Starting phenix.real_space_refine on Sat May 10 05:51:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jin_36321/05_2025/8jin_36321.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jin_36321/05_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_36321/05_2025/8jin_36321.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jin_36321/05_2025/8jin_36321.map" model { file = "/net/cci-nas-00/data/ceres_data/8jin_36321/05_2025/8jin_36321.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jin_36321/05_2025/8jin_36321.cif" } resolution = 2.45 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 5.27, per 1000 atoms: 1.00 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: 1.26 Conformation dependent library (CDL) restraints added in 652.4 milliseconds 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: 0.59 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: 1.36 Time building geometry restraints manager: 1.50 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: 0.010 Normalize map: mean=0, sd=1: 6.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 17.450 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.690 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.010 0.001 TRP P 98 HIS 0.001 0.000 HIS P 159 PHE 0.006 0.001 PHE P 151 TYR 0.007 0.001 TYR B 220 ARG 0.002 0.000 ARG B 161 Details of bonding type rmsd hydrogen bonds : bond 0.26391 ( 131) hydrogen bonds : angle 10.72137 ( 333) SS BOND : bond 0.00173 ( 6) SS BOND : angle 0.49088 ( 12) covalent geometry : bond 0.00221 ( 5384) covalent geometry : angle 0.53730 ( 7315) *********************** 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 : 0.595 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: 0.8588 time to fit residues: 172.7750 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 : 0.559 ------------------------------------------------------------------------------- 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 55 optimal weight: 0.5980 chunk 50 optimal weight: 0.7980 chunk 27 optimal weight: 0.4980 chunk 17 optimal weight: 0.9990 chunk 33 optimal weight: 0.7980 chunk 26 optimal weight: 0.2980 chunk 51 optimal weight: 0.5980 chunk 20 optimal weight: 0.9980 chunk 31 optimal weight: 0.0980 chunk 38 optimal weight: 0.8980 chunk 59 optimal weight: 0.7980 overall best weight: 0.4180 ------------------------------------------------------------------------------- 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 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 96 GLN B 126 GLN B 162 GLN A 417 ASN A 422 ASN A 439 ASN A 474 GLN A 477 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.129887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.122415 restraints weight = 8024.860| |-----------------------------------------------------------------------------| r_work (start): 0.3818 rms_B_bonded: 1.68 r_work: 0.3738 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3620 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.2167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.071 5390 Z= 0.295 Angle : 0.704 7.554 7327 Z= 0.353 Chirality : 0.049 0.169 776 Planarity : 0.005 0.044 950 Dihedral : 6.953 56.407 783 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.30 % Allowed : 9.84 % Favored : 89.87 % Rotamer: Outliers : 7.43 % Allowed : 16.11 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.25 (0.31), residues: 671 helix: -3.48 (0.70), residues: 28 sheet: -1.63 (0.34), residues: 243 loop : -2.48 (0.28), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 436 HIS 0.003 0.001 HIS P 159 PHE 0.018 0.002 PHE B 173 TYR 0.019 0.002 TYR P 226 ARG 0.007 0.001 ARG B 197 Details of bonding type rmsd hydrogen bonds : bond 0.04242 ( 131) hydrogen bonds : angle 6.53877 ( 333) SS BOND : bond 0.00276 ( 6) SS BOND : angle 0.80377 ( 12) covalent geometry : bond 0.00668 ( 5384) covalent geometry : angle 0.70339 ( 7315) *********************** 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 183 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 141 time to evaluate : 0.552 Fit side-chains REVERT: P 27 SER cc_start: 0.8272 (m) cc_final: 0.7784 (t) REVERT: P 94 ASP cc_start: 0.7003 (p0) cc_final: 0.6643 (p0) REVERT: P 236 TYR cc_start: 0.8472 (p90) cc_final: 0.7939 (p90) REVERT: B 11 LEU cc_start: 0.7300 (mt) cc_final: 0.6951 (mt) REVERT: B 38 GLN cc_start: 0.8165 (tt0) cc_final: 0.7933 (tt0) REVERT: B 97 TYR