chunk 26 optimal weight: 0.2980 chunk 25 optimal weight: 0.9990 chunk 18 optimal weight: 0.8980 chunk 59 optimal weight: 0.3980 chunk 30 optimal weight: 3.9990 chunk 6 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.4088 r_free = 0.4088 target = 0.189723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.145301 restraints weight = 5753.280| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 2.12 r_work: 0.3266 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.1784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 5816 Z= 0.112 Angle : 0.478 9.554 7934 Z= 0.241 Chirality : 0.036 0.109 868 Planarity : 0.004 0.043 946 Dihedral : 4.039 16.847 724 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.40 % Favored : 92.60 % Rotamer: Outliers : 2.68 % Allowed : 15.10 % Favored : 82.21 % 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: 0.95 (0.35), residues: 662 helix: 1.85 (0.25), residues: 486 sheet: None (None), residues: 0 loop : -3.08 (0.45), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 95 TYR 0.015 0.001 TYR A 55 PHE 0.011 0.001 PHE B 313 TRP 0.012 0.001 TRP B 321 HIS 0.001 0.000 HIS B 317 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.11 ( 5814) covalent geometry : angle 0.47772 / 0.24 ( 7930) SS BOND : bond 0.00091 / 0.06 ( 2) SS BOND : angle 0.33495 / 0.24 ( 4) hydrogen bonds : bond 0.03241 / 2.16 ( 347) hydrogen bonds : angle 3.84166 / 2.74 ( 1023) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 40 time to evaluate : 0.151 Fit side-chains REVERT: A 88 PHE cc_start: 0.7937 (OUTLIER) cc_final: 0.7648 (m-10) REVERT: A 95 ARG cc_start: 0.6871 (OUTLIER) cc_final: 0.5231 (mpp80) REVERT: A 243 ARG cc_start: 0.7784 (mtp180) cc_final: 0.6065 (mmt180) REVERT: B 88 PHE cc_start: 0.8077 (OUTLIER) cc_final: 0.7357 (m-10) REVERT: B 95 ARG cc_start: 0.6973 (tmm-80) cc_final: 0.5306 (mpp80) outliers start: 16 outliers final: 13 residues processed: 52 average time/residue: 0.0601 time to fit residues: 4.3100 Evaluate side-chains 56 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 40 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 88 PHE Chi-restraints excluded: chain A residue 95 ARG Chi-restraints excluded: chain A residue 97 HIS Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 226 ASN Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 88 PHE Chi-restraints excluded: chain B residue 204 MET Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 225 CYS Chi-restraints excluded: chain B residue 226 ASN Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 399 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 56 optimal weight: 0.6980 chunk 26 optimal weight: 0.0570 chunk 28 optimal weight: 0.6980 chunk 13 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 16 optimal weight: 0.6980 chunk 12 optimal weight: 4.9990 chunk 42 optimal weight: 0.7980 chunk 11 optimal weight: 9.9990 chunk 64 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 41 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.181964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.134496 restraints weight = 5939.170| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 2.22 r_work: 0.3258 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.1845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 5816 Z= 0.112 Angle : 0.479 9.963 7934 Z= 0.241 Chirality : 0.036 0.109 868 Planarity : 0.004 0.043 946 Dihedral : 3.983 16.773 724 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.85 % Favored : 92.15 % Rotamer: Outliers : 3.19 % Allowed : 14.60 % Favored : 82.21 % 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: 1.00 (0.35), residues: 662 helix: 1.88 (0.25), residues: 486 sheet: None (None), residues: 0 loop : -3.06 (0.45), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 95 TYR 0.016 0.001 TYR A 55 PHE 0.011 0.001 PHE B 313 TRP 0.012 0.001 TRP B 321 HIS 0.001 0.000 HIS A 317 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.11 ( 5814) covalent geometry : angle 0.47943 / 0.24 ( 7930) SS BOND : bond 0.00106 / 0.07 ( 2) SS BOND : angle 0.33693 / 0.25 ( 4) hydrogen bonds : bond 0.03226 / 2.15 ( 347) hydrogen bonds : angle 3.81281 / 2.72 ( 1023) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 40 time to evaluate : 0.195 Fit side-chains REVERT: A 88 PHE cc_start: 0.7863 (OUTLIER) cc_final: 0.7559 (m-10) REVERT: A 95 ARG cc_start: 0.6837 (OUTLIER) cc_final: 0.5105 (mpp80) REVERT: A 243 ARG cc_start: 0.7761 (mtp180) cc_final: 0.5973 (mmt180) REVERT: B 88 PHE cc_start: 0.8015 (OUTLIER) cc_final: 0.7295 (m-10) REVERT: B 95 ARG cc_start: 0.6913 (tmm-80) cc_final: 0.5214 (mpp80) REVERT: B 172 HIS cc_start: 0.6998 (OUTLIER) cc_final: 0.6704 (t70) outliers start: 19 outliers final: 14 residues processed: 54 average time/residue: 0.0709 time to fit residues: 5.2903 Evaluate side-chains 58 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 40 time to evaluate : 0.