Starting phenix.real_space_refine on Wed Sep 17 05:09:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9j3n_61120/09_2025/9j3n_61120.cif Found real_map, /net/cci-nas-00/data/ceres_data/9j3n_61120/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/9j3n_61120/09_2025/9j3n_61120.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9j3n_61120/09_2025/9j3n_61120.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9j3n_61120/09_2025/9j3n_61120.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9j3n_61120/09_2025/9j3n_61120.map" } resolution = 2.72 write_initial_geo_file = False refinement { macro_cycles = 10 } 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-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 1.37, per 1000 atoms: 0.28 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: 0.34 Conformation dependent library (CDL) restraints added in 119.4 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 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: 0.16 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: 0.74 Time building geometry restraints manager: 0.44 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: 1.170 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: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 6.080 Find NCS groups from input model: 0.010 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:6.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.010 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.003 0.000 ARG A 283 TYR 0.006 0.001 TYR B 33 PHE 0.015 0.001 PHE B 47 TRP 0.012 0.001 TRP A 332 HIS 0.001 0.000 HIS A 22 Details of bonding type rmsd covalent geometry : bond 0.00468 ( 4934) covalent geometry : angle 0.77966 ( 6707) SS BOND : bond 0.00224 ( 1) SS BOND : angle 0.38328 ( 2) hydrogen bonds : bond 0.14877 ( 324) hydrogen bonds : angle 6.98627 ( 951) *********************** 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 : 0.162 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: 0.8680 (p) REVERT: B 87 ASN cc_start: 0.8142 (m-40) cc_final: 0.7897 (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: 0.2721 time to fit residues: 28.4147 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 : 0.211 ------------------------------------------------------------------------------- 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 54 optimal weight: 6.9990 chunk 24 optimal weight: 0.9980 chunk 48 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 2 optimal weight: 4.9990 chunk 16 optimal weight: 0.8980 chunk 32 optimal weight: 0.9980 chunk 31 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 58 optimal weight: 0.5980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 3 GLN A 20 HIS A 431 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.147770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.105964 restraints weight = 5791.464| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 2.58 r_work: 0.3150 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6771 moved from start: 0.0927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 4935 Z= 0.191 Angle : 0.625 7.586 6709 Z= 0.322 Chirality : 0.041 0.176 766 Planarity : 0.004 0.030 814 Dihedral : 8.504 54.587 691 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.45 % Favored : 94.38 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.96 (0.34), residues: 605 helix: 0.19 (0.26), residues: 378 sheet: -2.69 (0.69), residues: 46 loop : -1.66 (0.49), residues: 181 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 210 TYR 0.007 0.001 TYR B 80 PHE 0.020 0.002 PHE A 494 TRP 0.013 0.001 TRP A 332 HIS 0.002 0.001 HIS A 121 Details of bonding type rmsd covalent geometry : bond 0.00435 ( 4934) covalent geometry : angle 0.62493 ( 6707) SS BOND : bond 0.00378 ( 1) SS BOND : angle 0.60384 ( 2) hydrogen bonds : bond 0.04331 ( 324) hydrogen bonds : angle 5.37828 ( 951) *********************** 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 102 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 90 time to evaluate : 0.187 Fit side-chains revert: symmetry clash REVERT: B 17 SER cc_start: 0.7353 (m) cc_final: 0.7112 (t) REVERT: B 60 TYR cc_start: 0.8594 (m-80) cc_final: 0.8293 (m-80) REVERT: B 85 SER cc_start: 0.9018 (m) cc_final: 0.8274 (p) REVERT: B 87 ASN cc_start: 0.7701 (m-40) cc_final: 0.7355 (m-40) REVERT: A 190 ILE cc_start: 0.7921 (tt) cc_final: 0.7690 (tt) outliers start: 12 outliers final: 6 residues processed: 93 average time/residue: 0.2963 time to fit residues: 29.6890 Evaluate side-chains 91 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 85 time to evaluate : 0.180 ------------------------------------------------------------------------------- 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 410 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 47 optimal weight: 0.5980 chunk 0 optimal weight: 7.9990 chunk 26 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 chunk 12 optimal weight: 0.0040 chunk 4 optimal weight: 0.6980 chunk 37 optimal weight: 20.0000 chunk 40 optimal weight: 0.9980 chunk 8 optimal weight: 4.9990 chunk 59 optimal weight: 3.9990 overall best weight: 0.