cc_start: 0.8296 (m-80) cc_final: 0.7777 (m-80) REVERT: B 106 GLU cc_start: 0.6978 (OUTLIER) cc_final: 0.6771 (pm20) REVERT: B 108 LYS cc_start: 0.6918 (OUTLIER) cc_final: 0.6262 (ptpp) REVERT: B 173 PHE cc_start: 0.8294 (OUTLIER) cc_final: 0.8026 (p90) REVERT: B 196 SER cc_start: 0.8718 (p) cc_final: 0.8500 (t) REVERT: A 380 TYR cc_start: 0.8475 (m-80) cc_final: 0.8213 (m-80) REVERT: A 386 LYS cc_start: 0.8551 (mtmt) cc_final: 0.8328 (mtmt) REVERT: A 405 ASN cc_start: 0.7594 (m-40) cc_final: 0.7374 (m-40) REVERT: A 440 LYS cc_start: 0.8291 (mppt) cc_final: 0.8020 (mppt) REVERT: A 472 ILE cc_start: 0.8488 (OUTLIER) cc_final: 0.8240 (mm) REVERT: A 501 TYR cc_start: 0.7891 (m-10) cc_final: 0.7629 (m-10) outliers start: 42 outliers final: 21 residues processed: 162 average time/residue: 0.8607 time to fit residues: 147.2483 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 : 0.581 ------------------------------------------------------------------------------- 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 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 33 LEU 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 106 GLU 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 173 PHE Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 194 THR 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 51 optimal weight: 0.5980 chunk 57 optimal weight: 0.0980 chunk 53 optimal weight: 0.7980 chunk 35 optimal weight: 0.9990 chunk 32 optimal weight: 0.0870 chunk 54 optimal weight: 0.1980 chunk 46 optimal weight: 0.0980 chunk 5 optimal weight: 0.9990 chunk 50 optimal weight: 0.1980 chunk 33 optimal weight: 0.0030 chunk 14 optimal weight: 0.5980 overall best weight: 0.0968 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 6 GLN B 89 GLN B 96 GLN B 126 GLN A 370 ASN A 439 ASN A 487 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.130445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.123247 restraints weight = 8062.425| |-----------------------------------------------------------------------------| r_work (start): 0.3861 rms_B_bonded: 1.66 r_work: 0.3784 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3668 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.2412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 5390 Z= 0.110 Angle : 0.615 11.280 7327 Z= 0.298 Chirality : 0.046 0.200 776 Planarity : 0.004 0.038 950 Dihedral : 5.894 44.408 776 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.11 % Favored : 93.74 % Rotamer: Outliers : 6.73 % Allowed : 18.76 % Favored : 74.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.66 (0.31), residues: 671 helix: -2.47 (0.93), residues: 22 sheet: -1.13 (0.36), residues: 231 loop : -2.19 (0.29), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 94 HIS 0.001 0.000 HIS P 159 PHE 0.007 0.001 PHE P 151 TYR 0.019 0.001 TYR P 226 ARG 0.008 0.000 ARG B 45 Details of bonding type rmsd hydrogen bonds : bond 0.03131 ( 131) hydrogen bonds : angle 5.98270 ( 333) SS BOND : bond 0.00597 ( 6) SS BOND : angle 2.10681 ( 12) covalent geometry : bond 0.00244 ( 5384) covalent geometry : angle 0.60943 ( 7315) *********************** 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 162 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 124 time to evaluate : 0.530 Fit side-chains REVERT: P 27 SER cc_start: 0.8354 (m) cc_final: 0.7915 (t) REVERT: P 94 ASP cc_start: 0.6902 (p0) cc_final: 0.6506 (p0) REVERT: P 236 TYR cc_start: 0.8420 (p90) cc_final: 0.7859 (p90) REVERT: B 11 LEU cc_start: 0.7179 (mt) cc_final: 0.6937 (mt) REVERT: B 38 GLN cc_start: 0.8104 (tt0) cc_final: 0.7847 (tt0) REVERT: B 108 LYS cc_start: 0.6804 (OUTLIER) cc_final: 0.6234 (ptpp) REVERT: B 130 SER cc_start: 0.8124 (p) cc_final: 0.7801 (m) REVERT: B 196 SER cc_start: 0.8719 (p) cc_final: 0.8474 (t) REVERT: A 386 LYS cc_start: 0.8379 (mtmt) cc_final: 0.8177 (mtmt) REVERT: A 472 ILE cc_start: 0.8443 (OUTLIER) cc_final: 0.8236 (mm) outliers start: 38 outliers final: 21 residues processed: 148 average time/residue: 0.7567 time to fit residues: 119.1154 Evaluate side-chains 142 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 119 time to evaluate : 0.535 ------------------------------------------------------------------------------- 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 96 LEU Chi-restraints excluded: chain P residue 99 VAL Chi-restraints excluded: chain P residue 107 THR