Starting phenix.real_space_refine on Fri Aug 22 15:46:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jin_36321/08_2025/8jin_36321.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jin_36321/08_2025/8jin_36321.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jin_36321/08_2025/8jin_36321.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jin_36321/08_2025/8jin_36321.map" model { file = "/net/cci-nas-00/data/ceres_data/8jin_36321/08_2025/8jin_36321.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jin_36321/08_2025/8jin_36321.cif" } resolution = 2.45 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 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 22 5.16 5 C 3318 2.51 5 N 889 2.21 5 O 1020 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 39 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 5249 Number of models: 1 Model: "" Number of chains: 3 Chain: "P" Number of atoms: 1764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1764 Classifications: {'peptide': 235} Link IDs: {'PTRANS': 11, 'TRANS': 223} Chain breaks: 1 Chain: "B" Number of atoms: 1907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1907 Classifications: {'peptide': 247} Link IDs: {'PTRANS': 10, 'TRANS': 236} Chain breaks: 1 Chain: "A" Number of atoms: 1578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1578 Classifications: {'peptide': 199} Link IDs: {'PTRANS': 13, 'TRANS': 185} Time building chain proxies: 1.28, per 1000 atoms: 0.24 Number of scatterers: 5249 At special positions: 0 Unit cell: (97.58, 78.54, 115.43, 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 22 16.00 O 1020 8.00 N 889 7.00 C 3318 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS P 22 " - pdb=" SG CYS P 89 " distance=2.03 Simple disulfide: pdb=" SG CYS P 146 " - pdb=" SG CYS P 220 " distance=2.03 Simple disulfide: pdb=" SG CYS B 145 " - pdb=" SG CYS B 221 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.40 Conformation dependent library (CDL) restraints added in 149.8 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 1342 Ramachandran restraints generated. 671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1228 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 14 sheets defined 6.2% alpha, 28.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing helix chain 'B' and resid 230 through 235 removed outlier: 4.424A pdb=" N GLY B 234 " --> pdb=" O ASP B 230 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N LEU B 235 " --> pdb=" O ILE B 231 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 230 through 235' Processing helix chain 'B' and resid 239 through 246 Processing helix chain 'A' and resid 337 through 341 Processing helix chain 'A' and resid 367 through 371 removed outlier: 3.676A pdb=" N PHE A 371 " --> pdb=" O ILE A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 390 removed outlier: 3.729A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU A 390 " --> pdb=" O LEU A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.776A pdb=" N SER A 408 " --> pdb=" O ASN A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 421 removed outlier: 3.705A pdb=" N TYR A 421 " --> pdb=" O ASN A 417 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'P' and resid 11 through 12 removed outlier: 3.567A pdb=" N GLY P 12 " --> pdb=" O THR P 107 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'P' and resid 18 through 23 removed outlier: 3.627A pdb=" N SER P 71 " --> pdb=" O SER P 68 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'P' and resid 46 through 49 removed outlier: 6.503A pdb=" N TRP P 36 " --> pdb=" O LEU P 48 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'P' and resid 90 through 93 removed outlier: 3.682A pdb=" N ASN P 97 " --> pdb=" O ASP P 93 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'P' and resid 192 through 197 removed outlier: 3.558A pdb=" N SER P 202 " --> pdb=" O ASP P 197 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N SER P 149 " --> pdb=" O GLN P 127 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLN P 127 " --> pdb=" O SER P 149 " (cutoff:3.500A) removed outlier: 8.299A pdb=" N LEU P 128 " --> pdb=" O GLN P 243 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'P' and resid 158 through 163 removed outlier: 6.964A pdb=" N MET P 158 " --> pdb=" O VAL P 174 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N VAL P 174 " --> pdb=" O MET P 158 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N TRP P 160 " --> pdb=" O VAL P 172 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'P' and resid 222 through 223 removed outlier: 3.615A pdb=" N VAL P 240 " --> pdb=" O LYS P 222 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 10 through 11 removed outlier: 6.342A pdb=" N PHE B 99 " --> pdb=" O GLN B 90 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N GLN B 90 " --> pdb=" O PHE B 99 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N GLN B 101 " --> pdb=" O CYS B 88 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N CYS B 88 " --> pdb=" O GLN B 101 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N LEU B 33 " --> pdb=" O TYR B 49 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N TYR B 49 " --> pdb=" O LEU B 33 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N TRP B 35 " --> pdb=" O LEU B 47 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 20 through 29 removed outlier: 5.656A pdb=" N THR B 69 " --> pdb=" O ALA B 25 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 127 through 130 removed outlier: 3.671A pdb=" N LEU B 141 " --> pdb=" O MET B 208 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N SER B 196 " --> pdb=" O TYR B 205 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 183 through 185 removed outlier: 6.440A pdb=" N LEU B 168 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N ALA B 163 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N TRP B 170 " --> pdb=" O ARG B 161 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N ARG B 161 " --> pdb=" O TRP B 170 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLY B 172 " --> pdb=" O TRP B 159 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N ALA B 156 " --> pdb=" O ASP B 224 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 356 through 358 removed outlier: 3.550A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB5, first strand: chain 'A' and resid 473 through 474 131 hydrogen bonds defined for protein. 