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 88 PHE Chi-restraints excluded: chain A residue 95 ARG Chi-restraints excluded: chain A residue 97 HIS Chi-restraints excluded: chain A residue 204 MET Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 226 ASN Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 88 PHE Chi-restraints excluded: chain B residue 172 HIS Chi-restraints excluded: chain B residue 204 MET Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 225 CYS Chi-restraints excluded: chain B residue 226 ASN Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 399 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 1 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 16 optimal weight: 0.1980 chunk 43 optimal weight: 7.9990 chunk 31 optimal weight: 0.7980 chunk 59 optimal weight: 0.5980 chunk 48 optimal weight: 0.5980 chunk 5 optimal weight: 0.0470 chunk 20 optimal weight: 0.9980 chunk 24 optimal weight: 0.7980 overall best weight: 0.4478 ------------------------------------------------------------------------------- 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 = 0.4112 r_free = 0.4112 target = 0.192488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.147656 restraints weight = 5841.305| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 2.17 r_work: 0.3322 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.1938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 5816 Z= 0.098 Angle : 0.467 10.036 7934 Z= 0.234 Chirality : 0.036 0.106 868 Planarity : 0.004 0.042 946 Dihedral : 3.897 16.277 724 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.95 % Favored : 93.05 % Rotamer: Outliers : 2.52 % Allowed : 15.27 % Favored : 82.21 % 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: 1.13 (0.36), residues: 662 helix: 1.96 (0.25), residues: 488 sheet: None (None), residues: 0 loop : -3.00 (0.46), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 323 TYR 0.016 0.001 TYR B 55 PHE 0.010 0.001 PHE B 170 TRP 0.012 0.001 TRP B 321 HIS 0.001 0.000 HIS B 317 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.10 ( 5814) covalent geometry : angle 0.46733 / 0.23 ( 7930) SS BOND : bond 0.00084 / 0.06 ( 2) SS BOND : angle 0.33396 / 0.25 ( 4) hydrogen bonds : bond 0.02994 / 1.99 ( 347) hydrogen bonds : angle 3.73763 / 2.66 ( 1023) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 41 time to evaluate : 0.189 Fit side-chains REVERT: A 88 PHE cc_start: 0.7799 (OUTLIER) cc_final: 0.7533 (m-10) REVERT: A 95 ARG cc_start: 0.6843 (tmm-80) cc_final: 0.5203 (mpp80) REVERT: A 243 ARG cc_start: 0.7752 (mtp180) cc_final: 0.5954 (mmt180) REVERT: B 88 PHE cc_start: 0.8011 (OUTLIER) cc_final: 0.7296 (m-10) REVERT: B 95 ARG cc_start: 0.6813 (tmm-80) cc_final: 0.5143 (mpp80) outliers start: 15 outliers final: 11 residues processed: 52 average time/residue: 0.0651 time to fit residues: 4.7533 Evaluate side-chains 53 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 40 time to evaluate : 0.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 88 PHE Chi-restraints excluded: chain A residue 97 HIS Chi-restraints excluded: chain A residue 204 MET Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 88 PHE Chi-restraints excluded: chain B residue 204 MET Chi-restraints excluded: chain B residue 225 CYS Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 399 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 41 optimal weight: 0.7980 chunk 39 optimal weight: 0.5980 chunk 18 optimal weight: 0.5980 chunk 16 optimal weight: 0.3980 chunk 15 optimal weight: 0.8980 chunk 19 optimal weight: 0.8980 chunk 8 optimal weight: 0.9990 chunk 21 optimal weight: 0.8980 chunk 17 optimal weight: 0.9980 chunk 40 optimal weight: 0.5980 chunk 56 optimal weight: 0.6980 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 = 0.3998 r_free = 0.3998 target = 0.182760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.135510 restraints weight = 5913.257| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 2.20 r_work: 0.3265 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 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 : 0.003 0.021 5816 Z= 0.110 Angle : 0.477 10.073 7934 Z= 0.238 Chirality : 0.036 0.109 868 Planarity : 0.004 0.043 946 Dihedral : 3.907 16.557 724 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.70 % Favored : 92.30 % Rotamer: Outliers : 2.52 % Allowed : 15.44 % Favored : 82.05 % 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: 1.10 (0.36), residues: 662 helix: 1.92 (0.25), residues: 488 sheet: None (None), residues: 0 loop : -2.97 (0.47), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 95 TYR 0.016 0.001 TYR A 55 PHE 0.010 0.001 PHE B 313 TRP 0.012 0.001 TRP B 321 HIS 0.001 0.000 HIS B 317 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.11 ( 5814) covalent geometry : angle 0.47700 / 0.24 ( 7930) SS BOND : bond 0.00093 / 0.06 ( 2) SS BOND : angle 0.34590 / 0.25 ( 4) hydrogen bonds : bond 0.03169 / 2.11 ( 347) hydrogen bonds : angle 3.76121 / 2.68 ( 1023) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1383.32 seconds wall clock time: 24 minutes 24.21 seconds (1464.21 seconds total)