Starting phenix.real_space_refine on Sun Apr 27 09:42:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jin_36321/04_2025/8jin_36321.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jin_36321/04_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_36321/04_2025/8jin_36321.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jin_36321/04_2025/8jin_36321.map" model { file = "/net/cci-nas-00/data/ceres_data/8jin_36321/04_2025/8jin_36321.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jin_36321/04_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-5669/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: 7.20, per 1000 atoms: 1.37 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: 1.28 Conformation dependent library (CDL) restraints added in 692.7 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: 0.68 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: 1.59 Time building geometry restraints manager: 1.56 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: 9.540 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: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 20.860 Find NCS groups from input model: 0.060 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:17.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.320 ------------------------------------------------------------------------------- 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 : 0.635 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: 0.8609 time to fit residues: 173.3333 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 : 0.547 ------------------------------------------------------------------------------- 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: 0.2980 chunk 38 optimal weight: 0.6980 chunk 59 optimal weight: 0.7980 overall best weight: 0.4580 ------------------------------------------------------------------------------- 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 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 = 0.3905 r_free = 0.3905 target = 0.129528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.121988 restraints weight = 8019.444| |-----------------------------------------------------------------------------| r_work (start): 0.3813 rms_B_bonded: 1.69 r_work: 0.3733 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3613 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.2248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.080 5390 Z= 0.321 Angle : 0.721 7.422 7327 Z= 0.364 Chirality : 0.049 0.170 776 Planarity : 0.005 0.045 950 Dihedral : 7.050 56.060 783 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 : 7.61 % Allowed : 15.93 % 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: -3.26 (0.31), residues: 671 helix: -3.49 (0.69), residues: 28 sheet: -1.60 (0.33), residues: 256 loop : -2.52 (0.29), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 436 HIS 0.004 0.001 HIS P 159 PHE 0.020 0.003 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 0.04306 ( 131) hydrogen bonds : angle 6.58001 ( 333) SS BOND : bond 0.00302 ( 6) SS BOND : angle 0.82735 ( 12) covalent geometry : bond 0.00728 ( 5384) covalent geometry : angle 0.72103 ( 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 184 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 141 time to evaluate : 0.529 Fit side-chains REVERT: P 27 SER cc_start: 0.8284 (m) cc_final: 0.7778 (t) REVERT: P 94 ASP cc_start: 0.7009 (p0) cc_final: 0.6648 (p0) REVERT: P 236 TYR cc_start: 0.8477 (p90) cc_final: 0.7956 (p90) REVERT: B 11 LEU cc_start: 0.7325 (mt) cc_final: 0.7015 (mt) REVERT: B 38 GLN cc_start: 0.8173 (tt0) cc_final: 0.7926 (tt0) REVERT: B 94 TRP cc_start: 0.7561 (OUTLIER) cc_final: 0.7151 (t-100) REVERT: B 97 TYR cc_start: 0.8311 (m-80) cc_final: 0.7710 (m-80) REVERT: B 108 LYS cc_start: 0.6919 (OUTLIER) cc_final: 0.6266 (ptpp) REVERT: B 173 PHE cc_start: 0.8288 (OUTLIER) cc_final: 0.8016 (p90) REVERT: B 196 SER cc_start: 0.8728 (p) cc_final: 0.8510 (t) REVERT: A 380 TYR cc_start: 0.8497 (m-80) cc_final: 0.8243 (m-80) REVERT: A 386 LYS cc_start: 0.8569 (mtmt) cc_final: 0.8352 (mtmt) REVERT: A 405 ASN cc_start: 