333 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.62 Time building geometry restraints manager: 0.55 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: 1694 1.34 - 1.46: 1332 1.46 - 1.58: 2330 1.58 - 1.69: 0 1.69 - 1.81: 28 Bond restraints: 5384 Sorted by residual: bond pdb=" CA GLY P 69 " pdb=" C GLY P 69 " ideal model delta sigma weight residual 1.514 1.530 -0.016 1.41e-02 5.03e+03 1.27e+00 bond pdb=" N GLY P 69 " pdb=" CA GLY P 69 " ideal model delta sigma weight residual 1.449 1.464 -0.015 1.45e-02 4.76e+03 1.04e+00 bond pdb=" C SER B 14 " pdb=" N PRO B 15 " ideal model delta sigma weight residual 1.330 1.340 -0.010 1.25e-02 6.40e+03 6.18e-01 bond pdb=" C SER P 68 " pdb=" N GLY P 69 " ideal model delta sigma weight residual 1.331 1.320 0.010 1.46e-02 4.69e+03 5.14e-01 bond pdb=" C GLY P 69 " pdb=" O GLY P 69 " ideal model delta sigma weight residual 1.235 1.225 0.009 1.35e-02 5.49e+03 4.82e-01 ... (remaining 5379 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.05: 6949 1.05 - 2.10: 287 2.10 - 3.16: 52 3.16 - 4.21: 20 4.21 - 5.26: 7 Bond angle restraints: 7315 Sorted by residual: angle pdb=" N ALA A 372 " pdb=" CA ALA A 372 " pdb=" C ALA A 372 " ideal model delta sigma weight residual 108.22 110.48 -2.26 9.00e-01 1.23e+00 6.33e+00 angle pdb=" N THR A 523 " pdb=" CA THR A 523 " pdb=" C THR A 523 " ideal model delta sigma weight residual 114.39 110.82 3.57 1.45e+00 4.76e-01 6.06e+00 angle pdb=" N ASP A 420 " pdb=" CA ASP A 420 " pdb=" C ASP A 420 " ideal model delta sigma weight residual 114.39 110.91 3.48 1.45e+00 4.76e-01 5.77e+00 angle pdb=" N ALA A 419 " pdb=" CA ALA A 419 " pdb=" C ALA A 419 " ideal model delta sigma weight residual 113.89 110.14 3.75 1.58e+00 4.01e-01 5.65e+00 angle pdb=" C SER P 51 " pdb=" N ASN P 52 " pdb=" CA ASN P 52 " ideal model delta sigma weight residual 121.54 125.97 -4.43 1.91e+00 2.74e-01 5.38e+00 ... (remaining 7310 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.56: 2981 17.56 - 35.12: 146 35.12 - 52.68: 23 52.68 - 70.23: 5 70.23 - 87.79: 1 Dihedral angle restraints: 3156 sinusoidal: 1208 harmonic: 1948 Sorted by residual: dihedral pdb=" CA GLN P 137 " pdb=" C GLN P 137 " pdb=" N PRO P 138 " pdb=" CA PRO P 138 " ideal model delta harmonic sigma weight residual -180.00 -153.15 -26.85 0 5.00e+00 4.00e-02 2.88e+01 dihedral pdb=" CA ARG B 91 " pdb=" CB ARG B 91 " pdb=" CG ARG B 91 " pdb=" CD ARG B 91 " ideal model delta sinusoidal sigma weight residual -180.00 -121.51 -58.49 3 1.50e+01 4.44e-03 9.47e+00 dihedral pdb=" N LEU B 141 " pdb=" CA LEU B 141 " pdb=" CB LEU B 141 " pdb=" CG LEU B 141 " ideal model delta sinusoidal sigma weight residual -60.00 -118.06 58.06 3 1.50e+01 4.44e-03 9.46e+00 ... (remaining 3153 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 421 0.026 - 0.053: 227 0.053 - 0.079: 73 0.079 - 0.105: 34 0.105 - 0.131: 21 Chirality restraints: 776 Sorted by residual: chirality pdb=" CA ILE B 75 " pdb=" N ILE B 75 " pdb=" C ILE B 75 " pdb=" CB ILE B 75 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.32e-01 chirality pdb=" CA VAL B 258 " pdb=" N VAL B 258 " pdb=" C VAL B 258 " pdb=" CB VAL B 258 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.18e-01 chirality pdb=" CA ILE B 174 " pdb=" N ILE B 174 " pdb=" C ILE B 174 " pdb=" CB ILE B 174 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.59e-01 ... (remaining 773 not shown) Planarity restraints: 950 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER B 236 " 0.026 5.00e-02 4.00e+02 3.92e-02 2.46e+00 pdb=" N PRO B 237 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO B 237 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 237 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS B 136 " -0.020 5.00e-02 4.00e+02 2.96e-02 1.41e+00 pdb=" N PRO B 137 " 0.051 5.00e-02 4.00e+02 pdb=" CA PRO B 137 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO B 137 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN P 137 " -0.019 5.00e-02 4.00e+02 2.81e-02 1.27e+00 pdb=" N PRO P 138 " 0.049 5.00e-02 4.00e+02 pdb=" CA PRO P 138 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO P 138 " -0.015 5.00e-02 4.00e+02 ... (remaining 947 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 579 2.75 - 3.29: 4939 3.29 - 3.83: 8570 3.83 - 4.36: 10412 4.36 - 4.90: 18142 Nonbonded interactions: 42642 Sorted by model distance: nonbonded pdb=" O ASN A 439 " pdb=" OG SER A 443 " model vdw 2.214 3.040 nonbonded pdb=" O THR B 5 " pdb=" NH1 ARG B 24 " model vdw 2.296 3.120 nonbonded pdb=" N VAL P 34 " pdb=" OD1 ASN P 52 " model vdw 2.305 3.120 nonbonded pdb=" OE1 GLN B 37 " pdb=" NH2 ARG B 45 " model vdw 2.320 3.120 nonbonded pdb=" O GLY P 24 " pdb=" OG1 THR P 70 " model vdw 2.320 3.040 ... (remaining 42637 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 11.000 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: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.480 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7371 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 : 0.002 0.029 5390 Z= 0.117 Angle : 0.537 5.260 7327 Z= 0.309 Chirality : 0.041 0.131 776 Planarity : 0.004 0.039 950 Dihedral : 10.470 87.791 1910 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.15 % Favored : 92.70 % Rotamer: Outliers : 5.49 % Allowed : 7.08 % Favored : 87.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.97 (0.29), residues: 671 helix: -3.92 (0.64), residues: 28 sheet: -2.22 (0.34), residues: 222 loop : -2.91 (0.26), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 161 TYR 0.007 0.001 TYR B 220 PHE 0.006 0.001 PHE P 151 TRP 0.010 0.001 TRP P 98 HIS 0.001 0.000 HIS P 159 Details of bonding type rmsd covalent geometry : bond 0.00221 ( 5384) covalent geometry : angle 0.53730 ( 7315) SS BOND : bond 0.00173 ( 6) SS BOND : angle 0.49088 ( 12) hydrogen bonds : bond 0.26391 ( 131) hydrogen bonds : angle 10.72137 ( 333) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1342 Ramachandran restraints generated. 671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1342 Ramachandran restraints generated. 