Chi-restraints excluded: chain P residue 193 SER Chi-restraints excluded: chain P residue 212 THR Chi-restraints excluded: chain P residue 250 SER 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 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 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 47 optimal weight: 0.7980 chunk 13 optimal weight: 0.9990 chunk 8 optimal weight: 0.7980 chunk 38 optimal weight: 0.6980 chunk 45 optimal weight: 0.6980 chunk 14 optimal weight: 0.8980 chunk 61 optimal weight: 0.0040 chunk 17 optimal weight: 0.6980 chunk 54 optimal weight: 0.6980 chunk 29 optimal weight: 0.9980 chunk 20 optimal weight: 0.0870 overall best weight: 0.4370 ------------------------------------------------------------------------------- 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 162 GLN B 207 GLN A 370 ASN A 394 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 = 0.3877 r_free = 0.3877 target = 0.126186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.118902 restraints weight = 8264.610| |-----------------------------------------------------------------------------| r_work (start): 0.3805 rms_B_bonded: 1.67 r_work: 0.3723 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3605 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.2888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.075 5390 Z= 0.311 Angle : 0.727 9.349 7327 Z= 0.362 Chirality : 0.050 0.264 776 Planarity : 0.005 0.044 950 Dihedral : 6.605 46.662 776 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.30 % Allowed : 9.39 % Favored : 90.31 % Rotamer: Outliers : 8.32 % Allowed : 17.88 % Favored : 73.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.72 (0.32), residues: 671 helix: -3.28 (0.72), residues: 34 sheet: -0.99 (0.34), residues: 253 loop : -2.31 (0.30), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 436 HIS 0.004 0.001 HIS P 159 PHE 0.017 0.002 PHE A 515 TYR 0.017 0.002 TYR B 49 ARG 0.009 0.001 ARG B 45 Details of bonding type rmsd hydrogen bonds : bond 0.03541 ( 131) hydrogen bonds : angle 6.15336 ( 333) SS BOND : bond 0.00446 ( 6) SS BOND : angle 2.67657 ( 12) covalent geometry : bond 0.00709 ( 5384) covalent geometry : angle 0.71933 ( 7315) *********************** 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 177 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 130 time to evaluate : 0.608 Fit side-chains revert: symmetry clash REVERT: P 27 SER cc_start: 0.8281 (m) cc_final: 0.7858 (t) REVERT: P 236 TYR cc_start: 0.8513 (p90) cc_final: 0.7969 (p90) REVERT: B 11 LEU cc_start: 0.7221 (mt) cc_final: 0.6868 (mt) REVERT: B 38 GLN cc_start: 0.8100 (tt0) cc_final: 0.7861 (tt0) REVERT: B 97 TYR cc_start: 0.8284 (m-80) cc_final: 0.7818 (m-80) REVERT: B 106 GLU cc_start: 0.6973 (pm20) cc_final: 0.6765 (pm20) REVERT: B 108 LYS cc_start: 0.6904 (OUTLIER) cc_final: 0.6192 (ptpp) REVERT: B 127 LEU cc_start: 0.8710 (OUTLIER) cc_final: 0.8468 (pt) REVERT: B 130 SER cc_start: 0.8177 (OUTLIER) cc_final: 0.7899 (m) REVERT: B 252 GLN cc_start: 0.7813 (mp10) cc_final: 0.7431 (mp10) REVERT: A 405 ASN cc_start: 0.7721 (m-40) cc_final: 0.7478 (m-40) REVERT: A 440 LYS cc_start: 0.8268 (mppt) cc_final: 0.8014 (mppt) REVERT: A 468 ILE cc_start: 0.8521 (OUTLIER) cc_final: 0.8278 (mm) REVERT: A 472 ILE cc_start: 0.8539 (OUTLIER) cc_final: 0.8289 (mm) REVERT: A 518 LEU cc_start: 0.7730 (OUTLIER) cc_final: 0.7266 (pp) outliers start: 47 outliers final: 21 residues processed: 158 average time/residue: 0.9905 time to fit residues: 164.0596 Evaluate side-chains 149 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 122 time to evaluate : 0.541 ------------------------------------------------------------------------------- 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 212 THR Chi-restraints excluded: chain P residue 245 THR Chi-restraints excluded: chain B residue 17 GLU 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 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 183 THR Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 255 THR Chi-restraints excluded: chain A residue 332 ILE 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 468 ILE Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 478 LYS Chi-restraints excluded: chain A residue 518 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 42 optimal weight: 0.8980 chunk 49 optimal weight: 0.4980 chunk 10 optimal weight: 0.0670 chunk 