Starting phenix.real_space_refine on Sat May 10 03:15:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9j3n_61120/05_2025/9j3n_61120.cif Found real_map, /net/cci-nas-00/data/ceres_data/9j3n_61120/05_2025/9j3n_61120.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.72 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9j3n_61120/05_2025/9j3n_61120.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9j3n_61120/05_2025/9j3n_61120.map" model { file = "/net/cci-nas-00/data/ceres_data/9j3n_61120/05_2025/9j3n_61120.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9j3n_61120/05_2025/9j3n_61120.cif" } resolution = 2.72 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= 0.071 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: 5 Type Number sf(0) Gaussians P 3 5.49 5 S 27 5.16 5 C 3171 2.51 5 N 776 2.21 5 O 832 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 4809 Number of models: 1 Model: "" Number of chains: 3 Chain: "B" Number of atoms: 949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 949 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 2, 'TRANS': 118} Chain: "A" Number of atoms: 3829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 488, 3829 Classifications: {'peptide': 488} Link IDs: {'PTRANS': 21, 'TRANS': 466} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.22, per 1000 atoms: 0.67 Number of scatterers: 4809 At special positions: 0 Unit cell: (89.24, 78.2, 107.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 27 16.00 P 3 15.00 O 832 8.00 N 776 7.00 C 3171 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " 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 539.8 milliseconds 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1124 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 3 sheets defined 72.4% alpha, 8.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing helix chain 'B' and resid 28 through 30 No H-bonds generated for 'chain 'B' and resid 28 through 30' Processing helix chain 'B' and resid 87 through 91 removed outlier: 3.529A pdb=" N THR B 91 " --> pdb=" O PRO B 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 23 through 54 Proline residue: A 29 - end of helix removed outlier: 3.689A pdb=" N ASP A 49 " --> pdb=" O ARG A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 70 removed outlier: 4.168A pdb=" N PHE A 65 " --> pdb=" O GLU A 61 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N PHE A 68 " --> pdb=" O PRO A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 86 Processing helix chain 'A' and resid 90 through 112 Proline residue: A 101 - end of helix Proline residue: A 110 - end of helix Processing helix chain 'A' and resid 116 through 121 Processing helix chain 'A' and resid 122 through 131 Processing helix chain 'A' and resid 134 through 136 No H-bonds generated for 'chain 'A' and resid 134 through 136' Processing helix chain 'A' and resid 137 through 146 removed outlier: 3.825A pdb=" N ILE A 143 " --> pdb=" O GLY A 139 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU A 144 " --> pdb=" O LEU A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 166 removed outlier: 3.937A pdb=" N LEU A 164 " --> pdb=" O GLY A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 176 Processing helix chain 'A' and resid 177 through 209 removed outlier: 4.484A pdb=" N LYS A 182 " --> pdb=" O ILE A 178 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N ARG A 183 " --> pdb=" O HIS A 179 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASN A 193 " --> pdb=" O GLY A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 249 removed outlier: 3.685A pdb=" N SER A 223 " --> pdb=" O PRO A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 266 Processing helix chain 'A' and resid 274 through 279 Processing helix chain 'A' and resid 280 through 283 Processing helix chain 'A' and resid 284 through 316 removed outlier: 3.589A pdb=" N ASN A 302 " --> pdb=" O GLY A 298 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ILE A 304 " --> pdb=" O CYS A 300 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLU A 305 " --> pdb=" O ILE A 301 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N VAL A 306 " --> pdb=" O ASN A 302 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N THR A 307 " --> pdb=" O LEU A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 344 Processing helix chain 'A' and resid 346 through 378 removed outlier: 3.949A pdb=" N ARG A 350 " --> pdb=" O GLY A 346 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N TRP A 354 " --> pdb=" O ARG A 350 " (cutoff:3.500A) removed outlier: 9.637A pdb=" N LEU A 355 " --> pdb=" O LYS A 351 