671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 173 time to evaluate : 0.143 Fit side-chains REVERT: P 27 SER cc_start: 0.8133 (m) cc_final: 0.7378 (t) REVERT: P 94 ASP cc_start: 0.6541 (p0) cc_final: 0.6073 (p0) REVERT: P 193 SER cc_start: 0.7817 (t) cc_final: 0.7509 (p) REVERT: P 236 TYR cc_start: 0.8392 (p90) cc_final: 0.7669 (p90) REVERT: B 38 GLN cc_start: 0.8189 (tt0) cc_final: 0.7899 (tt0) REVERT: B 42 GLN cc_start: 0.7066 (mp10) cc_final: 0.6814 (mp10) REVERT: B 56 THR cc_start: 0.8437 (m) cc_final: 0.8218 (p) REVERT: B 97 TYR cc_start: 0.7886 (m-80) cc_final: 0.7498 (m-80) REVERT: B 108 LYS cc_start: 0.4909 (OUTLIER) cc_final: 0.4679 (ptpp) REVERT: B 141 LEU cc_start: 0.8128 (OUTLIER) cc_final: 0.7914 (tt) REVERT: B 196 SER cc_start: 0.8343 (p) cc_final: 0.8090 (t) REVERT: B 249 VAL cc_start: 0.8797 (t) cc_final: 0.8494 (m) REVERT: B 256 VAL cc_start: 0.8036 (t) cc_final: 0.7670 (m) REVERT: A 331 ASN cc_start: 0.6755 (OUTLIER) cc_final: 0.6386 (t0) REVERT: A 380 TYR cc_start: 0.8382 (m-80) cc_final: 0.8094 (m-80) REVERT: A 386 LYS cc_start: 0.8376 (mtmt) cc_final: 0.8144 (mtmt) REVERT: A 440 LYS cc_start: 0.7833 (mppt) cc_final: 0.7561 (mppt) REVERT: A 450 ASN cc_start: 0.8451 (m-40) cc_final: 0.7963 (m-40) REVERT: A 470 THR cc_start: 0.9001 (p) cc_final: 0.8798 (t) REVERT: A 472 ILE cc_start: 0.8203 (OUTLIER) cc_final: 0.7956 (mm) REVERT: A 501 TYR cc_start: 0.7261 (m-10) cc_final: 0.6892 (m-10) outliers start: 31 outliers final: 9 residues processed: 191 average time/residue: 0.3736 time to fit residues: 75.1817 Evaluate side-chains 148 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 135 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 86 ASP Chi-restraints excluded: chain P residue 89 CYS Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 108 LYS Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 478 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 49 optimal weight: 0.8980 chunk 53 optimal weight: 0.3980 chunk 5 optimal weight: 0.0060 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 0.4980 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.5980 chunk 38 optimal weight: 0.4980 chunk 61 optimal weight: 0.0030 chunk 45 optimal weight: 0.0770 chunk 27 optimal weight: 0.3980 overall best weight: 0.1764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 35 ASN P 80 GLN P 97 ASN P 127 GLN P 206 GLN P 208 ASN B 53 ASN B 89 GLN B 96 GLN B 162 GLN A 394 ASN A 417 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 439 ASN A 474 GLN A 477 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.133601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.125833 restraints weight = 8077.558| |-----------------------------------------------------------------------------| r_work (start): 0.3861 rms_B_bonded: 1.74 r_work: 0.3781 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3663 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.1820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 5390 Z= 0.144 Angle : 0.603 7.519 7327 Z= 0.298 Chirality : 0.045 0.154 776 Planarity : 0.004 0.042 950 Dihedral : 6.403 58.220 783 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.60 % Favored : 92.25 % Rotamer: Outliers : 6.19 % Allowed : 17.35 % Favored : 76.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.13 (0.31), residues: 671 helix: -3.63 (0.65), residues: 28 sheet: -1.51 (0.35), residues: 228 loop : -2.39 (0.28), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 197 TYR 0.020 0.001 TYR P 226 PHE 0.010 0.001 PHE B 173 TRP 0.008 0.001 TRP A 436 HIS 0.002 0.001 HIS P 159 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 5384) covalent geometry : angle 0.60325 ( 7315) SS BOND : bond 0.00140 ( 6) SS BOND : angle 0.69111 ( 12) hydrogen bonds : bond 0.03901 ( 131) hydrogen bonds : angle 6.30828 ( 333) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1342 Ramachandran restraints generated. 671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1342 Ramachandran restraints generated. 671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 160 time to evaluate : 0.175 Fit side-chains REVERT: P 27 SER cc_start: 0.8328 (m) cc_final: 0.7915 (t) REVERT: P 94 ASP cc_start: 0.6965 (p0) cc_final: 0.6632 (p0) REVERT: P 236 TYR cc_start: 0.8397 (p90) cc_final: 0.7859 (p90) REVERT: B 11 LEU cc_start: 0.7220 (mt) cc_final: 0.6829 (mt) REVERT: B 17 GLU cc_start: 0.5854 (OUTLIER) cc_final: 0.5598 (tm-30) REVERT: B 38 GLN cc_start: 0.8109 (tt0) cc_final: 0.7872 (tt0) REVERT: B 39 LYS cc_start: 0.8348 (mmtm) cc_final: 0.8127 (mmmm) REVERT: B 58 ILE cc_start: 0.6405 (OUTLIER) cc_final: 0.6197 (pt) REVERT: B 97 TYR cc_start: 0.8240 (m-80) cc_final: 0.7726 (m-80) REVERT: B 108 LYS cc_start: 0.6867 (OUTLIER) cc_final: 0.6214 (ptpp) REVERT: B 196 SER cc_start: 0.8717 (p) cc_final: 0.8509 (t) REVERT: A 440 LYS cc_start: 0.8148 (mppt) cc_final: 0.7885 (mppt) REVERT: A 472 ILE cc_start: 0.8438 (OUTLIER) cc_final: 0.8221 (mm) REVERT: A 501 TYR cc_start: 0.7712 (m-10) cc_final: 0.7497 (m-10) outliers start: 35 outliers final: 19 residues processed: 176 average time/residue: 0.3891 time to fit residues: 72.1416 Evaluate side-chains 163 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 140 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 86 ASP Chi-restraints excluded: chain P residue 89 CYS Chi-restraints excluded: chain P residue 129 VAL Chi-restraints excluded: chain P residue 212 THR Chi-restraints excluded: chain P residue 245 THR Chi-restraints excluded: chain P residue 250 SER Chi-restraints excluded: chain B residue 17 GLU Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 90 GLN Chi-restraints excluded: chain B residue 108 LYS Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 130 SER Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 424 LYS Chi-restraints excluded: chain A residue 444 LYS Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 478 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 38 optimal weight: 0.0570 chunk 3 optimal weight: 0.8980 chunk 40 optimal weight: 0.8980 chunk 14 optimal weight: 0.6980 chunk 16 optimal weight: 0.8980 chunk 23 optimal weight: 0.0370 chunk 53 optimal weight: 0.8980 chunk 32 optimal weight: 0.2980 chunk 1 optimal weight: 0.4980 chunk 46 optimal weight: 0.3980 chunk 17 optimal weight: 0.0870 overall best weight: 0.1754 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 89 GLN B 96 GLN B 162 GLN B 207 GLN A 370 ASN A 394 ASN A 448 ASN A 487 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.130629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.123223 restraints weight = 8102.051| |-----------------------------------------------------------------------------| r_work (start): 0.3860 rms_B_bonded: 1.69 r_work: 0.3781 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3663 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.2265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 5390 Z= 0.146 Angle : 0.627 9.909 7327 Z= 0.305 Chirality : 0.045 0.198 776 Planarity : 0.004 0.038 950 Dihedral : 5.988 42.784 779 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.30 % Favored : 92.55 % Rotamer: Outliers : 7.08 % Allowed : 18.23 % Favored : 74.