Starting phenix.real_space_refine on Thu Mar 6 07:10:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jin_36321/03_2025/8jin_36321.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jin_36321/03_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_36321/03_2025/8jin_36321.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jin_36321/03_2025/8jin_36321.map" model { file = "/net/cci-nas-00/data/ceres_data/8jin_36321/03_2025/8jin_36321.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jin_36321/03_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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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: 4.67, per 1000 atoms: 0.89 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: 1.15 Conformation dependent library (CDL) restraints added in 677.8 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: 1.31 Time building geometry restraints manager: 1.39 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: 4.620 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: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 16.980 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:16.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.650 ------------------------------------------------------------------------------- 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 : 0.510 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: 0.8300 time to fit residues: 167.7760 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 : 0.579 ------------------------------------------------------------------------------- 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: 0.2980 chunk 38 optimal weight: 0.6980 chunk 59 optimal weight: 0.7980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 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 = 0.3909 r_free = 0.3909 target = 0.129758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.122143 restraints weight = 7988.274| |-----------------------------------------------------------------------------| r_work (start): 0.3809 rms_B_bonded: 1.70 r_work: 0.3731 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3617 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.2255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.077 5384 Z= 0.449 Angle : 0.715 7.375 7315 Z= 0.360 Chirality : 0.049 0.171 776 Planarity : 0.005 0.044 950 Dihedral : 7.037 55.843 783 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.30 % Allowed : 9.84 % Favored : 89.87 % Rotamer: Outliers : 7.43 % Allowed : 16.11 % Favored : 76.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.27 (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 0.013 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 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1342 Ramachandran restraints generated. 671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1342 Ramachandran restraints generated. 671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 141 time to evaluate : 0.568 Fit side-chains REVERT: P 27 SER cc_start: 0.8230 (m) cc_final: 0.7777 (t) REVERT: P 94 ASP cc_start: 0.6969 (p0) cc_final: 0.6620 (p0) REVERT: P 236 TYR cc_start: 0.8461 (p90) cc_final: 0.7940 (p90) REVERT: B 11 LEU cc_start: 0.7298 (mt) cc_final: 0.6996 (mt) REVERT: B 38 GLN cc_start: 0.8159 (tt0) cc_final: 0.7934 (tt0) REVERT: B 94 TRP cc_start: 0.7544 (OUTLIER) cc_final: 0.7138 (t-100) REVERT: B 97 TYR cc_start: 0.8302 (m-80) cc_final: 0.7703 (m-80) REVERT: B 108 LYS cc_start: 0.6888 (OUTLIER) cc_final: 0.6243 (ptpp) REVERT: B 173 PHE cc_start: 0.8284 (OUTLIER) cc_final: 0.8010 (p90) REVERT: B 196 SER cc_start: 0.8695 (p) cc_final: 0.8481 (t) REVERT: A 380 TYR cc_start: 0.8469 (m-80) cc_final: 0.8211 (m-80) REVERT: A 405 ASN cc_start: 0.7600 (m-40) cc_final: 0.7393 (m-40) REVERT: A 440 LYS cc_start: 0.8201 (mppt) cc_final: 0.7952 (mppt) REVERT: A 472 ILE cc_start: 0.8481 (OUTLIER) cc_final: 0.8228 (mm) REVERT: A 501 TYR cc_start: 0.7925 (m-10) cc_final: 0.7710 (m-10) outliers start: 42 outliers final: 20 residues processed: 161 average time/residue: 0.8591 time to fit residues: 146.1789 Evaluate side-chains 148 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 124 time to evaluate : 0.571 ------------------------------------------------------------------------------- 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 