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 320 ASN A 431 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.149459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.107723 restraints weight = 5784.552| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 2.60 r_work: 0.3095 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6790 moved from start: 0.1263 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= 0.149 Angle : 0.579 7.423 6709 Z= 0.296 Chirality : 0.039 0.171 766 Planarity : 0.004 0.030 814 Dihedral : 8.062 55.374 687 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 3.16 % Allowed : 13.04 % Favored : 83.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.18 (0.35), residues: 605 helix: 0.85 (0.27), residues: 382 sheet: -2.83 (0.73), residues: 40 loop : -1.45 (0.49), residues: 183 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 72 TYR 0.009 0.001 TYR B 80 PHE 0.025 0.001 PHE A 494 TRP 0.012 0.001 TRP A 332 HIS 0.001 0.000 HIS A 121 Details of bonding type rmsd covalent geometry : bond 0.00337 ( 4934) covalent geometry : angle 0.57869 ( 6707) SS BOND : bond 0.00363 ( 1) SS BOND : angle 0.58902 ( 2) hydrogen bonds : bond 0.03855 ( 324) hydrogen bonds : angle 5.12555 ( 951) *********************** 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: 16 poor density : 88 time to evaluate : 0.199 Fit side-chains revert: symmetry clash REVERT: B 60 TYR cc_start: 0.8584 (m-80) cc_final: 0.8228 (m-80) REVERT: B 65 LYS cc_start: 0.7020 (tttp) cc_final: 0.6790 (ttpp) REVERT: B 85 SER cc_start: 0.9009 (m) cc_final: 0.8317 (p) REVERT: B 87 ASN cc_start: 0.7690 (m-40) cc_final: 0.7351 (m-40) REVERT: A 190 ILE cc_start: 0.7923 (tt) cc_final: 0.7685 (tt) outliers start: 16 outliers final: 8 residues processed: 95 average time/residue: 0.2905 time to fit residues: 29.7566 Evaluate side-chains 93 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 85 time to evaluate : 0.187 ------------------------------------------------------------------------------- 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 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 410 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 16 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 15 optimal weight: 0.5980 chunk 55 optimal weight: 0.7980 chunk 51 optimal weight: 3.9990 chunk 25 optimal weight: 0.7980 chunk 54 optimal weight: 6.9990 chunk 34 optimal weight: 2.9990 chunk 24 optimal weight: 0.5980 chunk 20 optimal weight: 0.8980 chunk 21 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 A 456 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.150257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.108513 restraints weight = 5770.673| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 2.43 r_work: 0.2888 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6577 moved from start: 0.1474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 4935 Z= 0.166 Angle : 0.586 7.697 6709 Z= 0.297 Chirality : 0.040 0.190 766 Planarity : 0.004 0.029 814 Dihedral : 7.418 50.763 687 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 3.36 % Allowed : 14.03 % Favored : 82.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.15 (0.35), residues: 605 helix: 1.11 (0.27), residues: 381 sheet: -2.71 (0.73), residues: 40 loop : -1.29 (0.49), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 72 TYR 0.008 0.001 TYR A 297 PHE 0.025 0.002 PHE A 494 TRP 0.011 0.001 TRP A 332 HIS 0.001 0.000 HIS A 121 Details of bonding type rmsd covalent geometry : bond 0.00382 ( 4934) covalent geometry : angle 0.58562 ( 6707) SS BOND : bond 0.00435 ( 1) SS BOND : angle 0.75321 ( 2) hydrogen bonds : bond 0.03785 ( 324) hydrogen bonds : angle 5.03325 ( 951) *********************** 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: 17 poor density : 91 time to evaluate : 0.129 Fit side-chains revert: symmetry clash REVERT: B 17 SER cc_start: 0.7425 (m) cc_final: 0.7181 (t) REVERT: B 65 LYS cc_start: 0.6783 (tttp) cc_final: 0.6555 (ttpp) REVERT: B 72 ARG cc_start: 0.7207 (ptm160) cc_final: 0.6996 (ptm160) REVERT: B 85 SER cc_start: 0.8852 (m) cc_final: 0.8192 (p) REVERT: B 87 ASN cc_start: 0.7549 (m-40) cc_final: 0.7197 (m-40) REVERT: A 190 ILE cc_start: 0.7645 (tt) cc_final: 0.7393 (tt) outliers start: 17 outliers final: 10 residues processed: 99 average time/residue: 0.2681 time to fit residues: 28.6301 Evaluate side-chains 98 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 88 time to evaluate : 0.139 ------------------------------------------------------------------------------- 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 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 392 THR Chi-restraints excluded: chain A residue 410 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 42 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 chunk 40 optimal weight: 0.3980 chunk 35 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 9 optimal weight: 4.9990 chunk 53 optimal weight: 0.9990 chunk 6 optimal weight: 0.7980 chunk 51 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 = 0.3710 r_free = 0.3710 target = 0.149757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.108080 restraints weight = 5769.121| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 2.43 r_work: 0.2885 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6589 moved from start: 0.1697 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= 0.173 Angle : 0.591 8.202 6709 Z= 0.301 Chirality : 0.041 0.183 766 Planarity : 0.003 0.029 814 Dihedral : 6.846 45.736 687 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 4.15 % Allowed : 13.83 % Favored : 82.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.36 (0.35), residues: 605 helix: 1.35 (0.27), residues: 373 sheet: -2.61 (0.73), residues: 39 loop : -1.30 (0.48), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 210 TYR 0.007 0.001 TYR B 80 PHE 0.026 0.002 PHE A 494 TRP 0.011 0.001 TRP A 332 HIS 0.001 0.000 HIS A 121 Details of bonding type rmsd covalent geometry : bond 0.00396 ( 4934) covalent geometry : angle 0.59069 ( 6707) SS BOND : bond 0.00405 ( 1) SS BOND : angle 0.68103 ( 2) hydrogen bonds : bond 0.03782 ( 324) hydrogen bonds : angle 5.00594 ( 951) *********************** 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 110 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 89 time to evaluate : 0.128 Fit side-chains revert: symmetry clash REVERT: B 65 LYS cc_start: 0.6794 (tttp) cc_final: 0.6566 (ttpp) REVERT: B 85 SER cc_start: 0.8852 (m) cc_final: 0.8215 (p) REVERT: B 87 ASN cc_start: 0.7469 (m-40) cc_final: 0.7133 (m-40) REVERT: A 190 ILE cc_start: 0.7624 (tt) cc_final: 0.7392 (tt) REVERT: A 274 MET cc_start: 0.6759 (tpp) cc_final: 0.6142 (tpp) outliers start: 21 outliers final: 10 residues processed: 100 average time/residue: 0.2641 time to fit residues: 28.5652 Evaluate side-chains 97 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 87 time to evaluate : 0.176 ------------------------------------------------------------------------------- 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 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 392 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 41 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 45 optimal weight: 4.9990 chunk 52 optimal weight: 0.7980 chunk 42 optimal weight: 0.0970 chunk 11 optimal weight: 0.1980 chunk 10 optimal weight: 0.9990 chunk 50 optimal weight: 0.9980 chunk 9 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 55 optimal weight: 0.6980 overall best weight: 0.5578 ------------------------------------------------------------------------------- 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 = 0.3722 r_free = 0.3722 target = 0.150996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.109042 restraints weight = 5863.824| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 2.46 r_work: 0.2906 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6594 moved from start: 0.1822 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= 0.141 Angle : 0.574 7.424 6709 Z= 0.291 Chirality : 0.040 0.174 766 Planarity : 0.003 0.028 814 Dihedral : 6.318 40.578 687 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 3.36 % Allowed : 15.02 % Favored : 81.