Starting phenix.real_space_refine on Thu Nov 14 08:57:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jin_36321/11_2024/8jin_36321.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jin_36321/11_2024/8jin_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jin_36321/11_2024/8jin_36321.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jin_36321/11_2024/8jin_36321.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jin_36321/11_2024/8jin_36321.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jin_36321/11_2024/8jin_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-5513/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: 6.24, per 1000 atoms: 1.19 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: 1.12 Conformation dependent library (CDL) restraints added in 693.3 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: 0.70 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: 1.50 Time building geometry restraints manager: 1.37 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: 10.530 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: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.070 Process input model: 18.840 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:14.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.870 ------------------------------------------------------------------------------- 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 5384 Z= 0.144 Angle : 0.537 5.260 7315 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 *********************** 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 : 0.592 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: 0.8895 time to fit residues: 179.2797 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 : 0.607 ------------------------------------------------------------------------------- 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: 0.4980 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: 0.3980 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.2133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 5384 Z= 0.410 Angle : 0.693 7.378 7315 Z= 0.348 Chirality : 0.048 0.170 776 Planarity : 0.005 0.044 950 Dihedral : 6.894 56.325 783 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.30 % Allowed : 9.69 % Favored : 90.01 % Rotamer: Outliers : 7.08 % Allowed : 16.28 % Favored : 76.64 % 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: -3.27 (0.30), residues: 671 helix: -3.48 (0.70), residues: 28 sheet: -1.62 (0.35), residues: 236 loop : -2.51 (0.28), residues: 407 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 0.006 0.001 ARG B 197 *********************** 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 179 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 139 time to evaluate : 0.603 Fit side-chains REVERT: P 27 SER cc_start: 0.8105 (m) cc_final: 0.7440 (t) REVERT: P 94 ASP cc_start: 0.6602 (p0) cc_final: 0.6199 (p0) REVERT: P 193 SER cc_start: 0.7994 (t) cc_final: 0.7693 (p) REVERT: P 236 TYR cc_start: 0.8419 (p90) cc_final: 0.7779 (p90) REVERT: B 11 LEU cc_start: 0.6885 (mt) cc_final: 0.6452 (mt) REVERT: B 38 GLN cc_start: 0.8128 (tt0) cc_final: 0.7847 (tt0) REVERT: B 39 LYS cc_start: 0.8279 (mmtm) cc_final: 0.8019 (mmmm) REVERT: B 97 TYR cc_start: 0.8158 (m-80) cc_final: 0.7713 (m-80) REVERT: B 106 GLU cc_start: 0.6574 (OUTLIER) cc_final: 0.6359 (pm20) REVERT: B 108 LYS cc_start: 0.4926 (OUTLIER) cc_final: 0.4617 (ptpp) REVERT: B 196 SER cc_start: 0.8429 (p) cc_final: 0.8140 (t) REVERT: B 249 VAL cc_start: 0.8757 (t) cc_final: 0.8374 (m) REVERT: A 380 TYR cc_start: 0.8438 (m-80) cc_final: 0.8154 (m-80) REVERT: A 386 LYS cc_start: 0.8437 (mtmt) cc_final: 0.8176 (mtmt) REVERT: A 440 LYS cc_start: 0.8029 (mppt) cc_final: 0.7765 (mppt) REVERT: A 470 THR cc_start: 0.9051 (p) cc_final: 0.8818 (t) REVERT: A 472 ILE cc_start: 0.8300 (OUTLIER) cc_final: 0.8035 (mm) REVERT: A 501 TYR cc_start: 0.7546 (m-10) cc_final: 0.7280 (m-10) REVERT: A 518 LEU cc_start: 0.7700 (OUTLIER) cc_final: 0.7495 (pp) outliers start: 40 outliers final: 20 residues processed: 158 average time/residue: 0.9138 time to fit residues: 153.1052 Evaluate side-chains 147 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 123 time to evaluate : 0.693 ------------------------------------------------------------------------------- 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 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 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 Chi-restraints excluded: chain A residue 518 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 33 optimal weight: 0.2980 chunk 18 optimal weight: 0.9980 chunk 49 optimal weight: 0.0040 chunk 40 optimal weight: 0.6980 chunk 16 optimal weight: 0.8980 chunk 60 optimal weight: 0.4980 chunk 64 optimal weight: 0.0670 chunk 53 optimal weight: 0.7980 chunk 59 optimal weight: 0.6980 chunk 20 optimal weight: 0.0670 chunk 48 optimal weight: 0.4980 overall best weight: 0.1868 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 32 ASN B 89 GLN B 96 GLN B 126 GLN A 370 ASN A 439 ASN A 487 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 moved from start: 0.2469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 5384 Z= 0.221 Angle : 0.619 7.916 7315 Z= 0.306 Chirality : 0.046 0.207 776 Planarity : 0.004 0.039 950 Dihedral : 6.103 44.610 776 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.71 % Favored : 93.14 % Rotamer: Outliers : 7.26 % Allowed : 18.23 % 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: -2.83 (0.31), residues: 671 helix: -3.08 (0.76), residues: 28 sheet: -1.20 (0.35), residues: 232 loop : -2.29 (0.29), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 436 HIS 0.002 0.000 HIS P 159 PHE 0.014 0.001 PHE B 173 TYR 0.020 0.001 TYR P 226 ARG 0.008 0.001 ARG B 45 *********************** 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: 41 poor density : 126 time to evaluate : 0.618 Fit side-chains REVERT: P 27 SER cc_start: 0.8190 (m) cc_final: 0.7495 (t) REVERT: P 94 ASP cc_start: 0.6545 (p0) cc_final: 0.6103 (p0) REVERT: P 236 TYR cc_start: 0.8404 (p90) cc_final: 0.7796 (p90) REVERT: B 11 LEU cc_start: 0.6790 (mt) cc_final: 0.6349 (mt) REVERT: B 17 GLU cc_start: 0.5508 (OUTLIER) cc_final: 0.5041 (tm-30) REVERT: B 38 GLN cc_start: 0.8111 (tt0) cc_final: 0.7836 (tt0) REVERT: B 56 THR cc_start: 0.8485 (m) cc_final: 0.8232 (p) REVERT: B 94 TRP cc_start: 0.7486 (OUTLIER) cc_final: 0.6860 (t-100) REVERT: B 97 TYR cc_start: 0.8103 (m-80) cc_final: 0.7313 (m-80) REVERT: B 106 GLU cc_start: 0.6430 (OUTLIER) cc_final: 0.6148 (pm20) REVERT: B 108 LYS cc_start: 0.4908 (OUTLIER) cc_final: 0.4627 (ptpp) REVERT: B 130 SER cc_start: 0.7978 (p) cc_final: 0.7585 (m) REVERT: B 249 VAL cc_start: 0.8794 (t) cc_final: 0.8462 (m) REVERT: A 386 LYS cc_start: 0.8350 (mtmt) cc_final: 0.8117 (mtmt) REVERT: A 440 LYS cc_start: 0.8037 (mppt) cc_final: 0.7779 (mppt) REVERT: A 470 THR cc_start: 0.9015 (p) cc_final: 0.8796 (t) REVERT: A 472 ILE cc_start: 0.8306 (OUTLIER) cc_final: 0.8062 (mm) REVERT: A 518 LEU cc_start: 0.7569 (OUTLIER) cc_final: 0.6936 (pp) outliers start: 41 outliers final: 21 residues processed: 149 average time/residue: 0.8356 time to fit residues: 132.3582 Evaluate side-chains 148 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 121 time to evaluate : 0.604 ------------------------------------------------------------------------------- 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 129 VAL Chi-restraints excluded: chain P residue 212 THR Chi-restraints excluded: chain P residue 245 THR Chi-restraints excluded: chain P residue 250 SER Chi-restraints excluded: chain B residue 17 GLU Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 94 TRP Chi-restraints excluded: chain B residue 106 GLU 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 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 Chi-restraints excluded: chain A residue 518 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 59 optimal weight: 0.8980 chunk 45 optimal weight: 0.0170 chunk 31 optimal weight: 0.0980 chunk 6 optimal weight: 0.8980 chunk 28 optimal weight: 0.0020 chunk 40 optimal weight: 0.5980 chunk 60 optimal weight: 0.5980 chunk 63 optimal weight: 0.3980 chunk 57 optimal weight: 0.0970 chunk 17 optimal weight: 0.8980 chunk 53 optimal weight: 0.9980 overall best weight: 0.1224 ------------------------------------------------------------------------------- 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 207 GLN A 370 ASN A 439 ASN A 487 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7435 moved from start: 0.2621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 5384 Z= 0.176 Angle : 0.601 8.313 7315 Z= 0.294 Chirality : 0.045 0.212 776 Planarity : 0.004 0.038 950 Dihedral : 5.905 44.116 776 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.60 % Favored : 92.25 % Rotamer: Outliers : 6.55 % Allowed : 19.82 % 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: -2.46 (0.32), residues: 671 helix: -2.82 (0.80), residues: 28 sheet: -0.87 (0.36), residues: 224 loop : -2.07 (0.29), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 436 HIS 0.001 0.001 HIS P 159 PHE 0.012 0.001 PHE B 173 TYR 0.020 0.001 TYR P 226 ARG 0.008 0.000 ARG B 45 *********************** 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: 37 poor density : 140 time to evaluate : 0.577 Fit side-chains REVERT: P 27 SER cc_start: 0.8158 (m) cc_final: 0.7659 (t) REVERT: P 96 LEU cc_start: 0.8288 (mt) cc_final: 0.8073 (mm) REVERT: P 236 TYR cc_start: 0.8392 (p90) cc_final: 0.7753 (p90) REVERT: B 11 LEU cc_start: 0.6797 (mt) cc_final: 0.6277 (mt) REVERT: B 17 GLU cc_start: 0.5326 (OUTLIER) cc_final: 0.5116 (tm-30) REVERT: B 38 GLN cc_start: 0.8080 (tt0) cc_final: 0.7813 (tt0) REVERT: B 56 THR cc_start: 0.8456 (m) cc_final: 0.8230 (p) REVERT: B 94 TRP cc_start: 0.7348 (OUTLIER) cc_final: 0.7096 (t-100) REVERT: B 97 TYR cc_start: 0.8063 (m-80) cc_final: 0.7438 (m-80) REVERT: B 106 GLU cc_start: 0.6450 (OUTLIER) cc_final: 0.6139 (pm20) REVERT: B 108 LYS cc_start: 0.4967 (OUTLIER) cc_final: 0.4710 (ptpp) REVERT: B 130 SER cc_start: 0.7946 (p) cc_final: 0.7584 (m) REVERT: B 249 VAL cc_start: 0.8754 (t) cc_final: 0.8460 (m) REVERT: A 386 LYS cc_start: 0.8316 (mtmt) cc_final: 0.8075 (mtmt) REVERT: A 440 LYS cc_start: 0.7917 (mppt) cc_final: 0.7659 (mppt) REVERT: A 468 ILE cc_start: 0.8369 (OUTLIER) cc_final: 0.8086 (mm) REVERT: A 472 ILE cc_start: 0.8309 (OUTLIER) cc_final: 0.8076 (mm) outliers start: 37 outliers final: 15 residues processed: 159 average time/residue: 1.0057 time to fit residues: 168.0208 Evaluate side-chains 155 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 134 time to evaluate : 0.589 ------------------------------------------------------------------------------- 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 B residue 17 GLU 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 106 GLU 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 