Starting phenix.real_space_refine on Wed Feb 12 10:10:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6rd6_4807/02_2025/6rd6_4807.cif Found real_map, /net/cci-nas-00/data/ceres_data/6rd6_4807/02_2025/6rd6_4807.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6rd6_4807/02_2025/6rd6_4807.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6rd6_4807/02_2025/6rd6_4807.map" model { file = "/net/cci-nas-00/data/ceres_data/6rd6_4807/02_2025/6rd6_4807.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6rd6_4807/02_2025/6rd6_4807.cif" } resolution = 2.75 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= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 6 5.16 5 C 4940 2.51 5 N 1289 2.21 5 O 1523 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 72 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 7758 Number of models: 1 Model: "" Number of chains: 10 Chain: "2" Number of atoms: 3163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3163 Classifications: {'peptide': 441} Link IDs: {'PTRANS': 17, 'TRANS': 423} Chain: "4" Number of atoms: 2177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2177 Classifications: {'peptide': 290} Link IDs: {'PTRANS': 9, 'TRANS': 280} Chain: "7" Number of atoms: 1347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1347 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 5, 'TRANS': 170} Chain: "P" Number of atoms: 665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 665 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "T" Number of atoms: 374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 374 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 4, 'TRANS': 41} Chain: "2" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "4" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "7" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "T" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Time building chain proxies: 6.39, per 1000 atoms: 0.82 Number of scatterers: 7758 At special positions: 0 Unit cell: (128.466, 75.816, 114.777, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 6 16.00 O 1523 8.00 N 1289 7.00 C 4940 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 1.75 Conformation dependent library (CDL) restraints added in 911.0 milliseconds 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1962 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 5 sheets defined 71.2% alpha, 6.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.78 Creating SS restraints... Processing helix chain '2' and resid 7 through 19 Processing helix chain '2' and resid 25 through 39 Processing helix chain '2' and resid 44 through 58 removed outlier: 3.760A pdb=" N TRP 2 48 " --> pdb=" O ASN 2 44 " (cutoff:3.500A) Processing helix chain '2' and resid 62 through 77 Processing helix chain '2' and resid 80 through 87 Processing helix chain '2' and resid 87 through 95 Processing helix chain '2' and resid 96 through 98 No H-bonds generated for 'chain '2' and resid 96 through 98' Processing helix chain '2' and resid 99 through 113 Processing helix chain '2' and resid 117 through 131 Processing helix chain '2' and resid 136 through 150 Processing helix chain '2' and resid 154 through 168 Processing helix chain '2' and resid 171 through 186 Processing helix chain '2' and resid 189 through 199 removed outlier: 3.826A pdb=" N VAL 2 193 " --> pdb=" O ASP 2 189 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ASP 2 194 " --> pdb=" O LYS 2 190 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ALA 2 195 " --> pdb=" O ALA 2 191 " (cutoff:3.500A) Processing helix chain '2' and resid 206 through 220 removed outlier: 3.688A pdb=" N ALA 2 210 " --> pdb=" O SER 2 206 " (cutoff:3.500A) Processing helix chain '2' and resid 225 through 235 Processing helix chain '2' and resid 236 through 239 Processing helix chain '2' and resid 240 through 255 Processing helix chain '2' and resid 258 through 276 Proline residue: 2 271 - end of helix Processing helix chain '2' and resid 281 through 296 Processing helix chain '2' and resid 300 through 321 Processing helix chain '2' and resid 323 through 341 Processing helix chain '2' and resid 345 through 357 removed outlier: 3.871A pdb=" N VAL 2 357 " --> pdb=" O VAL 2 353 " (cutoff:3.500A) Processing helix chain '2' and resid 383 through 387 Processing helix chain '2' and resid 396 through 409 removed outlier: 3.778A pdb=" N ALA 2 400 " --> pdb=" O LEU 2 396 " (cutoff:3.500A) Processing helix chain '2' and resid 418 through 423 Processing helix chain '2' and resid 426 through 442 Processing helix chain '4' and resid 7 through 14 removed outlier: 3.719A pdb=" N LEU 4 11 " --> pdb=" O LYS 4 7 " (cutoff:3.500A) Processing helix chain '4' and resid 18 through 35 Processing helix chain '4' and resid 46 through 67 Proline residue: 4 64 - end of helix removed outlier: 3.800A pdb=" N HIS 4 67 " --> pdb=" O GLU 4 63 " (cutoff:3.500A) Processing helix chain '4' and resid 78 through 95 Processing helix chain '4' and resid 99 through 112 Processing helix chain '4' and resid 117 through 125 Processing helix chain '4' and resid 130 through 149 Processing helix chain '4' and resid 158 through 175 Processing helix chain '4' and resid 178 through 188 Processing helix chain '4' and resid 191 through 234 Processing helix chain '4' and resid 236 through 258 removed outlier: 3.978A pdb=" N ALA 4 258 " --> pdb=" O ARG 4 254 " (cutoff:3.500A) Processing helix chain '4' and resid 261 through 284 removed outlier: 3.570A pdb=" N ALA 4 284 " --> pdb=" O SER 4 280 " (cutoff:3.500A) Processing helix chain '7' and resid 63 through 70 removed outlier: 4.159A pdb=" N SER 7 70 " --> pdb=" O LEU 7 66 " (cutoff:3.500A) Processing helix chain '7' and resid 83 through 106 Processing helix chain '7' and resid 109 through 114 removed outlier: 3.690A pdb=" N THR 7 112 " --> pdb=" O ASP 7 109 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N TYR 7 114 " --> pdb=" O THR 7 111 " (cutoff:3.500A) Processing helix chain '7' and resid 115 through 122 removed outlier: 3.703A pdb=" N ALA 7 122 " --> pdb=" O PHE 7 118 " (cutoff:3.500A) Processing helix chain '7' and resid 123 through 145 Processing helix chain '7' and resid 146 through 148 No H-bonds generated for 'chain '7' and resid 146 through 148' Processing helix chain '7' and resid 149 through 155 Processing helix chain '7' and resid 157 through 166 removed outlier: 3.636A pdb=" N TYR 7 161 " --> pdb=" O VAL 7 157 " (cutoff:3.500A) Processing helix chain '7' and resid 174 through 188 Processing helix chain 'P' and resid 163 through 175 Processing helix chain 'P' and resid 210 through 229 Processing helix chain 'T' and resid 44 through 49 Processing helix chain 'T' and resid 55 through 76 Proline residue: T 68 - end of helix Processing sheet with id=AA1, first strand: chain '2' and resid 78 through 79 Processing sheet with id=AA2, first strand: chain '2' and resid 358 through 359 Processing sheet with id=AA3, first strand: chain '2' and resid 368 through 372 removed outlier: 4.330A pdb=" N ILE 2 368 " --> pdb=" O VAL 2 379 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N LYS 2 376 " --> pdb=" O ALA 2 412 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N ALA 2 414 " --> pdb=" O LYS 2 376 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N LEU 2 378 " --> pdb=" O ALA 2 414 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N VAL 2 416 " --> pdb=" O LEU 2 378 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N GLN 2 380 " --> pdb=" O VAL 2 416 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain '7' and resid 36 through 41 Processing sheet with id=AA5, first strand: chain 'P' and resid 183 through 190 removed outlier: 4.179A pdb=" N ARG P 205 " --> pdb=" O PHE P 202 " (cutoff:3.500A) 551 hydrogen bonds defined for protein. 1629 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: 2.36 Time building geometry restraints manager: 2.09 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: 2476 1.34 - 1.46: 1086 1.46 - 1.57: 4288 1.57 - 1.69: 0 1.69 - 1.81: 9 Bond restraints: 7859 Sorted by residual: bond pdb=" C GLN 4 51 " pdb=" N LEU 4 52 " ideal model delta sigma weight residual 1.335 1.438 -0.103 1.36e-02 5.41e+03 5.75e+01 bond pdb=" C ILE T 67 " pdb=" N PRO T 68 " ideal model delta sigma weight residual 1.336 1.379 -0.044 1.23e-02 6.61e+03 1.27e+01 bond pdb=" N ILE 4 49 " pdb=" CA ILE 4 49 " ideal model delta sigma weight residual 1.460 1.495 -0.035 1.21e-02 6.83e+03 8.36e+00 bond pdb=" C VAL 7 158 " pdb=" N PRO 7 159 " ideal model delta sigma weight residual 1.334 1.393 -0.060 2.34e-02 1.83e+03 6.47e+00 bond pdb=" N ASP 4 44 " pdb=" CA ASP 4 44 " ideal model delta sigma weight residual 1.458 1.487 -0.030 1.17e-02 7.31e+03 6.38e+00 ... (remaining 7854 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.10: 10343 2.10 - 4.19: 271 4.19 - 6.29: 26 6.29 - 8.38: 10 8.38 - 10.48: 2 Bond angle restraints: 10652 Sorted by residual: angle pdb=" C VAL 7 157 " pdb=" N VAL 7 158 " pdb=" CA VAL 7 158 " ideal model delta sigma weight residual 120.33 125.51 -5.18 8.00e-01 1.56e+00 4.18e+01 angle pdb=" CA GLN 4 51 " pdb=" C GLN 4 51 " pdb=" N LEU 4 52 " ideal model delta sigma weight residual 117.63 123.49 -5.86 1.25e+00 6.40e-01 2.20e+01 angle pdb=" C SER 4 6 " pdb=" N LYS 4 7 " pdb=" CA LYS 4 7 " ideal model delta sigma weight residual 121.54 130.13 -8.59 1.91e+00 2.74e-01 2.02e+01 angle pdb=" CA TYR 4 210 " pdb=" CB TYR 4 210 " pdb=" CG TYR 4 210 " ideal model delta sigma weight residual 113.90 121.83 -7.93 1.80e+00 3.09e-01 1.94e+01 angle pdb=" C TYR 2 345 " pdb=" N ARG 2 346 " pdb=" CA ARG 2 346 " ideal model