0.7625 (m-40) cc_final: 0.7412 (m-40) REVERT: A 440 LYS cc_start: 0.8252 (mppt) cc_final: 0.7982 (mppt) REVERT: A 472 ILE cc_start: 0.8505 (OUTLIER) cc_final: 0.8252 (mm) REVERT: A 501 TYR cc_start: 0.7925 (m-10) cc_final: 0.7698 (m-10) outliers start: 43 outliers final: 21 residues processed: 163 average time/residue: 0.8491 time to fit residues: 146.3330 Evaluate side-chains 149 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 124 time to evaluate : 0.504 ------------------------------------------------------------------------------- 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 94 TRP 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: 0.2980 chunk 53 optimal weight: 0.7980 chunk 35 optimal weight: 0.9990 chunk 32 optimal weight: 0.0970 chunk 54 optimal weight: 0.1980 chunk 46 optimal weight: 0.0000 chunk 5 optimal weight: 0.0020 chunk 50 optimal weight: 0.0970 chunk 33 optimal weight: 0.0980 chunk 14 optimal weight: 0.6980 overall best weight: 0.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 6 GLN P 52 ASN 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.131092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.123852 restraints weight = 8084.584| |-----------------------------------------------------------------------------| r_work (start): 0.3869 rms_B_bonded: 1.67 r_work: 0.3792 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3678 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.2450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 5390 Z= 0.100 Angle : 0.607 10.901 7327 Z= 0.294 Chirality : 0.045 0.194 776 Planarity : 0.004 0.038 950 Dihedral : 5.834 44.573 776 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 6.19 % Allowed : 18.94 % Favored : 74.87 % 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: -2.60 (0.32), residues: 671 helix: -2.49 (0.91), residues: 22 sheet: -1.09 (0.36), residues: 231 loop : -2.14 (0.29), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 436 HIS 0.001 0.000 HIS P 159 PHE 0.010 0.001 PHE B 150 TYR 0.019 0.001 TYR P 226 ARG 0.008 0.000 ARG B 45 Details of bonding type rmsd hydrogen bonds : bond 0.03008 ( 131) hydrogen bonds : angle 5.94574 ( 333) SS BOND : bond 0.00418 ( 6) SS BOND : angle 2.08248 ( 12) covalent geometry : bond 0.00219 ( 5384) covalent geometry : angle 0.60188 ( 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 167 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 132 time to evaluate : 0.517 Fit side-chains REVERT: P 27 SER cc_start: 0.8329 (m) cc_final: 0.7932 (t) REVERT: P 94 ASP cc_start: 0.6866 (p0) cc_final: 0.6470 (p0) REVERT: P 236 TYR cc_start: 0.8400 (p90) cc_final: 0.7816 (p90) REVERT: B 11 LEU cc_start: 0.7295 (mt) cc_final: 0.6942 (mt) REVERT: B 38 GLN cc_start: 0.8093 (tt0) cc_final: 0.7849 (tt0) REVERT: B 97 TYR cc_start: 0.8248 (m-80) cc_final: 0.7734 (m-80) REVERT: B 108 LYS cc_start: 0.6800 (OUTLIER) cc_final: 0.6215 (ptpp) REVERT: B 130 SER cc_start: 0.8090 (p) cc_final: 0.7792 (m) REVERT: B 196 SER cc_start: 0.8717 (p) cc_final: 0.8473 (t) REVERT: A 386 LYS cc_start: 0.8368 (mtmt) cc_final: 0.8168 (mtmt) outliers start: 35 outliers final: 17 residues processed: 154 average time/residue: 0.7828 time to fit residues: 127.8555 Evaluate side-chains 145 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 127 time to evaluate : 0.515 ------------------------------------------------------------------------------- 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 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 189 VAL Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 444 LYS Chi-restraints excluded: chain A residue 458 LYS 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: 0.0970 chunk 38 optimal weight: 0.7980 chunk 45 optimal weight: 0.9980 chunk 14 optimal weight: 0.4980 chunk 61 optimal weight: 0.0870 chunk 17 optimal weight: 0.8980 chunk 54 optimal weight: 0.3980 chunk 29 optimal weight: 0.9990 chunk 20 optimal weight: 0.8980 overall best weight: 0.3756 ------------------------------------------------------------------------------- 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 = 0.3886 