18 optimal weight: 0.9990 chunk 50 optimal weight: 0.1980 chunk 41 optimal weight: 0.3980 chunk 12 optimal weight: 0.3980 chunk 3 optimal weight: 0.4980 chunk 21 optimal weight: 0.3980 chunk 53 optimal weight: 0.2980 chunk 17 optimal weight: 0.1980 overall best weight: 0.2318 ------------------------------------------------------------------------------- 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 101 GLN B 126 GLN B 162 GLN A 370 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 = 0.3910 r_free = 0.3910 target = 0.129933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.122464 restraints weight = 8110.425| |-----------------------------------------------------------------------------| r_work (start): 0.3824 rms_B_bonded: 1.69 r_work: 0.3743 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3624 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.2910 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= 0.182 Angle : 0.647 9.228 7327 Z= 0.319 Chirality : 0.047 0.245 776 Planarity : 0.004 0.041 950 Dihedral : 6.385 48.945 776 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.86 % Favored : 93.00 % Rotamer: Outliers : 7.08 % Allowed : 20.18 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.40 (0.32), residues: 671 helix: -2.63 (0.85), residues: 28 sheet: -0.73 (0.35), residues: 239 loop : -2.14 (0.29), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 94 HIS 0.002 0.001 HIS P 159 PHE 0.011 0.002 PHE B 173 TYR 0.023 0.001 TYR P 226 ARG 0.006 0.000 ARG B 45 Details of bonding type rmsd hydrogen bonds : bond 0.03030 ( 131) hydrogen bonds : angle 5.90360 ( 333) SS BOND : bond 0.00445 ( 6) SS BOND : angle 2.57572 ( 12) covalent geometry : bond 0.00418 ( 5384) covalent geometry : angle 0.63887 ( 7315) *********************** 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 161 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 121 time to evaluate : 0.575 Fit side-chains REVERT: P 236 TYR cc_start: 0.8466 (p90) cc_final: 0.7901 (p90) REVERT: B 11 LEU cc_start: 0.7195 (mt) cc_final: 0.6904 (mt) REVERT: B 38 GLN cc_start: 0.8131 (tt0) cc_final: 0.7869 (tt0) REVERT: B 97 TYR cc_start: 0.8244 (m-80) cc_final: 0.7759 (m-80) REVERT: B 108 LYS cc_start: 0.6879 (OUTLIER) cc_final: 0.6237 (ptpp) REVERT: B 127 LEU cc_start: 0.8610 (OUTLIER) cc_final: 0.8356 (pt) REVERT: B 130 SER cc_start: 0.8125 (p) cc_final: 0.7839 (m) REVERT: B 252 GLN cc_start: 0.7598 (mp10) cc_final: 0.7234 (mp10) REVERT: A 380 TYR cc_start: 0.8167 (OUTLIER) cc_final: 0.7946 (m-80) REVERT: A 440 LYS cc_start: 0.8241 (mppt) cc_final: 0.8009 (mppt) REVERT: A 468 ILE cc_start: 0.8578 (OUTLIER) cc_final: 0.8343 (mm) REVERT: A 472 ILE cc_start: 0.8522 (OUTLIER) cc_final: 0.8291 (mm) outliers start: 40 outliers final: 21 residues processed: 143 average time/residue: 0.8665 time to fit residues: 130.7899 Evaluate side-chains 146 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 120 time to evaluate : 0.509 ------------------------------------------------------------------------------- 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 193 SER Chi-restraints excluded: chain P residue 211 ARG 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 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 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 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 7 optimal weight: 0.9990 chunk 47 optimal weight: 0.7980 chunk 1 optimal weight: 0.3980 chunk 45 optimal weight: 0.0270 chunk 33 optimal weight: 0.0870 chunk 38 optimal weight: 0.0040 chunk 40 optimal weight: 0.2980 chunk 53 optimal weight: 0.9990 chunk 44 optimal weight: 0.0010 chunk 27 optimal weight: 0.8980 chunk 0 optimal weight: 0.6980 overall best weight: 0.0834 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 89 GLN B 126 GLN B 162 GLN A 370 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.130103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.122991 restraints weight = 8134.363| |-----------------------------------------------------------------------------| r_work (start): 0.3858 rms_B_bonded: 1.65 r_work: 0.3780 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3664 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.2926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 5390 Z= 0.112 Angle : 0.628 13.034 7327 Z= 0.300 Chirality : 0.046 0.263 776 Planarity : 0.004 0.044 950 Dihedral : 5.967 44.954 776 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.15 % Favored : 92.85 % Rotamer: Outliers : 6.73 % Allowed : 20.00 % Favored : 73.