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N THR A 356 " --> pdb=" O PHE A 352 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLY A 357 " --> pdb=" O GLY A 353 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N THR A 361 " --> pdb=" O GLY A 357 " (cutoff:3.500A) Proline residue: A 362 - end of helix removed outlier: 3.667A pdb=" N PHE A 372 " --> pdb=" O THR A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 383 Processing helix chain 'A' and resid 386 through 390 Processing helix chain 'A' and resid 392 through 411 Processing helix chain 'A' and resid 416 through 424 Processing helix chain 'A' and resid 428 through 463 removed outlier: 4.490A pdb=" N ALA A 444 " --> pdb=" O ASP A 440 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N ARG A 445 " --> pdb=" O VAL A 441 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLY A 447 " --> pdb=" O ALA A 443 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N LYS A 448 " --> pdb=" O ALA A 444 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLN A 455 " --> pdb=" O GLY A 451 " (cutoff:3.500A) Processing helix chain 'A' and resid 464 through 503 Proline residue: A 470 - end of helix removed outlier: 3.609A pdb=" N LYS A 492 " --> pdb=" O THR A 488 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLN A 503 " --> pdb=" O ALA A 499 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 10 through 11 removed outlier: 5.875A pdb=" N GLY B 10 " --> pdb=" O THR B 115 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N VAL B 93 " --> pdb=" O GLN B 39 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N MET B 34 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N THR B 50 " --> pdb=" O MET B 34 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N TRP B 36 " --> pdb=" O VAL B 48 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 10 through 11 removed outlier: 5.875A pdb=" N GLY B 10 " --> pdb=" O THR B 115 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 17 through 20 removed outlier: 3.998A pdb=" N THR B 78 " --> pdb=" O ASP B 73 " (cutoff:3.500A) 328 hydrogen bonds defined for protein. 951 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: 1.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1397 1.34 - 1.45: 868 1.45 - 1.57: 2616 1.57 - 1.69: 5 1.69 - 1.81: 48 Bond restraints: 4934 Sorted by residual: bond pdb=" C4 ATP A 601 " pdb=" C5 ATP A 601 " ideal model delta sigma weight residual 1.388 1.469 -0.081 1.00e-02 1.00e+04 6.58e+01 bond pdb=" C5 ATP A 601 " pdb=" C6 ATP A 601 " ideal model delta sigma weight residual 1.409 1.473 -0.064 1.00e-02 1.00e+04 4.15e+01 bond pdb=" C4 ATP A 601 " pdb=" N9 ATP A 601 " ideal model delta sigma weight residual 1.374 1.327 0.047 1.00e-02 1.00e+04 2.18e+01 bond pdb=" C8 ATP A 601 " pdb=" N7 ATP A 601 " ideal model delta sigma weight residual 1.310 1.355 -0.045 1.00e-02 1.00e+04 2.02e+01 bond pdb=" C5 ATP A 601 " pdb=" N7 ATP A 601 " ideal model delta sigma weight residual 1.387 1.343 0.044 1.00e-02 1.00e+04 1.92e+01 ... (remaining 4929 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.58: 6682 4.58 - 9.16: 23 9.16 - 13.75: 0 13.75 - 18.33: 0 18.33 - 22.91: 2 Bond angle restraints: 6707 Sorted by residual: angle pdb=" PA ATP A 601 " pdb=" O3A ATP A 601 " pdb=" PB ATP A 601 " ideal model delta sigma weight residual 136.83 113.92 22.91 1.00e+00 1.00e+00 5.25e+02 angle pdb=" PB ATP A 601 " pdb=" O3B ATP A 601 " pdb=" PG ATP A 601 " ideal model delta sigma weight residual 139.87 121.46 18.41 1.00e+00 1.00e+00 3.39e+02 angle pdb=" C5 ATP A 601 " pdb=" C4 ATP A 601 " pdb=" N3 ATP A 601 " ideal model delta sigma weight residual 126.80 119.27 7.53 1.00e+00 1.00e+00 5.68e+01 angle pdb=" N3 ATP A 601 " pdb=" C4 ATP A 601 " pdb=" N9 ATP A 601 " ideal model delta sigma weight residual 127.04 134.79 -7.75 1.15e+00 7.59e-01 4.56e+01 angle pdb=" N1 ATP A 601 " pdb=" C2 ATP A 601 " pdb=" N3 ATP A 601 " ideal model delta sigma weight residual 128.69 123.36 5.33 1.00e+00 1.00e+00 2.84e+01 ... (remaining 6702 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.44: 2625 16.44 - 32.89: 190 32.89 - 49.33: 59 49.33 - 65.77: 11 65.77 - 82.22: 4 Dihedral angle restraints: 2889 sinusoidal: 1132 harmonic: 1757 Sorted by residual: dihedral pdb=" CA THR A 411 " pdb=" C THR A 411 " pdb=" N LYS A 412 " pdb=" CA LYS A 412 " ideal model delta harmonic sigma weight residual 180.00 157.17 22.83 0 5.00e+00 4.00e-02 2.09e+01 dihedral pdb=" CA MET A 274 " pdb=" C MET A 274 " pdb=" N LYS A 275 " pdb=" CA LYS A 275 " ideal model delta harmonic sigma weight residual -180.00 -161.65 -18.35 0 5.00e+00 4.00e-02 1.35e+01 dihedral pdb=" CA LYS A 275 " pdb=" C LYS A 275 " pdb=" N ASP A 