r_free = 0.3886 target = 0.126872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.119662 restraints weight = 8254.407| |-----------------------------------------------------------------------------| r_work (start): 0.3813 rms_B_bonded: 1.66 r_work: 0.3731 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3614 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.2795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 5390 Z= 0.270 Angle : 0.705 8.961 7327 Z= 0.347 Chirality : 0.050 0.252 776 Planarity : 0.005 0.042 950 Dihedral : 6.220 45.620 774 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.30 % Allowed : 9.54 % Favored : 90.16 % Rotamer: Outliers : 8.14 % Allowed : 18.05 % 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: -2.62 (0.31), residues: 671 helix: -2.81 (0.82), residues: 28 sheet: -1.03 (0.35), residues: 236 loop : -2.18 (0.29), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 436 HIS 0.003 0.001 HIS P 159 PHE 0.019 0.002 PHE B 173 TYR 0.016 0.002 TYR P 218 ARG 0.009 0.001 ARG B 45 Details of bonding type rmsd hydrogen bonds : bond 0.03445 ( 131) hydrogen bonds : angle 6.05274 ( 333) SS BOND : bond 0.00495 ( 6) SS BOND : angle 2.68224 ( 12) covalent geometry : bond 0.00619 ( 5384) covalent geometry : angle 0.69749 ( 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 174 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 128 time to evaluate : 0.526 Fit side-chains REVERT: P 27 SER cc_start: 0.8274 (m) cc_final: 0.7707 (t) REVERT: P 94 ASP cc_start: 0.6913 (p0) cc_final: 0.6536 (p0) REVERT: P 236 TYR cc_start: 0.8477 (p90) cc_final: 0.7888 (p90) REVERT: B 11 LEU cc_start: 0.7232 (mt) cc_final: 0.6938 (mt) REVERT: B 17 GLU cc_start: 0.6161 (OUTLIER) cc_final: 0.5306 (tm-30) REVERT: B 18 ARG cc_start: 0.6765 (ttp-110) cc_final: 0.5866 (tmm-80) REVERT: B 38 GLN cc_start: 0.8117 (tt0) cc_final: 0.7886 (tt0) REVERT: B 94 TRP cc_start: 0.7392 (OUTLIER) cc_final: 0.6923 (t-100) REVERT: B 97 TYR cc_start: 0.8297 (m-80) cc_final: 0.7610 (m-80) REVERT: B 108 LYS cc_start: 0.6892 (OUTLIER) cc_final: 0.6189 (ptpp) REVERT: B 127 LEU cc_start: 0.8686 (OUTLIER) cc_final: 0.8455 (pt) REVERT: B 130 SER cc_start: 0.8146 (OUTLIER) cc_final: 0.7841 (m) REVERT: B 173 PHE cc_start: 0.8230 (OUTLIER) cc_final: 0.7884 (p90) REVERT: B 252 GLN cc_start: 0.7814 (mp10) cc_final: 0.7435 (mp10) REVERT: A 440 LYS cc_start: 0.8261 (mppt) cc_final: 0.8014 (mppt) REVERT: A 468 ILE cc_start: 0.8554 (OUTLIER) cc_final: 0.8306 (mm) REVERT: A 501 TYR cc_start: 0.7855 (m-10) cc_final: 0.7626 (m-10) REVERT: A 518 LEU cc_start: 0.7723 (OUTLIER) cc_final: 0.7270 (pp) outliers start: 46 outliers final: 18 residues processed: 155 average time/residue: 1.0540 time to fit residues: 171.0105 Evaluate side-chains 151 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 125 time to evaluate : 0.565 ------------------------------------------------------------------------------- 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 94 TRP 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 255 THR Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 362 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 468 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: 0.9990 chunk 49 optimal weight: 0.4980 chunk 10 optimal weight: 0.9980 chunk 18 optimal weight: 0.8980 chunk 50 optimal weight: 0.9990 chunk 41 optimal weight: 0.0570 chunk 12 optimal weight: 0.3980 chunk 3 optimal weight: 0.2980 chunk 21 optimal weight: 0.0980 chunk 53 optimal weight: 0.4980 chunk 17 optimal weight: 0.0980 overall best weight: 0.1898 ------------------------------------------------------------------------------- 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 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 = 0.3905 r_free = 0.3905 target = 0.128485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.121386 restraints weight = 8141.065| |-----------------------------------------------------------------------------| r_work (start): 0.3837 rms_B_bonded: 1.65 r_work: 0.3758 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3641 