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.64 (0.31), residues: 671 helix: -2.35 (0.92), residues: 22 sheet: -1.02 (0.37), residues: 217 loop : -2.22 (0.28), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG P 17 TYR 0.019 0.001 TYR P 226 PHE 0.009 0.001 PHE B 99 TRP 0.010 0.001 TRP A 436 HIS 0.002 0.001 HIS P 156 Details of bonding type rmsd covalent geometry : bond 0.00330 ( 5384) covalent geometry : angle 0.62148 ( 7315) SS BOND : bond 0.00273 ( 6) SS BOND : angle 2.12470 ( 12) hydrogen bonds : bond 0.03263 ( 131) hydrogen bonds : angle 5.95428 ( 333) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1342 Ramachandran restraints generated. 671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1342 Ramachandran restraints generated. 671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 131 time to evaluate : 0.122 Fit side-chains REVERT: P 27 SER cc_start: 0.8330 (m) cc_final: 0.7875 (t) REVERT: P 94 ASP cc_start: 0.6922 (p0) cc_final: 0.6541 (p0) REVERT: P 236 TYR cc_start: 0.8401 (p90) cc_final: 0.7835 (p90) REVERT: B 11 LEU cc_start: 0.7204 (mt) cc_final: 0.6936 (mt) REVERT: B 17 GLU cc_start: 0.5812 (OUTLIER) cc_final: 0.5565 (tm-30) REVERT: B 38 GLN cc_start: 0.8093 (tt0) cc_final: 0.7842 (tt0) REVERT: B 91 ARG cc_start: 0.8266 (mtp85) cc_final: 0.8041 (mtp85) REVERT: B 97 TYR cc_start: 0.8190 (m-80) cc_final: 0.7670 (m-80) REVERT: B 108 LYS cc_start: 0.6862 (OUTLIER) cc_final: 0.6243 (ptpp) REVERT: B 127 LEU cc_start: 0.8571 (OUTLIER) cc_final: 0.8297 (pt) REVERT: B 130 SER cc_start: 0.8125 (p) cc_final: 0.7807 (m) REVERT: B 196 SER cc_start: 0.8730 (p) cc_final: 0.8516 (t) REVERT: B 197 ARG cc_start: 0.8723 (OUTLIER) cc_final: 0.8443 (ptp-110) REVERT: B 208 MET cc_start: 0.8066 (mtt) cc_final: 0.7817 (mtt) REVERT: A 423 TYR cc_start: 0.8083 (t80) cc_final: 0.7861 (t80) REVERT: A 440 LYS cc_start: 0.8219 (mppt) cc_final: 0.7946 (mppt) REVERT: A 472 ILE cc_start: 0.8456 (OUTLIER) cc_final: 0.8236 (mm) outliers start: 40 outliers final: 20 residues processed: 153 average time/residue: 0.4276 time to fit residues: 68.6037 Evaluate side-chains 151 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 126 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 5 THR Chi-restraints excluded: chain P residue 86 ASP Chi-restraints excluded: chain P residue 99 VAL Chi-restraints excluded: chain P residue 107 THR Chi-restraints excluded: chain P residue 129 VAL Chi-restraints excluded: chain P residue 212 THR Chi-restraints excluded: chain B residue 17 GLU Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 90 GLN Chi-restraints excluded: chain B residue 108 LYS Chi-restraints excluded: chain B residue 126 GLN Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 424 LYS Chi-restraints excluded: chain A residue 444 LYS Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 478 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 34 optimal weight: 0.9980 chunk 15 optimal weight: 0.6980 chunk 53 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 chunk 44 optimal weight: 0.0980 chunk 1 optimal weight: 0.5980 chunk 61 optimal weight: 0.3980 chunk 37 optimal weight: 0.7980 chunk 49 optimal weight: 0.5980 chunk 56 optimal weight: 0.6980 chunk 63 optimal weight: 0.4980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 32 ASN B 89 GLN B 96 GLN B 126 GLN B 162 GLN B 207 GLN A 370 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 487 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.128955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.121672 restraints weight = 8034.786| |-----------------------------------------------------------------------------| r_work (start): 0.3811 rms_B_bonded: 1.65 r_work: 0.3730 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3612 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.2745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.072 5390 Z= 0.308 Angle : 0.728 11.272 7327 Z= 0.361 Chirality : 0.049 0.257 776 Planarity : 0.005 0.041 950 Dihedral : 6.630 45.778 778 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.30 % Allowed : 9.69 % Favored : 90.01 % Rotamer: Outliers : 9.03 % Allowed : 17.35 % Favored : 73.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.75 (0.31), residues: 671 helix: -3.21 (0.73), residues: 34 sheet: -1.08 (0.35), residues: 235 loop : -2.24 (0.29), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 45 TYR 0.022 0.002 TYR P 226 PHE 0.018 0.002 PHE A 515 TRP 0.015 0.002 TRP A 436 HIS 0.004 0.001 HIS P 159 Details of bonding type rmsd covalent geometry : bond 0.00700 ( 5384) covalent geometry : angle 0.71999 ( 7315) SS BOND : bond 0.00478 ( 6) SS BOND : angle 2.76927 ( 12) hydrogen bonds : bond 0.03510 ( 131) hydrogen bonds : angle 6.21841 ( 333) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1342 Ramachandran restraints generated. 671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1342 Ramachandran restraints generated. 