Starting phenix.real_space_refine on Wed Feb 4 01:45:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9qju_53211/02_2026/9qju_53211.cif Found real_map, /net/cci-nas-00/data/ceres_data/9qju_53211/02_2026/9qju_53211.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.34 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9qju_53211/02_2026/9qju_53211.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9qju_53211/02_2026/9qju_53211.map" model { file = "/net/cci-nas-00/data/ceres_data/9qju_53211/02_2026/9qju_53211.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9qju_53211/02_2026/9qju_53211.cif" } resolution = 3.34 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= 0.020 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: 4 Type Number sf(0) Gaussians S 34 5.16 5 C 5468 2.51 5 N 1228 2.21 5 O 1422 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 34 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8152 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" Number of atoms: 4076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 495, 4076 Classifications: {'peptide': 495} Link IDs: {'PTRANS': 23, 'TRANS': 471} Chain breaks: 5 Chain: "A" Number of atoms: 4076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 495, 4076 Classifications: {'peptide': 495} Link IDs: {'PTRANS': 23, 'TRANS': 471} Chain breaks: 5 Time building chain proxies: 1.82, per 1000 atoms: 0.22 Number of scatterers: 8152 At special positions: 0 Unit cell: (115.878, 97.65, 101.556, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 34 16.00 O 1422 8.00 N 1228 7.00 C 5468 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: 0.78 Conformation dependent library (CDL) restraints added in 288.3 milliseconds 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1940 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 2 sheets defined 79.1% alpha, 3.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'B' and resid 4 through 9 Processing helix chain 'B' and resid 17 through 23 removed outlier: 4.091A pdb=" N ASN B 23 " --> pdb=" O THR B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 33 Processing helix chain 'B' and resid 34 through 36 No H-bonds generated for 'chain 'B' and resid 34 through 36' Processing helix chain 'B' and resid 60 through 71 removed outlier: 3.552A pdb=" N ASP B 71 " --> pdb=" O LEU B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 97 removed outlier: 3.713A pdb=" N SER B 97 " --> pdb=" O SER B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 116 removed outlier: 3.554A pdb=" N LEU B 108 " --> pdb=" O LYS B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 147 Proline residue: B 136 - end of helix Processing helix chain 'B' and resid 148 through 152 removed outlier: 3.778A pdb=" N TYR B 152 " --> pdb=" O ASN B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 176 Processing helix chain 'B' and resid 177 through 188 removed outlier: 3.742A pdb=" N ARG B 184 " --> pdb=" O PHE B 180 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N LEU B 185 " --> pdb=" O TRP B 181 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N SER B 186 " --> pdb=" O SER B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 217 Processing helix chain 'B' and resid 218 through 246 Processing helix chain 'B' and resid 251 through 278 removed outlier: 3.795A pdb=" N PHE B 257 " --> pdb=" O SER B 253 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LEU B 258 " --> pdb=" O ILE B 254 " (cutoff:3.500A) Proline residue: B 259 - end of helix Proline residue: B 268 - end of helix Processing helix chain 'B' and resid 278 through 287 Processing helix chain 'B' and resid 290 through 320 removed outlier: 4.211A pdb=" N VAL B 304 " --> pdb=" O ALA B 300 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N ILE B 305 " --> pdb=" O LYS B 301 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE B 306 " --> pdb=" O ASN B 302 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL B 312 " --> pdb=" O LEU B 308 " (cutoff:3.500A) Proline residue: B 313 - end of helix Processing helix chain 'B' and resid 326 through 330 removed outlier: 4.337A pdb=" N ALA B 330 " --> pdb=" O LEU B 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 358 through 369 Processing helix chain 'B' and resid 369 through 379 Processing helix chain 'B' and resid 413 through 428 Processing helix chain 'B' and resid 429 through 433 Processing helix chain 'B' and resid 436 through 455 removed outlier: 3.863A pdb=" N LYS B 443 " --> pdb=" O ALA B 439 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LEU B 444 " --> pdb=" O ASN B 440 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER B 455 " --> pdb=" O LEU B 451 " (cutoff:3.500A) Processing helix chain 'B' and resid 460 through 483 removed outlier: 3.730A pdb=" N ARG B 478 " --> pdb=" O GLN B 474 " (cutoff:3.500A) Processing helix chain 'B' and resid 509 through 534 removed outlier: 3.560A pdb=" N SER B 513 " --> pdb=" O GLY B 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 562 through 590 removed outlier: 3.814A pdb=" N VAL B 567 " --> pdb=" O TRP B 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 4 through 9 Processing helix chain 'A' and resid 17 through 23 removed outlier: 4.062A pdb=" N ASN A 23 " --> pdb=" O THR A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 24 through 33 Processing helix chain 'A' and resid 60 through 71 removed outlier: 3.750A pdb=" N ASN A 69 " --> pdb=" O SER A 65 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ASP A 71 " --> pdb=" O LEU A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 97 removed outlier: 3.613A pdb=" N SER A 97 " --> pdb=" O SER A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 115 removed outlier: 3.790A pdb=" N LEU A 108 " --> pdb=" O LYS A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 147 Proline residue: A 136 - end of helix Processing helix chain 'A' and resid 148 through 152 removed outlier: 3.768A pdb=" N TYR A 152 " --> pdb=" O ASN A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 176 Processing helix chain 'A' and resid 177 through 188 removed outlier: 3.770A pdb=" N ARG A 184 " --> pdb=" O PHE A 180 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LEU A 185 " --> pdb=" O TRP A 181 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N SER A 186 " --> pdb=" O SER A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 217 removed outlier: 3.513A pdb=" N CYS A 217 " --> pdb=" O LEU A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 246 Processing helix chain 'A' and resid 251 through 278 removed outlier: 3.524A pdb=" N LEU A 255 " --> pdb=" O MET A 251 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N PHE A 257 " --> pdb=" O SER A 253 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LEU A 258 " --> pdb=" O ILE A 254 " (cutoff:3.500A) Proline residue: A 259 - end of helix Proline residue: A 268 - end of helix Processing helix chain 'A' and resid 278 through 287 Processing helix chain 'A' and resid 290 through 311 removed outlier: 4.174A pdb=" N VAL A 304 " --> pdb=" O ALA A 300 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N ILE A 305 " --> pdb=" O LYS A 301 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ILE A 306 " --> pdb=" O ASN A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 320 Processing helix chain 'A' and resid 326 through 330 removed outlier: 4.187A pdb=" N ALA A 330 " --> pdb=" O LEU A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 369 Processing helix chain 'A' and resid 369 through 379 Processing helix chain 'A' and resid 413 through 428 Processing helix chain 'A' and resid 429 through 433 Processing helix chain 'A' and resid 436 through 454 removed outlier: 3.909A pdb=" N LYS A 443 " --> pdb=" O ALA A 439 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LEU A 444 " --> pdb=" O ASN A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 483 removed outlier: 3.710A pdb=" N ARG A 478 " --> pdb=" O GLN A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 534 removed outlier: 3.549A pdb=" N SER A 513 " --> pdb=" O GLY A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 591 removed outlier: 3.831A pdb=" N VAL A 567 " --> pdb=" O TRP A 563 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N SER A 591 " --> pdb=" O ILE A 587 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 38 through 42 removed outlier: 6.818A pdb=" N VAL B 13 " --> pdb=" O ILE B 76 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N ILE B 76 " --> pdb=" O VAL B 13 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N VAL B 15 " --> pdb=" O GLU B 74 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 38 through 42 550 hydrogen bonds defined for protein. 1614 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: 1.00 Time building geometry restraints manager: 1.