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: 0.4980 chunk 57 optimal weight: 0.2980 chunk 53 optimal weight: 0.7980 chunk 35 optimal weight: 0.6980 chunk 32 optimal weight: 0.0370 chunk 54 optimal weight: 0.1980 chunk 46 optimal weight: 0.3980 chunk 5 optimal weight: 0.8980 chunk 50 optimal weight: 0.1980 chunk 33 optimal weight: 0.0980 chunk 14 optimal weight: 0.4980 overall best weight: 0.1658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 6 GLN 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.131601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.124037 restraints weight = 8007.875| |-----------------------------------------------------------------------------| r_work (start): 0.3840 rms_B_bonded: 1.70 r_work: 0.3759 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3641 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.2472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 5384 Z= 0.208 Angle : 0.632 11.643 7315 Z= 0.308 Chirality : 0.046 0.213 776 Planarity : 0.004 0.039 950 Dihedral : 6.166 45.163 776 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.56 % Favored : 93.29 % Rotamer: Outliers : 7.26 % Allowed : 18.41 % Favored : 74.34 % 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: -2.74 (0.31), residues: 671 helix: -2.41 (0.95), residues: 22 sheet: -1.17 (0.35), residues: 232 loop : -2.27 (0.28), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 436 HIS 0.002 0.001 HIS P 159 PHE 0.009 0.001 PHE B 99 TYR 0.019 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 173 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 132 time to evaluate : 0.613 Fit side-chains REVERT: P 27 SER cc_start: 0.8376 (m) cc_final: 0.7848 (t) REVERT: P 94 ASP cc_start: 0.6903 (p0) cc_final: 0.6501 (p0) REVERT: P 236 TYR cc_start: 0.8436 (p90) cc_final: 0.7913 (p90) REVERT: B 11 LEU cc_start: 0.7229 (mt) cc_final: 0.6981 (mt) REVERT: B 17 GLU cc_start: 0.5997 (OUTLIER) cc_final: 0.5731 (tm-30) REVERT: B 38 GLN cc_start: 0.8118 (tt0) cc_final: 0.7876 (tt0) REVERT: B 97 TYR cc_start: 0.8282 (m-80) cc_final: 0.7798 (m-80) REVERT: B 108 LYS cc_start: 0.6867 (OUTLIER) cc_final: 0.6249 (ptpp) REVERT: B 130 SER cc_start: 0.8153 (p) cc_final: 0.7833 (m) REVERT: B 196 SER cc_start: 0.8718 (p) cc_final: 0.8487 (t) REVERT: A 440 LYS cc_start: 0.8174 (mppt) cc_final: 0.7900 (mppt) REVERT: A 472 ILE cc_start: 0.8487 (OUTLIER) cc_final: 0.8266 (mm) REVERT: A 501 TYR cc_start: 0.7812 (m-10) cc_final: 0.7606 (m-10) outliers start: 41 outliers final: 21 residues processed: 153 average time/residue: 0.8413 time to fit residues: 136.6060 Evaluate side-chains 145 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 121 time to evaluate : 0.618 ------------------------------------------------------------------------------- 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 193 SER 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 108 LYS Chi-restraints excluded: chain B residue 126 GLN Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 424 LYS Chi-restraints excluded: chain A residue 444 LYS Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 478 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 47 optimal weight: 0.7980 chunk 13 optimal weight: 0.9980 chunk 8 optimal weight: 0.6980 chunk 38 optimal weight: 0.0070 chunk 45 optimal weight: 0.5980 chunk 14 optimal weight: 0.7980 chunk 61 optimal weight: 0.0010 chunk 17 optimal weight: 0.5980 chunk 54 optimal weight: 0.5980 chunk 29 optimal weight: 0.9990 chunk 20 optimal weight: 0.2980 overall best weight: 0.3004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 89 GLN B 162 GLN B 207 GLN A 370 ASN A 394 ASN A 487 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.129857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.122442 restraints weight = 8215.447| |-----------------------------------------------------------------------------| r_work (start): 0.3822 rms_B_bonded: 1.68 r_work: 0.3740 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3622 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.2764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 5384 Z= 0.321 Angle : 0.662 8.482 7315 Z= 0.328 Chirality : 0.048 0.237 776 Planarity : 0.005 0.040 950 Dihedral : 6.378 45.824 776 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.35 % Favored : 91.51 % Rotamer: Outliers : 7.79 % Allowed : 18.41 % 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: -2.61 (0.31), residues: 671 helix: -2.78 (0.83), residues: 28 sheet: -1.07 (0.35), residues: 236 loop : -2.15 (0.29), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 436 HIS 0.002 0.001 HIS P 159 PHE 0.014 0.002 PHE B 173 TYR 0.022 0.002 TYR P 226 ARG 0.009 0.001 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 171 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 127 time to evaluate : 0.585 Fit side-chains REVERT: P 236 TYR cc_start: 0.8473 (p90) cc_final: 0.7888 (p90) REVERT: B 11 LEU cc_start: 0.7210 (mt) cc_final: 0.6872 (mt) REVERT: B 17 GLU cc_start: 0.5826 (OUTLIER) cc_final: 0.5486 (tm-30) REVERT: B 38 GLN cc_start: 0.8110 (tt0) cc_final: 0.7848 (tt0) REVERT: B 94 TRP cc_start: 0.7337 (OUTLIER) cc_final: 0.6848 (t-100) REVERT: B 97 TYR cc_start: 0.8297 (m-80) cc_final: 0.7561 (m-80) REVERT: B 108 LYS cc_start: 0.6888 (OUTLIER) cc_final: 0.6201 (ptpp) REVERT: B 127 LEU cc_start: 0.8667 (OUTLIER) cc_final: 0.8394 (pt) REVERT: B 130 SER cc_start: 0.8128 (p) cc_final: 0.7822 (m) REVERT: A 440 LYS cc_start: 0.8257 (mppt) cc_final: 0.8007 (mppt) REVERT: A 468 ILE cc_start: 0.8563 (OUTLIER) cc_final: 0.8312 (mm) REVERT: A 472 ILE cc_start: 0.8532 (OUTLIER) cc_final: 0.8299 (mm) outliers start: 44 outliers final: 20 residues processed: 154 average time/residue: 0.9862 time to fit residues: 159.4068 Evaluate side-chains 148 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 122 time to evaluate : 0.564 ------------------------------------------------------------------------------- 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 130 GLU 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 29 VAL Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 90 GLN Chi-restraints excluded: chain B residue 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 42 optimal weight: 0.9990 chunk 49 optimal weight: 0.6980 chunk 10 optimal weight: 0.8980 chunk 18 optimal weight: 0.7980 chunk 50 optimal weight: 0.9980 chunk 41 optimal weight: 0.1980 chunk 12 optimal weight: 0.3980 chunk 3 optimal weight: 0.8980 chunk 21 optimal weight: 0.4980 chunk 53 optimal weight: 0.4980 chunk 17 optimal weight: 0.3980 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 52 ASN B 89 GLN B 96 GLN B 162 GLN A 370 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.126534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.119332 restraints weight = 8109.506| |-----------------------------------------------------------------------------| r_work (start): 0.3807 rms_B_bonded: 1.64 r_work: 0.3726 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3611 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.2961 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= 0.414 Angle : 0.697 8.841 7315 Z= 0.347 Chirality : 0.050 0.268 776 Planarity : 0.005 0.043 950 Dihedral : 6.720 49.800 776 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.05 % Favored : 91.80 % Rotamer: Outliers : 7.61 % Allowed : 20.35 % Favored : 72.04 % 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: -2.49 (0.32), residues: 671 helix: -2.72 (0.84), residues: 28 sheet: -0.91 (0.34), residues: 250 loop : -2.15 (0.30), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 436 HIS 0.003 0.001 HIS P 159 PHE 0.015 0.002 PHE A 429 TYR 0.020 0.002 TYR P 226 ARG 0.007 0.001 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 160 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 117 time to evaluate : 0.521 Fit side-chains REVERT: P 236 TYR cc_start: 0.8532 (p90) cc_final: 0.8005 (p90) REVERT: B 11 LEU cc_start: 0.7196 (mt) cc_final: 0.6884 (mt) REVERT: B 17 GLU cc_start: 0.5953 (OUTLIER) cc_final: 0.5437 (tm-30) REVERT: B 38 GLN cc_start: 0.8128 (tt0) cc_final: 0.7850 (tt0) REVERT: B 97 TYR cc_start: 0.8312 (m-80) cc_final: 0.7719 (m-80) REVERT: B 108 LYS cc_start: 0.6888 (OUTLIER) cc_final: 0.6249 (ptpp) REVERT: B 130 SER cc_start: 0.8147 (p) cc_final: 0.7863 (m) REVERT: B 252 GLN cc_start: 0.7735 (mp10) cc_final: 0.7356 (mp10) REVERT: A 440 LYS cc_start: 0.8259 (mppt) cc_final: 0.8025 (mppt) REVERT: A 468 ILE cc_start: 0.8587 (OUTLIER) cc_final: 0.8351 (mm) REVERT: A 472 ILE cc_start: 0.8553 (OUTLIER) cc_final: 0.8310 (mm) outliers start: 43 outliers final: 25 residues processed: 142 average time/residue: 0.8035 time to fit residues: 120.8776 Evaluate side-chains 144 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 