delta sigma weight residual 120.09 125.19 -5.10 1.25e+00 6.40e-01 1.67e+01 ... (remaining 10647 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.70: 4374 17.70 - 35.41: 334 35.41 - 53.11: 44 53.11 - 70.81: 16 70.81 - 88.52: 7 Dihedral angle restraints: 4775 sinusoidal: 1747 harmonic: 3028 Sorted by residual: dihedral pdb=" CA LYS P 193 " pdb=" C LYS P 193 " pdb=" N LEU P 194 " pdb=" CA LEU P 194 " ideal model delta harmonic sigma weight residual 180.00 159.53 20.47 0 5.00e+00 4.00e-02 1.68e+01 dihedral pdb=" CA LEU P 162 " pdb=" C LEU P 162 " pdb=" N ASP P 163 " pdb=" CA ASP P 163 " ideal model delta harmonic sigma weight residual 180.00 160.73 19.27 0 5.00e+00 4.00e-02 1.48e+01 dihedral pdb=" CA LEU 2 299 " pdb=" C LEU 2 299 " pdb=" N PRO 2 300 " pdb=" CA PRO 2 300 " ideal model delta harmonic sigma weight residual 180.00 162.24 17.76 0 5.00e+00 4.00e-02 1.26e+01 ... (remaining 4772 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 972 0.048 - 0.096: 209 0.096 - 0.144: 59 0.144 - 0.192: 11 0.192 - 0.240: 2 Chirality restraints: 1253 Sorted by residual: chirality pdb=" CG LEU 2 424 " pdb=" CB LEU 2 424 " pdb=" CD1 LEU 2 424 " pdb=" CD2 LEU 2 424 " both_signs ideal model delta sigma weight residual False -2.59 -2.35 -0.24 2.00e-01 2.50e+01 1.44e+00 chirality pdb=" CA THR 2 391 " pdb=" N THR 2 391 " pdb=" C THR 2 391 " pdb=" CB THR 2 391 " both_signs ideal model delta sigma weight residual False 2.53 2.33 0.20 2.00e-01 2.50e+01 9.60e-01 chirality pdb=" CA ALA 4 45 " pdb=" N ALA 4 45 " pdb=" C ALA 4 45 " pdb=" CB ALA 4 45 " both_signs ideal model delta sigma weight residual False 2.48 2.29 0.19 2.00e-01 2.50e+01 9.22e-01 ... (remaining 1250 not shown) Planarity restraints: 1357 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER 2 99 " -0.041 5.00e-02 4.00e+02 6.22e-02 6.19e+00 pdb=" N PRO 2 100 " 0.108 5.00e-02 4.00e+02 pdb=" CA PRO 2 100 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO 2 100 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR 2 391 " -0.040 5.00e-02 4.00e+02 5.97e-02 5.71e+00 pdb=" N PRO 2 392 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO 2 392 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO 2 392 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU 2 299 " 0.039 5.00e-02 4.00e+02 5.84e-02 5.46e+00 pdb=" N PRO 2 300 " -0.101 5.00e-02 4.00e+02 pdb=" CA PRO 2 300 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO 2 300 " 0.032 5.00e-02 4.00e+02 ... (remaining 1354 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.82: 2462 2.82 - 3.34: 7184 3.34 - 3.86: 13238 3.86 - 4.38: 15197 4.38 - 4.90: 26175 Nonbonded interactions: 64256 Sorted by model distance: nonbonded pdb=" O GLY 7 180 " pdb=" OG1 THR 7 183 " model vdw 2.306 3.040 nonbonded pdb=" OH TYR 4 84 " pdb=" OH TYR 7 161 " model vdw 2.316 3.040 nonbonded pdb=" OD2 ASP 2 316 " pdb=" OG1 THR 4 41 " model vdw 2.323 3.040 nonbonded pdb=" O LYS T 52 " pdb=" O HOH T 601 " model vdw 2.337 3.040 nonbonded pdb=" O LYS P 189 " pdb=" O HOH P 301 " model vdw 2.345 3.040 ... (remaining 64251 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.390 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: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 21.850 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.040 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:12.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 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 : 0.006 0.103 7859 Z= 0.368 Angle : 0.819 10.478 10652 Z= 0.493 Chirality : 0.046 0.240 1253 Planarity : 0.008 0.062 1357 Dihedral : 13.672 88.518 2813 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 0.38 % Allowed : 4.19 % Favored : 95.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.09 (0.20), residues: 1025 helix: -2.01 (0.14), residues: 705 sheet: -0.50 (0.72), residues: 61 loop : -1.90 (0.31), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.004 TRP 7 107 HIS 0.009 0.002 HIS 4 232 PHE 0.014 0.002 PHE P 218 TYR 0.026 0.002 TYR 4 210 ARG 0.003 0.001 ARG 2 322 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 128 time to evaluate : 0.866 Fit side-chains REVERT: 2 44 ASN cc_start: 0.9004 (t0) cc_final: 0.8766 (t0) REVERT: 7 56 LYS cc_start: 0.7997 (mttm) cc_final: 0.7570 (mmtp) REVERT: P 183 LYS cc_start: 0.7493 (mtmm) cc_final: 0.7194 (mttp) REVERT: T 50 LYS cc_start: 0.8653 (ptpt) cc_final: 0.8452 (ptpt) outliers start: 3 outliers final: 0 residues processed: 129 average time/residue: 1.2617 time to fit residues: 171.9432 Evaluate side-chains 82 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 86 optimal weight: 0.1980 chunk 77 optimal weight: 0.2980 chunk 42 optimal weight: 0.7980 chunk 26 optimal weight: 0.7980 chunk 52 optimal weight: 0.5980 chunk 41 optimal weight: 1.9990 chunk 79 optimal weight: 0.5980 chunk 