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.16 (0.32), residues: 671 helix: -2.47 (0.87), residues: 28 sheet: -0.63 (0.37), residues: 226 loop : -1.90 (0.30), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 94 HIS 0.001 0.000 HIS P 159 PHE 0.009 0.001 PHE B 173 TYR 0.014 0.001 TYR P 226 ARG 0.010 0.000 ARG B 45 Details of bonding type rmsd hydrogen bonds : bond 0.02725 ( 131) hydrogen bonds : angle 5.55921 ( 333) SS BOND : bond 0.00873 ( 6) SS BOND : angle 2.81553 ( 12) covalent geometry : bond 0.00267 ( 5384) covalent geometry : angle 0.61807 ( 7315) *********************** 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 162 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 124 time to evaluate : 0.594 Fit side-chains REVERT: P 206 GLN cc_start: 0.7677 (OUTLIER) cc_final: 0.7475 (tm-30) REVERT: P 236 TYR cc_start: 0.8444 (p90) cc_final: 0.7834 (p90) REVERT: B 38 GLN cc_start: 0.8117 (tt0) cc_final: 0.7871 (tt0) REVERT: B 97 TYR cc_start: 0.8204 (m-80) cc_final: 0.7711 (m-80) REVERT: B 108 LYS cc_start: 0.6808 (OUTLIER) cc_final: 0.6167 (ptpp) REVERT: B 127 LEU cc_start: 0.8535 (OUTLIER) cc_final: 0.8207 (pt) REVERT: B 130 SER cc_start: 0.8042 (p) cc_final: 0.7720 (m) REVERT: B 173 PHE cc_start: 0.8133 (OUTLIER) cc_final: 0.7917 (p90) REVERT: A 380 TYR cc_start: 0.8040 (OUTLIER) cc_final: 0.7421 (m-80) REVERT: A 440 LYS cc_start: 0.8194 (mppt) cc_final: 0.7991 (mppt) REVERT: A 468 ILE cc_start: 0.8581 (OUTLIER) cc_final: 0.8360 (mm) REVERT: A 472 ILE cc_start: 0.8490 (OUTLIER) cc_final: 0.8282 (mm) outliers start: 38 outliers final: 19 residues processed: 143 average time/residue: 0.9293 time to fit residues: 140.1239 Evaluate side-chains 149 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 123 time to evaluate : 0.550 ------------------------------------------------------------------------------- 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 193 SER Chi-restraints excluded: chain P residue 206 GLN Chi-restraints excluded: chain P residue 211 ARG 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 126 GLN Chi-restraints excluded: chain B residue 127 LEU 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 424 LYS 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 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 32 optimal weight: 0.0770 chunk 40 optimal weight: 0.1980 chunk 19 optimal weight: 0.2980 chunk 45 optimal weight: 0.9990 chunk 23 optimal weight: 0.8980 chunk 62 optimal weight: 0.7980 chunk 22 optimal weight: 0.9990 chunk 31 optimal weight: 0.4980 chunk 51 optimal weight: 0.3980 chunk 38 optimal weight: 0.0060 chunk 8 optimal weight: 0.0040 overall best weight: 0.1166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 89 GLN B 126 GLN B 162 GLN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 487 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.130273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.123106 restraints weight = 8022.482| |-----------------------------------------------------------------------------| r_work (start): 0.3857 rms_B_bonded: 1.65 r_work: 0.3779 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3665 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.3011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.095 5390 Z= 0.128 Angle : 0.659 14.681 7327 Z= 0.312 Chirality : 0.046 0.320 776 Planarity : 0.004 0.048 950 Dihedral : 5.901 44.706 776 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.30 % Favored : 92.55 % Rotamer: Outliers : 5.66 % Allowed : 21.59 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.99 (0.33), residues: 671 helix: -2.37 (0.88), residues: 28 sheet: -0.50 (0.37), residues: 231 loop : -1.81 (0.30), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 94 HIS 0.001 0.000 HIS P 159 PHE 0.010 0.001 PHE B 173 TYR 0.011 0.001 TYR P 226 ARG 0.012 0.000 ARG B 45 Details of bonding type rmsd hydrogen bonds : bond 0.02813 ( 131) hydrogen bonds : angle 5.26600 ( 333) SS BOND : bond 0.00657 ( 6) SS BOND : angle 3.03553 ( 12) covalent geometry : bond 0.00310 ( 5384) covalent geometry : angle 0.64819 ( 7315) *********************** 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 161 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 129 time to