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 468 ILE Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 478 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 36 optimal weight: 0.2980 chunk 0 optimal weight: 0.7980 chunk 47 optimal weight: 0.7980 chunk 26 optimal weight: 0.6980 chunk 54 optimal weight: 0.3980 chunk 44 optimal weight: 0.0970 chunk 32 optimal weight: 0.3980 chunk 57 optimal weight: 0.0970 chunk 16 optimal weight: 0.9990 chunk 21 optimal weight: 0.3980 chunk 12 optimal weight: 0.5980 overall best weight: 0.2576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 89 GLN B 162 GLN B 207 GLN A 370 ASN A 394 ASN A 487 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 moved from start: 0.2821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 5384 Z= 0.286 Angle : 0.640 9.397 7315 Z= 0.315 Chirality : 0.047 0.245 776 Planarity : 0.004 0.039 950 Dihedral : 6.217 43.655 776 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.35 % Favored : 91.51 % Rotamer: Outliers : 8.32 % Allowed : 17.70 % Favored : 73.98 % 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: -2.37 (0.32), residues: 671 helix: -2.56 (0.87), residues: 28 sheet: -0.84 (0.36), residues: 230 loop : -2.02 (0.29), residues: 413 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 0.013 0.002 PHE B 173 TYR 0.014 0.002 TYR P 226 ARG 0.005 0.000 ARG B 45 *********************** 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 170 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 123 time to evaluate : 0.589 Fit side-chains REVERT: P 27 SER cc_start: 0.8174 (m) cc_final: 0.7637 (t) REVERT: P 236 TYR cc_start: 0.8413 (p90) cc_final: 0.7796 (p90) REVERT: B 11 LEU cc_start: 0.6792 (mt) cc_final: 0.6329 (mt) REVERT: B 17 GLU cc_start: 0.5533 (OUTLIER) cc_final: 0.5138 (tm-30) REVERT: B 38 GLN cc_start: 0.8082 (tt0) cc_final: 0.7813 (tt0) REVERT: B 56 THR cc_start: 0.8458 (m) cc_final: 0.8221 (p) REVERT: B 94 TRP cc_start: 0.7376 (OUTLIER) cc_final: 0.7152 (t-100) REVERT: B 97 TYR cc_start: 0.8129 (m-80) cc_final: 0.7503 (m-80) REVERT: B 106 GLU cc_start: 0.6545 (OUTLIER) cc_final: 0.6246 (pm20) REVERT: B 108 LYS cc_start: 0.4916 (OUTLIER) cc_final: 0.4617 (ptpp) REVERT: B 130 SER cc_start: 0.7979 (OUTLIER) cc_final: 0.7601 (m) REVERT: B 249 VAL cc_start: 0.8735 (t) cc_final: 0.8411 (m) REVERT: B 252 GLN cc_start: 0.7230 (mp10) cc_final: 0.6798 (mp10) REVERT: A 386 LYS cc_start: 0.8389 (mtmt) cc_final: 0.8142 (mtmt) REVERT: A 440 LYS cc_start: 0.8001 (mppt) cc_final: 0.7763 (mppt) REVERT: A 468 ILE cc_start: 0.8359 (OUTLIER) cc_final: 0.8093 (mm) REVERT: A 472 ILE cc_start: 0.8359 (OUTLIER) cc_final: 0.8097 (mm) REVERT: A 501 TYR cc_start: 0.7473 (m-10) cc_final: 0.7155 (m-10) outliers start: 47 outliers final: 20 residues processed: 152 average time/residue: 0.8383 time to fit residues: 135.2953 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 : 0.580 ------------------------------------------------------------------------------- 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 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 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 183 THR Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 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 37 optimal weight: 0.4980 chunk 15 optimal weight: 0.0670 chunk 63 optimal weight: 0.3980 chunk 53 optimal weight: 0.9980 chunk 29 optimal weight: 0.9980 chunk 5 optimal weight: 0.0010 chunk 21 optimal weight: 0.0670 chunk 33 optimal weight: 0.1980 chunk 61 optimal weight: 0.0870 chunk 7 optimal weight: 0.9990 chunk 36 optimal weight: 0.0970 overall best weight: 0.0638 ------------------------------------------------------------------------------- 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 162 GLN A 487 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7402 moved from start: 0.2906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.071 5384 Z= 0.154 Angle : 0.593 9.444 7315 Z= 0.284 Chirality : 0.045 0.255 776 Planarity : 0.004 0.040 950 Dihedral : 5.693 43.493 776 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 6.19 % Allowed : 20.00 % 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: -2.09 (0.32), residues: 671 helix: -2.48 (0.86), residues: 28 sheet: -0.67 (0.37), residues: 228 loop : -1.79 (0.30), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 94 HIS 0.001 0.000 HIS P 159 PHE 0.011 0.001 PHE B 173 TYR 0.012 0.001 TYR A 380 ARG 0.010 0.000 ARG B 45 *********************** 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 167 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 132 time to evaluate : 0.594 Fit side-chains REVERT: P 236 TYR cc_start: 0.8368 (p90) cc_final: 0.7703 (p90) REVERT: B 11 LEU cc_start: 0.6588 (mt) cc_final: 0.5880 (mt) REVERT: B 38 GLN cc_start: 0.8073 (tt0) cc_final: 0.7804 (tt0) REVERT: B 56 THR cc_start: 0.8442 (m) cc_final: 0.8229 (p) REVERT: B 97 TYR cc_start: 0.8033 (m-80) cc_final: 0.7475 (m-80) REVERT: B 106 GLU cc_start: 0.6456 (OUTLIER) cc_final: 0.6157 (pm20) REVERT: B 108 LYS cc_start: 0.5051 (OUTLIER) cc_final: 0.4836 (ptpp) REVERT: B 130 SER cc_start: 0.7864 (p) cc_final: 0.7476 (m) REVERT: B 249 VAL cc_start: 0.8756 (t) cc_final: 0.8524 (m) REVERT: A 440 LYS cc_start: 0.7886 (mppt) cc_final: 0.7676 (mppt) REVERT: A 468 ILE cc_start: 0.8374 (OUTLIER) cc_final: 0.8130 (mt) REVERT: A 472 ILE cc_start: 0.8333 (OUTLIER) cc_final: 0.8103 (mm) outliers start: 35 outliers final: 16 residues processed: 149 average time/residue: 0.8879 time to fit residues: 139.7250 Evaluate side-chains 149 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 129 time to evaluate : 0.634 ------------------------------------------------------------------------------- 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 3 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 106 GLU Chi-restraints excluded: chain B residue 108 LYS Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain A residue 332 ILE 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 46 optimal weight: 0.1980 chunk 36 optimal weight: 0.8980 chunk 53 optimal weight: 0.4980 chunk 35 optimal weight: 0.0070 chunk 63 optimal weight: 0.5980 chunk 39 optimal weight: 0.0570 chunk 38 optimal weight: 0.6980 chunk 29 optimal weight: 0.9980 chunk 25 optimal weight: 0.2980 chunk 37 optimal weight: 0.0970 chunk 19 optimal weight: 0.0570 overall best weight: 0.0832 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 201 ASN B 89 GLN B 96 GLN B 162 GLN B 207 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7400 moved from start: 0.2950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.100 5384 Z= 0.173 Angle : 0.632 17.408 7315 Z= 0.300 Chirality : 0.045 0.312 776 Planarity : 0.004 0.047 950 Dihedral : 5.567 42.352 776 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.86 % Favored : 93.14 % Rotamer: Outliers : 5.13 % Allowed : 22.30 % Favored : 72.57 % 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: -1.90 (0.33), residues: 671 helix: -2.45 (0.86), residues: 28 sheet: -0.46 (0.37), residues: 226 loop : -1.70 (0.30), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 436 HIS 0.001 0.000 HIS P 159 PHE 0.008 0.001 PHE A 400 TYR 0.010 0.001 TYR A 380 ARG 0.011 0.000 ARG B 45 *********************** 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 165 