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2347 1.34 - 1.46: 1983 1.46 - 1.58: 4010 1.58 - 1.69: 0 1.69 - 1.81: 52 Bond restraints: 8392 Sorted by residual: bond pdb=" CG1 ILE B 493 " pdb=" CD1 ILE B 493 " ideal model delta sigma weight residual 1.513 1.479 0.034 3.90e-02 6.57e+02 7.71e-01 bond pdb=" C TRP A 458 " pdb=" O TRP A 458 " ideal model delta sigma weight residual 1.249 1.242 0.007 8.50e-03 1.38e+04 7.10e-01 bond pdb=" C PRO B 558 " pdb=" N ILE B 559 " ideal model delta sigma weight residual 1.334 1.323 0.010 1.24e-02 6.50e+03 7.01e-01 bond pdb=" N ILE A 77 " pdb=" CA ILE A 77 " ideal model delta sigma weight residual 1.454 1.461 -0.006 7.70e-03 1.69e+04 6.89e-01 bond pdb=" CA HIS A 326 " pdb=" CB HIS A 326 " ideal model delta sigma weight residual 1.529 1.542 -0.013 1.64e-02 3.72e+03 6.47e-01 ... (remaining 8387 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.35: 11157 1.35 - 2.69: 194 2.69 - 4.04: 29 4.04 - 5.39: 22 5.39 - 6.74: 4 Bond angle restraints: 11406 Sorted by residual: angle pdb=" CA MET A 251 " pdb=" CB MET A 251 " pdb=" CG MET A 251 " ideal model delta sigma weight residual 114.10 119.45 -5.35 2.00e+00 2.50e-01 7.14e+00 angle pdb=" CA MET B 251 " pdb=" CB MET B 251 " pdb=" CG MET B 251 " ideal model delta sigma weight residual 114.10 119.37 -5.27 2.00e+00 2.50e-01 6.95e+00 angle pdb=" CA LEU B 70 " pdb=" CB LEU B 70 " pdb=" CG LEU B 70 " ideal model delta sigma weight residual 116.30 123.04 -6.74 3.50e+00 8.16e-02 3.70e+00 angle pdb=" C TYR A 188 " pdb=" N SER A 189 " pdb=" CA SER A 189 " ideal model delta sigma weight residual 121.54 125.00 -3.46 1.91e+00 2.74e-01 3.27e+00 angle pdb=" C TYR B 188 " pdb=" N SER B 189 " pdb=" CA SER B 189 " ideal model delta sigma weight residual 121.54 124.86 -3.32 1.91e+00 2.74e-01 3.01e+00 ... (remaining 11401 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.71: 4157 17.71 - 35.42: 528 35.42 - 53.13: 177 53.13 - 70.84: 29 70.84 - 88.55: 9 Dihedral angle restraints: 4900 sinusoidal: 1926 harmonic: 2974 Sorted by residual: dihedral pdb=" CA PHE B 191 " pdb=" C PHE B 191 " pdb=" N SER B 192 " pdb=" CA SER B 192 " ideal model delta harmonic sigma weight residual 180.00 161.15 18.85 0 5.00e+00 4.00e-02 1.42e+01 dihedral pdb=" CA PHE A 191 " pdb=" C PHE A 191 " pdb=" N SER A 192 " pdb=" CA SER A 192 " ideal model delta harmonic sigma weight residual 180.00 162.03 17.97 0 5.00e+00 4.00e-02 1.29e+01 dihedral pdb=" CA ASP A 71 " pdb=" CB ASP A 71 " pdb=" CG ASP A 71 " pdb=" OD1 ASP A 71 " ideal model delta sinusoidal sigma weight residual -30.00 -91.46 61.46 1 2.00e+01 2.50e-03 1.25e+01 ... (remaining 4897 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 743 0.027 - 0.054: 326 0.054 - 0.082: 165 0.082 - 0.109: 51 0.109 - 0.136: 19 Chirality restraints: 1304 Sorted by residual: chirality pdb=" CA THR B 267 " pdb=" N THR B 267 " pdb=" C THR B 267 " pdb=" CB THR B 267 " both_signs ideal model delta sigma weight residual False 2.53 2.39 0.14 2.00e-01 2.50e+01 4.64e-01 chirality pdb=" CB ILE A 76 " pdb=" CA ILE A 76 " pdb=" CG1 ILE A 76 " pdb=" CG2 ILE A 76 " both_signs ideal model delta sigma weight residual False 2.64 2.51 0.13 2.00e-01 2.50e+01 4.44e-01 chirality pdb=" CA ILE B 39 " pdb=" N ILE B 39 " pdb=" C ILE B 39 " pdb=" CB ILE B 39 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.03e-01 ... (remaining 1301 not shown) Planarity restraints: 1374 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 322 " -0.023 5.00e-02 4.00e+02 3.47e-02 1.92e+00 pdb=" N PRO A 323 " 0.060 5.00e-02 4.00e+02 pdb=" CA PRO A 323 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 323 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 15 " -0.007 2.00e-02 2.50e+03 1.36e-02 1.85e+00 pdb=" C VAL A 15 " 0.023 2.00e-02 2.50e+03 pdb=" O VAL A 15 " -0.009 2.00e-02 2.50e+03 pdb=" N PHE A 16 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU B 322 " 0.020 5.00e-02 4.00e+02 2.96e-02 1.40e+00 pdb=" N PRO B 323 " -0.051 5.00e-02 4.00e+02 pdb=" CA PRO B 323 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO B 323 " 0.017 5.00e-02 4.00e+02 ... (remaining 1371 not shown) Histogram of nonbonded interaction distances: 2.59 - 3.06: 5566 3.06 - 3.52: 9387 3.52 - 3.98: 12723 3.98 - 4.44: 15660 4.44 - 4.90: 23613 Nonbonded interactions: 66949 Sorted by model distance: nonbonded pdb=" O THR A 151 " pdb=" OG1 THR A 151 " model vdw 2.595 3.040 nonbonded pdb=" C SER B 484 " pdb=" OG SER B 484 " model vdw 2.621 2.616 nonbonded pdb=" C SER A 484 " pdb=" OG SER A 484 " model vdw 2.622 2.616 nonbonded pdb=" ND1 HIS A 326 " pdb=" N LEU A 327 " model vdw 2.622 3.200 nonbonded pdb=" C SER B 38 " pdb=" OG SER B 38 " model vdw 2.625 2.616 ... (remaining 66944 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: 0.940 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: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 8.660 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7305 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 0.034 8392 Z= 0.126 Angle : 0.509 6.736 11406 Z= 0.274 Chirality : 0.040 0.136 1304 Planarity : 0.004 0.035 1374 Dihedral : 17.835 88.552 2960 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 4.62 % Allowed : 25.81 % Favored : 69.57 % 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: 1.69 (0.29), residues: 966 helix: 1.79 (0.20), residues: 708 sheet: -1.98 (0.92), residues: 34 loop : -0.43 (0.49), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 33 TYR 0.010 0.001 TYR B 569 PHE 0.019 0.001 PHE A 237 TRP 0.008 0.001 TRP A 563 HIS 0.005 0.001 HIS A 326 Details of bonding type rmsd covalent geometry : bond 0.00252 ( 8392) covalent geometry : angle 0.50913 (11406) hydrogen bonds : bond 0.13804 ( 550) hydrogen bonds : angle 6.16873 ( 1614) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 243 time to evaluate : 0.227 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 13 VAL cc_start: 0.8516 (m) cc_final: 0.8146 (t) REVERT: B 34 LEU cc_start: 0.6634 (pt) cc_final: 0.5679 (pp) REVERT: B 35 ASN cc_start: 0.5399 (OUTLIER) cc_final: 0.2514 (m110) REVERT: B 54 ARG cc_start: 0.8335 (tpp80) cc_final: 0.7989 (tpp80) REVERT: B 55 ILE cc_start: 0.8911 (pt) cc_final: 0.8603 (mt) REVERT: B 66 PHE cc_start: 0.5914 (t80) cc_final: 0.5711 (t80) REVERT: B 68 GLN cc_start: 0.7362 (tp-100) cc_final: 0.6901 (tp-100) REVERT: B 84 LEU cc_start: 0.8788 (tp) cc_final: 0.8411 (tp) REVERT: B 110 ASN cc_start: 0.7725 (m-40) cc_final: 0.7495 (t0) REVERT: B 129 ASN cc_start: 0.7656 (t0) cc_final: 0.7296 (t0) REVERT: B 140 PHE cc_start: 0.7650 (t80) cc_final: 0.7377 (t80) REVERT: B 172 PHE cc_start: 0.8105 (m-80) cc_final: 0.7819 (m-80) REVERT: B 182 SER cc_start: 0.8590 (t) cc_final: 0.8228 (p) REVERT: B 212 MET cc_start: 0.8241 (mmm) cc_final: 0.7955 (tmm) REVERT: B 214 LYS cc_start: 0.8257 (mtmt) cc_final: 0.7431 (mttp) REVERT: B 232 PHE cc_start: 0.7723 (t80) cc_final: 0.7388 (t80) REVERT: B 262 LEU cc_start: 0.8315 (OUTLIER) cc_final: 0.7954 (mm) REVERT: B 276 LYS cc_start: 0.8226 (ttmm) cc_final: 0.7917 (ttpt) REVERT: B 286 GLU cc_start: 0.7783 (mt-10) cc_final: 0.7525 (mt-10) REVERT: B 326 HIS cc_start: 0.8197 (p-80) cc_final: 0.7977 (p90) REVERT: B 411 GLN cc_start: 0.8941 (pm20) cc_final: 0.8709 (pm20) REVERT: B 421 SER cc_start: 0.8468 (m) cc_final: 0.8030 (p) REVERT: B 438 ASP cc_start: 0.8241 (m-30) cc_final: 0.7909 (m-30) REVERT: B 531 TYR cc_start: 0.8056 (t80) cc_final: 0.7821 (t80) REVERT: B 569 TYR cc_start: 0.7748 (t80) cc_final: 0.7442 (t80) REVERT: B 574 GLU cc_start: 0.7333 (tt0) cc_final: 0.7031 (tt0) REVERT: B 589 LYS cc_start: 0.7793 (ttmt) cc_final: 0.7462 (mtpp) REVERT: A 35 ASN cc_start: 0.5695 (OUTLIER) cc_final: 0.3762 (m-40) REVERT: A 54 ARG cc_start: 0.8248 (tpp80) cc_final: 0.7747 (tpp80) REVERT: A 84 LEU cc_start: 0.8742 (tp) cc_final: 0.8428 (tp) REVERT: A 93 SER cc_start: 0.8063 (p) cc_final: 0.7787 (p) REVERT: A 104 LYS cc_start: 0.8274 (mppt) cc_final: 0.7777 (mmmm) REVERT: A 116 ASN cc_start: 0.7493 (m-40) cc_final: 0.7269 (t0) REVERT: A 119 LYS cc_start: 0.7666 (mttp) cc_final: 0.7390 (mttp) REVERT: A 151 THR cc_start: 0.7856 (p) cc_final: 0.7543 (m) REVERT: A 172 PHE cc_start: 0.8111 (m-80) cc_final: 0.7867 (m-80) REVERT: A 212 MET cc_start: 0.8093 (tpp) cc_final: 0.7733 (tmm) REVERT: A 233 GLN cc_start: 0.8353 (mt0) cc_final: 0.7994 (mt0) REVERT: A 262 LEU cc_start: 0.8221 (mm) cc_final: 0.7867 (mm) REVERT: A 282 MET cc_start: 0.6689 (OUTLIER) cc_final: 0.6247 (mtp) REVERT: A 286 GLU cc_start: 0.7911 (mt-10) cc_final: 0.7518 (mt-10) REVERT: A 299 GLU cc_start: 0.7608 (mm-30) cc_final: 0.7288 (mm-30) REVERT: A 356 ASP cc_start: 0.8024 (t0) cc_final: 0.7717 (t0) REVERT: A 371 ASN cc_start: 0.6956 (t0) cc_final: 0.6621 (t0) REVERT: A 412 LEU cc_start: 0.8731 (OUTLIER) cc_final: 0.8313 (pt) REVERT: A 417 MET cc_start: 0.7751 (tpp) cc_final: 0.7244 (tpp) REVERT: A 418 LYS cc_start: 0.7929 (ttmm) cc_final: 0.7646 (ttmm) REVERT: A 421 SER cc_start: 0.8514 (m) cc_final: 0.8070 (p) REVERT: A 429 ASP cc_start: 0.8083 (m-30) cc_final: 0.7873 (m-30) REVERT: A 436 ASP cc_start: 0.7761 (t70) cc_final: 0.7425 (t0) REVERT: A 438 ASP cc_start: 0.8111 (m-30) cc_final: 0.7756 (m-30) REVERT: A 485 LYS cc_start: 0.8783 (tttt) cc_final: 0.8495 (ptmt) REVERT: A 589 LYS cc_start: 0.7878 (OUTLIER) cc_final: 0.7429 (mtpp) outliers start: 43 outliers final: 23 residues processed: 268 average time/residue: 0.0736 time to fit residues: 27.5740 Evaluate side-chains 266 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 237 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 58 ASP Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 156 SER Chi-restraints excluded: chain B residue 243 ILE Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 264 CYS Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 424 LYS Chi-restraints excluded: chain B residue 491 PHE Chi-restraints excluded: chain B residue 578 VAL Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 35 ASN Chi-restraints excluded: chain A residue 41 GLU Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain A residue 183 ASP Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 326 