671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 125 time to evaluate : 0.134 Fit side-chains REVERT: P 27 SER cc_start: 0.8274 (m) cc_final: 0.7675 (t) REVERT: P 94 ASP cc_start: 0.6967 (p0) cc_final: 0.6549 (p0) REVERT: P 236 TYR cc_start: 0.8505 (p90) cc_final: 0.7958 (p90) REVERT: B 11 LEU cc_start: 0.7208 (mt) cc_final: 0.6803 (mt) REVERT: B 38 GLN cc_start: 0.8178 (tt0) cc_final: 0.7925 (tt0) REVERT: B 97 TYR cc_start: 0.8265 (m-80) cc_final: 0.7715 (m-80) REVERT: B 106 GLU cc_start: 0.6959 (pm20) cc_final: 0.6744 (pm20) REVERT: B 108 LYS cc_start: 0.6914 (OUTLIER) cc_final: 0.6250 (ptpp) REVERT: B 127 LEU cc_start: 0.8711 (OUTLIER) cc_final: 0.8491 (pt) REVERT: B 130 SER cc_start: 0.8204 (p) cc_final: 0.7908 (m) REVERT: B 196 SER cc_start: 0.8716 (p) cc_final: 0.8511 (t) REVERT: B 197 ARG cc_start: 0.8902 (OUTLIER) cc_final: 0.8426 (ptp-110) REVERT: B 252 GLN cc_start: 0.7741 (mp10) cc_final: 0.7371 (mp10) REVERT: A 405 ASN cc_start: 0.7759 (m-40) cc_final: 0.7512 (m-40) REVERT: A 440 LYS cc_start: 0.8269 (mppt) cc_final: 0.8013 (mppt) REVERT: A 468 ILE cc_start: 0.8531 (OUTLIER) cc_final: 0.8287 (mm) REVERT: A 472 ILE cc_start: 0.8547 (OUTLIER) cc_final: 0.8291 (mm) outliers start: 51 outliers final: 25 residues processed: 156 average time/residue: 0.4524 time to fit residues: 74.1064 Evaluate side-chains 152 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 122 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 5 THR Chi-restraints excluded: chain P residue 19 THR Chi-restraints excluded: chain P residue 86 ASP Chi-restraints excluded: chain P residue 99 VAL Chi-restraints excluded: chain P residue 107 THR Chi-restraints excluded: chain P residue 129 VAL Chi-restraints excluded: chain P residue 130 GLU Chi-restraints excluded: chain P residue 131 SER Chi-restraints excluded: chain P residue 195 SER Chi-restraints excluded: chain P residue 212 THR Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 90 GLN Chi-restraints excluded: chain B residue 108 LYS Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 424 LYS Chi-restraints excluded: chain A residue 444 LYS Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 478 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 24 optimal weight: 0.6980 chunk 34 optimal weight: 0.9980 chunk 17 optimal weight: 0.1980 chunk 45 optimal weight: 0.3980 chunk 26 optimal weight: 0.6980 chunk 16 optimal weight: 0.7980 chunk 29 optimal weight: 0.4980 chunk 7 optimal weight: 0.9990 chunk 28 optimal weight: 0.0670 chunk 48 optimal weight: 0.5980 chunk 33 optimal weight: 0.0270 overall best weight: 0.2376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 52 ASN B 89 GLN B 96 GLN B 162 GLN B 207 GLN A 370 ASN A 422 ASN A 487 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.130442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.122901 restraints weight = 8167.763| |-----------------------------------------------------------------------------| r_work (start): 0.3826 rms_B_bonded: 1.69 r_work: 0.3745 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3626 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.2822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 5390 Z= 0.185 Angle : 0.647 9.228 7327 Z= 0.320 Chirality : 0.047 0.246 776 Planarity : 0.004 0.040 950 Dihedral : 6.364 48.785 778 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.45 % Favored : 92.40 % Rotamer: Outliers : 7.79 % Allowed : 19.47 % Favored : 72.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.38 (0.32), residues: 671 helix: -2.54 (0.88), residues: 28 sheet: -0.68 (0.35), residues: 239 loop : -2.16 (0.29), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 45 TYR 0.022 0.001 TYR P 226 PHE 0.010 0.002 PHE B 99 TRP 0.017 0.002 TRP B 94 HIS 0.002 0.001 HIS P 159 Details of bonding type rmsd covalent geometry : bond 0.00424 ( 5384) covalent geometry : angle 0.63793 ( 7315) SS BOND : bond 0.00559 ( 6) SS BOND : angle 2.73800 ( 12) hydrogen bonds : bond 0.03070 ( 131) hydrogen bonds : angle 5.92514 ( 333) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1342 Ramachandran restraints generated. 671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1342 Ramachandran restraints generated. 671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 125 time to evaluate : 0.208 Fit side-chains REVERT: P 27 SER cc_start: 0.8388 (m) cc_final: 0.7810 (t) REVERT: P 94 ASP cc_start: 0.6908 (p0) cc_final: 0.6500 (p0) REVERT: P 236 TYR cc_start: 0.8454 (p90) cc_final: 0.7886 (p90) REVERT: B 11 LEU cc_start: 0.7197 (mt) cc_final: 0.6919 (mt) REVERT: B 38 GLN cc_start: 0.8119 (tt0) cc_final: 0.7886 (tt0) REVERT: B 58 ILE cc_start: 0.6271 (OUTLIER) cc_final: 0.6019 (pt) REVERT: B 97 TYR cc_start: 0.8177 (m-80) cc_final: 0.7740 (m-80) REVERT: B 108 LYS cc_start: 0.6869 (OUTLIER) cc_final: 0.6230 (ptpp) REVERT: B 127 LEU cc_start: 0.8630 (OUTLIER) cc_final: 0.8411 (pt) REVERT: B 130 SER cc_start: 0.8142 (p) cc_final: 0.7857 (m) REVERT: B 173 PHE cc_start: 0.8197 (OUTLIER) cc_final: 0.7972 (p90) REVERT: B 197 ARG cc_start: 0.8846 (OUTLIER) cc_final: 0.8236 (ptp-110) REVERT: A 440 LYS cc_start: 0.8244 (mppt) cc_final: 0.8016 (mppt) REVERT: A 468 ILE cc_start: 0.8583 (OUTLIER) cc_final: 0.8350 (mm) REVERT: A 472 ILE cc_start: 0.8526 (OUTLIER) cc_final: 0.8293 (mm) outliers start: 44 outliers final: 17 residues processed: 152 average time/residue: 0.4364 time to fit residues: 69.6137 Evaluate side-chains 150 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 126 time to evaluate : 0.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 86 ASP Chi-restraints excluded: chain P residue 107 THR Chi-restraints excluded: chain P residue 131 SER Chi-restraints excluded: chain P residue 212 THR Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 108 LYS Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 173 PHE Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 424 LYS Chi-restraints excluded: chain A residue 444 LYS Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 478 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 56 optimal weight: 0.0980 chunk 26 optimal weight: 0.8980 chunk 46 optimal weight: 0.2980 chunk 33 optimal weight: 0.0870 chunk 32 optimal weight: 0.4980 chunk 2 optimal weight: 0.9980 chunk 9 optimal weight: 0.0980 chunk 7 optimal weight: 0.9990 chunk 63 optimal weight: 0.4980 chunk 48 optimal weight: 0.8980 chunk 8 optimal weight: 0.2980 overall best weight: 0.1758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 252 GLN A 370 ASN A 487 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.128848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.121620 restraints weight = 8255.644| |-----------------------------------------------------------------------------| r_work (start): 0.3838 rms_B_bonded: 1.66 r_work: 0.3759 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3643 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.2891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 5390 Z= 0.153 Angle : 0.636 10.107 7327 Z= 0.312 Chirality : 0.046 0.275 776 Planarity : 0.004 0.037 950 Dihedral : 6.170 46.818 778 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.90 % Favored : 91.95 % Rotamer: Outliers : 7.61 % Allowed : 20.18 % Favored : 72.