evaluate : 0.538 Fit side-chains REVERT: P 206 GLN cc_start: 0.7686 (OUTLIER) cc_final: 0.7423 (tm-30) REVERT: P 236 TYR cc_start: 0.8422 (p90) cc_final: 0.7879 (p90) REVERT: B 38 GLN cc_start: 0.8090 (tt0) cc_final: 0.7861 (tt0) REVERT: B 97 TYR cc_start: 0.8211 (m-80) cc_final: 0.7701 (m-80) REVERT: B 108 LYS cc_start: 0.6831 (OUTLIER) cc_final: 0.6192 (ptpp) REVERT: B 127 LEU cc_start: 0.8554 (OUTLIER) cc_final: 0.8226 (pt) REVERT: B 130 SER cc_start: 0.8054 (p) cc_final: 0.7747 (m) REVERT: B 173 PHE cc_start: 0.8127 (OUTLIER) cc_final: 0.7893 (p90) REVERT: B 197 ARG cc_start: 0.8893 (mtp85) cc_final: 0.8451 (mtp85) REVERT: A 380 TYR cc_start: 0.8060 (OUTLIER) cc_final: 0.7562 (m-80) REVERT: A 468 ILE cc_start: 0.8496 (OUTLIER) cc_final: 0.8291 (mm) REVERT: A 472 ILE cc_start: 0.8495 (OUTLIER) cc_final: 0.8286 (mm) REVERT: A 501 TYR cc_start: 0.7651 (m-10) cc_final: 0.7431 (m-10) outliers start: 32 outliers final: 16 residues processed: 148 average time/residue: 1.0558 time to fit residues: 163.4651 Evaluate side-chains 151 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 128 time to evaluate : 0.564 ------------------------------------------------------------------------------- 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 193 SER Chi-restraints excluded: chain P residue 206 GLN Chi-restraints excluded: chain P residue 211 ARG 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 126 GLN Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 173 PHE Chi-restraints excluded: chain B residue 183 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 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 46 optimal weight: 0.0770 chunk 39 optimal weight: 0.3980 chunk 0 optimal weight: 0.6980 chunk 42 optimal weight: 0.9990 chunk 61 optimal weight: 0.0970 chunk 14 optimal weight: 0.9990 chunk 37 optimal weight: 0.4980 chunk 34 optimal weight: 0.9990 chunk 35 optimal weight: 0.0270 chunk 40 optimal weight: 0.0980 chunk 43 optimal weight: 0.0970 overall best weight: 0.0792 ------------------------------------------------------------------------------- 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 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 487 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.130803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.123620 restraints weight = 8162.710| |-----------------------------------------------------------------------------| r_work (start): 0.3866 rms_B_bonded: 1.67 r_work: 0.3788 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3673 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.3122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 5390 Z= 0.114 Angle : 0.654 12.770 7327 Z= 0.310 Chirality : 0.046 0.282 776 Planarity : 0.004 0.041 950 Dihedral : 5.724 44.274 776 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.86 % Favored : 93.14 % Rotamer: Outliers : 5.31 % Allowed : 23.36 % Favored : 71.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.87 (0.33), residues: 671 helix: -2.36 (0.88), residues: 28 sheet: -0.29 (0.37), residues: 222 loop : -1.77 (0.30), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 94 HIS 0.001 0.000 HIS P 159 PHE 0.011 0.001 PHE A 400 TYR 0.010 0.001 TYR P 226 ARG 0.010 0.000 ARG B 45 Details of bonding type rmsd hydrogen bonds : bond 0.02763 ( 131) hydrogen bonds : angle 5.08115 ( 333) SS BOND : bond 0.00715 ( 6) SS BOND : angle 2.80482 ( 12) covalent geometry : bond 0.00279 ( 5384) covalent geometry : angle 0.64475 ( 7315) *********************** 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 168 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 138 time to evaluate : 0.590 Fit side-chains REVERT: P 236 TYR cc_start: 0.8425 (p90) cc_final: 0.7865 (p90) REVERT: B 38 GLN cc_start: 0.8100 (tt0) cc_final: 0.7879 (tt0) REVERT: B 97 TYR cc_start: 0.8187 (m-80) cc_final: 0.7653 (m-80) REVERT: B 108 LYS cc_start: 0.6808 (OUTLIER) cc_final: 0.6327 (ptpp) REVERT: B 127 LEU cc_start: 0.8598 (OUTLIER) cc_final: 0.8270 (pt) REVERT: B 130 SER cc_start: 0.8044 (p) cc_final: 0.7742 (m) REVERT: B 173 PHE cc_start: 0.8136 (OUTLIER) cc_final: 0.7905 (p90) REVERT: B 197 ARG cc_start: 0.8900 (mtp85) cc_final: 0.8465 (mtp85) REVERT: A 468 ILE cc_start: 0.8494 (OUTLIER) cc_final: 0.8283 (mm) REVERT: A 472 ILE cc_start: 0.8488 (OUTLIER) cc_final: 0.8279 (mm) REVERT: A 501 TYR cc_start: 0.7606 (m-10) cc_final: 