HIS Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 491 PHE Chi-restraints excluded: chain A residue 563 TRP Chi-restraints excluded: chain A residue 589 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 0.5980 chunk 61 optimal weight: 0.1980 chunk 45 optimal weight: 0.0170 overall best weight: 0.4218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 89 HIS ** B 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 128 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 = 0.3954 r_free = 0.3954 target = 0.159578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.141154 restraints weight = 13402.197| |-----------------------------------------------------------------------------| r_work (start): 0.3651 rms_B_bonded: 2.53 r_work: 0.3502 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7312 moved from start: 0.0810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 8392 Z= 0.137 Angle : 0.526 8.117 11406 Z= 0.272 Chirality : 0.041 0.175 1304 Planarity : 0.004 0.029 1374 Dihedral : 6.965 57.949 1099 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 3.33 % Allowed : 26.77 % Favored : 69.89 % 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: 1.87 (0.29), residues: 966 helix: 1.86 (0.20), residues: 714 sheet: -1.55 (0.79), residues: 44 loop : -0.17 (0.53), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 184 TYR 0.010 0.001 TYR A 569 PHE 0.026 0.001 PHE B 266 TRP 0.008 0.001 TRP B 563 HIS 0.005 0.001 HIS B 326 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 8392) covalent geometry : angle 0.52635 (11406) hydrogen bonds : bond 0.04205 ( 550) hydrogen bonds : angle 4.72598 ( 1614) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 242 time to evaluate : 0.318 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 13 VAL cc_start: 0.8542 (m) cc_final: 0.8178 (t) REVERT: B 54 ARG cc_start: 0.8313 (tpp80) cc_final: 0.8047 (tpp80) REVERT: B 55 ILE cc_start: 0.8885 (pt) cc_final: 0.8575 (mt) REVERT: B 68 GLN cc_start: 0.7379 (tp-100) cc_final: 0.6950 (tp-100) REVERT: B 84 LEU cc_start: 0.8796 (tp) cc_final: 0.8428 (tp) REVERT: B 129 ASN cc_start: 0.7675 (t0) cc_final: 0.7311 (t0) REVERT: B 140 PHE cc_start: 0.7692 (t80) cc_final: 0.7389 (t80) REVERT: B 150 PHE cc_start: 0.4267 (OUTLIER) cc_final: 0.3884 (m-10) REVERT: B 172 PHE cc_start: 0.8125 (m-80) cc_final: 0.7860 (m-80) REVERT: B 182 SER cc_start: 0.8517 (t) cc_final: 0.8139 (p) REVERT: B 212 MET cc_start: 0.7955 (mmm) cc_final: 0.7622 (tmm) REVERT: B 214 LYS cc_start: 0.8152 (mtmt) cc_final: 0.7378 (mttp) REVERT: B 232 PHE cc_start: 0.7870 (t80) cc_final: 0.7481 (t80) REVERT: B 271 THR cc_start: 0.7994 (t) cc_final: 0.7719 (m) REVERT: B 276 LYS cc_start: 0.8246 (ttmm) cc_final: 0.7867 (ttpt) REVERT: B 411 GLN cc_start: 0.8957 (pm20) cc_final: 0.8754 (pm20) REVERT: B 417 MET cc_start: 0.7662 (tpp) cc_final: 0.7387 (tpp) REVERT: B 421 SER cc_start: 0.8480 (m) cc_final: 0.8024 (p) REVERT: B 429 ASP cc_start: 0.7941 (m-30) cc_final: 0.7509 (t0) REVERT: B 438 ASP cc_start: 0.8191 (m-30) cc_final: 0.7932 (m-30) REVERT: B 531 TYR cc_start: 0.8005 (t80) cc_final: 0.7734 (t80) REVERT: B 561 HIS cc_start: 0.7778 (m-70) cc_final: 0.7345 (m-70) REVERT: B 569 TYR cc_start: 0.7863 (t80) cc_final: 0.7615 (t80) REVERT: B 589 LYS cc_start: 0.7830 (ttmt) cc_final: 0.7501 (mtpp) REVERT: A 13 VAL cc_start: 0.8469 (m) cc_final: 0.8177 (t) REVERT: A 34 LEU cc_start: 0.6231 (pt) cc_final: 0.5808 (pp) REVERT: A 54 ARG cc_start: 0.8294 (tpp80) cc_final: 0.7772 (tpp80) REVERT: A 55 ILE cc_start: 0.8958 (pt) cc_final: 0.8691 (mt) REVERT: A 84 LEU cc_start: 0.8754 (tp) cc_final: 0.8435 (tp) REVERT: A 93 SER cc_start: 0.8097 (p) cc_final: 0.7814 (p) REVERT: A 104 LYS cc_start: 0.8146 (mppt) cc_final: 0.7671 (mmmm) REVERT: A 172 PHE cc_start: 0.8110 (m-80) cc_final: 0.7872 (m-80) REVERT: A 233 GLN cc_start: 0.8355 (mt0) cc_final: 0.7988 (mt0) REVERT: A 282 MET cc_start: 0.6537 (OUTLIER) cc_final: 0.6159 (mtp) REVERT: A 286 GLU cc_start: 0.7913 (mt-10) cc_final: 0.7649 (mt-10) REVERT: A 299 GLU cc_start: 0.7658 (mm-30) cc_final: 0.7318 (mm-30) REVERT: A 356 ASP cc_start: 0.7958 (t0) cc_final: 0.7629 (t0) REVERT: A 371 ASN cc_start: 0.6915 (t0) cc_final: 0.6592 (t0) REVERT: A 412 LEU cc_start: 0.8733 (OUTLIER) cc_final: 0.8378 (pt) REVERT: A 417 MET cc_start: 0.7779 (tpp) cc_final: 0.7258 (tpp) REVERT: A 418 LYS cc_start: 0.7917 (ttmm) cc_final: 0.7651 (ttmm) REVERT: A 421 SER cc_start: 0.8535 (m) cc_final: 0.8081 (p) REVERT: A 429 ASP cc_start: 0.7875 (m-30) cc_final: 0.7626 (m-30) REVERT: A 436 ASP cc_start: 0.7726 (t70) cc_final: 0.7485 (t0) REVERT: A 438 ASP cc_start: 0.8065 (m-30) cc_final: 0.7663 (m-30) REVERT: A 589 LYS cc_start: 0.7889 (ttmt) cc_final: 0.7455 (mtpp) outliers start: 31 outliers final: 17 residues processed: 257 average time/residue: 0.0830 time to fit residues: 29.6107 Evaluate side-chains 260 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 240 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 150 PHE Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 282 MET Chi-restraints excluded: chain B residue 378 MET Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 451 LEU Chi-restraints excluded: chain B residue 484 SER Chi-restraints excluded: chain B residue 491 PHE Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 326 HIS Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 491 PHE Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 563 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 58 optimal weight: 0.0670 chunk 14 optimal weight: 0.0670 chunk 68 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 chunk 95 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 39 optimal weight: 0.5980 chunk 64 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 overall best weight: 0.4256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 275 ASN B 302 ASN ** A 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 117 ASN A 120 GLN ** A 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 372 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.152547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.134049 restraints weight = 13014.339| |-----------------------------------------------------------------------------| r_work (start): 0.3662 rms_B_bonded: 2.49 r_work: 0.3521 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7302 moved from start: 0.1170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8392 Z= 0.135 Angle : 0.550 9.860 11406 Z= 0.277 Chirality : 0.041 0.173 1304 Planarity : 0.004 0.031 1374 Dihedral : 5.822 59.174 1066 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 3.98 % Allowed : 26.34 % Favored : 69.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.90 (0.29), residues: 966 helix: 1.93 (0.20), residues: 702 sheet: -1.42 (0.78), residues: 44 loop : -0.24 (0.51), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG A 184 TYR 0.010 0.001 TYR A 569 PHE 0.028 0.001 PHE B 266 TRP 0.007 0.001 TRP A 173 HIS 0.005 0.001 HIS B 326 Details of bonding type rmsd covalent geometry : bond 0.00293 ( 8392) covalent geometry : angle 0.55010 (11406) hydrogen bonds : bond 0.04020 ( 550) hydrogen bonds : angle 4.56187 ( 1614) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 244 time to evaluate : 0.205 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 13 VAL cc_start: 0.8548 (m) cc_final: 0.8191 (t) REVERT: B 54 ARG cc_start: 0.8397 (tpp80) cc_final: 0.8169 (tpp80) REVERT: B 55 ILE cc_start: 0.8899 (pt) cc_final: 0.8613 (mt) REVERT: B 68 GLN cc_start: 0.7280 (tp-100) cc_final: 0.6872 (tp-100) REVERT: B 84 LEU cc_start: 0.8727 (tp) cc_final: 0.8438 (tp) REVERT: B 129 ASN cc_start: 0.7681 (t0) cc_final: 0.7240 (t0) REVERT: B 140 PHE cc_start: 0.7692 (t80) cc_final: 0.7392 (t80) REVERT: B 150 PHE cc_start: 0.4271 (OUTLIER) cc_final: 0.4028 (m-10) REVERT: B 172 PHE cc_start: 0.8150 (m-80) cc_final: 0.7881 (m-80) REVERT: B 212 MET cc_start: 0.8023 (mmm) cc_final: 0.7633 (tmm) REVERT: B 214 LYS cc_start: 0.8040 (mtmt) cc_final: 0.7747 (mttt) REVERT: B 232 PHE cc_start: 0.7877 (t80) cc_final: 0.7488 (t80) REVERT: B 271 THR cc_start: 0.8064 (OUTLIER) cc_final: 0.7807 (m) REVERT: B 276 LYS cc_start: 0.8253 (ttmm) cc_final: 0.7904 (ttpt) REVERT: B 302 ASN cc_start: 0.8698 (OUTLIER) cc_final: 0.8283 (m110) REVERT: B 411 GLN cc_start: 0.8830 (pm20) cc_final: 0.8558 (pm20) REVERT: B 417 MET cc_start: 0.7563 (tpp) cc_final: 0.7179 (tpp) REVERT: B 421 SER cc_start: 0.8494 (m) cc_final: 0.8051 (p) REVERT: B 429 ASP cc_start: 0.7924 (m-30) cc_final: 0.7535 (t0) REVERT: B 438 ASP cc_start: 0.8101 (m-30) cc_final: 0.7845 (m-30) REVERT: B 531 TYR cc_start: 0.8019 (t80) cc_final: 0.7766 (t80) REVERT: B 561 HIS cc_start: 0.7784 (m-70) cc_final: 0.7293 (m-70) REVERT: B 569 TYR cc_start: 0.7855 (t80) cc_final: 0.7634 (t80) REVERT: B 589 LYS cc_start: 0.7833 (ttmt) cc_final: 0.7504 (mtpp) REVERT: A 13 VAL cc_start: 0.8484 (m) cc_final: 0.8213 (t) REVERT: A 54 ARG cc_start: 0.8362 (tpp80) cc_final: 0.8116 (tpp80) REVERT: A 55 ILE cc_start: 0.8973 (pt) cc_final: 0.8707 (mt) REVERT: A 84 LEU cc_start: 0.8747 (tp) cc_final: 0.8428 (tp) REVERT: A 93 SER cc_start: 0.8131 (p) cc_final: 0.7835 (p) REVERT: A 104 LYS cc_start: 0.8158 (mppt) cc_final: 0.7672 (mmmm) REVERT: A 120 GLN cc_start: 0.8046 (mt0) cc_final: 0.7762 (mt0) REVERT: A 172 PHE cc_start: 0.8148 (m-80) cc_final: 0.7897 (m-80) REVERT: A 178 GLU cc_start: 0.8027 (tp30) cc_final: 0.7767 (tp30) REVERT: A 214 LYS cc_start: 0.7890 (mtmt) cc_final: 0.7084 (mttp) REVERT: A 233 GLN cc_start: 0.8344 (mt0) cc_final: 0.7985 (mt0) REVERT: A 282 MET cc_start: 0.6594 (mtp) cc_final: 0.6186 (mtp) REVERT: A 286 GLU cc_start: 0.7936 (mt-10) cc_final: 0.7675 (mt-10) REVERT: A 299 GLU cc_start: 0.7645 (mm-30) cc_final: 0.7324 (mm-30) REVERT: A 356 ASP cc_start: 0.7979 (t0) cc_final: 0.7641 (t0) REVERT: A 371 ASN cc_start: 0.6991 (t0) cc_final: 0.6685 (t0) REVERT: A 412 LEU cc_start: 0.8738 (OUTLIER) cc_final: 0.8311 (pt) REVERT: A 417 MET cc_start: 0.7751 (tpp) cc_final: 0.7185 (tpp) REVERT: A 418 LYS cc_start: 0.7863 (ttmm) cc_final: 0.7601 (ttmm) REVERT: A 421 SER cc_start: 0.8550 (m) cc_final: 0.8095 (p) REVERT: A 429 ASP cc_start: 0.7832 (m-30) cc_final: 0.7608 (m-30) REVERT: A 436 ASP cc_start: 0.7761 (t70) cc_final: 0.7374 (t0) REVERT: A 438 ASP cc_start: 0.8053 (m-30) cc_final: 0.7640 (m-30) REVERT: A 589 LYS cc_start: 0.7919 (ttmt) cc_final: 0.7492 (mtpp) outliers start: 37 outliers final: 20 residues processed: 265 average time/residue: 0.0702 time to fit residues: 25.9381 Evaluate side-chains 260 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 236 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 58 ASP Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 150 PHE Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 302 ASN Chi-restraints excluded: chain B residue 378 MET Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 451 LEU Chi-restraints excluded: chain B residue 484 SER Chi-restraints excluded: chain B residue 491 PHE Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 41 GLU Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 326 HIS Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 491 PHE Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 563 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 52 optimal weight: 2.9990 chunk 13 optimal weight: 0.0070 chunk 92 optimal weight: 0.5980 chunk 65 optimal weight: 0.9980 chunk 11 optimal weight: 0.7980 chunk 73 optimal weight: 0.8980 chunk 22 optimal weight: 0.6980 chunk 87 optimal weight: 0.7980 chunk 89 optimal weight: 0.9980 chunk 88 optimal weight: 0.0770 chunk 25 optimal weight: 0.9980 overall best weight: 0.4356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 302 ASN ** A 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 293 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.152619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.134200 restraints weight = 13314.200| |-----------------------------------------------------------------------------| r_work (start): 0.3664 rms_B_bonded: 2.52 r_work: 0.3525 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7302 moved from start: 0.1357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 8392 Z= 0.135 Angle : 0.530 7.653 11406 Z= 0.270 Chirality : 0.041 0.161 1304 Planarity : 0.004 0.029 1374 Dihedral : 5.618 59.335 1063 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 4.09 % Allowed : 26.88 % Favored : 69.03 % 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: 1.95 (0.29), residues: 966 helix: 1.95 (0.20), residues: 702 sheet: -1.41 (0.78), residues: 44 loop : -0.20 (0.51), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG B 33 TYR 0.010 0.001 TYR A 569 PHE 0.029 0.001 PHE B 266 TRP 0.007 0.001 TRP A 173 HIS 0.005 0.001 HIS B 326 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 8392) covalent geometry : angle 0.52963 (11406) hydrogen bonds : bond 0.03921 ( 550) hydrogen bonds : angle 4.48196 ( 1614) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 235 time to evaluate : 0.212 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 13 VAL cc_start: 0.8596 (m) cc_final: 0.8274 (t) REVERT: B 15 VAL cc_start: 0.7631 (OUTLIER) cc_final: 0.7380 (m) REVERT: B 35 ASN cc_start: 0.5593 (OUTLIER) cc_final: 0.2778 (m-40) REVERT: B 55 ILE cc_start: 0.8867 (pt) cc_final: 0.8608 (mt) REVERT: B 68 GLN cc_start: 0.7264 (tp-100) cc_final: 0.6850 (tp-100) REVERT: B 84 LEU cc_start: 0.8686 (tp) cc_final: 0.8442 (tp) REVERT: B 129 ASN cc_start: 0.7663 (t0) cc_final: 0.7234 (t0) REVERT: B 140 PHE cc_start: 0.7711 (t80) cc_final: 0.7427 (t80) REVERT: B 150 PHE cc_start: 0.4302 (OUTLIER) cc_final: 0.4079 (m-10) REVERT: B 172 PHE cc_start: 0.8156 (m-80) cc_final: 0.7900 (m-80) REVERT: B 212 MET cc_start: 0.8027 (mmm) cc_final: 0.7613 (tmm) REVERT: B 232 PHE cc_start: 0.7851 (t80) cc_final: 0.7529 (t80) REVERT: B 271 THR cc_start: 0.8098 (OUTLIER) cc_final: 0.7834 (m) REVERT: B 276 LYS cc_start: 0.8230 (ttmm) cc_final: 0.7854 (ttpt) REVERT: B 411 GLN cc_start: 0.8852 (pm20) cc_final: 0.8564 (pm20) REVERT: B 417 MET cc_start: 0.7524 (tpp) cc_final: 0.7147 (tpp) REVERT: B 421 SER cc_start: 0.8520 (m) cc_final: 0.8072 (p) REVERT: B 429 ASP cc_start: 0.7963 (m-30) cc_final: 0.7618 (t0) REVERT: B 438 ASP cc_start: 0.8057 (m-30) cc_final: 0.7809 (m-30) REVERT: B 531 TYR cc_start: 0.8046 (t80) cc_final: 0.7758 (t80) REVERT: B 561 HIS cc_start: 0.7756 (m-70) cc_final: 0.7297 (m-70) REVERT: B 574 GLU cc_start: 0.7422 (tm-30) cc_final: 0.7059 (tt0) REVERT: B 589 LYS cc_start: 0.7835 (ttmt) cc_final: 0.7512 (mtpp) REVERT: A 13 VAL cc_start: 0.8495 (m) cc_final: 0.8242 (t) REVERT: A 54 ARG cc_start: 0.8379 (tpp80) cc_final: 0.8139 (tpp80) REVERT: A 55 ILE cc_start: 0.8954 (pt) cc_final: 0.8715 (mt) REVERT: A 84 LEU cc_start: 0.8766 (tp) cc_final: 0.8456 (tp) REVERT: A 93 SER cc_start: 0.8158 (p) cc_final: 0.7874 (p) REVERT: A 104 LYS cc_start: 0.8154 (mppt) cc_final: 0.7682 (mmmm) REVERT: A 172 PHE cc_start: 0.8158 (m-80) cc_final: 0.7835 (m-80) REVERT: A 178 GLU cc_start: 0.7953 (tp30) cc_final: 0.7654 (tp30) REVERT: A 233 GLN cc_start: 0.8366 (mt0) cc_final: 0.7990 (mt0) REVERT: A 262 LEU cc_start: 0.8328 (OUTLIER) cc_final: 0.7990 (mm) REVERT: A 282 MET cc_start: 0.6652 (OUTLIER) cc_final: 0.6212 (mtp) REVERT: A 286 GLU cc_start: 0.7924 (mt-10) cc_final: 0.7646 (mt-10) REVERT: A 299 GLU cc_start: 0.7631 (mm-30) cc_final: 0.7299 (mm-30) REVERT: A 356 ASP cc_start: 0.8028 (t0) cc_final: 0.7782 (t0) REVERT: A 371 ASN cc_start: 0.7057 (t0) cc_final: 0.6751 (t0) REVERT: A 412 LEU cc_start: 0.8724 (OUTLIER) cc_final: 0.8285 (pt) REVERT: A 417 MET cc_start: 0.7639 (tpp) cc_final: 0.7067 (tpp) REVERT: A 418 LYS cc_start: 0.7845 (ttmm) cc_final: 0.7598 (ttmm) REVERT: A 421 SER cc_start: 0.8549 (m) cc_final: 0.8100 (p) REVERT: A 429 ASP cc_start: 0.7827 (m-30) cc_final: 0.7603 (m-30) REVERT: A 436 ASP cc_start: 0.7684 (t70) cc_final: 0.7398 (t0) REVERT: A 438 ASP cc_start: 0.8047 (m-30) cc_final: 0.7621 (m-30) REVERT: A 488 TYR cc_start: 0.8235 (m-10) cc_final: 0.8029 (m-10) REVERT: A 589 LYS cc_start: 0.7930 (ttmt) cc_final: 0.7488 (mtpp) outliers start: 38 outliers final: 26 residues processed: 256 average time/residue: 0.0695 time to fit residues: 25.3053 Evaluate side-chains 264 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 231 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 58 ASP Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 150 PHE Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 282 MET Chi-restraints excluded: chain B residue 302 ASN Chi-restraints excluded: chain B residue 378 MET Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 451 LEU Chi-restraints excluded: chain B residue 484 SER Chi-restraints excluded: chain B residue 491 PHE Chi-restraints excluded: chain B residue 578 VAL Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 41 GLU Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 244 LYS Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 326 HIS Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 484 SER Chi-restraints excluded: chain A residue 491 PHE Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 563 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 60 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 chunk 42 optimal weight: 0.7980 chunk 12 optimal weight: 0.9980 chunk 37 optimal weight: 0.7980 chunk 50 optimal weight: 0.9990 chunk 73 optimal weight: 0.6980 chunk 55 optimal weight: 0.9990 chunk 83 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 302 ASN ** A 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 128 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 = 0.3915 r_free = 0.3915 target = 0.150568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.132102 restraints weight = 13207.033| |-----------------------------------------------------------------------------| r_work (start): 0.3635 rms_B_bonded: 2.50 r_work: 0.3492 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7340 moved from start: 0.1528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 8392 Z= 0.194 Angle : 0.554 9.714 11406 Z= 0.287 Chirality : 0.043 0.142 1304 Planarity : 0.004 0.031 1374 Dihedral : 5.578 58.961 1062 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 4.52 % Allowed : 27.63 % Favored : 67.