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 136 time to evaluate : 0.571 Fit side-chains REVERT: P 27 SER cc_start: 0.8192 (m) cc_final: 0.7585 (t) REVERT: P 202 SER cc_start: 0.8211 (p) cc_final: 0.8002 (p) REVERT: P 236 TYR cc_start: 0.8383 (p90) cc_final: 0.7691 (p90) REVERT: B 11 LEU cc_start: 0.6606 (mt) cc_final: 0.5886 (mt) REVERT: B 38 GLN cc_start: 0.8067 (tt0) cc_final: 0.7824 (tt0) REVERT: B 106 GLU cc_start: 0.6537 (OUTLIER) cc_final: 0.6217 (pm20) REVERT: B 108 LYS cc_start: 0.5090 (OUTLIER) cc_final: 0.4864 (ptpp) REVERT: B 127 LEU cc_start: 0.8569 (OUTLIER) cc_final: 0.8345 (pt) REVERT: B 130 SER cc_start: 0.7868 (p) cc_final: 0.7466 (m) REVERT: B 197 ARG cc_start: 0.8700 (mtp85) cc_final: 0.8305 (mtp85) REVERT: B 249 VAL cc_start: 0.8745 (t) cc_final: 0.8489 (m) REVERT: A 440 LYS cc_start: 0.7896 (mppt) cc_final: 0.7687 (mppt) REVERT: A 468 ILE cc_start: 0.8321 (OUTLIER) cc_final: 0.8110 (mm) REVERT: A 472 ILE cc_start: 0.8326 (OUTLIER) cc_final: 0.8093 (mm) outliers start: 29 outliers final: 17 residues processed: 147 average time/residue: 1.1299 time to fit residues: 174.9418 Evaluate side-chains 157 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 135 time to evaluate : 0.611 ------------------------------------------------------------------------------- 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 3 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 106 GLU Chi-restraints excluded: chain B residue 108 LYS Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 362 VAL 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 12 optimal weight: 0.5980 chunk 40 optimal weight: 0.9990 chunk 43 optimal weight: 0.8980 chunk 31 optimal weight: 0.1980 chunk 5 optimal weight: 0.0670 chunk 50 optimal weight: 0.9980 chunk 57 optimal weight: 0.0670 chunk 60 optimal weight: 0.8980 chunk 55 optimal weight: 0.8980 chunk 59 optimal weight: 0.0770 chunk 35 optimal weight: 0.9980 overall best weight: 0.2014 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 207 GLN B 252 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 moved from start: 0.3040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 5384 Z= 0.250 Angle : 0.672 15.747 7315 Z= 0.323 Chirality : 0.048 0.308 776 Planarity : 0.004 0.042 950 Dihedral : 5.924 41.965 776 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.05 % Favored : 91.80 % Rotamer: Outliers : 6.19 % Allowed : 22.48 % 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: -2.34 (0.90), residues: 28 sheet: -0.45 (0.37), residues: 234 loop : -1.69 (0.30), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 436 HIS 0.002 0.001 HIS A 339 PHE 0.013 0.002 PHE A 400 TYR 0.011 0.001 TYR P 226 ARG 0.010 0.001 ARG B 45 *********************** 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: 35 poor density : 133 time to evaluate : 0.530 Fit side-chains REVERT: P 27 SER cc_start: 0.8136 (m) cc_final: 0.7554 (t) REVERT: P 236 TYR cc_start: 0.8397 (p90) cc_final: 0.7722 (p90) REVERT: P 248 THR cc_start: 0.7046 (t) cc_final: 0.6808 (t) REVERT: B 11 LEU cc_start: 0.6585 (mt) cc_final: 0.6003 (mt) REVERT: B 38 GLN cc_start: 0.8075 (tt0) cc_final: 0.7811 (tt0) REVERT: B 94 TRP cc_start: 0.7455 (OUTLIER) cc_final: 0.6970 (t-100) REVERT: B 108 LYS cc_start: 0.4911 (OUTLIER) cc_final: 0.4641 (ptpp) REVERT: B 130 SER cc_start: 0.7913 (p) cc_final: 0.7512 (m) REVERT: B 197 ARG cc_start: 0.8716 (mtp85) cc_final: 0.8255 (mtp85) REVERT: B 249 VAL cc_start: 0.8725 (t) cc_final: 0.8442 (m) REVERT: A 440 LYS cc_start: 0.7987 (mppt) cc_final: 0.7786 (mppt) REVERT: A 468 ILE cc_start: 0.8341 (OUTLIER) cc_final: 0.8125 (mm) REVERT: A 472 ILE cc_start: 0.8366 (OUTLIER) cc_final: 