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.2857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 5390 Z= 0.159 Angle : 0.641 8.801 7327 Z= 0.314 Chirality : 0.047 0.242 776 Planarity : 0.004 0.039 950 Dihedral : 5.971 46.330 774 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.86 % Favored : 93.00 % Rotamer: Outliers : 6.37 % Allowed : 20.00 % 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 (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: -2.59 (0.85), residues: 28 sheet: -0.80 (0.36), residues: 230 loop : -2.08 (0.29), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 436 HIS 0.002 0.001 HIS A 519 PHE 0.011 0.001 PHE B 173 TYR 0.022 0.001 TYR P 226 ARG 0.006 0.000 ARG B 45 Details of bonding type rmsd hydrogen bonds : bond 0.02968 ( 131) hydrogen bonds : angle 5.79968 ( 333) SS BOND : bond 0.00498 ( 6) SS BOND : angle 2.57576 ( 12) covalent geometry : bond 0.00366 ( 5384) covalent geometry : angle 0.63269 ( 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 168 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 132 time to evaluate : 0.515 Fit side-chains REVERT: P 27 SER cc_start: 0.8362 (m) cc_final: 0.7886 (t) REVERT: P 94 ASP cc_start: 0.6857 (p0) cc_final: 0.6453 (p0) REVERT: P 236 TYR cc_start: 0.8466 (p90) cc_final: 0.7857 (p90) REVERT: B 11 LEU cc_start: 0.7205 (mt) cc_final: 0.6985 (mt) REVERT: B 38 GLN cc_start: 0.8112 (tt0) cc_final: 0.7858 (tt0) REVERT: B 94 TRP cc_start: 0.7397 (OUTLIER) cc_final: 0.6924 (t-100) REVERT: B 97 TYR cc_start: 0.8281 (m-80) cc_final: 0.7516 (m-80) REVERT: B 108 LYS cc_start: 0.6828 (OUTLIER) cc_final: 0.6163 (ptpp) REVERT: B 127 LEU cc_start: 0.8605 (OUTLIER) cc_final: 0.8316 (pt) REVERT: B 130 SER cc_start: 0.8108 (p) cc_final: 0.7808 (m) REVERT: B 173 PHE cc_start: 0.8173 (OUTLIER) cc_final: 0.7925 (p90) REVERT: A 440 LYS cc_start: 0.8248 (mppt) cc_final: 0.8003 (mppt) REVERT: A 468 ILE cc_start: 0.8571 (OUTLIER) cc_final: 0.8312 (mt) outliers start: 36 outliers final: 20 residues processed: 155 average time/residue: 0.9658 time to fit residues: 157.1225 Evaluate side-chains 154 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 129 time to evaluate : 0.511 ------------------------------------------------------------------------------- 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 107 THR Chi-restraints excluded: chain P residue 130 GLU 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 58 ILE Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 94 TRP 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 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 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 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: 0.0370 chunk 33 optimal weight: 0.1980 chunk 38 optimal weight: 0.0050 chunk 40 optimal weight: 0.4980 chunk 53 optimal weight: 0.9980 chunk 44 optimal weight: 0.0270 chunk 27 optimal weight: 0.6980 chunk 0 optimal weight: 0.6980 overall best weight: 0.1330 ------------------------------------------------------------------------------- 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 487 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.129266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.122135 restraints weight = 8139.934| |-----------------------------------------------------------------------------| r_work (start): 0.3847 rms_B_bonded: 1.65 r_work: 0.3769 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3653 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.2918 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= 0.132 Angle : 0.649 13.749 7327 Z= 0.310 Chirality : 0.046 0.271 776 Planarity : 0.004 0.036 950 Dihedral : 5.773 43.945 774 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.05 % Favored : 91.80 % Rotamer: Outliers : 6.37 % Allowed : 19.47 % Favored : 74.16 % 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: -2.18 (0.32), residues: 671 helix: -2.48 (0.87), residues: 28 sheet: -0.60 (0.37), residues: 221 loop : -1.93 (0.29), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 436 HIS 0.001 0.000 HIS P 159 PHE 0.008 0.001 PHE P 151 TYR 0.018 0.001 TYR B 205 ARG 0.005 