30 optimal weight: 0.5980 chunk 48 optimal weight: 0.7980 chunk 59 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 68 ASN 2 122 ASN 2 243 GLN ** 4 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 239 GLN 7 60 GLN 7 123 HIS 7 170 HIS 7 184 ASN P 220 ASN P 223 ASN T 60 GLN T 64 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.128078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.094722 restraints weight = 9834.378| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 1.82 r_work: 0.2924 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2793 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.1420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7859 Z= 0.173 Angle : 0.493 6.343 10652 Z= 0.264 Chirality : 0.038 0.133 1253 Planarity : 0.005 0.049 1357 Dihedral : 4.269 19.230 1092 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.90 % Allowed : 8.76 % Favored : 89.34 % 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: 0.01 (0.25), residues: 1025 helix: 0.54 (0.18), residues: 706 sheet: -0.15 (0.70), residues: 61 loop : -1.19 (0.34), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP 4 205 HIS 0.004 0.001 HIS 7 123 PHE 0.010 0.001 PHE 4 161 TYR 0.027 0.002 TYR 4 210 ARG 0.005 0.000 ARG P 205 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 94 time to evaluate : 0.885 Fit side-chains REVERT: 2 136 LYS cc_start: 0.7404 (OUTLIER) cc_final: 0.7051 (pttp) REVERT: 2 204 THR cc_start: 0.8046 (OUTLIER) cc_final: 0.7820 (m) REVERT: 2 409 GLN cc_start: 0.8213 (mt0) cc_final: 0.7906 (mt0) REVERT: 4 18 ASP cc_start: 0.7458 (t70) cc_final: 0.6952 (t70) REVERT: 7 56 LYS cc_start: 0.7674 (mttm) cc_final: 0.7084 (mmtp) REVERT: P 183 LYS cc_start: 0.7296 (mtmm) cc_final: 0.6911 (mttp) REVERT: P 186 MET cc_start: 0.8267 (mtm) cc_final: 0.8050 (mtm) outliers start: 15 outliers final: 4 residues processed: 101 average time/residue: 1.3446 time to fit residues: 143.8303 Evaluate side-chains 84 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 78 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 130 SER Chi-restraints excluded: chain 2 residue 136 LYS Chi-restraints excluded: chain 2 residue 204 THR Chi-restraints excluded: chain 2 residue 370 ILE Chi-restraints excluded: chain 2 residue 391 THR Chi-restraints excluded: chain 7 residue 75 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 82 optimal weight: 0.9990 chunk 87 optimal weight: 0.6980 chunk 18 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 27 optimal weight: 0.5980 chunk 77 optimal weight: 9.9990 chunk 22 optimal weight: 0.9980 chunk 79 optimal weight: 2.9990 chunk 67 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 74 ASN 4 110 GLN ** 4 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 60 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.126275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.092231 restraints weight = 10022.659| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 1.85 r_work: 0.2903 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2772 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.1623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7859 Z= 0.240 Angle : 0.508 7.217 10652 Z= 0.268 Chirality : 0.039 0.137 1253 Planarity : 0.004 0.045 1357 Dihedral : 4.076 18.301 1092 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.28 % Allowed : 10.53 % Favored : 87.18 % 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: 0.99 (0.26), residues: 1025 helix: 1.28 (0.19), residues: 717 sheet: 0.18 (0.72), residues: 57 loop : -0.92 (0.36), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP 4 205 HIS 0.005 0.001 HIS 7 123 PHE 0.012 0.002 PHE 4 161 TYR 0.027 0.002 TYR 4 210 ARG 0.003 0.000 ARG P 205 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 92 time to evaluate : 0.940 Fit side-chains REVERT: 2 409 GLN cc_start: 0.8179 (mt0) cc_final: 0.7923 (mt0) REVERT: 4 47 GLU cc_start: 0.7815 (mm-30) cc_final: 0.7560 (mp0) REVERT: 7 56 LYS cc_start: 0.7672 (mttm) cc_final: 0.7053 (mmtp) REVERT: P 183 LYS cc_start: 0.7332 (mtmm) cc_final: 0.6908 (mttp) REVERT: P 186 MET cc_start: 0.8438 (mtm) cc_final: 0.8172 (mtm) outliers start: 18 outliers final: 7 residues processed: 100 average time/residue: 1.2877 time to fit residues: 136.6266 Evaluate side-chains 89 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 82 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 130 SER Chi-restraints excluded: chain 2 residue 370 ILE Chi-restraints excluded: chain 2 residue 391 THR Chi-restraints excluded: chain 7 residue 34 SER Chi-restraints excluded: chain 7 residue 35 ILE Chi-restraints excluded: chain 7 residue 60 GLN Chi-restraints excluded: chain 7 residue 75 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 100 optimal weight: 0.5980 chunk 47 optimal weight: 6.9990 chunk 63 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 71 optimal weight: 0.6980 chunk 19 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 86 optimal weight: 0.5980 chunk 2 optimal weight: 0.8980 chunk 35 optimal weight: 0.7980 chunk 93 optimal weight: 5.