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.58 (0.35), residues: 605 helix: 1.49 (0.27), residues: 374 sheet: -2.73 (0.72), residues: 40 loop : -1.09 (0.48), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 72 TYR 0.007 0.001 TYR A 153 PHE 0.026 0.001 PHE A 494 TRP 0.012 0.001 TRP A 332 HIS 0.001 0.000 HIS A 121 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 4934) covalent geometry : angle 0.57449 ( 6707) SS BOND : bond 0.00414 ( 1) SS BOND : angle 0.49035 ( 2) hydrogen bonds : bond 0.03616 ( 324) hydrogen bonds : angle 4.92509 ( 951) *********************** 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 100 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 83 time to evaluate : 0.186 Fit side-chains revert: symmetry clash REVERT: B 17 SER cc_start: 0.7505 (m) cc_final: 0.7254 (t) REVERT: B 65 LYS cc_start: 0.6786 (tttp) cc_final: 0.6561 (ttpp) REVERT: B 85 SER cc_start: 0.8877 (m) cc_final: 0.8248 (p) REVERT: B 87 ASN cc_start: 0.7460 (m-40) cc_final: 0.7114 (m-40) REVERT: A 190 ILE cc_start: 0.7628 (tt) cc_final: 0.7397 (tt) REVERT: A 274 MET cc_start: 0.6843 (tpp) cc_final: 0.6213 (tpp) outliers start: 17 outliers final: 12 residues processed: 92 average time/residue: 0.3126 time to fit residues: 30.8007 Evaluate side-chains 94 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 82 time to evaluate : 0.173 ------------------------------------------------------------------------------- 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 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 23 optimal weight: 0.0570 chunk 48 optimal weight: 0.9980 chunk 17 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 15 optimal weight: 0.9980 chunk 49 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 overall best weight: 0.7098 ------------------------------------------------------------------------------- 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 = 0.3717 r_free = 0.3717 target = 0.150411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.108705 restraints weight = 5825.597| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 2.45 r_work: 0.2896 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6598 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 : 0.004 0.046 4935 Z= 0.161 Angle : 0.607 9.547 6709 Z= 0.302 Chirality : 0.041 0.221 766 Planarity : 0.004 0.029 814 Dihedral : 6.008 36.659 687 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 3.56 % Allowed : 16.21 % Favored : 80.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.66 (0.35), residues: 605 helix: 1.45 (0.26), residues: 380 sheet: -2.56 (0.73), residues: 39 loop : -0.92 (0.50), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 72 TYR 0.007 0.001 TYR A 153 PHE 0.026 0.001 PHE A 494 TRP 0.011 0.001 TRP A 332 HIS 0.001 0.000 HIS A 121 Details of bonding type rmsd covalent geometry : bond 0.00369 ( 4934) covalent geometry : angle 0.60722 ( 6707) SS BOND : bond 0.00454 ( 1) SS BOND : angle 0.57936 ( 2) hydrogen bonds : bond 0.03687 ( 324) hydrogen bonds : angle 4.93613 ( 951) *********************** 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 100 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 82 time to evaluate : 0.186 Fit side-chains revert: symmetry clash REVERT: B 17 SER cc_start: 0.7578 (m) cc_final: 0.7333 (t) REVERT: B 45 ARG cc_start: 0.7667 (ttm110) cc_final: 0.7420 (ttm170) REVERT: B 72 ARG cc_start: 0.7178 (ptm160) cc_final: 0.6906 (ptm160) REVERT: B 85 SER cc_start: 0.8843 (m) cc_final: 0.8200 (p) REVERT: B 87 ASN cc_start: 0.7463 (m-40) cc_final: 0.7132 (m-40) REVERT: A 190 ILE cc_start: 0.7653 (tt) cc_final: 0.7418 (tt) REVERT: A 274 MET cc_start: 0.6842 (tpp) cc_final: 0.6255 (tpp) outliers start: 18 outliers final: 13 residues processed: 91 average time/residue: 0.3041 time to fit residues: 29.7929 Evaluate side-chains 95 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 82 time to evaluate : 0.178 ------------------------------------------------------------------------------- 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 71 SER 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 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 469 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 22 optimal weight: 0.9980 chunk 3 optimal weight: 0.8980 chunk 28 optimal weight: 3.9990 chunk 49 optimal weight: 0.5980 chunk 2 optimal weight: 0.6980 chunk 1 optimal weight: 0.0670 chunk 41 optimal weight: 0.9980 chunk 50 optimal weight: 0.5980 chunk 6 optimal weight: 0.9980 chunk 54 optimal weight: 0.9980 chunk 47 optimal weight: 0.7980 overall best weight: 0.5518 ------------------------------------------------------------------------------- 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 = 0.3728 r_free = 0.3728 target = 0.151601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.109811 restraints weight = 5872.046| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 2.46 r_work: 0.2913 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6585 moved from start: 0.2037 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= 0.140 Angle : 0.572 8.414 6709 Z= 0.289 Chirality : 0.040 0.198 766 Planarity : 0.003 0.029 814 Dihedral : 5.659 35.428 687 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 3.75 % Allowed : 15.81 % Favored : 80.