0.8114 (mm) outliers start: 35 outliers final: 17 residues processed: 152 average time/residue: 1.0760 time to fit residues: 171.3607 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 : 0.595 ------------------------------------------------------------------------------- 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 212 THR Chi-restraints excluded: chain P residue 245 THR Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 94 TRP Chi-restraints excluded: chain B residue 108 LYS Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 362 VAL 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 25 optimal weight: 0.6980 chunk 46 optimal weight: 0.4980 chunk 18 optimal weight: 0.9990 chunk 53 optimal weight: 0.9990 chunk 56 optimal weight: 0.0970 chunk 59 optimal weight: 0.8980 chunk 38 optimal weight: 0.0010 chunk 62 optimal weight: 0.0050 chunk 29 optimal weight: 0.6980 chunk 43 optimal weight: 0.0980 chunk 65 optimal weight: 0.0980 overall best weight: 0.0598 ------------------------------------------------------------------------------- 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 101 GLN B 162 GLN A 487 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7381 moved from start: 0.3248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 5384 Z= 0.157 Angle : 0.641 15.007 7315 Z= 0.304 Chirality : 0.046 0.264 776 Planarity : 0.004 0.036 950 Dihedral : 5.406 41.791 774 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 4.25 % Allowed : 24.96 % 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: -2.94 (0.74), residues: 34 sheet: -0.37 (0.37), residues: 228 loop : -1.48 (0.31), residues: 409 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 B 173 TYR 0.013 0.001 TYR P 226 ARG 0.008 0.000 ARG B 45 *********************** 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 163 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 139 time to evaluate : 0.594 Fit side-chains REVERT: P 27 SER cc_start: 0.8060 (m) cc_final: 0.7731 (t) REVERT: P 236 TYR cc_start: 0.8366 (p90) cc_final: 0.7694 (p90) REVERT: P 248 THR cc_start: 0.6890 (t) cc_final: 0.6670 (t) REVERT: B 11 LEU cc_start: 0.6787 (mt) cc_final: 0.6311 (mt) REVERT: B 38 GLN cc_start: 0.8071 (tt0) cc_final: 0.7811 (tt0) REVERT: B 97 TYR cc_start: 0.7947 (m-80) cc_final: 0.7443 (m-80) REVERT: B 130 SER cc_start: 0.7893 (p) cc_final: 0.7494 (m) REVERT: B 197 ARG cc_start: 0.8708 (mtp85) cc_final: 0.8242 (mtp85) REVERT: A 440 LYS cc_start: 0.7885 (mppt) cc_final: 0.7685 (mppt) REVERT: A 472 ILE cc_start: 0.8343 (OUTLIER) cc_final: 0.8108 (mm) REVERT: A 501 TYR cc_start: 0.7126 (m-10) cc_final: 0.6893 (m-10) outliers start: 24 outliers final: 16 residues processed: 150 average time/residue: 1.0269 time to fit residues: 161.9193 Evaluate side-chains 158 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 141 time to evaluate : 0.617 ------------------------------------------------------------------------------- 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 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 A residue 332 ILE Chi-restraints excluded: chain A residue 362 VAL 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 60 optimal weight: 0.6980 chunk 52 optimal weight: 0.9990 chunk 5 optimal weight: 0.0570 chunk 40 optimal weight: 0.3980 chunk 32 optimal weight: 0.3980 chunk 41 optimal weight: 0.7980 chunk 55 optimal weight: 0.5980 chunk 16 optimal weight: 0.8980 chunk 48 optimal weight: 0.9990 chunk 7 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 overall best weight: 0.4298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 201 ASN A 394 ASN A 487 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 