276 " pdb=" CA ASP A 276 " ideal model delta harmonic sigma weight residual 180.00 162.50 17.50 0 5.00e+00 4.00e-02 1.22e+01 ... (remaining 2886 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 486 0.033 - 0.065: 207 0.065 - 0.098: 55 0.098 - 0.130: 14 0.130 - 0.163: 4 Chirality restraints: 766 Sorted by residual: chirality pdb=" CA THR A 469 " pdb=" N THR A 469 " pdb=" C THR A 469 " pdb=" CB THR A 469 " both_signs ideal model delta sigma weight residual False 2.53 2.36 0.16 2.00e-01 2.50e+01 6.64e-01 chirality pdb=" CB VAL A 72 " pdb=" CA VAL A 72 " pdb=" CG1 VAL A 72 " pdb=" CG2 VAL A 72 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.15 2.00e-01 2.50e+01 6.00e-01 chirality pdb=" CB ILE B 51 " pdb=" CA ILE B 51 " pdb=" CG1 ILE B 51 " pdb=" CG2 ILE B 51 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.14 2.00e-01 2.50e+01 5.14e-01 ... (remaining 763 not shown) Planarity restraints: 814 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA A 444 " 0.017 2.00e-02 2.50e+03 3.37e-02 1.14e+01 pdb=" C ALA A 444 " -0.058 2.00e-02 2.50e+03 pdb=" O ALA A 444 " 0.022 2.00e-02 2.50e+03 pdb=" N ARG A 445 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 162 " 0.010 2.00e-02 2.50e+03 2.11e-02 4.44e+00 pdb=" C VAL A 162 " -0.036 2.00e-02 2.50e+03 pdb=" O VAL A 162 " 0.014 2.00e-02 2.50e+03 pdb=" N MET A 163 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR A 114 " 0.023 5.00e-02 4.00e+02 3.49e-02 1.95e+00 pdb=" N PRO A 115 " -0.060 5.00e-02 4.00e+02 pdb=" CA PRO A 115 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 115 " 0.020 5.00e-02 4.00e+02 ... (remaining 811 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1146 2.78 - 3.31: 4762 3.31 - 3.84: 8173 3.84 - 4.37: 9837 4.37 - 4.90: 16653 Nonbonded interactions: 40571 Sorted by model distance: nonbonded pdb=" OD1 ASN A 173 " pdb=" OH TYR A 185 " model vdw 2.252 3.040 nonbonded pdb=" OD1 ASP B 73 " pdb=" OG SER B 75 " model vdw 2.254 3.040 nonbonded pdb=" NE2 HIS A 121 " pdb=" OG1 THR A 148 " model vdw 2.309 3.120 nonbonded pdb=" O MET A 364 " pdb=" OG1 THR A 368 " model vdw 2.324 3.040 nonbonded pdb=" O SER B 63 " pdb=" NH2 ARG B 67 " model vdw 2.334 3.120 ... (remaining 40566 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: 0.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.060 Process input model: 14.540 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:14.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7242 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 : 0.005 0.081 4935 Z= 0.281 Angle : 0.780 22.911 6709 Z= 0.546 Chirality : 0.040 0.163 766 Planarity : 0.004 0.035 814 Dihedral : 13.386 82.217 1762 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.27 % Favored : 92.56 % Rotamer: Outliers : 0.20 % Allowed : 2.77 % Favored : 97.04 % 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: -2.76 (0.31), residues: 605 helix: -1.35 (0.23), residues: 389 sheet: -3.30 (0.68), residues: 39 loop : -2.17 (0.48), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 332 HIS 0.001 0.000 HIS A 22 PHE 0.015 0.001 PHE B 47 TYR 0.006 0.001 TYR B 33 ARG 0.003 0.000 ARG A 283 Details of bonding type rmsd hydrogen bonds : bond 0.14877 ( 324) hydrogen bonds : angle 6.98627 ( 951) SS BOND : bond 0.00224 ( 1) SS BOND : angle 0.38328 ( 2) covalent geometry : bond 0.00468 ( 4934) covalent geometry : angle 0.77966 ( 6707) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 96 time to evaluate : 0.523 Fit side-chains revert: symmetry clash REVERT: B 60 TYR cc_start: 0.8808 (m-80) cc_final: 0.8592 (m-80) REVERT: B 85 SER cc_start: 0.9398 (m) cc_final: 0.8696 (p) REVERT: B 87 ASN cc_start: 0.8142 (m-40) cc_final: 0.7898 (m-40) REVERT: A 190 ILE cc_start: 0.8259 (tt) cc_final: 0.7991 (tt) REVERT: A 261 MET cc_start: 0.5909 (tpt) cc_final: 0.5661 (tpt) REVERT: A 445 ARG cc_start: 0.7980 (OUTLIER) cc_final: 0.6766 (mtp180) outliers start: 1 outliers final: 0 residues processed: 97 average time/residue: 0.5741 time to fit residues: 60.2464 Evaluate side-chains 87 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 86 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 445 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 50 optimal weight: 0.5980 chunk 45 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 15 optimal weight: 0.8980 chunk 30 optimal weight: 0.4980 chunk 24 optimal weight: 0.7980 chunk 47 optimal weight: 0.5980 chunk 18 optimal weight: 0.5980 chunk 28 optimal weight: 3.9990 chunk 35 optimal weight: 0.0670 chunk 54 optimal weight: 6.9990 overall best weight: 0.4718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 3 GLN A 431 GLN A 456 