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 74 ASN 4 110 GLN 4 232 HIS 7 60 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.126387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.092442 restraints weight = 9844.321| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 1.82 r_work: 0.2914 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2784 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7859 Z= 0.207 Angle : 0.485 7.589 10652 Z= 0.256 Chirality : 0.038 0.133 1253 Planarity : 0.004 0.043 1357 Dihedral : 3.991 18.683 1092 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.16 % Allowed : 12.18 % Favored : 85.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.26), residues: 1025 helix: 1.65 (0.19), residues: 717 sheet: 0.49 (0.70), residues: 57 loop : -0.75 (0.37), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP 4 205 HIS 0.004 0.001 HIS 7 123 PHE 0.010 0.001 PHE 4 161 TYR 0.025 0.002 TYR 4 210 ARG 0.005 0.000 ARG P 205 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 87 time to evaluate : 0.834 Fit side-chains REVERT: 2 409 GLN cc_start: 0.8147 (mt0) cc_final: 0.7904 (mt0) REVERT: 4 47 GLU cc_start: 0.7843 (mm-30) cc_final: 0.7595 (mp0) REVERT: 7 56 LYS cc_start: 0.7659 (mttm) cc_final: 0.7035 (mmtp) REVERT: P 183 LYS cc_start: 0.7354 (mtmm) cc_final: 0.6932 (mttp) REVERT: P 186 MET cc_start: 0.8432 (mtm) cc_final: 0.8201 (mtm) outliers start: 17 outliers final: 9 residues processed: 97 average time/residue: 1.3046 time to fit residues: 133.9240 Evaluate side-chains 97 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 88 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 130 SER Chi-restraints excluded: chain 2 residue 223 LYS Chi-restraints excluded: chain 2 residue 370 ILE Chi-restraints excluded: chain 2 residue 391 THR Chi-restraints excluded: chain 7 residue 34 SER Chi-restraints excluded: chain 7 residue 35 ILE Chi-restraints excluded: chain 7 residue 60 GLN Chi-restraints excluded: chain 7 residue 75 SER Chi-restraints excluded: chain 7 residue 144 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 46 optimal weight: 0.6980 chunk 20 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 chunk 49 optimal weight: 0.8980 chunk 63 optimal weight: 1.9990 chunk 50 optimal weight: 0.0970 chunk 11 optimal weight: 0.9990 chunk 7 optimal weight: 0.9980 chunk 65 optimal weight: 0.9980 overall best weight: 0.7378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 74 ASN 7 60 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.126457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.092416 restraints weight = 9885.353| |-----------------------------------------------------------------------------| r_work (start): 0.3019 rms_B_bonded: 1.83 r_work: 0.2901 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2770 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.1842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7859 Z= 0.212 Angle : 0.486 7.883 10652 Z= 0.255 Chirality : 0.039 0.132 1253 Planarity : 0.004 0.042 1357 Dihedral : 3.941 18.762 1092 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.41 % Allowed : 12.69 % Favored : 84.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.74 (0.26), residues: 1025 helix: 1.81 (0.19), residues: 717 sheet: 0.81 (0.72), residues: 57 loop : -0.63 (0.37), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP 4 205 HIS 0.004 0.001 HIS 4 232 PHE 0.011 0.001 PHE P 218 TYR 0.025 0.002 TYR 4 210 ARG 0.003 0.000 ARG P 205 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 94 time to evaluate : 0.938 Fit side-chains REVERT: 2 136 LYS cc_start: 0.7567 (OUTLIER) cc_final: 0.6998 (pttp) REVERT: 2 409 GLN cc_start: 0.8122 (mt0) cc_final: 0.7918 (mt0) REVERT: 4 47 GLU cc_start: 0.7838 (mm-30) cc_final: 0.7576 (mp0) REVERT: 7 56 LYS cc_start: 0.7621 (mttm) cc_final: 0.7003 (mmtp) REVERT: P 183 LYS cc_start: 0.7342 (mtmm) cc_final: 0.6957 (mttp) REVERT: P 186 MET cc_start: 0.8469 (mtm) cc_final: 0.8197 (mtm) outliers start: 19 outliers final: 10 residues processed: 104 average time/residue: 1.3218 time to fit residues: 145.2855 Evaluate side-chains 100 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 89 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 13 LYS Chi-restraints excluded: chain 2 residue 104 SER Chi-restraints excluded: chain 2 residue 136 LYS Chi-restraints excluded: chain 2 residue 370 ILE Chi-restraints excluded: chain 2 residue 391 THR Chi-restraints excluded: chain 2 residue 432 GLN Chi-restraints excluded: chain 7 residue 34 SER