0.7390 (m-10) outliers start: 30 outliers final: 16 residues processed: 157 average time/residue: 0.9718 time to fit residues: 160.4752 Evaluate side-chains 156 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 135 time to evaluate : 0.753 ------------------------------------------------------------------------------- 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 193 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 127 LEU Chi-restraints excluded: chain B residue 173 PHE 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 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 32 optimal weight: 0.0370 chunk 43 optimal weight: 0.2980 chunk 18 optimal weight: 0.9980 chunk 60 optimal weight: 0.0570 chunk 16 optimal weight: 0.8980 chunk 6 optimal weight: 0.9990 chunk 19 optimal weight: 0.0770 chunk 24 optimal weight: 0.6980 chunk 17 optimal weight: 0.3980 chunk 54 optimal weight: 0.8980 chunk 46 optimal weight: 0.4980 overall best weight: 0.1734 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 201 ASN B 96 GLN B 101 GLN B 207 GLN B 252 GLN A 487 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.129614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.122481 restraints weight = 8081.286| |-----------------------------------------------------------------------------| r_work (start): 0.3849 rms_B_bonded: 1.63 r_work: 0.3773 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3659 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.3200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.096 5390 Z= 0.156 Angle : 0.708 17.451 7327 Z= 0.337 Chirality : 0.047 0.300 776 Planarity : 0.004 0.038 950 Dihedral : 5.939 44.035 776 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.05 % Favored : 91.80 % Rotamer: Outliers : 4.96 % Allowed : 23.89 % Favored : 71.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.85 (0.33), residues: 671 helix: -2.34 (0.88), residues: 28 sheet: -0.47 (0.36), residues: 239 loop : -1.67 (0.31), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 436 HIS 0.002 0.001 HIS P 159 PHE 0.015 0.001 PHE A 400 TYR 0.012 0.001 TYR P 226 ARG 0.009 0.001 ARG B 45 Details of bonding type rmsd hydrogen bonds : bond 0.02994 ( 131) hydrogen bonds : angle 5.12321 ( 333) SS BOND : bond 0.00806 ( 6) SS BOND : angle 2.88194 ( 12) covalent geometry : bond 0.00373 ( 5384) covalent geometry : angle 0.69906 ( 7315) *********************** 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 162 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 134 time to evaluate : 0.551 Fit side-chains REVERT: P 206 GLN cc_start: 0.7693 (OUTLIER) cc_final: 0.7473 (tm-30) REVERT: P 211 ARG cc_start: 0.8406 (mtt180) cc_final: 0.8157 (ptp-170) REVERT: P 236 TYR cc_start: 0.8441 (p90) cc_final: 0.7860 (p90) REVERT: B 38 GLN cc_start: 0.8127 (tt0) cc_final: 0.7904 (tt0) REVERT: B 97 TYR cc_start: 0.8162 (m-80) cc_final: 0.7675 (m-80) REVERT: B 108 LYS cc_start: 0.6830 (OUTLIER) cc_final: 0.6247 (ptpp) REVERT: B 130 SER cc_start: 0.8104 (p) cc_final: 0.7803 (m) REVERT: B 173 PHE cc_start: 0.8176 (OUTLIER) cc_final: 0.7937 (p90) REVERT: B 197 ARG cc_start: 0.8929 (mtp85) cc_final: 0.8469 (mtp85) REVERT: A 468 ILE cc_start: 0.8499 (OUTLIER) cc_final: 0.8296 (mm) REVERT: A 472 ILE cc_start: 0.8517 (OUTLIER) cc_final: 0.8291 (mm) REVERT: A 501 TYR cc_start: 0.7660 (m-10) cc_final: 0.7451 (m-10) outliers start: 28 outliers final: 17 residues processed: 152 average time/residue: 1.0183 time to fit residues: 162.4832 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 : 0.624 ------------------------------------------------------------------------------- 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 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 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 36 optimal weight: 0.0970 chunk 24 optimal weight: 0.1980 chunk 55 optimal weight: 0.8980 chunk 59 optimal weight: 0.2980 chunk 61 optimal weight: 0.5980 chunk 7 optimal weight: 0.6980 chunk 64 optimal weight: 0.0040 chunk 0 optimal weight: 0.7980 chunk 9 optimal weight: 0.0570 chunk 15 optimal weight: 0.8980 chunk 32 optimal weight: 0.0570 overall best weight: 0.0826 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 101 GLN B 207 GLN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 487 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.134110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.126696 