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.150043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.108564 restraints weight = 5771.067| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 2.59 r_work: 0.3107 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6787 moved from start: 0.1025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 4935 Z= 0.142 Angle : 0.604 7.439 6709 Z= 0.310 Chirality : 0.040 0.166 766 Planarity : 0.004 0.029 814 Dihedral : 8.348 56.044 691 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.29 % Favored : 94.55 % Rotamer: Outliers : 2.37 % Allowed : 11.46 % Favored : 86.17 % 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: -0.86 (0.34), residues: 605 helix: 0.28 (0.26), residues: 380 sheet: -2.68 (0.68), residues: 46 loop : -1.65 (0.49), residues: 179 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 332 HIS 0.002 0.001 HIS A 121 PHE 0.020 0.001 PHE A 494 TYR 0.008 0.001 TYR A 297 ARG 0.002 0.000 ARG A 210 Details of bonding type rmsd hydrogen bonds : bond 0.04108 ( 324) hydrogen bonds : angle 5.30107 ( 951) SS BOND : bond 0.00106 ( 1) SS BOND : angle 0.54189 ( 2) covalent geometry : bond 0.00312 ( 4934) covalent geometry : angle 0.60393 ( 6707) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 88 time to evaluate : 0.520 Fit side-chains revert: symmetry clash REVERT: B 17 SER cc_start: 0.7355 (m) cc_final: 0.7106 (t) REVERT: B 60 TYR cc_start: 0.8581 (m-80) cc_final: 0.8249 (m-80) REVERT: B 85 SER cc_start: 0.9010 (m) cc_final: 0.8267 (p) REVERT: B 87 ASN cc_start: 0.7706 (m-40) cc_final: 0.7354 (m-40) REVERT: A 190 ILE cc_start: 0.7912 (tt) cc_final: 0.7677 (tt) outliers start: 12 outliers final: 7 residues processed: 92 average time/residue: 0.5679 time to fit residues: 56.5394 Evaluate side-chains 91 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 84 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 290 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 55 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 10 optimal weight: 4.9990 chunk 11 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 52 optimal weight: 0.3980 chunk 23 optimal weight: 0.0020 chunk 50 optimal weight: 0.9990 chunk 45 optimal weight: 3.9990 overall best weight: 0.6590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 82 GLN A 320 ASN A 431 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.149525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.107754 restraints weight = 5804.306| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 2.61 r_work: 0.3094 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6794 moved from start: 0.1306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 4935 Z= 0.155 Angle : 0.580 7.462 6709 Z= 0.296 Chirality : 0.040 0.170 766 Planarity : 0.004 0.029 814 Dihedral : 7.862 54.181 687 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 3.56 % Allowed : 12.85 % Favored : 83.60 % 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: -0.15 (0.35), residues: 605 helix: 0.88 (0.26), residues: 382 sheet: -2.75 (0.73), residues: 40 loop : -1.46 (0.49), residues: 183 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 332 HIS 0.001 0.000 HIS A 179 PHE 0.024 0.001 PHE A 494 TYR 0.008 0.001 TYR B 80 ARG 0.004 0.000 ARG B 72 Details of bonding type rmsd hydrogen bonds : bond 0.03876 ( 324) hydrogen bonds : angle 5.09107 ( 951) SS BOND : bond 0.00403 ( 1) SS BOND : angle 0.61547 ( 2) covalent geometry : bond 0.00350 ( 4934) covalent geometry : angle 0.58039 ( 6707) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 86 time to evaluate : 0.525 Fit side-chains revert: symmetry clash REVERT: B 60 TYR cc_start: 0.8587 (m-80) cc_final: 0.8227 (m-80) REVERT: B 65 LYS cc_start: 0.7010 (tttp) cc_final: 0.6778 (ttpp) REVERT: B 85 SER cc_start: 0.9017 (m) cc_final: 0.8321 (p) REVERT: B 87 ASN cc_start: 0.7693 (m-40) cc_final: 0.7325 (m-40) REVERT: A 190 ILE cc_start: 0.7900 (tt) cc_final: 0.7658 (tt) outliers start: 18 outliers final: 10 residues processed: 94 average time/residue: 0.5912 time to fit residues: 60.3666 Evaluate side-chains 96 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 86 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 410 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 16 optimal weight: 0.9990 chunk 35 optimal weight: 0.0370 chunk 54 optimal weight: 3.9990 chunk 53 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 chunk 52 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 6 optimal weight: 0.1980 overall best weight: 0.6460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN A 320 ASN A 431 