0.000 ARG B 45 Details of bonding type rmsd hydrogen bonds : bond 0.02818 ( 131) hydrogen bonds : angle 5.62276 ( 333) SS BOND : bond 0.00486 ( 6) SS BOND : angle 2.80858 ( 12) covalent geometry : bond 0.00315 ( 5384) covalent geometry : angle 0.63985 ( 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 170 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 134 time to evaluate : 0.526 Fit side-chains REVERT: P 27 SER cc_start: 0.8336 (m) cc_final: 0.8030 (t) REVERT: P 236 TYR cc_start: 0.8459 (p90) cc_final: 0.7927 (p90) REVERT: B 38 GLN cc_start: 0.8127 (tt0) cc_final: 0.7879 (tt0) REVERT: B 97 TYR cc_start: 0.8236 (m-80) cc_final: 0.7735 (m-80) REVERT: B 108 LYS cc_start: 0.6847 (OUTLIER) cc_final: 0.6208 (ptpp) REVERT: B 127 LEU cc_start: 0.8563 (OUTLIER) cc_final: 0.8272 (pt) REVERT: B 130 SER cc_start: 0.8050 (p) cc_final: 0.7786 (m) REVERT: A 440 LYS cc_start: 0.8218 (mppt) cc_final: 0.7991 (mppt) REVERT: A 468 ILE cc_start: 0.8566 (OUTLIER) cc_final: 0.8311 (mt) outliers start: 36 outliers final: 18 residues processed: 153 average time/residue: 1.0242 time to fit residues: 164.0661 Evaluate side-chains 151 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 130 time to evaluate : 0.572 ------------------------------------------------------------------------------- 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 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 146 THR Chi-restraints excluded: chain B residue 183 THR 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 430 THR Chi-restraints excluded: chain A residue 444 LYS Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 468 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: 0.0020 chunk 40 optimal weight: 0.9980 chunk 19 optimal weight: 0.6980 chunk 45 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 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: 0.0170 chunk 8 optimal weight: 0.2980 overall best weight: 0.2426 ------------------------------------------------------------------------------- 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 394 ASN A 487 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.128202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.121020 restraints weight = 7996.322| |-----------------------------------------------------------------------------| r_work (start): 0.3831 rms_B_bonded: 1.64 r_work: 0.3753 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3637 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.2954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.098 5390 Z= 0.196 Angle : 0.711 14.752 7327 Z= 0.340 Chirality : 0.049 0.348 776 Planarity : 0.004 0.039 950 Dihedral : 6.015 44.393 774 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.64 % Favored : 91.21 % Rotamer: Outliers : 5.84 % Allowed : 22.30 % Favored : 71.86 % 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: -2.14 (0.32), residues: 671 helix: -2.47 (0.87), residues: 28 sheet: -0.65 (0.36), residues: 231 loop : -1.87 (0.30), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 436 HIS 0.002 0.001 HIS P 159 PHE 0.011 0.002 PHE B 152 TYR 0.015 0.002 TYR B 205 ARG 0.004 0.000 ARG B 142 Details of bonding type rmsd hydrogen bonds : bond 0.03125 ( 131) hydrogen bonds : angle 5.54903 ( 333) SS BOND : bond 0.00904 ( 6) SS BOND : angle 3.28021 ( 12) covalent geometry : bond 0.00461 ( 5384) covalent geometry : angle 0.69907 ( 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 162 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 129 time to evaluate : 0.544 Fit side-chains REVERT: P 236 TYR cc_start: 0.8471 (p90) cc_final: 0.7945 (p90) REVERT: B 38 GLN cc_start: 0.8129 (tt0) cc_final: 0.7884 (tt0) REVERT: B 97 TYR cc_start: 0.8307 (m-80) cc_final: 0.7668 (m-80) REVERT: B 108 LYS cc_start: 0.6811 (OUTLIER) cc_final: 0.6198 (ptpp) REVERT: B 127 LEU cc_start: 0.8624 (OUTLIER) cc_final: 0.8379 (pt) REVERT: B 130 SER cc_start: 0.8117 (p) cc_final: 0.7852 (m) REVERT: B 173 PHE cc_start: 0.8179 (OUTLIER) cc_final: 0.7962 (p90) REVERT: A 440 LYS cc_start: 0.8255 (mppt) cc_final: 0.8029 (mppt) REVERT: A 468 ILE cc_start: 0.8519 (OUTLIER) cc_final: 0.8248 (mm) outliers start: 33 outliers final: 18 residues processed: 148 average time/residue: 1.0382 time to fit residues: 161.2765 Evaluate side-chains 151 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 129 time to evaluate : 0.528 ------------------------------------------------------------------------------- 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 212 THR Chi-restraints excluded: chain P residue 245 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 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 478 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 46 optimal weight: 0.4980 chunk 39 optimal weight: 0.0970 chunk 0 optimal weight: 0.6980 chunk 42 optimal weight: 0.4980 chunk 61 optimal weight: 0.2980 chunk 14 optimal weight: 0.8980 chunk 37 optimal weight: 0.0970 chunk 34 optimal weight: 0.8980 chunk 35 optimal weight: 0.3980 chunk 40 optimal weight: 0.1980 chunk 43 optimal weight: 0.3980 overall best weight: 0.2176 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.130869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.123415 restraints weight = 8085.278| |-----------------------------------------------------------------------------| r_work (start): 0.3831 rms_B_bonded: 1.67 r_work: 0.3752 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3635 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.3053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 5390 Z= 0.178 Angle : 0.696 12.763 7327 Z= 0.334 Chirality : 0.048 0.310 776 Planarity : 0.004 0.046 950 Dihedral : 6.008 45.612 774 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.75 % Favored : 92.10 % Rotamer: Outliers : 5.49 % Allowed : 23.36 % 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: -2.11 (0.32), residues: 671 helix: -2.42 (0.87), residues: 28 sheet: -0.67 (0.36), residues: 231 loop : -1.82 (0.30), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 94 HIS 0.002 0.001 HIS P 159 PHE 0.011 0.002 PHE A 400 TYR 0.012 0.001 TYR P 226 ARG 0.006 0.000 ARG B 142 Details of bonding type rmsd hydrogen bonds : bond 0.03133 ( 131) hydrogen bonds : angle 5.46895 ( 333) SS BOND : bond 0.00801 ( 6) SS BOND : angle 3.00188 ( 12) covalent geometry : bond 0.00420 ( 5384) covalent geometry : angle 0.68625 ( 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 159 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 128 time to evaluate : 0.576 Fit side-chains REVERT: P 236 TYR cc_start: 0.8466 (p90) cc_final: 0.7938 (p90) REVERT: P 249 VAL cc_start: 0.8175 (OUTLIER) cc_final: 0.7880 (m) REVERT: B 38 GLN cc_start: 0.8166 (tt0) cc_final: 0.7938 (tt0) REVERT: B 97 TYR cc_start: 0.8258 (m-80) cc_final: 0.7803 (m-80) REVERT: B 108 LYS cc_start: 0.6821 (OUTLIER) cc_final: 0.6242 (ptpp) REVERT: B 127 LEU cc_start: 0.8631 (OUTLIER) cc_final: 0.8383 (pt) REVERT: B 130 SER cc_start: 0.8079 (p) cc_final: 0.7823 (m) REVERT: B 173 PHE cc_start: 0.8182 (OUTLIER) cc_final: 0.7955 (p90) REVERT: A 440 LYS cc_start: 0.8220 (mppt) cc_final: 0.8013 (mppt) REVERT: A 468 ILE cc_start: 0.8518 (OUTLIER) cc_final: 0.8270 (mt) outliers start: 31 outliers final: 20 residues processed: 148 average time/residue: 0.9631 time to fit residues: 150.0269 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 : 0.571 ------------------------------------------------------------------------------- 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 212 THR Chi-restraints excluded: chain P residue 245 THR Chi-restraints excluded: chain P residue 249 VAL 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 A residue 332 ILE Chi-restraints excluded: chain A residue 383 SER 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 478 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 32 optimal weight: 0.2980 chunk 43 optimal weight: 0.7980 chunk 18 optimal weight: 0.9990 chunk 60 optimal weight: 0.6980 chunk 16 optimal weight: 0.7980 chunk 6 optimal weight: 0.1980 chunk 19 optimal weight: 0.3980 chunk 24 optimal weight: 0.4980 chunk 17 optimal weight: 0.2980 chunk 54 optimal weight: 0.3980 chunk 46 optimal weight: 0.0970 overall best weight: 