Starting phenix.real_space_refine on Thu Jun 5 01:54:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9j3n_61120/06_2025/9j3n_61120.cif Found real_map, /net/cci-nas-00/data/ceres_data/9j3n_61120/06_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_61120/06_2025/9j3n_61120.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9j3n_61120/06_2025/9j3n_61120.map" model { file = "/net/cci-nas-00/data/ceres_data/9j3n_61120/06_2025/9j3n_61120.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9j3n_61120/06_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 3.84, per 1000 atoms: 0.80 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: 1.39 Conformation dependent library (CDL) restraints added in 632.3 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: 0.58 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: 1.39 Time building geometry restraints manager: 1.64 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: 1.080 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: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 16.960 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.890 ------------------------------------------------------------------------------- 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 : 0.480 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: 0.5755 time to fit residues: 60.3667 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 : 0.543 ------------------------------------------------------------------------------- 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 = 0.108565 restraints weight = 5771.066| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 2.59 r_work: 0.3107 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6786 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 : 0.513 Fit side-chains revert: symmetry clash REVERT: B 17 SER cc_start: 0.7353 (m) cc_final: 0.7105 (t) REVERT: B 60 TYR cc_start: 0.8580 (m-80) cc_final: 0.8248 (m-80) REVERT: B 85 SER cc_start: 0.9009 (m) cc_final: 0.8266 (p) REVERT: B 87 ASN cc_start: 0.7707 (m-40) cc_final: 0.7355 (m-40) REVERT: A 190 ILE cc_start: 0.7911 (tt) cc_final: 0.7677 (tt) outliers start: 12 outliers final: 7 residues processed: 92 average time/residue: 0.6137 time to fit residues: 61.0635 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 : 0.540 ------------------------------------------------------------------------------- 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: 0.9990 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: 0.9980 chunk 23 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 45 optimal weight: 4.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- 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 = 0.3707 r_free = 0.3707 target = 0.147175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.104998 restraints weight = 5823.445| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 2.61 r_work: 0.3061 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6810 moved from start: 0.1242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 4935 Z= 0.226 Angle : 0.616 7.654 6709 Z= 0.316 Chirality : 0.042 0.199 766 Planarity : 0.004 0.031 814 Dihedral : 7.933 54.291 687 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 3.56 % Allowed : 13.04 % Favored : 83.40 % 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: -0.37 (0.35), residues: 605 helix: 0.71 (0.26), residues: 381 sheet: -2.83 (0.73), residues: 40 loop : -1.53 (0.49), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 332 HIS 0.001 0.000 HIS B 57 PHE 0.024 0.002 PHE A 494 TYR 0.008 0.001 TYR B 80 ARG 0.003 0.000 ARG B 72 Details of bonding type rmsd hydrogen bonds : bond 0.04134 ( 324) hydrogen bonds : angle 5.20234 ( 951) SS BOND : bond 0.00586 ( 1) SS BOND : angle 0.96822 ( 2) covalent geometry : bond 0.00519 ( 4934) covalent geometry : angle 0.61562 ( 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 105 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 87 time to evaluate : 1.101 Fit side-chains revert: symmetry clash REVERT: B 60 TYR cc_start: 0.8632 (m-80) cc_final: 0.8314 (m-80) REVERT: B 65 LYS cc_start: 0.6979 (tttp) cc_final: 0.6747 (ttpp) REVERT: B 85 SER cc_start: 0.9014 (m) cc_final: 0.8330 (p) REVERT: B 87 ASN cc_start: 0.7620 (m-40) cc_final: 0.7267 (m-40) REVERT: A 190 ILE cc_start: 0.7956 (tt) cc_final: 0.7715 (tt) outliers start: 18 outliers final: 9 residues processed: 95 average time/residue: 0.6701 time to fit residues: 68.6032 Evaluate side-chains 94 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 85 time to evaluate : 0.828 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain A residue 425 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 16 optimal weight: 0.7980 chunk 35 optimal weight: 0.6980 chunk 54 optimal weight: 7.9990 chunk 53 