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.149981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.108094 restraints weight = 5881.181| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 2.61 r_work: 0.3099 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6769 moved from start: 0.1537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 4935 Z= 0.152 Angle : 0.568 7.399 6709 Z= 0.289 Chirality : 0.040 0.184 766 Planarity : 0.004 0.028 814 Dihedral : 7.358 53.892 687 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 3.56 % Allowed : 14.03 % Favored : 82.41 % 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: 0.24 (0.35), residues: 605 helix: 1.16 (0.27), residues: 382 sheet: -2.67 (0.74), residues: 40 loop : -1.22 (0.50), residues: 183 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 332 HIS 0.001 0.000 HIS A 121 PHE 0.024 0.002 PHE A 494 TYR 0.009 0.001 TYR A 297 ARG 0.005 0.000 ARG B 72 Details of bonding type rmsd hydrogen bonds : bond 0.03722 ( 324) hydrogen bonds : angle 4.99588 ( 951) SS BOND : bond 0.00321 ( 1) SS BOND : angle 0.60530 ( 2) covalent geometry : bond 0.00347 ( 4934) covalent geometry : angle 0.56807 ( 6707) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 90 time to evaluate : 0.506 Fit side-chains revert: symmetry clash REVERT: B 17 SER cc_start: 0.7555 (m) cc_final: 0.7254 (t) REVERT: B 65 LYS cc_start: 0.7007 (tttp) cc_final: 0.6784 (ttpp) REVERT: B 72 ARG cc_start: 0.7156 (ptm160) cc_final: 0.6890 (ptm160) REVERT: B 85 SER cc_start: 0.9006 (m) cc_final: 0.8309 (p) REVERT: B 87 ASN cc_start: 0.7636 (m-40) cc_final: 0.7253 (m-40) REVERT: A 23 GLU cc_start: 0.8645 (OUTLIER) cc_final: 0.8374 (mt-10) REVERT: A 190 ILE cc_start: 0.7826 (tt) cc_final: 0.7565 (tt) outliers start: 18 outliers final: 8 residues processed: 100 average time/residue: 0.5419 time to fit residues: 58.6761 Evaluate side-chains 96 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 87 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain A residue 23 GLU Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 290 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 54 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 36 optimal weight: 4.9990 chunk 49 optimal weight: 0.9990 chunk 35 optimal weight: 0.0570 chunk 59 optimal weight: 0.8980 chunk 26 optimal weight: 0.6980 chunk 1 optimal weight: 0.0040 chunk 28 optimal weight: 0.9990 chunk 9 optimal weight: 3.9990 chunk 56 optimal weight: 0.9990 overall best weight: 0.5312 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN A 320 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.151378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.109619 restraints weight = 5838.911| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 2.46 r_work: 0.2911 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6568 moved from start: 0.1769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 4935 Z= 0.138 Angle : 0.565 8.202 6709 Z= 0.288 Chirality : 0.040 0.172 766 Planarity : 0.003 0.027 814 Dihedral : 6.718 46.615 687 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 3.36 % Allowed : 14.43 % Favored : 82.21 % 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: 0.55 (0.36), residues: 605 helix: 1.48 (0.27), residues: 374 sheet: -2.64 (0.75), residues: 40 loop : -1.15 (0.49), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 332 HIS 0.001 0.000 HIS A 121 PHE 0.025 0.001 PHE A 494 TYR 0.007 0.001 TYR B 95 ARG 0.003 0.000 ARG B 72 Details of bonding type rmsd hydrogen bonds : bond 0.03614 ( 324) hydrogen bonds : angle 4.93403 ( 951) SS BOND : bond 0.00340 ( 1) SS BOND : angle 0.46999 ( 2) covalent geometry : bond 0.00311 ( 4934) covalent geometry : angle 0.56524 ( 6707) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 89 time to evaluate : 0.490 Fit side-chains revert: symmetry clash REVERT: B 65 LYS cc_start: 0.6786 (tttp) cc_final: 0.6558 (ttpp) REVERT: B 72 ARG cc_start: 0.6800 (ptm160) cc_final: 0.6501 (ptm160) REVERT: B 85 SER cc_start: 0.8852 (m) cc_final: 0.8212 (p) REVERT: B 87 ASN cc_start: 0.7509 (m-40) cc_final: 0.7142 (m-40) REVERT: A 23 GLU cc_start: 0.8454 (mt-10) cc_final: 0.8161 (mt-10) REVERT: A 190 ILE cc_start: 0.7579 (tt) cc_final: 0.7347 (tt) REVERT: A 274 MET cc_start: 0.6807 (tpp) cc_final: 0.6194 (tpp) outliers start: 17 outliers final: 10 residues processed: 99 average time/residue: 0.5924 time to fit residues: 63.1713 Evaluate side-chains 96 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 86 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 410 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 9 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 45 