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.24 (0.32), residues: 671 helix: -2.37 (0.90), residues: 28 sheet: -0.60 (0.35), residues: 240 loop : -2.07 (0.29), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 54 TYR 0.022 0.001 TYR P 226 PHE 0.009 0.001 PHE B 99 TRP 0.016 0.001 TRP B 94 HIS 0.002 0.001 HIS P 159 Details of bonding type rmsd covalent geometry : bond 0.00359 ( 5384) covalent geometry : angle 0.62576 ( 7315) SS BOND : bond 0.00607 ( 6) SS BOND : angle 2.90365 ( 12) hydrogen bonds : bond 0.02933 ( 131) hydrogen bonds : angle 5.67808 ( 333) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1342 Ramachandran restraints generated. 671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1342 Ramachandran restraints generated. 671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 128 time to evaluate : 0.206 Fit side-chains REVERT: P 27 SER cc_start: 0.8370 (m) cc_final: 0.7771 (t) REVERT: P 94 ASP cc_start: 0.6885 (p0) cc_final: 0.6474 (p0) REVERT: P 236 TYR cc_start: 0.8453 (p90) cc_final: 0.7860 (p90) REVERT: B 11 LEU cc_start: 0.7202 (mt) cc_final: 0.6924 (mt) REVERT: B 38 GLN cc_start: 0.8137 (tt0) cc_final: 0.7886 (tt0) REVERT: B 58 ILE cc_start: 0.6093 (OUTLIER) cc_final: 0.5832 (pt) REVERT: B 97 TYR cc_start: 0.8229 (m-80) cc_final: 0.7741 (m-80) REVERT: B 108 LYS cc_start: 0.6834 (OUTLIER) cc_final: 0.6246 (ptpp) REVERT: B 127 LEU cc_start: 0.8622 (OUTLIER) cc_final: 0.8399 (pt) REVERT: B 130 SER cc_start: 0.8117 (OUTLIER) cc_final: 0.7841 (m) REVERT: A 380 TYR cc_start: 0.7996 (OUTLIER) cc_final: 0.7527 (m-80) REVERT: A 440 LYS cc_start: 0.8261 (mppt) cc_final: 0.8041 (mppt) REVERT: A 468 ILE cc_start: 0.8529 (OUTLIER) cc_final: 0.8308 (mm) REVERT: A 472 ILE cc_start: 0.8520 (OUTLIER) cc_final: 0.8289 (mm) outliers start: 43 outliers final: 19 residues processed: 151 average time/residue: 0.4634 time to fit residues: 73.4792 Evaluate side-chains 148 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 122 time to evaluate : 0.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 5 THR Chi-restraints excluded: chain P residue 86 ASP Chi-restraints excluded: chain P residue 107 THR Chi-restraints excluded: chain P residue 131 SER Chi-restraints excluded: chain P residue 193 SER Chi-restraints excluded: chain P residue 212 THR Chi-restraints excluded: chain P residue 245 THR Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 108 LYS Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 130 SER Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 424 LYS Chi-restraints excluded: chain A residue 444 LYS Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 478 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 17 optimal weight: 0.7980 chunk 45 optimal weight: 0.6980 chunk 36 optimal weight: 0.5980 chunk 30 optimal weight: 0.9980 chunk 37 optimal weight: 0.3980 chunk 0 optimal weight: 0.6980 chunk 55 optimal weight: 0.8980 chunk 49 optimal weight: 0.4980 chunk 34 optimal weight: 0.0770 chunk 52 optimal weight: 0.0980 chunk 53 optimal weight: 0.0870 overall best weight: 0.2316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 89 GLN B 162 GLN A 370 ASN A 394 ASN A 487 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.130708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.123159 restraints weight = 8158.419| |-----------------------------------------------------------------------------| r_work (start): 0.3830 rms_B_bonded: 1.71 r_work: 0.3747 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3627 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.2992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.095 5390 Z= 0.188 Angle : 0.684 15.324 7327 Z= 0.335 Chirality : 0.047 0.338 776 Planarity : 0.004 0.038 950 Dihedral : 6.292 47.004 778 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.64 % Favored : 91.21 % Rotamer: Outliers : 6.73 % Allowed : 22.48 % Favored : 70.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.15 (0.32), residues: 671 helix: -2.38 (0.90), residues: 28 sheet: -0.66 (0.36), residues: 231 loop : -1.89 (0.30), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 54 TYR 0.016 0.001 TYR P 226 PHE 0.011 0.002 PHE A 400 TRP 0.013 0.001 TRP A 436 HIS 0.002 0.001 HIS P 159 Details of bonding type rmsd covalent geometry : bond 0.00446 ( 5384) covalent geometry : angle 0.67224 ( 7315) SS BOND : bond 0.00854 ( 6) SS BOND : angle 3.24002 ( 12) hydrogen bonds : bond 0.03080 ( 131) hydrogen bonds : angle 5.61039 ( 333) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1342 Ramachandran restraints generated. 671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1342 Ramachandran restraints generated. 671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 125 time to evaluate : 0.195 Fit side-chains REVERT: P 236 TYR cc_start: 0.8460 (p90) cc_final: 0.7954 (p90) REVERT: B 11 LEU cc_start: 0.7132 (mt) cc_final: 0.6928 (mt) REVERT: B 38 GLN cc_start: 0.8204 (tt0) cc_final: 0.7954 (tt0) REVERT: B 91 ARG cc_start: 0.8223 (mtp85) cc_final: 0.7949 (mtt90) REVERT: B 97 TYR cc_start: 0.8217 (m-80) cc_final: 0.7736 (m-80) REVERT: B 108 LYS cc_start: 0.6846 (OUTLIER) cc_final: 0.6247 (ptpp) REVERT: B 130 SER cc_start: 0.8133 (p) cc_final: 0.7866 (m) REVERT: A 440 LYS cc_start: 0.8271 (mppt) cc_final: 0.8054 (mppt) REVERT: A 468 ILE cc_start: 0.8535 (OUTLIER) cc_final: 0.8319 (mm) REVERT: A 472 ILE cc_start: 0.8540 (OUTLIER) cc_final: 0.8301 (mm) outliers start: 38 outliers final: 22 residues processed: 149 average time/residue: 0.4832 time to fit residues: 75.3810 Evaluate side-chains 148 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 123 time to evaluate : 0.