Chi-restraints excluded: chain 7 residue 60 GLN Chi-restraints excluded: chain 7 residue 75 SER Chi-restraints excluded: chain 7 residue 103 LEU Chi-restraints excluded: chain 7 residue 144 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 46 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 77 optimal weight: 10.0000 chunk 95 optimal weight: 0.8980 chunk 90 optimal weight: 0.0770 chunk 50 optimal weight: 0.7980 chunk 15 optimal weight: 0.6980 chunk 61 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 99 optimal weight: 0.5980 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 74 ASN 7 60 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.126925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.092889 restraints weight = 9828.631| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 1.83 r_work: 0.2900 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2770 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.1927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7859 Z= 0.188 Angle : 0.472 7.823 10652 Z= 0.249 Chirality : 0.038 0.130 1253 Planarity : 0.004 0.042 1357 Dihedral : 3.886 18.336 1092 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.54 % Allowed : 13.07 % Favored : 84.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.95 (0.26), residues: 1025 helix: 1.95 (0.19), residues: 718 sheet: 1.04 (0.71), residues: 58 loop : -0.55 (0.38), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP 4 205 HIS 0.004 0.001 HIS 4 232 PHE 0.011 0.001 PHE P 218 TYR 0.024 0.002 TYR 4 210 ARG 0.004 0.000 ARG P 205 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 94 time to evaluate : 0.931 Fit side-chains REVERT: 2 101 VAL cc_start: 0.8444 (OUTLIER) cc_final: 0.8204 (p) REVERT: 2 136 LYS cc_start: 0.7519 (OUTLIER) cc_final: 0.6863 (pttp) REVERT: 2 223 LYS cc_start: 0.8094 (OUTLIER) cc_final: 0.7505 (mppt) REVERT: 4 47 GLU cc_start: 0.7834 (mm-30) cc_final: 0.7582 (mp0) REVERT: 4 270 ASP cc_start: 0.8566 (m-30) cc_final: 0.8346 (m-30) REVERT: 7 56 LYS cc_start: 0.7615 (mttm) cc_final: 0.6995 (mmtp) REVERT: P 160 GLU cc_start: 0.8226 (mt-10) cc_final: 0.7509 (pt0) REVERT: P 183 LYS cc_start: 0.7412 (mtmm) cc_final: 0.6957 (mttp) REVERT: P 186 MET cc_start: 0.8472 (mtm) cc_final: 0.8225 (mtm) outliers start: 20 outliers final: 9 residues processed: 106 average time/residue: 1.2841 time to fit residues: 144.5098 Evaluate side-chains 99 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 87 time to evaluate : 1.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 101 VAL Chi-restraints excluded: chain 2 residue 104 SER Chi-restraints excluded: chain 2 residue 136 LYS Chi-restraints excluded: chain 2 residue 223 LYS Chi-restraints excluded: chain 2 residue 391 THR Chi-restraints excluded: chain 7 residue 25 ASP Chi-restraints excluded: chain 7 residue 34 SER Chi-restraints excluded: chain 7 residue 35 ILE Chi-restraints excluded: chain 7 residue 60 GLN Chi-restraints excluded: chain 7 residue 75 SER Chi-restraints excluded: chain 7 residue 103 LEU Chi-restraints excluded: chain 7 residue 144 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 8 optimal weight: 0.8980 chunk 35 optimal weight: 2.9990 chunk 4 optimal weight: 0.7980 chunk 12 optimal weight: 0.9980 chunk 72 optimal weight: 0.0270 chunk 92 optimal weight: 0.9990 chunk 56 optimal weight: 3.9990 chunk 6 optimal weight: 0.6980 chunk 74 optimal weight: 4.9990 chunk 20 optimal weight: 0.9980 chunk 59 optimal weight: 0.9990 overall best weight: 0.6838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 74 ASN 7 60 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.126758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.092703 restraints weight = 9854.677| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 1.83 r_work: 0.2904 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2774 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.1962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7859 Z= 0.200 Angle : 0.483 7.883 10652 Z= 0.252 Chirality : 0.038 0.130 1253 Planarity : 0.004 0.042 1357 Dihedral : 3.875 18.240 1092 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.16 % Allowed : 14.21 % Favored : 83.63 % 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: 2.04 (0.26), residues: 1025 helix: 2.00 (0.19), residues: 717 sheet: 0.89 (0.69), residues: 64 loop : -0.44 (0.39), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP 4 205 HIS 0.004 0.001 HIS 4 232 PHE 0.011 0.001 PHE P 218 TYR 0.024 0.002 TYR 4 210 ARG 0.003 0.000 ARG P 205 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 93 time to evaluate : 0.942 Fit side-chains REVERT: 2 101 VAL cc_start: 0.8467 (OUTLIER) cc_final: 0.8234 (p) REVERT: 2 136 LYS cc_start: 0.7583 (OUTLIER) cc_final: 0.6942 (pttp) REVERT: 2 223 LYS cc_start: 0.8132 (OUTLIER) cc_final: 