optimal weight: 4.9990 chunk 51 optimal weight: 3.9990 chunk 52 optimal weight: 0.8980 chunk 43 optimal weight: 0.5980 chunk 56 optimal weight: 0.9980 chunk 55 optimal weight: 0.9990 chunk 20 optimal weight: 0.5980 chunk 6 optimal weight: 0.0770 overall best weight: 0.5538 ------------------------------------------------------------------------------- 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 = 0.3744 r_free = 0.3744 target = 0.150490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.108486 restraints weight = 5866.028| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 2.63 r_work: 0.3101 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6788 moved from start: 0.1531 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= 0.140 Angle : 0.570 7.461 6709 Z= 0.289 Chirality : 0.039 0.180 766 Planarity : 0.004 0.029 814 Dihedral : 7.418 53.796 687 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 4.15 % Allowed : 13.24 % 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 (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: 0.20 (0.35), residues: 605 helix: 1.17 (0.27), residues: 379 sheet: -2.42 (0.70), residues: 46 loop : -1.33 (0.50), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 332 HIS 0.002 0.000 HIS A 121 PHE 0.025 0.001 PHE A 494 TYR 0.009 0.001 TYR A 297 ARG 0.004 0.000 ARG B 72 Details of bonding type rmsd hydrogen bonds : bond 0.03669 ( 324) hydrogen bonds : angle 5.02565 ( 951) SS BOND : bond 0.00264 ( 1) SS BOND : angle 0.49612 ( 2) covalent geometry : bond 0.00312 ( 4934) covalent geometry : angle 0.56998 ( 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 112 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 91 time to evaluate : 0.497 Fit side-chains revert: symmetry clash REVERT: B 17 SER cc_start: 0.7557 (m) cc_final: 0.7260 (t) REVERT: B 60 TYR cc_start: 0.8571 (m-80) cc_final: 0.8129 (m-80) REVERT: B 65 LYS cc_start: 0.6995 (tttp) cc_final: 0.6766 (ttpp) REVERT: B 85 SER cc_start: 0.8989 (m) cc_final: 0.8306 (p) REVERT: B 87 ASN cc_start: 0.7660 (m-40) cc_final: 0.7300 (m-40) REVERT: A 23 GLU cc_start: 0.8661 (mt-10) cc_final: 0.8394 (mt-10) REVERT: A 190 ILE cc_start: 0.7853 (tt) cc_final: 0.7597 (tt) outliers start: 21 outliers final: 10 residues processed: 101 average time/residue: 0.5445 time to fit residues: 59.6403 Evaluate side-chains 99 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 89 time to evaluate : 0.536 ------------------------------------------------------------------------------- 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 175 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 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: 0.8980 chunk 36 optimal weight: 2.9990 chunk 49 optimal weight: 0.7980 chunk 35 optimal weight: 0.9990 chunk 59 optimal weight: 0.9990 chunk 26 optimal weight: 0.6980 chunk 1 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.3703 r_free = 0.3703 target = 0.149257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.107474 restraints weight = 5857.708| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 2.44 r_work: 0.2882 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6622 moved from start: 0.1639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 4935 Z= 0.185 Angle : 0.590 7.543 6709 Z= 0.303 Chirality : 0.041 0.195 766 Planarity : 0.004 0.028 814 Dihedral : 6.858 47.452 687 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 3.95 % Allowed : 14.62 % Favored : 81.42 % 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: 0.38 (0.35), residues: 605 helix: 1.35 (0.27), residues: 373 sheet: -2.58 (0.75), residues: 39 loop : -1.26 (0.48), residues: 193 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 0.002 PHE A 494 TYR 0.007 0.001 TYR A 297 ARG 0.004 0.000 ARG B 72 Details of bonding type rmsd hydrogen bonds : bond 0.03820 ( 324) hydrogen bonds : angle 5.02649 ( 951) SS BOND : bond 0.00509 ( 1) SS BOND : angle 0.73026 ( 2) covalent geometry : bond 0.00423 ( 4934) covalent geometry : angle 0.58959 ( 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 107 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 87 time to evaluate : 0.948 Fit side-chains revert: symmetry clash REVERT: B 17 SER cc_start: 0.7448 (m) cc_final: 0.7178 (t) REVERT: B 60 TYR cc_start: 0.8440 (m-80) cc_final: 0.7989 (m-80) REVERT: B 65 LYS cc_start: 0.6815 (tttp) cc_final: 0.6585 (ttpp) REVERT: B 85 SER cc_start: 0.8862 (m) cc_final: 0.8224 (p) REVERT: B 87 ASN cc_start: 0.7548 (m-40) cc_final: 0.7209 (m-40) REVERT: A 23 GLU cc_start: 0.8528 (OUTLIER) cc_final: 0.8294 (mt-10) REVERT: A 190 ILE cc_start: 0.7687 (tt) cc_final: 0.7458 (tt) REVERT: A 274 MET cc_start: 0.6555 (tpp) cc_final: 0.6039 (tpp) outliers start: 20 outliers final: 14 residues processed: 96 average time/residue: 1.0746 time