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 5 THR Chi-restraints excluded: chain P residue 86 ASP Chi-restraints excluded: chain P residue 107 THR Chi-restraints excluded: chain P residue 131 SER Chi-restraints excluded: chain P residue 193 SER Chi-restraints excluded: chain P residue 212 THR Chi-restraints excluded: chain P residue 245 THR Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 96 GLN Chi-restraints excluded: chain B residue 108 LYS Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 424 LYS Chi-restraints excluded: chain A residue 444 LYS Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 478 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 42 optimal weight: 0.6980 chunk 2 optimal weight: 0.6980 chunk 60 optimal weight: 0.4980 chunk 5 optimal weight: 0.0770 chunk 27 optimal weight: 0.3980 chunk 9 optimal weight: 0.1980 chunk 64 optimal weight: 0.7980 chunk 62 optimal weight: 0.0970 chunk 41 optimal weight: 0.5980 chunk 58 optimal weight: 0.0270 chunk 18 optimal weight: 0.9990 overall best weight: 0.1594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 89 GLN B 162 GLN B 207 GLN A 370 ASN A 394 ASN A 487 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.129328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.122087 restraints weight = 8117.302| |-----------------------------------------------------------------------------| r_work (start): 0.3843 rms_B_bonded: 1.65 r_work: 0.3766 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3650 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.3077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 5390 Z= 0.148 Angle : 0.678 13.542 7327 Z= 0.326 Chirality : 0.047 0.300 776 Planarity : 0.004 0.036 950 Dihedral : 6.041 45.947 776 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.60 % Favored : 92.25 % Rotamer: Outliers : 6.73 % Allowed : 22.65 % Favored : 70.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.03 (0.32), residues: 671 helix: -2.33 (0.90), residues: 28 sheet: -0.54 (0.36), residues: 232 loop : -1.83 (0.30), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 54 TYR 0.014 0.001 TYR P 226 PHE 0.011 0.001 PHE A 400 TRP 0.014 0.001 TRP B 94 HIS 0.002 0.000 HIS P 159 Details of bonding type rmsd covalent geometry : bond 0.00356 ( 5384) covalent geometry : angle 0.66844 ( 7315) SS BOND : bond 0.00735 ( 6) SS BOND : angle 2.88135 ( 12) hydrogen bonds : bond 0.02981 ( 131) hydrogen bonds : angle 5.39024 ( 333) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1342 Ramachandran restraints generated. 671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1342 Ramachandran restraints generated. 671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 134 time to evaluate : 0.151 Fit side-chains REVERT: P 206 GLN cc_start: 0.7750 (OUTLIER) cc_final: 0.7479 (tm-30) REVERT: P 236 TYR cc_start: 0.8448 (p90) cc_final: 0.7929 (p90) REVERT: B 38 GLN cc_start: 0.8152 (tt0) cc_final: 0.7909 (tt0) REVERT: B 58 ILE cc_start: 0.6102 (OUTLIER) cc_final: 0.5814 (pt) REVERT: B 97 TYR cc_start: 0.8211 (m-80) cc_final: 0.7721 (m-80) REVERT: B 108 LYS cc_start: 0.6871 (OUTLIER) cc_final: 0.6330 (ptpp) REVERT: B 130 SER cc_start: 0.8114 (OUTLIER) cc_final: 0.7830 (m) REVERT: B 173 PHE cc_start: 0.8156 (OUTLIER) cc_final: 0.7935 (p90) REVERT: A 440 LYS cc_start: 0.8252 (mppt) cc_final: 0.8050 (mppt) REVERT: A 468 ILE cc_start: 0.8523 (OUTLIER) cc_final: 0.8312 (mm) REVERT: A 472 ILE cc_start: 0.8530 (OUTLIER) cc_final: 0.8296 (mm) REVERT: A 501 TYR cc_start: 0.7712 (m-10) cc_final: 0.7436 (m-10) outliers start: 38 outliers final: 24 residues processed: 157 average time/residue: 0.4411 time to fit residues: 72.6108 Evaluate side-chains 157 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 126 time to evaluate : 0.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 5 THR Chi-restraints excluded: chain P residue 86 ASP Chi-restraints excluded: chain P residue 107 THR Chi-restraints excluded: chain P residue 131 SER Chi-restraints excluded: chain P residue 144 LEU Chi-restraints excluded: chain P residue 193 SER Chi-restraints excluded: chain P residue 195 SER Chi-restraints excluded: chain P residue 206 GLN Chi-restraints excluded: chain P residue 212 THR Chi-restraints excluded: chain P residue 245 THR Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 96 GLN Chi-restraints excluded: chain B residue 108 LYS Chi-restraints excluded: chain B residue 130 SER Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 173 PHE Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 424 LYS Chi-restraints excluded: chain A residue 444 LYS Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 478 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 42 optimal weight: 0.9980 chunk 17 optimal weight: 0.7980 chunk 16 optimal weight: 0.7980 chunk 39 optimal weight: 0.4980 chunk 2 optimal weight: 0.0060 chunk 47 optimal weight: 0.6980 chunk 58 optimal weight: 0.0570 chunk 38 optimal weight: 0.0070 chunk 36 optimal weight: 0.3980 chunk 54 optimal weight: 0.4980 chunk 32 optimal weight: 0.0470 overall best weight: 0.1030 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 89 GLN B 162 GLN A 370 ASN A 394 ASN A 487 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.130322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.123054 restraints weight = 8192.863| |-----------------------------------------------------------------------------| r_work (start): 0.3840 rms_B_bonded: 1.67 r_work: 0.3764 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3649 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.3131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 5390 Z= 0.122 Angle : 0.656 12.645 7327 Z= 0.317 Chirality : 0.045 0.279 776 Planarity : 0.004 0.034 950 Dihedral : 5.858 44.096 776 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.00 % Favored : 92.85 % Rotamer: Outliers : 6.02 % Allowed : 24.42 % Favored : 69.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.85 (0.33), residues: 671 helix: -2.33 (0.89), residues: 28 sheet: -0.41 (0.36), residues: 228 loop : -1.69 (0.30), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 54 TYR 0.013 0.001 TYR P 226 PHE 0.010 0.001 PHE A 400 TRP 0.018 0.001 TRP B 94 HIS 0.001 0.000 HIS P 159 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 5384) covalent geometry : angle 0.64753 ( 7315) SS BOND : bond 0.00691 ( 6) SS BOND : angle 2.74262 ( 12) hydrogen bonds : bond 0.02975 ( 131) hydrogen bonds : angle 5.16491 ( 333) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1342 Ramachandran restraints generated. 671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1342 Ramachandran restraints generated. 