0.7548 (mppt) REVERT: 7 56 LYS cc_start: 0.7641 (mttm) cc_final: 0.7025 (mmtp) REVERT: P 160 GLU cc_start: 0.8207 (mt-10) cc_final: 0.7705 (pt0) REVERT: P 183 LYS cc_start: 0.7472 (mtmm) cc_final: 0.6982 (mttp) REVERT: P 186 MET cc_start: 0.8466 (mtm) cc_final: 0.8247 (mtm) outliers start: 17 outliers final: 13 residues processed: 103 average time/residue: 1.3829 time to fit residues: 150.9877 Evaluate side-chains 109 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 93 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 13 LYS Chi-restraints excluded: chain 2 residue 101 VAL Chi-restraints excluded: chain 2 residue 104 SER Chi-restraints excluded: chain 2 residue 136 LYS Chi-restraints excluded: chain 2 residue 223 LYS Chi-restraints excluded: chain 2 residue 293 THR Chi-restraints excluded: chain 2 residue 370 ILE Chi-restraints excluded: chain 2 residue 391 THR Chi-restraints excluded: chain 2 residue 432 GLN Chi-restraints excluded: chain 7 residue 25 ASP Chi-restraints excluded: chain 7 residue 34 SER Chi-restraints excluded: chain 7 residue 35 ILE Chi-restraints excluded: chain 7 residue 60 GLN Chi-restraints excluded: chain 7 residue 75 SER Chi-restraints excluded: chain 7 residue 103 LEU Chi-restraints excluded: chain 7 residue 144 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 43 optimal weight: 0.6980 chunk 12 optimal weight: 0.2980 chunk 18 optimal weight: 0.8980 chunk 6 optimal weight: 0.6980 chunk 23 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 76 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 7 60 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.127595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.093604 restraints weight = 9592.724| |-----------------------------------------------------------------------------| r_work (start): 0.3033 rms_B_bonded: 1.79 r_work: 0.2910 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2775 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.1980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7859 Z= 0.215 Angle : 0.498 7.913 10652 Z= 0.260 Chirality : 0.038 0.130 1253 Planarity : 0.004 0.042 1357 Dihedral : 3.875 15.262 1092 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.41 % Allowed : 14.97 % 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: 2.09 (0.26), residues: 1025 helix: 2.01 (0.19), residues: 717 sheet: 0.98 (0.69), residues: 64 loop : -0.36 (0.39), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP 4 205 HIS 0.004 0.001 HIS 4 232 PHE 0.011 0.001 PHE P 218 TYR 0.024 0.002 TYR 4 210 ARG 0.004 0.000 ARG P 205 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 91 time to evaluate : 0.814 Fit side-chains REVERT: 2 136 LYS cc_start: 0.7835 (OUTLIER) cc_final: 0.7628 (ptpp) REVERT: 2 223 LYS cc_start: 0.8259 (OUTLIER) cc_final: 0.7723 (mppt) REVERT: 2 226 LYS cc_start: 0.7895 (tppt) cc_final: 0.7596 (tttm) REVERT: 4 47 GLU cc_start: 0.7954 (mm-30) cc_final: 0.7704 (mp0) REVERT: 7 56 LYS cc_start: 0.7707 (mttm) cc_final: 0.7127 (mmtp) REVERT: P 160 GLU cc_start: 0.8157 (mt-10) cc_final: 0.7615 (pt0) REVERT: P 183 LYS cc_start: 0.7512 (mtmm) cc_final: 0.7014 (mttp) REVERT: P 186 MET cc_start: 0.8442 (mtm) cc_final: 0.8239 (mtm) outliers start: 19 outliers final: 13 residues processed: 103 average time/residue: 1.3642 time to fit residues: 148.4449 Evaluate side-chains 108 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 93 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 13 LYS Chi-restraints excluded: chain 2 residue 104 SER Chi-restraints excluded: chain 2 residue 136 LYS Chi-restraints excluded: chain 2 residue 223 LYS Chi-restraints excluded: chain 2 residue 293 THR Chi-restraints excluded: chain 2 residue 370 ILE Chi-restraints excluded: chain 2 residue 391 THR Chi-restraints excluded: chain 2 residue 432 GLN Chi-restraints excluded: chain 7 residue 25 ASP Chi-restraints excluded: chain 7 residue 34 SER Chi-restraints excluded: chain 7 residue 35 ILE Chi-restraints excluded: chain 7 residue 60 GLN Chi-restraints excluded: chain 7 residue 75 SER Chi-restraints excluded: chain 7 residue 103 LEU Chi-restraints excluded: chain 7 residue 144 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 79 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 44 optimal weight: 0.7980 chunk 69 optimal weight: 0.2980 chunk 20 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 chunk 74 optimal weight: 0.7980 chunk 95 optimal weight: 0.9990 chunk 101 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 7 60 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.127738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.094586 restraints weight = 9645.864| |-----------------------------------------------------------------------------| r_work (start): 0.3034 rms_B_bonded: 1.93 r_work: 0.2899 