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.81 (0.28), residues: 966 helix: 1.84 (0.20), residues: 702 sheet: -1.44 (0.75), residues: 44 loop : -0.19 (0.50), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 54 TYR 0.009 0.001 TYR B 130 PHE 0.025 0.001 PHE B 266 TRP 0.008 0.001 TRP A 173 HIS 0.005 0.001 HIS B 326 Details of bonding type rmsd covalent geometry : bond 0.00431 ( 8392) covalent geometry : angle 0.55429 (11406) hydrogen bonds : bond 0.04166 ( 550) hydrogen bonds : angle 4.53967 ( 1614) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 235 time to evaluate : 0.301 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 13 VAL cc_start: 0.8644 (m) cc_final: 0.8330 (t) REVERT: B 15 VAL cc_start: 0.7632 (OUTLIER) cc_final: 0.7387 (m) REVERT: B 34 LEU cc_start: 0.6261 (pt) cc_final: 0.5313 (pp) REVERT: B 35 ASN cc_start: 0.5572 (OUTLIER) cc_final: 0.2671 (m-40) REVERT: B 54 ARG cc_start: 0.8370 (tpp80) cc_final: 0.8006 (tpt-90) REVERT: B 55 ILE cc_start: 0.8877 (pt) cc_final: 0.8557 (mt) REVERT: B 68 GLN cc_start: 0.7307 (tp-100) cc_final: 0.6904 (tp-100) REVERT: B 84 LEU cc_start: 0.8724 (tp) cc_final: 0.8395 (tp) REVERT: B 129 ASN cc_start: 0.7715 (t0) cc_final: 0.7290 (t0) REVERT: B 135 ILE cc_start: 0.8664 (OUTLIER) cc_final: 0.8436 (mm) REVERT: B 140 PHE cc_start: 0.7699 (t80) cc_final: 0.7449 (t80) REVERT: B 172 PHE cc_start: 0.8158 (m-80) cc_final: 0.7912 (m-80) REVERT: B 212 MET cc_start: 0.8143 (mmm) cc_final: 0.7726 (tmm) REVERT: B 214 LYS cc_start: 0.8150 (mttt) cc_final: 0.7681 (mttp) REVERT: B 232 PHE cc_start: 0.7880 (t80) cc_final: 0.7518 (t80) REVERT: B 241 ILE cc_start: 0.8496 (tp) cc_final: 0.8155 (tp) REVERT: B 255 LEU cc_start: 0.8047 (OUTLIER) cc_final: 0.7574 (mm) REVERT: B 271 THR cc_start: 0.8134 (OUTLIER) cc_final: 0.7848 (m) REVERT: B 276 LYS cc_start: 0.8266 (ttmm) cc_final: 0.7870 (ttpt) REVERT: B 286 GLU cc_start: 0.7700 (mt-10) cc_final: 0.7444 (mt-10) REVERT: B 411 GLN cc_start: 0.8624 (pm20) cc_final: 0.8348 (pm20) REVERT: B 417 MET cc_start: 0.7624 (tpp) cc_final: 0.7355 (tpp) REVERT: B 421 SER cc_start: 0.8544 (m) cc_final: 0.8110 (p) REVERT: B 429 ASP cc_start: 0.8006 (m-30) cc_final: 0.7670 (t0) REVERT: B 438 ASP cc_start: 0.8084 (m-30) cc_final: 0.7856 (m-30) REVERT: B 531 TYR cc_start: 0.8160 (t80) cc_final: 0.7939 (t80) REVERT: B 561 HIS cc_start: 0.7762 (m-70) cc_final: 0.7401 (m-70) REVERT: B 589 LYS cc_start: 0.7802 (ttmt) cc_final: 0.7475 (mtpp) REVERT: A 13 VAL cc_start: 0.8504 (m) cc_final: 0.8268 (t) REVERT: A 14 ILE cc_start: 0.9168 (mm) cc_final: 0.8895 (mt) REVERT: A 34 LEU cc_start: 0.6000 (pt) cc_final: 0.5632 (pp) REVERT: A 54 ARG cc_start: 0.8412 (tpp80) cc_final: 0.8170 (tpp80) REVERT: A 55 ILE cc_start: 0.8953 (pt) cc_final: 0.8699 (mt) REVERT: A 79 TYR cc_start: 0.8151 (t80) cc_final: 0.7802 (t80) REVERT: A 84 LEU cc_start: 0.8754 (tp) cc_final: 0.8481 (tp) REVERT: A 93 SER cc_start: 0.8254 (p) cc_final: 0.7950 (p) REVERT: A 104 LYS cc_start: 0.8213 (mppt) cc_final: 0.7711 (mmmm) REVERT: A 120 GLN cc_start: 0.8032 (mt0) cc_final: 0.7779 (mt0) REVERT: A 172 PHE cc_start: 0.8170 (m-80) cc_final: 0.7862 (m-80) REVERT: A 178 GLU cc_start: 0.7955 (tp30) cc_final: 0.7654 (tp30) REVERT: A 233 GLN cc_start: 0.8346 (mt0) cc_final: 0.7969 (mt0) REVERT: A 262 LEU cc_start: 0.8359 (OUTLIER) cc_final: 0.8021 (mm) REVERT: A 282 MET cc_start: 0.6658 (OUTLIER) cc_final: 0.6201 (mtp) REVERT: A 286 GLU cc_start: 0.7980 (mt-10) cc_final: 0.7629 (mt-10) REVERT: A 299 GLU cc_start: 0.7659 (mm-30) cc_final: 0.7326 (mm-30) REVERT: A 319 PHE cc_start: 0.8084 (m-80) cc_final: 0.7795 (m-80) REVERT: A 356 ASP cc_start: 0.8028 (t0) cc_final: 0.7785 (t0) REVERT: A 412 LEU cc_start: 0.8728 (pt) cc_final: 0.8262 (pt) REVERT: A 417 MET cc_start: 0.7677 (tpp) cc_final: 0.7047 (tpp) REVERT: A 418 LYS cc_start: 0.7907 (ttmm) cc_final: 0.7666 (ttmm) REVERT: A 421 SER cc_start: 0.8618 (m) cc_final: 0.8214 (p) REVERT: A 429 ASP cc_start: 0.7844 (m-30) cc_final: 0.7638 (m-30) REVERT: A 438 ASP cc_start: 0.8065 (m-30) cc_final: 0.7708 (m-30) REVERT: A 589 LYS cc_start: 0.7958 (ttmt) cc_final: 0.7514 (mtpp) outliers start: 42 outliers final: 28 residues processed: 259 average time/residue: 0.0794 time to fit residues: 28.9815 Evaluate side-chains 268 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 233 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 58 ASP Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 282 MET Chi-restraints excluded: chain B residue 302 ASN Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain B residue 378 MET Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 451 LEU Chi-restraints excluded: chain B residue 484 SER Chi-restraints excluded: chain B residue 491 PHE Chi-restraints excluded: chain B residue 563 TRP Chi-restraints excluded: chain B residue 578 VAL Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 41 GLU Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 251 MET Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 326 HIS Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 484 SER Chi-restraints excluded: chain A residue 491 PHE Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 563 TRP Chi-restraints excluded: chain A residue 565 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 84 optimal weight: 0.7980 chunk 7 optimal weight: 0.4980 chunk 30 optimal weight: 0.5980 chunk 0 optimal weight: 0.9990 chunk 76 optimal weight: 2.9990 chunk 13 optimal weight: 0.6980 chunk 36 optimal weight: 0.9980 chunk 65 optimal weight: 0.9980 chunk 23 optimal weight: 0.8980 chunk 85 optimal weight: 0.3980 chunk 97 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 302 ASN ** A 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 275 ASN A 302 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.151674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.133524 restraints weight = 12902.936| |-----------------------------------------------------------------------------| r_work (start): 0.3669 rms_B_bonded: 2.38 r_work: 0.3534 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7306 moved from start: 0.1649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8392 Z= 0.158 Angle : 0.541 9.199 11406 Z= 0.278 Chirality : 0.042 0.171 1304 Planarity : 0.004 0.033 1374 Dihedral : 5.234 54.832 1058 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 5.16 % Allowed : 26.88 % Favored : 67.96 % 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: 1.80 (0.28), residues: 966 helix: 1.84 (0.20), residues: 702 sheet: -0.70 (0.87), residues: 34 loop : -0.48 (0.48), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 54 TYR 0.012 0.001 TYR A 569 PHE 0.023 0.001 PHE A 232 TRP 0.008 0.001 TRP A 173 HIS 0.005 0.001 HIS B 326 Details of bonding type rmsd covalent geometry : bond 0.00348 ( 8392) covalent geometry : angle 0.54069 (11406) hydrogen bonds : bond 0.04072 ( 550) hydrogen bonds : angle 4.48711 ( 1614) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 233 time to evaluate : 0.310 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 13 VAL cc_start: 0.8661 (m) cc_final: 0.8337 (t) REVERT: B 15 VAL cc_start: 0.7566 (OUTLIER) cc_final: 0.7357 (m) REVERT: B 34 LEU cc_start: 0.6354 (pt) cc_final: 0.5467 (pp) REVERT: B 35 ASN cc_start: 0.5508 (OUTLIER) cc_final: 0.2683 (m-40) REVERT: B 54 ARG cc_start: 0.8375 (tpp80) cc_final: 0.7967 (tpt-90) REVERT: B 55 ILE cc_start: 0.8902 (pt) cc_final: 0.8575 (mt) REVERT: B 68 GLN cc_start: 0.7310 (tp-100) cc_final: 0.6911 (tp-100) REVERT: B 84 LEU cc_start: 0.8749 (tp) cc_final: 0.8402 (tp) REVERT: B 129 ASN cc_start: 0.7669 (t0) cc_final: 0.7451 (t0) REVERT: B 140 PHE cc_start: 0.7681 (t80) cc_final: 0.7447 (t80) REVERT: B 172 PHE cc_start: 0.8143 (m-80) cc_final: 0.7883 (m-80) REVERT: B 212 MET cc_start: 0.8106 (mmm) cc_final: 0.7686 (tmm) REVERT: B 214 LYS cc_start: 0.8162 (mttt) cc_final: 0.7709 (mttp) REVERT: B 232 PHE cc_start: 0.7921 (t80) cc_final: 0.7544 (t80) REVERT: B 241 ILE cc_start: 0.8490 (tp) cc_final: 0.8133 (tp) REVERT: B 247 TYR cc_start: 0.7047 (t80) cc_final: 0.6841 (t80) REVERT: B 262 LEU cc_start: 0.8413 (OUTLIER) cc_final: 0.7990 (mm) REVERT: B 271 THR cc_start: 0.8149 (OUTLIER) cc_final: 0.7836 (m) REVERT: B 276 LYS cc_start: 0.8243 (ttmm) cc_final: 0.7799 (ttpp) REVERT: B 286 GLU cc_start: 0.7747 (mt-10) cc_final: 0.7542 (mt-10) REVERT: B 411 GLN cc_start: 0.8606 (pm20) cc_final: 0.8293 (pm20) REVERT: B 417 MET cc_start: 0.7579 (tpp) cc_final: 0.7290 (tpp) REVERT: B 421 SER cc_start: 0.8548 (m) cc_final: 0.8113 (p) REVERT: B 429 ASP cc_start: 0.7981 (m-30) cc_final: 0.7621 (t0) REVERT: B 438 ASP cc_start: 0.8092 (m-30) cc_final: 0.7854 (m-30) REVERT: B 531 TYR cc_start: 0.8122 (t80) cc_final: 0.7866 (t80) REVERT: B 561 HIS cc_start: 0.7741 (m-70) cc_final: 0.7381 (m-70) REVERT: B 589 LYS cc_start: 0.7798 (ttmt) cc_final: 0.7452 (mtpp) REVERT: A 13 VAL cc_start: 0.8513 (m) cc_final: 0.8270 (t) REVERT: A 14 ILE cc_start: 0.9163 (mm) cc_final: 0.8905 (mt) REVERT: A 32 LYS cc_start: 0.8178 (tptt) cc_final: 0.7947 (tptp) REVERT: A 34 LEU cc_start: 0.5970 (pt) cc_final: 0.5619 (pp) REVERT: A 54 ARG cc_start: 0.8419 (tpp80) cc_final: 0.8184 (tpp80) REVERT: A 55 ILE cc_start: 0.9019 (pt) cc_final: 0.8751 (mt) REVERT: A 66 PHE cc_start: 0.6532 (t80) cc_final: 0.6331 (t80) REVERT: A 79 TYR cc_start: 0.8134 (t80) cc_final: 0.7768 (t80) REVERT: A 84 LEU cc_start: 0.8796 (tp) cc_final: 0.8486 (tp) REVERT: A 93 SER cc_start: 0.8224 (p) cc_final: 0.7906 (p) REVERT: A 104 LYS cc_start: 0.8168 (mppt) cc_final: 0.7659 (mmmm) REVERT: A 120 GLN cc_start: 0.7968 (mt0) cc_final: 0.7720 (mt0) REVERT: A 172 PHE cc_start: 0.8133 (m-80) cc_final: 0.7772 (m-80) REVERT: A 178 GLU cc_start: 0.7912 (tp30) cc_final: 0.7591 (tp30) REVERT: A 214 LYS cc_start: 0.8012 (mtmt) cc_final: 0.7256 (mttp) REVERT: A 233 GLN cc_start: 0.8372 (mt0) cc_final: 0.7999 (mt0) REVERT: A 262 LEU cc_start: 0.8394 (OUTLIER) cc_final: 0.8030 (mm) REVERT: A 282 MET cc_start: 0.6663 (OUTLIER) cc_final: 0.6194 (mtp) REVERT: A 299 GLU cc_start: 0.7608 (mm-30) cc_final: 0.7271 (mm-30) REVERT: A 302 ASN cc_start: 0.8421 (OUTLIER) cc_final: 0.7949 (m110) REVERT: A 319 PHE cc_start: 0.8052 (m-80) cc_final: 0.7742 (m-80) REVERT: A 356 ASP cc_start: 0.7977 (t0) cc_final: 0.7703 (t0) REVERT: A 412 LEU cc_start: 0.8736 (pt) cc_final: 0.8275 (pt) REVERT: A 417 MET cc_start: 0.7672 (tpp) cc_final: 0.7042 (tpp) REVERT: A 418 LYS cc_start: 0.7876 (ttmm) cc_final: 0.7632 (ttmm) REVERT: A 421 SER cc_start: 0.8600 (m) cc_final: 0.8202 (p) REVERT: A 436 ASP cc_start: 0.7626 (t0) cc_final: 0.7224 (t0) REVERT: A 438 ASP cc_start: 0.8015 (m-30) cc_final: 0.7684 (m-30) REVERT: A 589 LYS cc_start: 0.7957 (ttmt) cc_final: 0.7494 (mtpp) outliers start: 48 outliers final: 33 residues processed: 261 average time/residue: 0.0786 time to fit residues: 28.9908 Evaluate side-chains 274 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 234 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 58 ASP Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 188 TYR Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 282 MET Chi-restraints excluded: chain B residue 302 ASN Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain B residue 378 MET Chi-restraints excluded: chain B residue 424 LYS Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 451 LEU Chi-restraints excluded: chain B residue 484 SER Chi-restraints excluded: chain B residue 491 PHE Chi-restraints excluded: chain B residue 563 TRP Chi-restraints excluded: chain B residue 578 VAL Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 41 GLU Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 251 MET Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 302 ASN Chi-restraints excluded: chain A residue 326 HIS Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 484 SER Chi-restraints excluded: chain A residue 491 PHE Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 563 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 26 optimal weight: 0.0570 chunk 28 optimal weight: 0.7980 chunk 46 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 chunk 94 optimal weight: 0.9990 chunk 93 optimal weight: 0.5980 chunk 78 optimal weight: 0.9980 chunk 84 optimal weight: 0.9980 chunk 11 optimal weight: 0.5980 chunk 38 optimal weight: 0.1980 chunk 89 optimal weight: 0.9980 overall best weight: 0.4498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 117 ASN B 120 GLN ** B 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 302 ASN ** A 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.158879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.140175 restraints weight = 13225.396| |-----------------------------------------------------------------------------| r_work (start): 0.3706 rms_B_bonded: 2.58 r_work: 0.3568 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7302 moved from start: 0.1722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 8392 Z= 0.138 Angle : 0.545 8.495 11406 Z= 0.277 Chirality : 0.042 0.148 1304 Planarity : 0.004 0.033 1374 Dihedral : 5.207 54.708 1058 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 4.95 % Allowed : 27.10 % Favored : 67.96 % 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: 1.84 (0.28), residues: 966 helix: 1.88 (0.20), residues: 702 sheet: -0.68 (0.85), residues: 34 loop : -0.48 (0.48), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 54 TYR 0.010 0.001 TYR A 569 PHE 0.025 0.001 PHE A 232 TRP 0.008 0.001 TRP A 173 HIS 0.005 0.001 HIS B 326 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 8392) covalent geometry : angle 0.54461 (11406) hydrogen bonds : bond 0.03983 ( 550) hydrogen bonds : angle 4.41549 ( 1614) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 232 time to evaluate : 0.319 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 13 VAL cc_start: 0.8647 (m) cc_final: 0.8349 (t) REVERT: B 34 LEU cc_start: 0.6337 (pt) cc_final: 0.5447 (pp) REVERT: B 35 ASN cc_start: 0.5557 (OUTLIER) cc_final: 0.2755 (m-40) REVERT: B 54 ARG cc_start: 0.8330 (tpp80) cc_final: 0.7932 (tpt-90) REVERT: B 55 ILE cc_start: 0.8897 (pt) cc_final: 0.8575 (mt) REVERT: B 68 GLN cc_start: 0.7306 (tp-100) cc_final: 0.6901 (tp-100) REVERT: B 84 LEU cc_start: 0.8764 (tp) cc_final: 0.8421 (tp) REVERT: B 129 ASN cc_start: 0.7653 (t0) cc_final: 0.7432 (t0) REVERT: B 135 ILE cc_start: 0.8659 (OUTLIER) cc_final: 0.8428 (mm) REVERT: B 140 PHE cc_start: 0.7679 (t80) cc_final: 0.7450 (t80) REVERT: B 172 PHE cc_start: 0.8164 (m-80) cc_final: 0.7908 (m-80) REVERT: B 212 MET cc_start: 0.8112 (mmm) cc_final: 0.7663 (tmm) REVERT: B 214 LYS cc_start: 0.8099 (mttt) cc_final: 0.7684 (mttp) REVERT: B 232 PHE cc_start: 0.7902 (t80) cc_final: 0.7519 (t80) REVERT: B 241 ILE cc_start: 0.8537 (tp) cc_final: 0.8208 (tp) REVERT: B 262 LEU cc_start: 0.8409 (OUTLIER) cc_final: 0.7975 (mm) REVERT: B 271 THR cc_start: 0.8185 (OUTLIER) cc_final: 0.7865 (m) REVERT: B 276 LYS cc_start: 0.8257 (ttmm) cc_final: 0.7811 (ttpp) REVERT: B 411 GLN cc_start: 0.8643 (pm20) cc_final: 0.8301 (pm20) REVERT: B 417 MET cc_start: 0.7568 (tpp) cc_final: 0.7322 (tpp) REVERT: B 421 SER cc_start: 0.8524 (m) cc_final: 0.8094 (p) REVERT: B 429 ASP cc_start: 0.7984 (m-30) cc_final: 0.7704 (t0) REVERT: B 438 ASP cc_start: 0.8052 (m-30) cc_final: 0.7763 (m-30) REVERT: B 531 TYR cc_start: 0.8100 (t80) cc_final: 0.7832 (t80) REVERT: B 561 HIS cc_start: 0.7752 (m-70) cc_final: 0.7459 (m-70) REVERT: B 574 GLU cc_start: 0.7391 (tm-30) cc_final: 0.6964 (tt0) REVERT: B 589 LYS cc_start: 0.7855 (ttmt) cc_final: 0.7503 (mtpp) REVERT: A 32 LYS cc_start: 0.8125 (tptt) cc_final: 0.7869 (tptp) REVERT: A 34 LEU cc_start: 0.5968 (pt) cc_final: 0.5608 (pp) REVERT: A 54 ARG cc_start: 0.8380 (tpp80) cc_final: 0.7980 (tpp80) REVERT: A 55 ILE cc_start: 0.8996 (pt) cc_final: 0.8705 (mt) REVERT: A 84 LEU cc_start: 0.8783 (tp) cc_final: 0.8514 (tp) REVERT: A 93 SER cc_start: 0.8198 (p) cc_final: 0.7890 (p) REVERT: A 104 LYS cc_start: 0.8176 (mppt) cc_final: 0.7674 (mmmm) REVERT: A 172 PHE cc_start: 0.8153 (m-80) cc_final: 0.7799 (m-80) REVERT: A 178 GLU cc_start: 0.7895 (tp30) cc_final: 0.7550 (tp30) REVERT: A 214 LYS cc_start: 0.7927 (mtmt) cc_final: 0.7111 (mttp) REVERT: A 233 GLN cc_start: 0.8407 (mt0) cc_final: 0.8033 (mt0) REVERT: A 299 GLU cc_start: 0.7574 (mm-30) cc_final: 0.7239 (mm-30) REVERT: A 356 ASP cc_start: 0.7991 (t0) cc_final: 0.7705 (t0) REVERT: A 412 LEU cc_start: 0.8709 (pt) cc_final: 0.8248 (pt) REVERT: A 417 MET cc_start: 0.7638 (tpp) cc_final: 0.7018 (tpp) REVERT: A 418 LYS cc_start: 0.7844 (ttmm) cc_final: 0.7602 (ttmm) REVERT: A 421 SER cc_start: 0.8578 (m) cc_final: 0.8148 (p) REVERT: A 429 ASP cc_start: 0.7985 (m-30) cc_final: 0.7678 (t70) REVERT: A 436 ASP cc_start: 0.7634 (t0) cc_final: 0.7416 (t0) REVERT: A 438 ASP cc_start: 0.8007 (m-30) cc_final: 0.7583 (m-30) REVERT: A 589 LYS cc_start: 0.7913 (ttmt) cc_final: 0.7452 (mtpp) outliers start: 46 outliers final: 34 residues processed: 258 average time/residue: 0.0785 time to fit residues: 28.5907 Evaluate side-chains 267 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 229 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 58 ASP Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 109 TYR Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 188 TYR Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 282 MET Chi-restraints excluded: chain B residue 302 ASN Chi-restraints excluded: chain B residue 424 LYS Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 451 LEU Chi-restraints excluded: chain B residue 484 SER Chi-restraints excluded: chain B residue 491 PHE Chi-restraints excluded: chain B residue 563 TRP Chi-restraints excluded: chain B residue 578 VAL Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 41 GLU Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 109 TYR Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 251 MET Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 326 HIS Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 484 SER Chi-restraints excluded: chain A residue 491 PHE Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 563 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 78 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 chunk 88 optimal weight: 0.6980 chunk 30 optimal weight: 0.8980 chunk 28 optimal weight: 0.7980 chunk 83 optimal weight: 5.9990 chunk 46 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 chunk 41 optimal weight: 0.6980 chunk 6 optimal weight: 0.8980 chunk 54 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 302 ASN ** A 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 128 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 = 0.3936 r_free = 0.3936 target = 0.157242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.138510 restraints weight = 13200.743| |-----------------------------------------------------------------------------| r_work (start): 0.3686 rms_B_bonded: 2.58 r_work: 0.3546 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7326 moved from start: 0.1851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8392 Z= 0.195 Angle : 0.576 7.906 11406 Z= 0.295 Chirality : 0.044 0.145 1304 Planarity : 0.004 0.034 1374 Dihedral : 5.245 54.771 1058 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 4.73 % Allowed : 26.99 % Favored : 68.28 % 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: 1.70 (0.28), residues: 966 helix: 1.77 (0.19), residues: 702 sheet: -0.76 (0.82), residues: 34 loop : -0.48 (0.47), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 54 TYR 0.008 0.001 TYR B 130 PHE 0.027 0.001 PHE A 232 TRP 0.008 0.001 TRP A 173 HIS 0.006 0.001 