to fit residues: 111.9428 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 : 1.234 ------------------------------------------------------------------------------- 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 23 GLU Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 175 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 493 LEU 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: 0.0570 chunk 5 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 45 optimal weight: 4.9990 chunk 27 optimal weight: 0.5980 chunk 6 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 overall best weight: 0.9100 ------------------------------------------------------------------------------- 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 = 0.3703 r_free = 0.3703 target = 0.149143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.106901 restraints weight = 5826.880| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 2.46 r_work: 0.2862 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6533 moved from start: 0.1727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 4935 Z= 0.188 Angle : 0.611 9.067 6709 Z= 0.308 Chirality : 0.041 0.199 766 Planarity : 0.004 0.029 814 Dihedral : 6.405 43.020 687 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 4.74 % Allowed : 14.43 % Favored : 80.83 % 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: 0.39 (0.35), residues: 605 helix: 1.29 (0.26), residues: 379 sheet: -2.77 (0.73), residues: 40 loop : -1.10 (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 0.026 0.002 PHE A 494 TYR 0.007 0.001 TYR A 82 ARG 0.005 0.000 ARG B 72 Details of bonding type rmsd hydrogen bonds : bond 0.03830 ( 324) hydrogen bonds : angle 5.02884 ( 951) SS BOND : bond 0.00483 ( 1) SS BOND : angle 0.82694 ( 2) covalent geometry : bond 0.00433 ( 4934) covalent geometry : angle 0.61104 ( 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 111 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 87 time to evaluate : 0.631 Fit side-chains revert: symmetry clash REVERT: B 17 SER cc_start: 0.7414 (m) cc_final: 0.7153 (t) REVERT: B 60 TYR cc_start: 0.8391 (m-80) cc_final: 0.7967 (m-80) REVERT: B 65 LYS cc_start: 0.6764 (tttp) cc_final: 0.6534 (ttpp) REVERT: B 85 SER cc_start: 0.8846 (m) cc_final: 0.8235 (p) REVERT: B 87 ASN cc_start: 0.7424 (m-40) cc_final: 0.7108 (m-40) REVERT: A 23 GLU cc_start: 0.8460 (OUTLIER) cc_final: 0.8259 (mt-10) REVERT: A 190 ILE cc_start: 0.7591 (tt) cc_final: 0.7359 (tt) REVERT: A 274 MET cc_start: 0.6555 (tpp) cc_final: 0.6061 (tpp) outliers start: 24 outliers final: 14 residues processed: 100 average time/residue: 1.0449 time to fit residues: 110.2063 Evaluate side-chains 100 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 85 time to evaluate : 0.919 ------------------------------------------------------------------------------- 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 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 175 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 493 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 17 optimal weight: 0.7980 chunk 48 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 18 optimal weight: 0.6980 chunk 10 optimal weight: 3.9990 chunk 1 optimal weight: 0.7980 chunk 50 optimal weight: 0.5980 chunk 3 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3708 r_free = 0.3708 target = 0.149681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.107592 restraints weight = 5759.794| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 2.44 r_work: 0.2883 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6602 moved from start: 0.1873 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= 0.168 Angle : 0.597 7.672 6709 Z= 0.301 Chirality : 0.041 0.227 766 Planarity : 0.004 0.029 814 Dihedral : 6.096 39.503 687 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 3.95 % Allowed : 15.42 % Favored : 80.63 % 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: 0.56 (0.35), residues: 605 helix: 1.41 (0.26), residues: 379 sheet: -2.60 (0.74), residues: 39 loop : -1.04 (0.49), residues: 187 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 0.026 0.001 PHE A 494 TYR 0.007 0.001 TYR B 95 ARG 0.006 0.000 ARG B 72 Details of bonding type rmsd hydrogen bonds : bond 0.03744 ( 324) hydrogen bonds : angle 5.01034 ( 951) SS BOND : bond 0.00416 ( 1) SS BOND : angle 0.54620 ( 2) covalent geometry : bond 0.00385 ( 4934) covalent geometry : angle 0.59729 ( 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 104 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 84 time to evaluate : 0.566 Fit side-chains revert: symmetry clash REVERT: B 17 SER cc_start: 0.7442 (m) cc_final: 0.7167 (t) REVERT: B 45 ARG cc_start: 0.7703 (ttm110) cc_final: 0.7442 (ttm170) REVERT: B 65 LYS cc_start: 0.6808 (tttp) cc_final: 0.6584 (ttpp) REVERT: B 85 SER cc_start: 0.8878 (m) cc_final: 0.8252 (p) REVERT: B 87 ASN cc_start: 0.7456 (m-40) cc_final: 0.7137 (m-40) REVERT: A 23 GLU cc_start: 0.8467 (OUTLIER) cc_final: 0.8260 (mt-10) REVERT: A 190 ILE cc_start: 0.7668 (tt) cc_final: 0.7439 (tt) REVERT: A 274 MET cc_start: 0.6618 (tpp) cc_final: 0.6155 (tpp) outliers start: 20 outliers final: 14 residues processed: 96 average time/residue: 0.9268 time to fit residues: 94.2459 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 : 0.551 ------------------------------------------------------------------------------- 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 38 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 5 optimal weight: 0.9980 chunk 11 optimal weight: 5.9990 chunk 13 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 6 optimal weight: 0.0470 chunk 41 optimal weight: 0.3980 chunk 23 optimal weight: 0.0270 overall best weight: 0.4536 ------------------------------------------------------------------------------- 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 = 0.3730 r_free = 0.3730 target = 0.151874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.110337 restraints weight = 5768.710| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 2.44 r_work: 0.2919 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6584 moved from start: 0.2002 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= 0.131 Angle : 0.610 12.055 6709 Z= 0.297 Chirality : 0.040 0.210 766 Planarity : 0.003 0.028 814 Dihedral : 5.725 36.175 687 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 6.58 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 (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: 0.76 (0.35), residues: 605 helix: 1.52 (0.27), residues: 380 sheet: -2.45 (0.75), residues: 39 loop : -0.88 (0.49), residues: 186 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 A 82 ARG 0.001 0.000 ARG A 45 Details of bonding type rmsd hydrogen bonds : bond 0.03557 ( 324) hydrogen bonds : angle 4.94125 ( 951) SS BOND : bond 0.00256 ( 1) SS BOND : angle 0.30688 ( 2) covalent geometry : bond 0.00293 ( 4934) covalent geometry : angle 0.60971 ( 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 104 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 85 time to evaluate : 0.598 Fit side-chains revert: symmetry clash REVERT: B 17 SER cc_start: 0.7631 (m) cc_final: 0.7338 (t) REVERT: B 45 ARG cc_start: 0.7688 (ttm110) cc_final: 0.7416 (ttm170) REVERT: B 65 LYS cc_start: 0.6785 (tttp) cc_final: 0.6559 (ttpp) REVERT: B 85 SER cc_start: 0.8871 (m) cc_final: 0.8241 (p) REVERT: B 87 ASN cc_start: 0.7525 (m-40) cc_final: 0.7196 (m-40) REVERT: A 23 GLU cc_start: 0.8403 (OUTLIER) cc_final: 0.8154 (mt-10) REVERT: A 190 ILE cc_start: 0.7603 (tt) cc_final: 0.7367 (tt) REVERT: A 274 MET cc_start: 0.6722 (tpp) cc_final: 0.6286 (tpp) outliers start: 19 outliers final: 11 residues processed: 95 average time/residue: 0.6962 time to fit residues: 70.6785 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 : 0.515 ------------------------------------------------------------------------------- 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 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 290 LEU Chi-restraints excluded: chain A residue 392 THR 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: 2.9990 chunk 39 optimal weight: 0.8980 chunk 59 optimal weight: 0.7980 chunk 23 optimal weight: 0.9980 chunk 35 optimal weight: 0.7980 chunk 49 optimal weight: 0.0980 chunk 54 optimal weight: 3.9990 chunk 58 optimal weight: 0.9990 chunk 52 optimal weight: 0.6980 chunk 46 optimal weight: 0.0970 overall best weight: 0.4978 ------------------------------------------------------------------------------- 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 = 0.152224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.110705 restraints weight = 5693.846| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 2.42 r_work: 0.2924 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6570 moved from start: 0.2113 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= 0.135 Angle : 0.604 11.529 6709 Z= 0.295 Chirality : 0.040 0.195 766 Planarity : 0.003 0.029 814 Dihedral : 5.510 36.775 687 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 2.96 % Allowed : 17.39 % 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 (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: 0.90 (0.35), residues: 605 helix: 1.60 (0.27), residues: 380 sheet: -2.37 (0.75), residues: 39 loop : -0.76 (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 A 153 ARG 0.004 0.000 ARG B 72 Details of bonding type rmsd hydrogen bonds : bond 0.03546 ( 324) hydrogen bonds : angle 4.88786 ( 951) SS BOND : bond 0.00255 ( 1) SS BOND : angle 0.61655 ( 