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 22 optimal weight: 0.6980 chunk 48 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN ** A 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 320 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.147410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.104985 restraints weight = 5851.813| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 2.44 r_work: 0.2844 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6636 moved from start: 0.1740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 4935 Z= 0.252 Angle : 0.643 8.677 6709 Z= 0.326 Chirality : 0.043 0.225 766 Planarity : 0.004 0.031 814 Dihedral : 6.381 43.101 687 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 4.74 % Allowed : 15.22 % Favored : 80.04 % 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: 0.32 (0.35), residues: 605 helix: 1.28 (0.26), residues: 373 sheet: -2.62 (0.76), residues: 39 loop : -1.22 (0.47), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 332 HIS 0.002 0.001 HIS A 121 PHE 0.026 0.002 PHE A 494 TYR 0.009 0.001 TYR A 322 ARG 0.002 0.000 ARG B 72 Details of bonding type rmsd hydrogen bonds : bond 0.04044 ( 324) hydrogen bonds : angle 5.10404 ( 951) SS BOND : bond 0.00719 ( 1) SS BOND : angle 1.39918 ( 2) covalent geometry : bond 0.00578 ( 4934) covalent geometry : angle 0.64219 ( 6707) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 84 time to evaluate : 0.482 Fit side-chains revert: symmetry clash REVERT: B 17 SER cc_start: 0.7380 (m) cc_final: 0.7114 (t) REVERT: B 60 TYR cc_start: 0.8464 (m-80) cc_final: 0.8034 (m-80) REVERT: B 65 LYS cc_start: 0.6872 (tttp) cc_final: 0.6645 (ttpp) REVERT: B 72 ARG cc_start: 0.7077 (ptm160) cc_final: 0.6784 (ptm160) REVERT: B 85 SER cc_start: 0.8890 (m) cc_final: 0.8229 (p) REVERT: B 87 ASN cc_start: 0.7496 (m-40) cc_final: 0.7149 (m-40) REVERT: A 23 GLU cc_start: 0.8531 (OUTLIER) cc_final: 0.8290 (mt-10) REVERT: A 190 ILE cc_start: 0.7731 (tt) cc_final: 0.7505 (tt) REVERT: A 274 MET cc_start: 0.6680 (tpp) cc_final: 0.6148 (tpp) outliers start: 24 outliers final: 13 residues processed: 97 average time/residue: 0.6018 time to fit residues: 62.9195 Evaluate side-chains 100 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 86 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain A residue 23 GLU Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 410 SER Chi-restraints excluded: chain A residue 469 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 17 optimal weight: 0.6980 chunk 48 optimal weight: 0.6980 chunk 47 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 chunk 10 optimal weight: 0.0980 chunk 1 optimal weight: 2.9990 chunk 50 optimal weight: 0.6980 chunk 3 optimal weight: 0.6980 chunk 52 optimal weight: 0.6980 chunk 2 optimal weight: 0.9980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN ** A 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 320 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.150243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.108418 restraints weight = 5736.177| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 2.43 r_work: 0.2896 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6580 moved from start: 0.1906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4935 Z= 0.145 Angle : 0.582 7.447 6709 Z= 0.294 Chirality : 0.040 0.178 766 Planarity : 0.003 0.028 814 Dihedral : 6.022 39.629 687 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 3.16 % Allowed : 16.80 % Favored : 80.04 % 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: 0.61 (0.35), residues: 605 helix: 1.53 (0.27), residues: 373 sheet: -2.56 (0.76), residues: 39 loop : -1.14 (0.47), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 332 HIS 0.001 0.000 HIS A 121 PHE 0.026 0.001 PHE A 494 TYR 0.007 0.001 TYR A 153 ARG 0.002 0.000 ARG B 72 Details of bonding type rmsd hydrogen bonds : bond 0.03682 ( 324) hydrogen bonds : angle 4.98985 ( 951) SS BOND : bond 0.00329 ( 1) SS BOND : angle 0.37546 ( 2) covalent geometry : bond 0.00329 ( 4934) covalent geometry : angle 0.58163 ( 6707) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 86 time to evaluate : 0.527 Fit side-chains revert: symmetry clash REVERT: B 17 SER cc_start: 0.7560 (m) cc_final: 0.7301 (t) REVERT: B 65 LYS cc_start: 0.6797 (tttp) cc_final: 0.6573 (ttpp) REVERT: B 72 ARG cc_start: 0.6848 (ptm160) cc_final: 0.6520 (ptm160) REVERT: B 85 SER cc_start: 0.8861 (m) cc_final: 0.8233 (p) REVERT: B 87 ASN cc_start: 0.7464 (m-40) cc_final: 0.7162 (m110) REVERT: A 23 GLU cc_start: 0.8452 (OUTLIER) cc_final: 0.8215 (mt-10) REVERT: A 190 ILE cc_start: 0.7625 (tt) cc_final: 0.7395 (tt) REVERT: A 274 MET cc_start: 0.6708 (tpp) cc_final: 0.6220 (tpp) outliers start: 16 outliers final: 10 residues processed: 96 average time/residue: 0.6963 time to fit residues: 72.0873 Evaluate side-chains 95 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 84 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain A residue 23 GLU Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 469 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 38 optimal weight: 5.9990 chunk 59 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 11 optimal weight: 5.9990 chunk 13 optimal weight: 0.9980 chunk 26 optimal weight: 0.5980 chunk 15 optimal weight: 0.6980 chunk 19 optimal weight: 2.9990 chunk 6 optimal weight: 0.1980 chunk 41 optimal weight: 0.6980 chunk 23 optimal weight: 0.2980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN ** A 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 320 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.151484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.109701 restraints weight = 5748.042| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 2.43 r_work: 0.2903 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6504 moved from start: 0.1983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 4935 Z= 0.137 Angle : 0.600 11.167 6709 Z= 0.296 Chirality : 0.040 0.178 766 Planarity : 0.003 0.028 814 Dihedral : 5.734 36.385 687 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 4.15 % Allowed : 16.01 % Favored : 79.84 % 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: 0.77 (0.35), residues: 605 helix: 1.61 (0.27), residues: 374 sheet: -2.51 (0.76), residues: 39 loop : -0.98 (0.47), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 332 HIS 0.001 0.000 HIS A 121 PHE 0.027 0.001 PHE A 494 TYR 0.007 0.001 TYR B 95 ARG 0.003 0.000 ARG B 72 Details of bonding type rmsd hydrogen bonds : bond 0.03607 ( 324) hydrogen bonds : angle 4.93645 ( 951) SS BOND : bond 0.00330 ( 1) SS BOND : angle 0.35982 ( 2) covalent geometry : bond 0.00311 ( 4934) covalent geometry : angle 0.60044 ( 6707) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 80 time to evaluate : 0.471 Fit side-chains revert: symmetry clash REVERT: B 45 ARG cc_start: 0.7676 (ttm110) cc_final: 0.7445 (ttm170) REVERT: B 85 SER cc_start: 0.8848 (m) cc_final: 0.8232 (p) REVERT: B 87 ASN cc_start: 0.7469 (m-40) cc_final: 0.7167 (m110) REVERT: A 190 ILE cc_start: 0.7525 (tt) cc_final: 0.7297 (tt) REVERT: A 274 MET cc_start: 0.6713 (tpp) cc_final: 0.6255 (tpp) outliers start: 21 outliers final: 13 residues processed: 92 average time/residue: 0.6318 time to fit residues: 62.4458 Evaluate side-chains 91 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 78 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 410 SER Chi-restraints excluded: chain A residue 441 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 4 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 59 optimal weight: 0.9980 chunk 23 optimal weight: 0.4980 chunk 35 optimal weight: 0.0570 chunk 49 optimal weight: 0.6980 chunk 54 optimal weight: 0.9980 chunk 58 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 46 optimal weight: 0.0570 overall best weight: 0.4616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN ** A 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 320 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.152470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.110977 restraints weight = 5680.717| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 2.41 r_work: 0.2929 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6585 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 : 0.003 0.041 4935 Z= 0.133 Angle : 0.596 8.966 6709 Z= 0.294 Chirality : 0.040 0.244 766 Planarity : 0.003 0.029 814 Dihedral : 5.544 36.922 687 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 3.36 % Allowed : 17.59 % Favored : 79.05 % 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: 0.89 (0.35), residues: 605 helix: 1.61 (0.26), residues: 380 sheet: -2.39 (0.76), residues: 39 loop : -0.79 (0.49), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 332 HIS 0.001 0.000 HIS A 121 PHE 0.027 0.001 PHE A 494 TYR 0.007 0.001 TYR B 33 ARG 0.001 0.000 ARG B 72 Details of bonding type rmsd hydrogen bonds : bond 0.03562 ( 324) hydrogen bonds : angle 4.87360 ( 951) SS BOND : bond 0.00257 ( 1) SS BOND : angle 0.54656 ( 2) covalent geometry : bond 0.00300 ( 4934) covalent geometry : angle 0.59636 ( 6707) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 84 time to evaluate : 0.495 Fit side-chains revert: symmetry clash REVERT: B 45 ARG cc_start: 0.7752 (ttm110) cc_final: 