671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 137 time to evaluate : 0.208 Fit side-chains REVERT: P 236 TYR cc_start: 0.8399 (p90) cc_final: 0.7883 (p90) REVERT: B 38 GLN cc_start: 0.8111 (tt0) cc_final: 0.7885 (tt0) REVERT: B 108 LYS cc_start: 0.6816 (OUTLIER) cc_final: 0.6240 (ptpp) REVERT: B 130 SER cc_start: 0.8106 (p) cc_final: 0.7794 (m) REVERT: B 173 PHE cc_start: 0.8107 (OUTLIER) cc_final: 0.7904 (p90) REVERT: A 472 ILE cc_start: 0.8501 (OUTLIER) cc_final: 0.8281 (mm) REVERT: A 501 TYR cc_start: 0.7632 (m-10) cc_final: 0.7426 (m-10) outliers start: 34 outliers final: 19 residues processed: 157 average time/residue: 0.4101 time to fit residues: 67.7657 Evaluate side-chains 153 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 131 time to evaluate : 0.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 5 THR Chi-restraints excluded: chain P residue 86 ASP Chi-restraints excluded: chain P residue 107 THR Chi-restraints excluded: chain P residue 130 GLU Chi-restraints excluded: chain P residue 131 SER Chi-restraints excluded: chain P residue 212 THR Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 108 LYS Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 173 PHE Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 444 LYS Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 478 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 63 optimal weight: 0.6980 chunk 15 optimal weight: 0.0970 chunk 23 optimal weight: 0.9990 chunk 53 optimal weight: 0.9990 chunk 62 optimal weight: 0.1980 chunk 46 optimal weight: 0.1980 chunk 13 optimal weight: 0.9990 chunk 27 optimal weight: 0.0370 chunk 56 optimal weight: 0.0670 chunk 42 optimal weight: 0.7980 chunk 38 optimal weight: 0.3980 overall best weight: 0.1194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN A 487 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.130982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.123727 restraints weight = 8211.108| |-----------------------------------------------------------------------------| r_work (start): 0.3863 rms_B_bonded: 1.65 r_work: 0.3787 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3674 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.3230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 5390 Z= 0.136 Angle : 0.709 16.999 7327 Z= 0.341 Chirality : 0.047 0.272 776 Planarity : 0.004 0.034 950 Dihedral : 5.800 43.892 774 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.60 % Favored : 92.25 % Rotamer: Outliers : 4.78 % Allowed : 26.37 % Favored : 68.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.80 (0.33), residues: 671 helix: -2.33 (0.90), residues: 28 sheet: -0.37 (0.36), residues: 228 loop : -1.66 (0.30), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 54 TYR 0.013 0.001 TYR B 205 PHE 0.014 0.001 PHE A 400 TRP 0.018 0.001 TRP B 94 HIS 0.001 0.000 HIS P 159 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 5384) covalent geometry : angle 0.70133 ( 7315) SS BOND : bond 0.00854 ( 6) SS BOND : angle 2.66834 ( 12) hydrogen bonds : bond 0.03025 ( 131) hydrogen bonds : angle 5.08045 ( 333) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1342 Ramachandran restraints generated. 671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1342 Ramachandran restraints generated. 671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 135 time to evaluate : 0.207 Fit side-chains REVERT: P 27 SER cc_start: 0.8303 (m) cc_final: 0.7984 (t) REVERT: P 211 ARG cc_start: 0.8444 (mtt180) cc_final: 0.8157 (ptp-170) REVERT: P 236 TYR cc_start: 0.8428 (p90) cc_final: 0.7887 (p90) REVERT: B 38 GLN cc_start: 0.8126 (tt0) cc_final: 0.7893 (tt0) REVERT: B 53 ASN cc_start: 0.7947 (m110) cc_final: 0.7683 (m-40) REVERT: B 108 LYS cc_start: 0.6774 (OUTLIER) cc_final: 0.6231 (ptpp) REVERT: B 130 SER cc_start: 0.8133 (p) cc_final: 0.7799 (m) REVERT: B 173 PHE cc_start: 0.8178 (OUTLIER) cc_final: 0.7946 (p90) REVERT: A 472 ILE cc_start: 0.8511 (OUTLIER) cc_final: 0.8286 (mm) REVERT: A 501 TYR cc_start: 0.7611 (m-10) cc_final: 0.7407 (m-10) outliers start: 27 outliers final: 19 residues processed: 150 average time/residue: 0.4437 time to fit residues: 70.0919 Evaluate side-chains 155 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 133 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 5 THR Chi-restraints excluded: chain P residue 86 ASP Chi-restraints excluded: chain P residue 107 THR Chi-restraints excluded: chain P residue 130 GLU Chi-restraints excluded: chain P residue 131 SER Chi-restraints excluded: chain P residue 212 THR Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 108 LYS Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 173 PHE Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 444 LYS Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 478 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 47 optimal weight: 0.6980 chunk 7 optimal weight: 0.9980 chunk 44 optimal weight: 0.1980 chunk 64 optimal weight: 0.0570 chunk 15 optimal weight: 0.0970 chunk 41 optimal weight: 0.5980 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 0.0970 chunk 42 optimal weight: 0.0980 chunk 37 optimal weight: 0.3980 chunk 38 optimal weight: 0.0370 overall best weight: 0.0772 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 370 ASN A 487 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.132478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.125294 restraints weight = 8258.533| |-----------------------------------------------------------------------------| r_work (start): 0.3866 rms_B_bonded: 1.65 r_work: 0.3793 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3680 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.3342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 5390 Z= 0.118 Angle : 0.702 16.319 7327 Z= 0.335 Chirality : 0.045 0.246 776 Planarity : 0.004 0.052 950 Dihedral : 5.538 43.426 774 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 4.78 % Allowed : 26.55 % Favored : 68.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.69 (0.33), residues: 671 helix: -2.35 (0.88), residues: 28 sheet: -0.26 (0.36), residues: 230 loop : -1.60 (0.30), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 45 TYR 0.012 0.001 TYR P 226 PHE 0.011 0.001 PHE B 173 TRP 0.022 0.001 TRP B 94 HIS 0.001 0.000 HIS P 159 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 5384) covalent geometry : angle 0.69616 ( 7315) SS BOND : bond 0.00784 ( 6) SS BOND : angle 2.42193 ( 12) hydrogen bonds : bond 0.02813 ( 131) hydrogen bonds : angle 4.95593 ( 333) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2874.96 seconds wall clock time: 49 minutes 37.03 seconds (2977.03 seconds total)