restraints weight = 8167.245| |-----------------------------------------------------------------------------| r_work (start): 0.3873 rms_B_bonded: 1.68 r_work: 0.3797 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3682 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.3329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 5390 Z= 0.118 Angle : 0.702 16.649 7327 Z= 0.329 Chirality : 0.046 0.259 776 Planarity : 0.004 0.035 950 Dihedral : 5.720 43.893 776 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer: Outliers : 4.96 % Allowed : 24.25 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.73 (0.33), residues: 671 helix: -2.34 (0.88), residues: 28 sheet: -0.25 (0.37), residues: 224 loop : -1.64 (0.30), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 94 HIS 0.001 0.001 HIS P 159 PHE 0.012 0.001 PHE A 400 TYR 0.011 0.001 TYR P 226 ARG 0.008 0.000 ARG B 45 Details of bonding type rmsd hydrogen bonds : bond 0.02840 ( 131) hydrogen bonds : angle 4.97090 ( 333) SS BOND : bond 0.00810 ( 6) SS BOND : angle 2.86190 ( 12) covalent geometry : bond 0.00289 ( 5384) covalent geometry : angle 0.69321 ( 7315) ********************** 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 164 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 136 time to evaluate : 0.569 Fit side-chains REVERT: P 211 ARG cc_start: 0.8432 (mtt180) cc_final: 0.8176 (ptp-170) REVERT: P 236 TYR cc_start: 0.8433 (p90) cc_final: 0.7870 (p90) REVERT: B 38 GLN cc_start: 0.8124 (tt0) cc_final: 0.7892 (tt0) REVERT: B 108 LYS cc_start: 0.6774 (OUTLIER) cc_final: 0.6305 (ptpp) REVERT: B 127 LEU cc_start: 0.8602 (OUTLIER) cc_final: 0.8328 (pt) REVERT: B 130 SER cc_start: 0.8088 (p) cc_final: 0.7775 (m) REVERT: B 173 PHE cc_start: 0.8174 (OUTLIER) cc_final: 0.7929 (p90) REVERT: B 197 ARG cc_start: 0.8924 (mtp85) cc_final: 0.8590 (mtp85) REVERT: A 423 TYR cc_start: 0.8041 (t80) cc_final: 0.7841 (t80) REVERT: A 472 ILE cc_start: 0.8520 (OUTLIER) cc_final: 0.8298 (mm) outliers start: 28 outliers final: 17 residues processed: 152 average time/residue: 0.9985 time to fit residues: 159.1008 Evaluate side-chains 156 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 135 time to evaluate : 0.535 ------------------------------------------------------------------------------- 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 144 LEU 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 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 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 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 11 optimal weight: 0.9990 chunk 1 optimal weight: 0.8980 chunk 62 optimal weight: 0.5980 chunk 2 optimal weight: 0.7980 chunk 3 optimal weight: 0.1980 chunk 10 optimal weight: 0.4980 chunk 26 optimal weight: 0.5980 chunk 0 optimal weight: 0.1980 chunk 41 optimal weight: 0.5980 chunk 5 optimal weight: 0.0970 chunk 50 optimal weight: 0.3980 overall best weight: 0.2778 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.130648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.123209 restraints weight = 8268.129| |-----------------------------------------------------------------------------| r_work (start): 0.3823 rms_B_bonded: 1.70 r_work: 0.3743 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3627 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.3322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 5390 Z= 0.224 Angle : 0.790 16.585 7327 Z= 0.375 Chirality : 0.049 0.281 776 Planarity : 0.004 0.040 950 Dihedral : 6.323 44.031 776 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.30 % Allowed : 8.20 % Favored : 91.51 % Rotamer: Outliers : 4.60 % Allowed : 24.96 % Favored : 70.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.87 (0.33), residues: 671 helix: -2.38 (0.87), residues: 28 sheet: -0.49 (0.36), residues: 234 loop : -1.66 (0.30), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 436 HIS 0.003 0.001 HIS P 159 PHE 0.015 0.002 PHE A 400 TYR 0.014 0.002 TYR B 49 ARG 0.008 0.001 ARG B 45 Details of bonding type rmsd hydrogen bonds : bond 0.03278 ( 131) hydrogen bonds : angle 5.34707 ( 333) SS BOND : bond 0.01059 ( 6) SS BOND : angle 3.27786 ( 12) covalent geometry : bond 0.00530 ( 5384) covalent geometry : angle 0.77894 ( 7315) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6080.24 seconds wall clock time: 105 minutes 16.60 seconds (6316.60 seconds total)