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.81 (0.35), residues: 605 helix: 1.55 (0.27), residues: 380 sheet: -2.48 (0.74), residues: 39 loop : -0.84 (0.49), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 72 TYR 0.007 0.001 TYR A 153 PHE 0.027 0.001 PHE A 494 TRP 0.012 0.001 TRP A 332 HIS 0.001 0.000 HIS A 121 Details of bonding type rmsd covalent geometry : bond 0.00318 ( 4934) covalent geometry : angle 0.57241 ( 6707) SS BOND : bond 0.00317 ( 1) SS BOND : angle 0.39310 ( 2) hydrogen bonds : bond 0.03572 ( 324) hydrogen bonds : angle 4.90318 ( 951) *********************** 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 103 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 84 time to evaluate : 0.157 Fit side-chains revert: symmetry clash REVERT: B 17 SER cc_start: 0.7623 (m) cc_final: 0.7354 (t) REVERT: B 45 ARG cc_start: 0.7664 (ttm110) cc_final: 0.7397 (ttm170) REVERT: B 72 ARG cc_start: 0.6986 (ptm160) cc_final: 0.6698 (ptm160) REVERT: B 85 SER cc_start: 0.8866 (m) cc_final: 0.8275 (p) REVERT: B 87 ASN cc_start: 0.7534 (m-40) cc_final: 0.7246 (m110) REVERT: A 190 ILE cc_start: 0.7625 (tt) cc_final: 0.7387 (tt) REVERT: A 274 MET cc_start: 0.6876 (tpp) cc_final: 0.6336 (tpp) REVERT: A 395 MET cc_start: 0.7969 (tpp) cc_final: 0.7369 (tpp) outliers start: 19 outliers final: 12 residues processed: 94 average time/residue: 0.2864 time to fit residues: 28.9789 Evaluate side-chains 93 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 81 time to evaluate : 0.174 ------------------------------------------------------------------------------- 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 71 SER 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 76 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 24 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 28 optimal weight: 0.5980 chunk 5 optimal weight: 0.0670 chunk 2 optimal weight: 0.9980 chunk 55 optimal weight: 3.9990 chunk 29 optimal weight: 0.6980 chunk 40 optimal weight: 0.8980 chunk 15 optimal weight: 0.8980 chunk 39 optimal weight: 0.6980 chunk 51 optimal weight: 2.9990 overall best weight: 0.5918 ------------------------------------------------------------------------------- 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 = 0.3731 r_free = 0.3731 target = 0.151766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.110225 restraints weight = 5790.930| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 2.43 r_work: 0.2915 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6601 moved from start: 0.2101 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= 0.146 Angle : 0.619 12.385 6709 Z= 0.302 Chirality : 0.040 0.192 766 Planarity : 0.003 0.028 814 Dihedral : 5.489 36.116 687 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 2.96 % Allowed : 17.19 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.88 (0.35), residues: 605 helix: 1.57 (0.26), residues: 381 sheet: -2.40 (0.75), residues: 39 loop : -0.73 (0.49), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 45 TYR 0.007 0.001 TYR A 153 PHE 0.027 0.001 PHE A 494 TRP 0.011 0.001 TRP A 332 HIS 0.001 0.000 HIS A 121 Details of bonding type rmsd covalent geometry : bond 0.00333 ( 4934) covalent geometry : angle 0.61923 ( 6707) SS BOND : bond 0.00308 ( 1) SS BOND : angle 0.69547 ( 2) hydrogen bonds : bond 0.03599 ( 324) hydrogen bonds : angle 4.86392 ( 951) *********************** 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 98 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 83 time to evaluate : 0.194 Fit side-chains revert: symmetry clash REVERT: B 17 SER cc_start: 0.7626 (m) cc_final: 0.7344 (t) REVERT: B 45 ARG cc_start: 0.7673 (ttm110) cc_final: 0.7408 (ttm170) REVERT: B 72 ARG cc_start: 0.7142 (ptm160) cc_final: 0.6781 (ptm160) REVERT: B 85 SER cc_start: 0.8868 (m) cc_final: 0.8276 (p) REVERT: B 87 ASN cc_start: 0.7470 (m-40) cc_final: 0.7184 (m110) REVERT: A 190 ILE cc_start: 0.7641 (tt) cc_final: 0.7403 (tt) REVERT: A 274 MET cc_start: 0.6877 (tpp) cc_final: 0.6371 (tpp) outliers start: 15 outliers final: 13 residues processed: 92 average time/residue: 0.3255 time to fit residues: 32.0059 