115 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 5 THR Chi-restraints excluded: chain P residue 40 LEU Chi-restraints excluded: chain P residue 86 ASP Chi-restraints excluded: chain P residue 107 THR Chi-restraints excluded: chain P residue 130 GLU Chi-restraints excluded: chain P residue 193 SER Chi-restraints excluded: chain P residue 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 29 VAL Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 108 LYS Chi-restraints excluded: chain B residue 126 GLN Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 194 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 444 LYS Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 478 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 7 optimal weight: 0.9980 chunk 47 optimal weight: 0.6980 chunk 1 optimal weight: 0.8980 chunk 45 optimal weight: 0.8980 chunk 33 optimal weight: 0.0980 chunk 38 optimal weight: 0.3980 chunk 40 optimal weight: 0.7980 chunk 53 optimal weight: 0.0980 chunk 44 optimal weight: 0.0970 chunk 27 optimal weight: 0.0870 chunk 0 optimal weight: 0.5980 overall best weight: 0.1556 ------------------------------------------------------------------------------- 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 = 0.3911 r_free = 0.3911 target = 0.128847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.121685 restraints weight = 8116.033| |-----------------------------------------------------------------------------| r_work (start): 0.3837 rms_B_bonded: 1.65 r_work: 0.3758 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3642 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.2899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 5384 Z= 0.209 Angle : 0.623 9.581 7315 Z= 0.304 Chirality : 0.046 0.269 776 Planarity : 0.004 0.043 950 Dihedral : 6.270 49.823 776 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.15 % Favored : 92.70 % Rotamer: Outliers : 6.37 % Allowed : 21.42 % Favored : 72.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % Twisted General : 0.00 % Rama-Z (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: -2.23 (0.32), residues: 671 helix: -2.54 (0.84), residues: 28 sheet: -0.63 (0.35), residues: 240 loop : -2.02 (0.30), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 94 HIS 0.002 0.001 HIS P 159 PHE 0.010 0.001 PHE B 173 TYR 0.015 0.001 TYR P 226 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 162 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 126 time to evaluate : 0.518 Fit side-chains REVERT: P 236 TYR cc_start: 0.8465 (p90) cc_final: 0.7904 (p90) REVERT: B 11 LEU cc_start: 0.7262 (mt) cc_final: 0.6972 (mt) REVERT: B 38 GLN cc_start: 0.8151 (tt0) cc_final: 0.7894 (tt0) REVERT: B 97 TYR cc_start: 0.8237 (m-80) cc_final: 0.7774 (m-80) REVERT: B 108 LYS cc_start: 0.6869 (OUTLIER) cc_final: 0.6259 (ptpp) REVERT: B 130 SER cc_start: 0.8090 (p) cc_final: 0.7830 (m) REVERT: A 380 TYR cc_start: 0.8034 (OUTLIER) cc_final: 0.7613 (m-80) REVERT: A 440 LYS cc_start: 0.8223 (mppt) cc_final: 0.7993 (mppt) REVERT: A 468 ILE cc_start: 0.8586 (OUTLIER) cc_final: 0.8336 (mm) REVERT: A 472 ILE cc_start: 0.8512 (OUTLIER) cc_final: 0.8297 (mm) REVERT: A 501 TYR cc_start: 0.7739 (m-10) cc_final: 0.7472 (m-10) outliers start: 36 outliers final: 22 residues processed: 149 average time/residue: 0.9910 time to fit residues: 155.0474 Evaluate side-chains 150 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 124 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 5 THR Chi-restraints excluded: chain P residue 86 ASP Chi-restraints excluded: chain P residue 107 THR Chi-restraints excluded: chain P residue 130 GLU Chi-restraints excluded: chain P residue 193 SER Chi-restraints excluded: chain P residue 212 THR Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 108 LYS Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 380 TYR 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 462 LYS Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 478 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 32 optimal weight: 0.1980 chunk 40 optimal weight: 0.0770 chunk 19 optimal weight: 0.0980 chunk 45 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 chunk 62 optimal weight: 0.9980 chunk 22 optimal weight: 0.8980 chunk 31 optimal weight: 0.2980 chunk 51 optimal weight: 0.1980 chunk 38 optimal weight: 0.0870 chunk 8 optimal weight: 