0.7530 (ttm170) REVERT: B 85 SER cc_start: 0.8885 (m) cc_final: 0.8263 (p) REVERT: B 87 ASN cc_start: 0.7518 (m-40) cc_final: 0.7245 (m110) REVERT: A 190 ILE cc_start: 0.7643 (tt) cc_final: 0.7407 (tt) REVERT: A 274 MET cc_start: 0.6741 (tpp) cc_final: 0.6281 (tpp) outliers start: 17 outliers final: 11 residues processed: 96 average time/residue: 0.6242 time to fit residues: 64.5859 Evaluate side-chains 94 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 83 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 410 SER Chi-restraints excluded: chain A residue 441 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 5 optimal weight: 2.9990 chunk 23 optimal weight: 0.0020 chunk 50 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 chunk 12 optimal weight: 0.9990 chunk 1 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 chunk 45 optimal weight: 4.9990 overall best weight: 0.7192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN A 320 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.151443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.109388 restraints weight = 5781.825| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 2.44 r_work: 0.2910 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6595 moved from start: 0.2100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 4935 Z= 0.164 Angle : 0.631 12.031 6709 Z= 0.307 Chirality : 0.040 0.191 766 Planarity : 0.003 0.029 814 Dihedral : 5.445 37.253 687 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 2.77 % Allowed : 17.79 % Favored : 79.45 % 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: 0.87 (0.35), residues: 605 helix: 1.56 (0.26), residues: 381 sheet: -2.42 (0.77), residues: 39 loop : -0.74 (0.49), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 332 HIS 0.001 0.000 HIS A 121 PHE 0.027 0.002 PHE A 494 TYR 0.007 0.001 TYR A 82 ARG 0.003 0.000 ARG B 72 Details of bonding type rmsd hydrogen bonds : bond 0.03657 ( 324) hydrogen bonds : angle 4.88510 ( 951) SS BOND : bond 0.00461 ( 1) SS BOND : angle 0.63396 ( 2) covalent geometry : bond 0.00379 ( 4934) covalent geometry : angle 0.63057 ( 6707) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 83 time to evaluate : 0.565 Fit side-chains revert: symmetry clash REVERT: B 45 ARG cc_start: 0.7680 (ttm110) cc_final: 0.7454 (ttm170) REVERT: B 85 SER cc_start: 0.8883 (m) cc_final: 0.8211 (p) REVERT: B 87 ASN cc_start: 0.7487 (m-40) cc_final: 0.7156 (m-40) REVERT: A 190 ILE cc_start: 0.7605 (tt) cc_final: 0.7369 (tt) REVERT: A 274 MET cc_start: 0.6787 (tpp) cc_final: 0.6398 (tpp) outliers start: 14 outliers final: 11 residues processed: 92 average time/residue: 0.6151 time to fit residues: 61.0075 Evaluate side-chains 94 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 83 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 410 SER Chi-restraints excluded: chain A residue 441 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 40 optimal weight: 0.9990 chunk 47 optimal weight: 0.5980 chunk 0 optimal weight: 7.9990 chunk 14 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 53 optimal weight: 0.2980 chunk 32 optimal weight: 0.8980 chunk 52 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 39 optimal weight: 0.9980 chunk 21 optimal weight: 0.0030 overall best weight: 0.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN A 320 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.152198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.110263 restraints weight = 5809.180| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 2.45 r_work: 0.2920 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6579 moved from start: 0.2224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 4935 Z= 0.142 Angle : 0.600 9.520 6709 Z= 0.295 Chirality : 0.040 0.177 766 Planarity : 0.003 0.029 814 Dihedral : 5.325 37.605 687 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 2.77 % Allowed : 17.79 % Favored : 79.45 % 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: 1.00 (0.36), residues: 605 helix: 1.62 (0.26), residues: 381 sheet: -1.50 (0.75), residues: 48 loop : -0.74 (0.51), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 332 HIS 0.001 0.000 HIS A 121 PHE 0.027 0.001 PHE A 494 TYR 0.006 0.001 TYR A 153 ARG 0.001 0.000 ARG B 72 Details of bonding type rmsd hydrogen bonds : bond 0.03561 ( 324) hydrogen bonds : angle 4.83855 ( 951) SS BOND : bond 0.00341 ( 1) SS BOND : angle 0.28630 ( 2) covalent geometry : bond 0.00323 ( 4934) covalent geometry : angle 0.60009 ( 6707) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3435.03 seconds wall clock time: 60 minutes 1.84 seconds (3601.84 seconds total)