0.2578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 96 GLN B 252 GLN A 394 ASN A 487 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.129956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.122548 restraints weight = 8181.604| |-----------------------------------------------------------------------------| r_work (start): 0.3817 rms_B_bonded: 1.69 r_work: 0.3737 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3619 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.3144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.091 5390 Z= 0.203 Angle : 0.736 17.865 7327 Z= 0.352 Chirality : 0.049 0.308 776 Planarity : 0.005 0.049 950 Dihedral : 6.140 46.470 774 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.49 % Favored : 91.36 % Rotamer: Outliers : 5.13 % Allowed : 24.07 % 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: -2.08 (0.32), residues: 671 helix: -2.40 (0.88), residues: 28 sheet: -0.64 (0.36), residues: 231 loop : -1.81 (0.30), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 94 HIS 0.002 0.001 HIS P 159 PHE 0.013 0.002 PHE B 152 TYR 0.013 0.002 TYR B 49 ARG 0.006 0.000 ARG B 142 Details of bonding type rmsd hydrogen bonds : bond 0.03219 ( 131) hydrogen bonds : angle 5.50199 ( 333) SS BOND : bond 0.00877 ( 6) SS BOND : angle 2.86565 ( 12) covalent geometry : bond 0.00476 ( 5384) covalent geometry : angle 0.72690 ( 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 160 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 131 time to evaluate : 0.546 Fit side-chains REVERT: P 27 SER cc_start: 0.8344 (m) cc_final: 0.8054 (t) REVERT: P 236 TYR cc_start: 0.8438 (p90) cc_final: 0.7916 (p90) REVERT: P 249 VAL cc_start: 0.8186 (OUTLIER) cc_final: 0.7891 (m) REVERT: B 38 GLN cc_start: 0.8142 (tt0) cc_final: 0.7912 (tt0) REVERT: B 54 ARG cc_start: 0.8496 (ttp80) cc_final: 0.8237 (ttp-110) REVERT: B 97 TYR cc_start: 0.8185 (m-80) cc_final: 0.7737 (m-80) REVERT: B 108 LYS cc_start: 0.6879 (OUTLIER) cc_final: 0.6315 (ptpp) REVERT: B 127 LEU cc_start: 0.8665 (OUTLIER) cc_final: 0.8428 (pt) REVERT: B 130 SER cc_start: 0.8026 (p) cc_final: 0.7806 (m) REVERT: A 468 ILE cc_start: 0.8496 (OUTLIER) cc_final: 0.8251 (mm) outliers start: 29 outliers final: 23 residues processed: 150 average time/residue: 1.0405 time to fit residues: 163.6291 Evaluate side-chains 160 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 133 time to evaluate : 0.570 ------------------------------------------------------------------------------- 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 144 LEU Chi-restraints excluded: chain P residue 211 ARG Chi-restraints excluded: chain P residue 212 THR Chi-restraints excluded: chain P residue 245 THR Chi-restraints excluded: chain P residue 249 VAL 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 183 THR Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 383 SER 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 478 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 36 optimal weight: 0.0980 chunk 24 optimal weight: 0.3980 chunk 55 optimal weight: 0.7980 chunk 59 optimal weight: 0.4980 chunk 61 optimal weight: 0.6980 chunk 7 optimal weight: 0.9990 chunk 64 optimal weight: 0.0770 chunk 0 optimal weight: 0.6980 chunk 9 optimal weight: 0.0980 chunk 15 optimal weight: 0.7980 chunk 32 optimal weight: 0.0870 overall best weight: 0.1516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 6 GLN B 89 GLN B 162 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.129162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.121961 restraints weight = 8143.673| |-----------------------------------------------------------------------------| r_work (start): 0.3844 rms_B_bonded: 1.64 r_work: 0.3767 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3652 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.3191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 5390 Z= 0.148 Angle : 0.712 17.032 7327 Z= 0.340 Chirality : 0.047 0.272 776 Planarity : 0.004 0.046 950 Dihedral : 5.955 45.890 774 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.86 % Favored : 93.00 % Rotamer: Outliers : 4.96 % Allowed : 24.42 % 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 (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: -1.96 (0.32), residues: 671 helix: -2.35 (0.88), residues: 28 sheet: -0.61 (0.36), residues: 226 loop : -1.68 (0.30), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 94 HIS 0.002 0.001 HIS P 159 PHE 0.010 0.001 PHE A 400 TYR 0.012 0.001 TYR P 226 ARG 0.005 0.000 ARG B 142 Details of bonding type rmsd hydrogen bonds : bond 0.03052 ( 131) hydrogen bonds : angle 5.38419 ( 333) SS BOND : bond 0.00848 ( 6) SS BOND : angle 2.59408 ( 12) covalent geometry : bond 0.00354 ( 5384) covalent geometry : angle 0.70431 ( 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 158 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 130 time to evaluate : 0.583 Fit side-chains REVERT: P 27 SER cc_start: 0.8369 (m) cc_final: 0.7878 (t) REVERT: P 94 ASP cc_start: 0.6867 (p0) cc_final: 0.6429 (p0) REVERT: P 236 TYR cc_start: 0.8442 (p90) cc_final: 0.7909 (p90) REVERT: P 249 VAL cc_start: 0.8180 (OUTLIER) cc_final: 0.7882 (m) REVERT: B 38 GLN cc_start: 0.8168 (tt0) cc_final: 0.7930 (tt0) REVERT: B 54 ARG cc_start: 0.8493 (ttp80) cc_final: 0.8227 (ttp-110) REVERT: B 108 LYS cc_start: 0.6776 (OUTLIER) cc_final: 0.6216 (ptpp) REVERT: B 127 LEU cc_start: 0.8629 (OUTLIER) cc_final: 0.8368 (pt) REVERT: B 130 SER cc_start: 0.8070 (p) cc_final: 0.7827 (m) REVERT: A 468 ILE cc_start: 0.8523 (OUTLIER) cc_final: 0.8261 (mm) outliers start: 28 outliers final: 19 residues processed: 148 average time/residue: 1.0058 time to fit residues: 156.4620 Evaluate side-chains 155 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 132 time to evaluate : 0.598 ------------------------------------------------------------------------------- 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 144 LEU Chi-restraints excluded: chain P residue 211 ARG Chi-restraints excluded: chain P residue 212 THR Chi-restraints excluded: chain P residue 245 THR Chi-restraints excluded: chain P residue 249 VAL 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 183 THR Chi-restraints excluded: chain A residue 332 ILE 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 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: 0.9980 chunk 62 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 3 optimal weight: 0.1980 chunk 10 optimal weight: 0.6980 chunk 26 optimal weight: 0.7980 chunk 0 optimal weight: 0.2980 chunk 41 optimal weight: 0.2980 chunk 5 optimal weight: 0.3980 chunk 50 optimal weight: 0.9990 overall best weight: 0.3780 ------------------------------------------------------------------------------- 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 = 0.3900 r_free = 0.3900 target = 0.129154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.121556 restraints weight = 8225.043| |-----------------------------------------------------------------------------| r_work (start): 0.3800 rms_B_bonded: 1.72 r_work: 0.3719 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3599 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.3299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.088 5390 Z= 0.280 Angle : 0.790 16.830 7327 Z= 0.382 Chirality : 0.051 0.299 776 Planarity : 0.005 0.072 950 Dihedral : 6.469 48.956 774 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.30 % Allowed : 9.54 % Favored : 90.16 % Rotamer: Outliers : 5.31 % Allowed : 24.42 % Favored : 70.27 % 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: -2.12 (0.32), residues: 671 helix: -2.89 (0.74), residues: 34 sheet: -0.74 (0.36), residues: 231 loop : -1.72 (0.30), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 94 HIS 0.004 0.001 HIS A 339 PHE 0.018 0.002 PHE B 152 TYR 0.017 0.002 TYR B 49 ARG 0.006 0.001 ARG P 143 Details of bonding type rmsd hydrogen bonds : bond 0.03518 ( 131) hydrogen bonds : angle 5.75256 ( 333) SS BOND : bond 0.00885 ( 6) SS BOND : angle 2.87460 ( 12) covalent geometry : bond 0.00651 ( 5384) covalent geometry : angle 0.78183 ( 7315) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6408.79 seconds wall clock time: 109 minutes 32.83 seconds (6572.83 seconds total)