moved from start: 0.3314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.083 5384 Z= 0.467 Angle : 0.808 14.841 7315 Z= 0.391 Chirality : 0.053 0.311 776 Planarity : 0.005 0.041 950 Dihedral : 6.330 46.732 770 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.30 % Allowed : 8.94 % Favored : 90.76 % Rotamer: Outliers : 3.54 % Allowed : 25.49 % Favored : 70.97 % 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: -2.03 (0.32), residues: 671 helix: -3.34 (0.65), residues: 40 sheet: -0.55 (0.36), residues: 233 loop : -1.66 (0.30), residues: 398 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 152 TYR 0.019 0.002 TYR P 218 ARG 0.009 0.001 ARG B 45 ********************** 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 149 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 129 time to evaluate : 0.561 Fit side-chains REVERT: P 236 TYR cc_start: 0.8401 (p90) cc_final: 0.7710 (p90) REVERT: P 248 THR cc_start: 0.7215 (t) cc_final: 0.7002 (t) REVERT: B 11 LEU cc_start: 0.6759 (mt) cc_final: 0.6477 (mt) REVERT: B 38 GLN cc_start: 0.8168 (tt0) cc_final: 0.7895 (tt0) REVERT: B 94 TRP cc_start: 0.7533 (OUTLIER) cc_final: 0.6937 (t-100) REVERT: B 97 TYR cc_start: 0.8263 (m-80) cc_final: 0.7332 (m-80) REVERT: B 130 SER cc_start: 0.8025 (p) cc_final: 0.7651 (m) REVERT: A 440 LYS cc_start: 0.8048 (mppt) cc_final: 0.7826 (mppt) REVERT: A 472 ILE cc_start: 0.8429 (OUTLIER) cc_final: 0.8147 (mm) outliers start: 20 outliers final: 14 residues processed: 140 average time/residue: 1.0738 time to fit residues: 157.4494 Evaluate side-chains 145 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 129 time to evaluate : 0.695 ------------------------------------------------------------------------------- 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 33 LEU 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 A residue 332 ILE Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 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 52 optimal weight: 0.6980 chunk 21 optimal weight: 0.0980 chunk 53 optimal weight: 0.8980 chunk 6 optimal weight: 0.3980 chunk 9 optimal weight: 0.1980 chunk 46 optimal weight: 0.1980 chunk 2 optimal weight: 0.0870 chunk 37 optimal weight: 0.3980 chunk 60 optimal weight: 0.0670 chunk 35 optimal weight: 0.0070 chunk 44 optimal weight: 0.3980 overall best weight: 0.0914 ------------------------------------------------------------------------------- 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 = 0.3936 r_free = 0.3936 target = 0.131219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.124101 restraints weight = 8086.058| |-----------------------------------------------------------------------------| r_work (start): 0.3864 rms_B_bonded: 1.63 r_work: 0.3790 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3678 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.3300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 5384 Z= 0.188 Angle : 0.694 14.907 7315 Z= 0.334 Chirality : 0.047 0.263 776 Planarity : 0.004 0.039 950 Dihedral : 5.779 47.250 770 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.41 % Favored : 93.44 % Rotamer: Outliers : 3.01 % Allowed : 27.26 % Favored : 69.73 % 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: -1.82 (0.33), residues: 671 helix: -2.86 (0.76), residues: 34 sheet: -0.49 (0.36), residues: 228 loop : -1.51 (0.31), residues: 409 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 0.016 0.001 PHE A 392 TYR 0.013 0.001 TYR P 226 ARG 0.008 0.000 ARG B 45 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3480.65 seconds wall clock time: 63 minutes 17.48 seconds (3797.48 seconds total)