2) covalent geometry : bond 0.00307 ( 4934) covalent geometry : angle 0.60421 ( 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 98 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 83 time to evaluate : 0.536 Fit side-chains revert: symmetry clash REVERT: B 85 SER cc_start: 0.8865 (m) cc_final: 0.8237 (p) REVERT: B 87 ASN cc_start: 0.7532 (m-40) cc_final: 0.7202 (m-40) REVERT: A 79 MET cc_start: 0.7311 (mmt) cc_final: 0.7108 (mmm) REVERT: A 190 ILE cc_start: 0.7623 (tt) cc_final: 0.7387 (tt) REVERT: A 274 MET cc_start: 0.6774 (tpp) cc_final: 0.6391 (tpp) outliers start: 15 outliers final: 11 residues processed: 92 average time/residue: 0.6449 time to fit residues: 63.9354 Evaluate side-chains 93 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 82 time to evaluate : 0.569 ------------------------------------------------------------------------------- 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 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 441 VAL Chi-restraints excluded: chain A residue 469 THR 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: 0.6980 chunk 50 optimal weight: 0.5980 chunk 36 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 1 optimal weight: 0.5980 chunk 11 optimal weight: 3.9990 chunk 16 optimal weight: 0.6980 chunk 20 optimal weight: 0.7980 chunk 29 optimal weight: 0.5980 chunk 45 optimal weight: 5.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.151671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.109650 restraints weight = 5786.780| |-----------------------------------------------------------------------------| 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: 0.6610 moved from start: 0.2125 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 : 0.605 11.510 6709 Z= 0.298 Chirality : 0.040 0.208 766 Planarity : 0.003 0.029 814 Dihedral : 5.391 37.197 687 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 2.96 % Allowed : 17.39 % 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 (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: 0.90 (0.35), residues: 605 helix: 1.58 (0.26), residues: 381 sheet: -2.31 (0.76), residues: 39 loop : -0.74 (0.49), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 332 HIS 0.001 0.000 HIS A 179 PHE 0.027 0.001 PHE A 494 TYR 0.007 0.001 TYR A 153 ARG 0.004 0.000 ARG B 72 Details of bonding type rmsd hydrogen bonds : bond 0.03618 ( 324) hydrogen bonds : angle 4.87922 ( 951) SS BOND : bond 0.00396 ( 1) SS BOND : angle 0.56395 ( 2) covalent geometry : bond 0.00348 ( 4934) covalent geometry : angle 0.60471 ( 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: 15 poor density : 82 time to evaluate : 0.504 Fit side-chains revert: symmetry clash REVERT: B 85 SER cc_start: 0.8898 (m) cc_final: 0.8298 (p) REVERT: B 87 ASN cc_start: 0.7485 (m-40) cc_final: 0.7210 (m110) REVERT: A 190 ILE cc_start: 0.7621 (tt) cc_final: 0.7386 (tt) REVERT: A 274 MET cc_start: 0.6833 (tpp) cc_final: 0.6441 (tpp) outliers start: 15 outliers final: 11 residues processed: 93 average time/residue: 0.6295 time to fit residues: 62.9778 Evaluate side-chains 93 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 82 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 VAL 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 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 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: 0.7980 chunk 0 optimal weight: 7.9990 chunk 14 optimal weight: 0.9990 chunk 51 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 52 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 21 optimal weight: 0.5980 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 = 0.3717 r_free = 0.3717 target = 0.150721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.108685 restraints weight = 5792.965| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 2.45 r_work: 0.2899 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6636 moved from start: 0.2138 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= 0.174 Angle : 0.639 12.322 6709 Z= 0.312 Chirality : 0.041 0.252 766 Planarity : 0.003 0.029 814 Dihedral : 5.372 37.421 687 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 3.16 % Allowed : 17.59 % Favored : 79.25 % 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: 380 sheet: -2.34 (0.76), residues: 39 loop : -0.75 (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 0.008 0.001 TYR B 95 ARG 0.006 0.000 ARG B 72 Details of bonding type rmsd hydrogen bonds : bond 0.03702 ( 324) hydrogen bonds : angle 4.89769 ( 951) SS BOND : bond 0.00475 ( 1) SS BOND : angle 0.63709 ( 2) covalent geometry : bond 0.00401 ( 4934) covalent geometry : angle 0.63923 ( 6707) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3947.70 seconds wall clock time: 70 minutes 37.26 seconds (4237.26 seconds total)