Evaluate side-chains 96 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 83 time to evaluate : 0.138 ------------------------------------------------------------------------------- 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 71 SER 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 31 optimal weight: 0.8980 chunk 41 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 56 optimal weight: 0.4980 chunk 11 optimal weight: 6.9990 chunk 57 optimal weight: 0.6980 chunk 2 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 42 optimal weight: 0.5980 chunk 49 optimal weight: 0.6980 chunk 44 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 A 320 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.151288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.109659 restraints weight = 5776.410| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 2.43 r_work: 0.2907 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6615 moved from start: 0.2105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 4935 Z= 0.155 Angle : 0.590 9.387 6709 Z= 0.295 Chirality : 0.040 0.194 766 Planarity : 0.003 0.029 814 Dihedral : 5.385 36.642 687 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 2.96 % Allowed : 17.19 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.88 (0.35), residues: 605 helix: 1.56 (0.26), residues: 381 sheet: -2.42 (0.75), residues: 39 loop : -0.71 (0.49), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 72 TYR 0.007 0.001 TYR A 153 PHE 0.027 0.001 PHE A 494 TRP 0.011 0.001 TRP A 332 HIS 0.001 0.000 HIS A 121 Details of bonding type rmsd covalent geometry : bond 0.00355 ( 4934) covalent geometry : angle 0.59038 ( 6707) SS BOND : bond 0.00421 ( 1) SS BOND : angle 0.76593 ( 2) hydrogen bonds : bond 0.03603 ( 324) hydrogen bonds : angle 4.88253 ( 951) ********************** 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 98 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 83 time to evaluate : 0.256 Fit side-chains revert: symmetry clash REVERT: B 17 SER cc_start: 0.7633 (m) cc_final: 0.7350 (t) REVERT: B 72 ARG cc_start: 0.7052 (ptm160) cc_final: 0.6760 (ptm160) REVERT: B 85 SER cc_start: 0.8893 (m) cc_final: 0.8283 (p) REVERT: B 87 ASN cc_start: 0.7475 (m-40) cc_final: 0.7187 (m110) REVERT: A 79 MET cc_start: 0.7372 (mmt) cc_final: 0.7165 (mmm) REVERT: A 190 ILE cc_start: 0.7659 (tt) cc_final: 0.7422 (tt) REVERT: A 274 MET cc_start: 0.6882 (tpp) cc_final: 0.6424 (tpp) outliers start: 15 outliers final: 13 residues processed: 92 average time/residue: 0.3122 time to fit residues: 30.7929 Evaluate side-chains 97 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 84 time to evaluate : 0.180 ------------------------------------------------------------------------------- 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 71 SER 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 57 optimal weight: 0.9990 chunk 23 optimal weight: 0.0670 chunk 53 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 45 optimal weight: 5.9990 chunk 16 optimal weight: 0.8980 chunk 48 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 chunk 44 optimal weight: 0.8980 chunk 21 optimal weight: 0.3980 overall best weight: 0.6118 ------------------------------------------------------------------------------- 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 = 0.151565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.109744 restraints weight = 5818.832| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 2.45 r_work: 0.2912 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6596 moved from start: 0.2195 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= 0.146 Angle : 0.585 9.574 6709 Z= 0.292 Chirality : 0.040 0.194 766 Planarity : 0.003 0.029 814 Dihedral : 5.292 36.988 687 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 2.57 % Allowed : 17.79 % Favored : 79.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.95 (0.35), residues: 605 helix: 1.62 (0.26), residues: 381 sheet: -2.42 (0.74), residues: 39 loop : -0.69 (0.49), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 45 TYR 0.007 0.001 TYR A 153 PHE 0.027 0.001 PHE A 494 TRP 0.011 0.001 TRP A 332 HIS 0.001 0.000 HIS A 121 Details of bonding type rmsd covalent geometry : bond 0.00333 ( 4934) covalent geometry : angle 0.58521 ( 6707) SS BOND : bond 0.00384 ( 1) SS BOND : angle 0.44768 ( 2) hydrogen bonds : bond 0.03567 ( 324) hydrogen bonds : angle 4.85560 ( 951) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1597.61 seconds wall clock time: 28 minutes 0.23 seconds (1680.23 seconds total)