0.1980 overall best weight: 0.1316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 96 GLN A 370 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.129322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.122127 restraints weight = 8015.087| |-----------------------------------------------------------------------------| r_work (start): 0.3844 rms_B_bonded: 1.66 r_work: 0.3765 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3651 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.3011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.092 5384 Z= 0.200 Angle : 0.637 14.239 7315 Z= 0.308 Chirality : 0.046 0.320 776 Planarity : 0.004 0.036 950 Dihedral : 6.086 46.990 776 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.15 % Favored : 92.70 % Rotamer: Outliers : 6.73 % Allowed : 21.59 % Favored : 71.68 % 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: -2.01 (0.32), residues: 671 helix: -2.37 (0.88), residues: 28 sheet: -0.48 (0.36), residues: 225 loop : -1.83 (0.30), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 94 HIS 0.001 0.000 HIS P 159 PHE 0.010 0.001 PHE B 173 TYR 0.012 0.001 TYR P 226 ARG 0.008 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 169 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 131 time to evaluate : 0.580 Fit side-chains REVERT: P 236 TYR cc_start: 0.8444 (p90) cc_final: 0.7932 (p90) REVERT: B 97 TYR cc_start: 0.8202 (m-80) cc_final: 0.7745 (m-80) REVERT: B 108 LYS cc_start: 0.6889 (OUTLIER) cc_final: 0.6281 (ptpp) REVERT: B 130 SER cc_start: 0.8038 (p) cc_final: 0.7786 (m) REVERT: A 380 TYR cc_start: 0.8011 (OUTLIER) cc_final: 0.7574 (m-80) REVERT: A 468 ILE cc_start: 0.8526 (OUTLIER) cc_final: 0.8306 (mm) REVERT: A 472 ILE cc_start: 0.8499 (OUTLIER) cc_final: 0.8289 (mm) REVERT: A 501 TYR cc_start: 0.7695 (m-10) cc_final: 0.7494 (m-10) outliers start: 38 outliers final: 21 residues processed: 153 average time/residue: 1.0441 time to fit residues: 167.4026 Evaluate side-chains 150 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 125 time to evaluate : 0.529 ------------------------------------------------------------------------------- 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 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 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 380 TYR Chi-restraints excluded: chain A residue 383 SER 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 462 LYS Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 478 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 46 optimal weight: 0.0570 chunk 39 optimal weight: 0.1980 chunk 0 optimal weight: 0.7980 chunk 42 optimal weight: 0.9980 chunk 61 optimal weight: 0.8980 chunk 14 optimal weight: 0.7980 chunk 37 optimal weight: 0.4980 chunk 34 optimal weight: 0.7980 chunk 35 optimal weight: 0.3980 chunk 40 optimal weight: 0.3980 chunk 43 optimal weight: 0.0970 overall best weight: 0.2296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 38 GLN B 89 GLN B 101 GLN B 207 GLN B 252 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.128481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.121123 restraints weight = 8069.196| |-----------------------------------------------------------------------------| r_work (start): 0.3811 rms_B_bonded: 1.67 r_work: 0.3730 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3613 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.3129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 5384 Z= 0.274 Angle : 0.693 12.288 7315 Z= 0.332 Chirality : 0.047 0.304 776 Planarity : 0.004 0.038 950 Dihedral : 6.314 47.319 776 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.20 % Favored : 91.65 % Rotamer: Outliers : 6.55 % Allowed : 21.95 % Favored : 71.50 % 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: -1.98 (0.32), residues: 671 helix: -2.40 (0.87), residues: 28 sheet: -0.49 (0.36), residues: 236 loop : -1.81 (0.30), residues: 407 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 A 400 TYR 0.024 0.002 TYR P 218 ARG 0.007 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 155 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 118 time to evaluate : 0.521 Fit side-chains REVERT: P 207 MET cc_start: 0.7506 (mtt) cc_final: 0.7302 (mtt) REVERT: P 211 ARG cc_start: 0.8428 (mtt180) cc_final: 0.8170 (ptp-170) REVERT: P 236 TYR cc_start: 0.8435 (p90) cc_final: 0.7930 (p90) REVERT: B 97 TYR cc_start: 0.8181 (m-80) cc_final: 0.7696 (m-80) REVERT: B 108 LYS cc_start: 0.6878 (OUTLIER) cc_final: 0.6284 (ptpp) REVERT: B 127 LEU cc_start: 0.8655 (OUTLIER) cc_final: 0.8409 (pt) REVERT: B 130 SER cc_start: 0.8138 (p) cc_final: 0.7883 (m) REVERT: B 173 PHE cc_start: 0.8124 (OUTLIER) cc_final: 0.7910 (p90) REVERT: A 468 ILE cc_start: 0.8533 (OUTLIER) cc_final: 0.8318 (mm) REVERT: A 472 ILE cc_start: 0.8549 (OUTLIER) cc_final: 0.8323 (mm) REVERT: A 501 TYR cc_start: 0.7692 (m-10) cc_final: 0.7463 (m-10) outliers start: 37 outliers final: 22 residues processed: 141 average time/residue: 0.9011 time to fit residues: 134.3296 Evaluate side-chains 147 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 120 time to evaluate : 0.574 ------------------------------------------------------------------------------- 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 130 GLU Chi-restraints excluded: chain P residue 193 SER Chi-restraints excluded: chain P residue 212 THR Chi-restraints excluded: chain P residue 245 THR Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 108 LYS Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 173 PHE Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 383 SER 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 472 ILE Chi-restraints excluded: chain A residue 478 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 32 optimal weight: 0.0470 chunk 43 optimal weight: 0.0870 chunk 18 optimal weight: 0.9990 chunk 60 optimal weight: 0.6980 chunk 16 optimal weight: 0.7980 chunk 6 optimal weight: 0.4980 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: 0.3980 overall best weight: 0.2456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 89 GLN B 207 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.128658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.121396 restraints weight = 8082.799| |-----------------------------------------------------------------------------| r_work (start): 0.3830 rms_B_bonded: 1.65 r_work: 0.3750 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3633 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.3195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.093 5384 Z= 0.292 Angle : 0.731 17.863 7315 Z= 0.351 Chirality : 0.048 0.306 776 Planarity : 0.005 0.054 950 Dihedral : 6.358 47.983 776 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.75 % Favored : 92.10 % Rotamer: Outliers : 5.49 % Allowed : 23.54 % 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: -1.94 (0.32), residues: 671 helix: -2.37 (0.88), residues: 28 sheet: -0.47 (0.36), residues: 236 loop : -1.77 (0.30), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 436 HIS 0.002 0.001 HIS P 159 PHE 0.014 0.002 PHE A 400 TYR 0.022 0.002 TYR P 218 ARG 0.014 0.001 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 155 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 124 time to evaluate : 0.534 Fit side-chains REVERT: P 211 ARG cc_start: 0.8397 (mtt180) cc_final: 0.8117 (ptp-170) REVERT: P 236 TYR cc_start: 0.8470 (p90) cc_final: 0.7959 (p90) REVERT: B 97 TYR cc_start: 0.8222 (m-80) cc_final: 0.7742 (m-80) REVERT: B 108 LYS cc_start: 0.6875 (OUTLIER) cc_final: 0.6309 (ptpp) REVERT: B 127 LEU cc_start: 0.8663 (OUTLIER) cc_final: 0.8432 (pt) REVERT: B 130 SER cc_start: 0.8127 (p) cc_final: 0.7861 (m) REVERT: A 468 ILE cc_start: 0.8516 (OUTLIER) cc_final: 0.8296 (mm) REVERT: A 472 ILE cc_start: 0.8585 (OUTLIER) cc_final: 0.8355 (mm) REVERT: A 501 TYR cc_start: 0.7781 (m-10) cc_final: 0.7544 (m-10) outliers start: 31 outliers final: 21 residues processed: 144 average time/residue: 0.8779 time to fit residues: 133.3760 Evaluate side-chains 146 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 121 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 5 THR Chi-restraints excluded: chain P residue 86 ASP Chi-restraints excluded: chain P residue 99 VAL Chi-restraints excluded: chain P residue 107 THR Chi-restraints excluded: chain P residue 144 LEU Chi-restraints excluded: chain P residue 193 SER 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 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 398 ASP 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 472 ILE Chi-restraints excluded: chain A residue 478 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 36 optimal weight: 0.5980 chunk 24 optimal weight: 0.0770 chunk 55 