HIS B 326 Details of bonding type rmsd covalent geometry : bond 0.00434 ( 8392) covalent geometry : angle 0.57551 (11406) hydrogen bonds : bond 0.04196 ( 550) hydrogen bonds : angle 4.47578 ( 1614) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 234 time to evaluate : 0.307 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 13 VAL cc_start: 0.8658 (m) cc_final: 0.8358 (t) REVERT: B 35 ASN cc_start: 0.5790 (OUTLIER) cc_final: 0.3366 (m-40) REVERT: B 54 ARG cc_start: 0.8364 (tpp80) cc_final: 0.7975 (tpt-90) REVERT: B 55 ILE cc_start: 0.8974 (pt) cc_final: 0.8624 (mt) REVERT: B 68 GLN cc_start: 0.7372 (tp-100) cc_final: 0.6997 (tp-100) REVERT: B 84 LEU cc_start: 0.8783 (tp) cc_final: 0.8428 (tp) REVERT: B 129 ASN cc_start: 0.7665 (t0) cc_final: 0.7464 (t0) REVERT: B 135 ILE cc_start: 0.8648 (OUTLIER) cc_final: 0.8417 (mm) REVERT: B 140 PHE cc_start: 0.7667 (t80) cc_final: 0.7453 (t80) REVERT: B 144 ILE cc_start: 0.8491 (tp) cc_final: 0.8266 (tt) REVERT: B 172 PHE cc_start: 0.8156 (m-80) cc_final: 0.7908 (m-80) REVERT: B 212 MET cc_start: 0.8177 (mmm) cc_final: 0.7698 (tmm) REVERT: B 214 LYS cc_start: 0.8136 (mttt) cc_final: 0.7700 (mttp) REVERT: B 232 PHE cc_start: 0.7938 (t80) cc_final: 0.7539 (t80) REVERT: B 241 ILE cc_start: 0.8535 (tp) cc_final: 0.8201 (tp) REVERT: B 262 LEU cc_start: 0.8431 (OUTLIER) cc_final: 0.8018 (mm) REVERT: B 271 THR cc_start: 0.8209 (OUTLIER) cc_final: 0.7886 (m) REVERT: B 276 LYS cc_start: 0.8274 (ttmm) cc_final: 0.7832 (ttpp) REVERT: B 411 GLN cc_start: 0.8720 (pm20) cc_final: 0.8342 (pm20) REVERT: B 417 MET cc_start: 0.7632 (tpp) cc_final: 0.7339 (tpp) REVERT: B 421 SER cc_start: 0.8539 (m) cc_final: 0.8125 (p) REVERT: B 429 ASP cc_start: 0.8004 (m-30) cc_final: 0.7735 (t0) REVERT: B 438 ASP cc_start: 0.8032 (m-30) cc_final: 0.7787 (m-30) REVERT: B 569 TYR cc_start: 0.7901 (t80) cc_final: 0.7644 (t80) REVERT: B 574 GLU cc_start: 0.7397 (tm-30) cc_final: 0.6991 (tt0) REVERT: A 32 LYS cc_start: 0.8000 (tptt) cc_final: 0.7728 (tptp) REVERT: A 34 LEU cc_start: 0.6111 (pt) cc_final: 0.5480 (pp) REVERT: A 35 ASN cc_start: 0.5237 (OUTLIER) cc_final: 0.3154 (m110) REVERT: A 54 ARG cc_start: 0.8384 (tpp80) cc_final: 0.7992 (tpp80) REVERT: A 55 ILE cc_start: 0.8982 (pt) cc_final: 0.8687 (mt) REVERT: A 84 LEU cc_start: 0.8770 (tp) cc_final: 0.8506 (tp) REVERT: A 93 SER cc_start: 0.8266 (p) cc_final: 0.7952 (p) REVERT: A 104 LYS cc_start: 0.8155 (mppt) cc_final: 0.7648 (mmmm) REVERT: A 120 GLN cc_start: 0.7989 (mt0) cc_final: 0.7739 (mt0) REVERT: A 135 ILE cc_start: 0.8464 (mm) cc_final: 0.8238 (mm) REVERT: A 172 PHE cc_start: 0.8153 (m-80) cc_final: 0.7822 (m-80) REVERT: A 178 GLU cc_start: 0.7907 (tp30) cc_final: 0.7590 (tp30) REVERT: A 233 GLN cc_start: 0.8403 (mt0) cc_final: 0.8016 (mt0) REVERT: A 262 LEU cc_start: 0.8428 (OUTLIER) cc_final: 0.8064 (mm) REVERT: A 299 GLU cc_start: 0.7568 (mm-30) cc_final: 0.7223 (mm-30) REVERT: A 356 ASP cc_start: 0.8014 (t0) cc_final: 0.7739 (t0) REVERT: A 412 LEU cc_start: 0.8717 (pt) cc_final: 0.8239 (pt) REVERT: A 417 MET cc_start: 0.7689 (tpp) cc_final: 0.7044 (tpp) REVERT: A 418 LYS cc_start: 0.7874 (ttmm) cc_final: 0.7628 (ttmm) REVERT: A 421 SER cc_start: 0.8621 (m) cc_final: 0.8193 (p) REVERT: A 429 ASP cc_start: 0.7996 (m-30) cc_final: 0.7689 (t70) REVERT: A 438 ASP cc_start: 0.8043 (m-30) cc_final: 0.7719 (m-30) REVERT: A 589 LYS cc_start: 0.7967 (ttmt) cc_final: 0.7508 (mtpp) outliers start: 44 outliers final: 36 residues processed: 259 average time/residue: 0.0785 time to fit residues: 28.7721 Evaluate side-chains 273 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 231 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 58 ASP Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 109 TYR Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 282 MET Chi-restraints excluded: chain B residue 302 ASN Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain B residue 378 MET Chi-restraints excluded: chain B residue 424 LYS Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 451 LEU Chi-restraints excluded: chain B residue 484 SER Chi-restraints excluded: chain B residue 491 PHE Chi-restraints excluded: chain B residue 563 TRP Chi-restraints excluded: chain B residue 578 VAL Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 35 ASN Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 41 GLU Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 109 TYR Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 251 MET Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 326 HIS Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 484 SER Chi-restraints excluded: chain A residue 491 PHE Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 563 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 7 optimal weight: 0.9980 chunk 51 optimal weight: 0.7980 chunk 65 optimal weight: 0.9980 chunk 57 optimal weight: 0.8980 chunk 69 optimal weight: 0.9990 chunk 87 optimal weight: 0.6980 chunk 71 optimal weight: 0.7980 chunk 47 optimal weight: 0.5980 chunk 64 optimal weight: 0.5980 chunk 90 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 302 ASN ** A 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 128 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 = 0.3942 r_free = 0.3942 target = 0.157833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.139347 restraints weight = 13282.613| |-----------------------------------------------------------------------------| r_work (start): 0.3666 rms_B_bonded: 2.56 r_work: 0.3524 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7327 moved from start: 0.1924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 8392 Z= 0.182 Angle : 0.587 9.447 11406 Z= 0.298 Chirality : 0.044 0.147 1304 Planarity : 0.004 0.034 1374 Dihedral : 5.286 55.558 1058 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 4.73 % Allowed : 27.96 % Favored : 67.31 % 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: 1.61 (0.28), residues: 966 helix: 1.77 (0.19), residues: 702 sheet: -1.32 (0.79), residues: 38 loop : -0.67 (0.46), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 54 TYR 0.010 0.001 TYR B 488 PHE 0.028 0.001 PHE A 232 TRP 0.008 0.001 TRP A 173 HIS 0.006 0.001 HIS B 326 Details of bonding type rmsd covalent geometry : bond 0.00403 ( 8392) covalent geometry : angle 0.58653 (11406) hydrogen bonds : bond 0.04180 ( 550) hydrogen bonds : angle 4.45668 ( 1614) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 230 time to evaluate : 0.252 Fit side-chains revert: symmetry clash REVERT: B 13 VAL cc_start: 0.8665 (m) cc_final: 0.8460 (t) REVERT: B 34 LEU cc_start: 0.6651 (pt) cc_final: 0.5648 (pp) REVERT: B 35 ASN cc_start: 0.5654 (OUTLIER) cc_final: 0.3056 (m-40) REVERT: B 54 ARG cc_start: 0.8423 (tpp80) cc_final: 0.8035 (tpt-90) REVERT: B 55 ILE cc_start: 0.9004 (pt) cc_final: 0.8649 (mt) REVERT: B 68 GLN cc_start: 0.7429 (tp-100) cc_final: 0.7113 (tp-100) REVERT: B 84 LEU cc_start: 0.8772 (tp) cc_final: 0.8425 (tp) REVERT: B 135 ILE cc_start: 0.8655 (OUTLIER) cc_final: 0.8419 (mm) REVERT: B 140 PHE cc_start: 0.7645 (t80) cc_final: 0.7427 (t80) REVERT: B 144 ILE cc_start: 0.8459 (tp) cc_final: 0.8233 (tt) REVERT: B 172 PHE cc_start: 0.8147 (m-80) cc_final: 0.7895 (m-80) REVERT: B 212 MET cc_start: 0.8239 (mmm) cc_final: 0.7754 (tmm) REVERT: B 214 LYS cc_start: 0.8150 (mttt) cc_final: 0.7666 (mttp) REVERT: B 232 PHE cc_start: 0.7917 (t80) cc_final: 0.7515 (t80) REVERT: B 241 ILE cc_start: 0.8539 (tp) cc_final: 0.8204 (tp) REVERT: B 262 LEU cc_start: 0.8423 (OUTLIER) cc_final: 0.8009 (mm) REVERT: B 271 THR cc_start: 0.8197 (OUTLIER) cc_final: 0.7871 (m) REVERT: B 276 LYS cc_start: 0.8266 (ttmm) cc_final: 0.7810 (ttpp) REVERT: B 411 GLN cc_start: 0.8762 (pm20) cc_final: 0.8360 (pm20) REVERT: B 417 MET cc_start: 0.7604 (tpp) cc_final: 0.7302 (tpp) REVERT: B 421 SER cc_start: 0.8564 (m) cc_final: 0.8157 (p) REVERT: B 429 ASP cc_start: 0.8045 (m-30) cc_final: 0.7760 (t0) REVERT: B 438 ASP cc_start: 0.8044 (m-30) cc_final: 0.7812 (m-30) REVERT: B 569 TYR cc_start: 0.7870 (t80) cc_final: 0.7609 (t80) REVERT: B 574 GLU cc_start: 0.7463 (tm-30) cc_final: 0.7059 (tt0) REVERT: A 32 LYS cc_start: 0.7901 (tptt) cc_final: 0.7661 (tptp) REVERT: A 34 LEU cc_start: 0.6120 (pt) cc_final: 0.5474 (pp) REVERT: A 35 ASN cc_start: 0.5202 (OUTLIER) cc_final: 0.3127 (m110) REVERT: A 54 ARG cc_start: 0.8418 (tpp80) cc_final: 0.8026 (tpp80) REVERT: A 55 ILE cc_start: 0.8991 (pt) cc_final: 0.8701 (mt) REVERT: A 73 ILE cc_start: 0.7746 (OUTLIER) cc_final: 0.7041 (pt) REVERT: A 84 LEU cc_start: 0.8755 (tp) cc_final: 0.8473 (tp) REVERT: A 93 SER cc_start: 0.8281 (p) cc_final: 0.7966 (p) REVERT: A 104 LYS cc_start: 0.8151 (mppt) cc_final: 0.7637 (mmmm) REVERT: A 135 ILE cc_start: 0.8474 (mm) cc_final: 0.8235 (mm) REVERT: A 172 PHE cc_start: 0.8124 (m-80) cc_final: 0.7764 (m-80) REVERT: A 178 GLU cc_start: 0.7855 (tp30) cc_final: 0.7621 (tp30) REVERT: A 233 GLN cc_start: 0.8382 (mt0) cc_final: 0.8005 (mt0) REVERT: A 241 ILE cc_start: 0.8591 (tp) cc_final: 0.8277 (tp) REVERT: A 262 LEU cc_start: 0.8435 (OUTLIER) cc_final: 0.8052 (mm) REVERT: A 299 GLU cc_start: 0.7532 (mm-30) cc_final: 0.7184 (mm-30) REVERT: A 356 ASP cc_start: 0.8011 (t0) cc_final: 0.7734 (t0) REVERT: A 412 LEU cc_start: 0.8725 (pt) cc_final: 0.8261 (pt) REVERT: A 417 MET cc_start: 0.7662 (tpp) cc_final: 0.7016 (tpp) REVERT: A 418 LYS cc_start: 0.7917 (ttmm) cc_final: 0.7682 (ttmm) REVERT: A 421 SER cc_start: 0.8623 (m) cc_final: 0.8204 (p) REVERT: A 429 ASP cc_start: 0.7995 (m-30) cc_final: 0.7695 (t70) REVERT: A 438 ASP cc_start: 0.8072 (m-30) cc_final: 0.7727 (m-30) REVERT: A 589 LYS cc_start: 0.7976 (ttmt) cc_final: 0.7516 (mtpp) outliers start: 44 outliers final: 35 residues processed: 255 average time/residue: 0.0824 time to fit residues: 29.3859 Evaluate side-chains 269 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 227 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 58 ASP Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 109 TYR Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 282 MET Chi-restraints excluded: chain B residue 302 ASN Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain B residue 378 MET Chi-restraints excluded: chain B residue 424 LYS Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 451 LEU Chi-restraints excluded: chain B residue 484 SER Chi-restraints excluded: chain B residue 491 PHE Chi-restraints excluded: chain B residue 563 TRP Chi-restraints excluded: chain B residue 578 VAL Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 35 ASN Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 41 GLU Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 251 MET Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 326 HIS Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 484 SER Chi-restraints excluded: chain A residue 491 PHE Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 563 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 61 optimal weight: 0.1980 chunk 52 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 chunk 12 optimal weight: 0.1980 chunk 23 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 56 optimal weight: 0.4980 chunk 11 optimal weight: 0.0870 chunk 30 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 15 optimal weight: 0.0770 overall best weight: 0.2116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 117 ASN ** A 128 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 = 0.3955 r_free = 0.3955 target = 0.153766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.134978 restraints weight = 13107.000| |-----------------------------------------------------------------------------| r_work (start): 0.3736 rms_B_bonded: 2.58 r_work: 0.3600 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7278 moved from start: 0.1963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 8392 Z= 0.115 Angle : 0.563 9.287 11406 Z= 0.282 Chirality : 0.042 0.146 1304 Planarity : 0.004 0.034 1374 Dihedral : 5.204 55.714 1058 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 3.66 % Allowed : 29.14 % Favored : 67.20 % 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: 1.91 (0.28), residues: 966 helix: 1.95 (0.19), residues: 702 sheet: -0.45 (0.83), residues: 34 loop : -0.58 (0.46), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 54 TYR 0.007 0.001 TYR A 106 PHE 0.031 0.001 PHE B 66 TRP 0.007 0.001 TRP B 511 HIS 0.005 0.001 HIS B 326 Details of bonding type rmsd covalent geometry : bond 0.00236 ( 8392) covalent geometry : angle 0.56290 (11406) hydrogen bonds : bond 0.03843 ( 550) hydrogen bonds : angle 4.30350 ( 1614) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 238 time to evaluate : 0.201 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 13 VAL cc_start: 0.8639 (m) cc_final: 0.8424 (t) REVERT: B 34 LEU cc_start: 0.6459 (pt) cc_final: 0.5540 (pp) REVERT: B 35 ASN cc_start: 0.5254 (OUTLIER) cc_final: 0.3443 (m110) REVERT: B 54 ARG cc_start: 0.8395 (tpp80) cc_final: 0.8028 (tpt-90) REVERT: B 55 ILE cc_start: 0.9018 (pt) cc_final: 0.8661 (mt) REVERT: B 68 GLN cc_start: 0.7457 (tp-100) cc_final: 0.7126 (tp-100) REVERT: B 84 LEU cc_start: 0.8783 (tp) cc_final: 0.8424 (tp) REVERT: B 135 ILE cc_start: 0.8636 (OUTLIER) cc_final: 0.8395 (mm) REVERT: B 140 PHE cc_start: 0.7677 (t80) cc_final: 0.7395 (t80) REVERT: B 144 ILE cc_start: 0.8441 (tp) cc_final: 0.8211 (tt) REVERT: B 172 PHE cc_start: 0.8143 (m-80) cc_final: 0.7889 (m-80) REVERT: B 212 MET cc_start: 0.8172 (mmm) cc_final: 0.7727 (tmm) REVERT: B 214 LYS cc_start: 0.8099 (mttt) cc_final: 0.7801 (mttp) REVERT: B 232 PHE cc_start: 0.7917 (t80) cc_final: 0.7537 (t80) REVERT: B 241 ILE cc_start: 0.8523 (tp) cc_final: 0.8179 (tp) REVERT: B 255 LEU cc_start: 0.8015 (OUTLIER) cc_final: 0.7700 (mm) REVERT: B 262 LEU cc_start: 0.8400 (OUTLIER) cc_final: 0.7968 (mm) REVERT: B 271 THR cc_start: 0.8169 (OUTLIER) cc_final: 0.7831 (m) REVERT: B 276 LYS cc_start: 0.8255 (ttmm) cc_final: 0.7808 (ttpp) REVERT: B 288 HIS cc_start: 0.8917 (m170) cc_final: 0.8664 (m170) REVERT: B 411 GLN cc_start: 0.8756 (pm20) cc_final: 0.8363 (pm20) REVERT: B 417 MET cc_start: 0.7512 (tpp) cc_final: 0.7250 (tpp) REVERT: B 421 SER cc_start: 0.8533 (m) cc_final: 0.8106 (p) REVERT: B 429 ASP cc_start: 0.7945 (m-30) cc_final: 0.7648 (t0) REVERT: B 438 ASP cc_start: 0.8005 (m-30) cc_final: 0.7788 (m-30) REVERT: B 569 TYR cc_start: 0.7866 (t80) cc_final: 0.7595 (t80) REVERT: B 574 GLU cc_start: 0.7364 (tm-30) cc_final: 0.7018 (tt0) REVERT: B 589 LYS cc_start: 0.7853 (ttmt) cc_final: 0.7500 (mtpp) REVERT: A 32 LYS cc_start: 0.7859 (tptt) cc_final: 0.7630 (tptt) REVERT: A 34 LEU cc_start: 0.5936 (pt) cc_final: 0.5558 (pp) REVERT: A 54 ARG cc_start: 0.8408 (tpp80) cc_final: 0.8025 (tpp80) REVERT: A 55 ILE cc_start: 0.8993 (pt) cc_final: 0.8737 (mt) REVERT: A 73 ILE cc_start: 0.7650 (OUTLIER) cc_final: 0.6929 (pt) REVERT: A 84 LEU cc_start: 0.8765 (tp) cc_final: 0.8465 (tp) REVERT: A 93 SER cc_start: 0.8266 (p) cc_final: 0.7943 (p) REVERT: A 104 LYS cc_start: 0.8140 (mppt) cc_final: 0.7621 (mmmm) REVERT: A 135 ILE cc_start: 0.8425 (mm) cc_final: 0.8177 (mm) REVERT: A 144 ILE cc_start: 0.8323 (tp) cc_final: 0.8119 (tt) REVERT: A 172 PHE cc_start: 0.8138 (m-80) cc_final: 0.7788 (m-80) REVERT: A 178 GLU cc_start: 0.7737 (tp30) cc_final: 0.7400 (tp30) REVERT: A 211 ILE cc_start: 0.8273 (mt) cc_final: 0.7574 (tt) REVERT: A 214 LYS cc_start: 0.7999 (mtmt) cc_final: 0.7087 (mptt) REVERT: A 233 GLN cc_start: 0.8391 (mt0) cc_final: 0.8004 (mt0) REVERT: A 239 LEU cc_start: 0.8702 (tp) cc_final: 0.8492 (tt) REVERT: A 241 ILE cc_start: 0.8592 (tp) cc_final: 0.8278 (tp) REVERT: A 299 GLU cc_start: 0.7531 (mm-30) cc_final: 0.7159 (mm-30) REVERT: A 356 ASP cc_start: 0.7987 (t0) cc_final: 0.7692 (t0) REVERT: A 412 LEU cc_start: 0.8706 (pt) cc_final: 0.8285 (pt) REVERT: A 417 MET cc_start: 0.7580 (tpp) cc_final: 0.6956 (tpp) REVERT: A 418 LYS cc_start: 0.7855 (ttmm) cc_final: 0.7607 (ttmm) REVERT: A 421 SER cc_start: 0.8562 (m) cc_final: 0.8130 (p) REVERT: A 429 ASP cc_start: 0.7986 (m-30) cc_final: 0.7699 (t70) REVERT: A 436 ASP cc_start: 0.7673 (t0) cc_final: 0.7448 (t0) REVERT: A 438 ASP cc_start: 0.8039 (m-30) cc_final: 0.7607 (m-30) REVERT: A 569 TYR cc_start: 0.7778 (t80) cc_final: 0.7525 (t80) REVERT: A 589 LYS cc_start: 0.7939 (ttmt) cc_final: 0.7490 (mtpp) outliers start: 34 outliers final: 21 residues processed: 257 average time/residue: 0.0787 time to fit residues: 28.3275 Evaluate side-chains 259 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 232 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 58 ASP Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 282 MET Chi-restraints excluded: chain B residue 451 LEU Chi-restraints excluded: chain B residue 484 SER Chi-restraints excluded: chain B residue 491 PHE Chi-restraints excluded: chain B residue 578 VAL Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 251 MET Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 326 HIS Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 491 PHE Chi-restraints excluded: chain A residue 529 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 77 optimal weight: 0.5980 chunk 36 optimal weight: 0.0980 chunk 32 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 25 optimal weight: 0.4980 chunk 11 optimal weight: 0.5980 chunk 23 optimal weight: 0.0870 chunk 38 optimal weight: 0.7980 chunk 12 optimal weight: 0.4980 chunk 6 optimal weight: 0.0170 chunk 56 optimal weight: 0.6980 overall best weight: 0.2396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 89 HIS ** A 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 128 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 = 0.3989 r_free = 0.3989 target = 0.161488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.142958 restraints weight = 13203.450| |-----------------------------------------------------------------------------| r_work (start): 0.3712 rms_B_bonded: 2.58 r_work: 0.3568 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7276 moved from start: 0.2066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8392 Z= 0.117 Angle : 0.565 10.357 11406 Z= 0.283 Chirality : 0.042 0.143 1304 Planarity : 0.004 0.032 1374 Dihedral : 5.004 54.851 1056 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.80 % Allowed : 30.75 % Favored : 66.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.90 (0.28), residues: 966 helix: 1.98 (0.19), residues: 714 sheet: -0.84 (0.80), residues: 44 loop : -0.78 (0.47), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 54 TYR 0.016 0.001 TYR A 531 PHE 0.040 0.001 PHE B 66 TRP 0.013 0.001 TRP A 563 HIS 0.005 0.001 HIS B 326 Details of bonding type rmsd covalent geometry : bond 0.00245 ( 8392) covalent geometry : angle 0.56470 (11406) hydrogen bonds : bond 0.03714 ( 550) hydrogen bonds : angle 4.22552 ( 1614) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1780.53 seconds wall clock time: 31 minutes 25.39 seconds (1885.39 seconds total)