optimal weight: 0.7980 chunk 59 optimal weight: 0.4980 chunk 61 optimal weight: 0.6980 chunk 7 optimal weight: 0.9980 chunk 64 optimal weight: 0.4980 chunk 0 optimal weight: 0.7980 chunk 9 optimal weight: 0.1980 chunk 15 optimal weight: 0.8980 chunk 32 optimal weight: 0.1980 overall best weight: 0.2938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 89 GLN B 101 GLN B 207 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.127839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.120581 restraints weight = 8146.175| |-----------------------------------------------------------------------------| r_work (start): 0.3802 rms_B_bonded: 1.64 r_work: 0.3724 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3608 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.3313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.091 5384 Z= 0.332 Angle : 0.738 17.118 7315 Z= 0.356 Chirality : 0.048 0.295 776 Planarity : 0.005 0.056 950 Dihedral : 6.523 49.406 776 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.90 % Favored : 91.95 % Rotamer: Outliers : 4.78 % Allowed : 24.42 % 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: -1.90 (0.32), residues: 671 helix: -2.44 (0.86), residues: 28 sheet: -0.48 (0.36), residues: 236 loop : -1.71 (0.30), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 436 HIS 0.002 0.001 HIS P 159 PHE 0.014 0.002 PHE A 429 TYR 0.027 0.002 TYR P 218 ARG 0.013 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 152 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 125 time to evaluate : 0.593 Fit side-chains REVERT: P 211 ARG cc_start: 0.8380 (mtt180) cc_final: 0.8122 (ptp-170) REVERT: P 236 TYR cc_start: 0.8440 (p90) cc_final: 0.7939 (p90) REVERT: B 97 TYR cc_start: 0.8217 (m-80) cc_final: 0.7738 (m-80) REVERT: B 108 LYS cc_start: 0.6848 (OUTLIER) cc_final: 0.6217 (ptpp) REVERT: B 127 LEU cc_start: 0.8698 (OUTLIER) cc_final: 0.8466 (pt) REVERT: B 130 SER cc_start: 0.8133 (p) cc_final: 0.7866 (m) REVERT: A 468 ILE cc_start: 0.8514 (OUTLIER) cc_final: 0.8292 (mm) REVERT: A 472 ILE cc_start: 0.8598 (OUTLIER) cc_final: 0.8369 (mm) outliers start: 27 outliers final: 19 residues processed: 143 average time/residue: 0.9449 time to fit residues: 142.3265 Evaluate side-chains 146 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 123 time to evaluate : 0.575 ------------------------------------------------------------------------------- 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 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 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 380 TYR Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 444 LYS Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 478 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 11 optimal weight: 0.9990 chunk 1 optimal weight: 0.7980 chunk 62 optimal weight: 0.9990 chunk 2 optimal weight: 0.6980 chunk 3 optimal weight: 0.6980 chunk 10 optimal weight: 0.5980 chunk 26 optimal weight: 0.5980 chunk 0 optimal weight: 0.0670 chunk 41 optimal weight: 0.0170 chunk 5 optimal weight: 0.0670 chunk 50 optimal weight: 0.9990 overall best weight: 0.2694 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 89 GLN B 207 GLN A 370 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.128048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.120707 restraints weight = 8235.492| |-----------------------------------------------------------------------------| r_work (start): 0.3822 rms_B_bonded: 1.67 r_work: 0.3742 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3624 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.3330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 5384 Z= 0.310 Angle : 0.751 16.902 7315 Z= 0.361 Chirality : 0.048 0.282 776 Planarity : 0.005 0.053 950 Dihedral : 6.508 50.633 776 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.75 % Favored : 92.10 % Rotamer: Outliers : 5.31 % Allowed : 24.07 % 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: -1.88 (0.33), residues: 671 helix: -2.34 (0.88), residues: 28 sheet: -0.54 (0.35), residues: 242 loop : -1.66 (0.30), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 436 HIS 0.002 0.001 HIS P 159 PHE 0.013 0.002 PHE A 429 TYR 0.015 0.002 TYR P 226 ARG 0.013 0.001 ARG B 45 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6010.70 seconds wall clock time: 102 minutes 47.05 seconds (6167.05 seconds total)