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2764 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.2034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7859 Z= 0.206 Angle : 0.497 7.881 10652 Z= 0.258 Chirality : 0.038 0.129 1253 Planarity : 0.004 0.042 1357 Dihedral : 3.868 16.617 1092 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.78 % Allowed : 15.48 % Favored : 82.74 % 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: 2.15 (0.26), residues: 1025 helix: 2.04 (0.19), residues: 717 sheet: 1.04 (0.69), residues: 64 loop : -0.29 (0.39), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP 4 205 HIS 0.004 0.001 HIS 4 232 PHE 0.011 0.001 PHE P 218 TYR 0.024 0.002 TYR 4 210 ARG 0.004 0.000 ARG P 205 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 92 time to evaluate : 0.867 Fit side-chains REVERT: 2 136 LYS cc_start: 0.7837 (OUTLIER) cc_final: 0.7281 (pttp) REVERT: 2 226 LYS cc_start: 0.7768 (tppt) cc_final: 0.7485 (tttm) REVERT: 4 47 GLU cc_start: 0.7904 (mm-30) cc_final: 0.7625 (mp0) REVERT: 7 56 LYS cc_start: 0.7676 (mttm) cc_final: 0.7084 (tptm) REVERT: P 160 GLU cc_start: 0.8208 (mt-10) cc_final: 0.7709 (pt0) REVERT: P 183 LYS cc_start: 0.7528 (mtmm) cc_final: 0.7091 (mttp) outliers start: 14 outliers final: 11 residues processed: 100 average time/residue: 1.3063 time to fit residues: 138.0921 Evaluate side-chains 97 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 85 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 104 SER Chi-restraints excluded: chain 2 residue 136 LYS Chi-restraints excluded: chain 2 residue 293 THR Chi-restraints excluded: chain 2 residue 370 ILE Chi-restraints excluded: chain 2 residue 391 THR Chi-restraints excluded: chain 2 residue 432 GLN Chi-restraints excluded: chain 7 residue 34 SER Chi-restraints excluded: chain 7 residue 35 ILE Chi-restraints excluded: chain 7 residue 60 GLN Chi-restraints excluded: chain 7 residue 75 SER Chi-restraints excluded: chain 7 residue 103 LEU Chi-restraints excluded: chain 7 residue 144 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 67 optimal weight: 0.5980 chunk 32 optimal weight: 0.6980 chunk 82 optimal weight: 0.0470 chunk 55 optimal weight: 3.9990 chunk 2 optimal weight: 0.8980 chunk 62 optimal weight: 0.0010 chunk 27 optimal weight: 0.9990 chunk 59 optimal weight: 0.9980 chunk 75 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 overall best weight: 0.4284 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 40 GLN 7 60 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.128767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.094837 restraints weight = 9611.879| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 1.80 r_work: 0.2930 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2798 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.2096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 7859 Z= 0.164 Angle : 0.480 8.047 10652 Z= 0.248 Chirality : 0.038 0.128 1253 Planarity : 0.004 0.043 1357 Dihedral : 3.809 17.140 1092 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.78 % Allowed : 15.48 % Favored : 82.74 % 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: 2.27 (0.26), residues: 1025 helix: 2.14 (0.19), residues: 717 sheet: 1.07 (0.69), residues: 64 loop : -0.27 (0.40), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP 4 205 HIS 0.004 0.001 HIS 4 232 PHE 0.011 0.001 PHE P 218 TYR 0.023 0.001 TYR 4 210 ARG 0.004 0.000 ARG P 205 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 89 time to evaluate : 0.846 Fit side-chains REVERT: 2 136 LYS cc_start: 0.7829 (OUTLIER) cc_final: 0.7286 (pttp) REVERT: 2 223 LYS cc_start: 0.8230 (OUTLIER) cc_final: 0.7690 (mppt) REVERT: 2 226 LYS cc_start: 0.7738 (tppt) cc_final: 0.7491 (tttp) REVERT: 4 47 GLU cc_start: 0.7879 (mm-30) cc_final: 0.7597 (mp0) REVERT: 7 56 LYS cc_start: 0.7685 (mttm) cc_final: 0.7122 (tptm) REVERT: P 160 GLU cc_start: 0.8209 (mt-10) cc_final: 0.7743 (pt0) REVERT: P 183 LYS cc_start: 0.7446 (mtmm) cc_final: 0.6948 (mttp) REVERT: T 50 LYS cc_start: 0.9035 (ptpt) cc_final: 0.7946 (ptmt) outliers start: 14 outliers final: 10 residues processed: 98 average time/residue: 1.3652 time to fit residues: 141.5100 Evaluate side-chains 99 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 87 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 13 LYS Chi-restraints excluded: chain 2 residue 104 SER Chi-restraints excluded: chain 2 residue 136 LYS Chi-restraints excluded: chain 2 residue 223 LYS Chi-restraints excluded: chain 2 residue 293 THR Chi-restraints excluded: chain 2 residue 370 ILE Chi-restraints excluded: chain 2 residue 391 THR Chi-restraints excluded: chain 7 residue 34 SER Chi-restraints excluded: chain 7 residue 60 GLN Chi-restraints excluded: chain 7 residue 75 SER Chi-restraints excluded: chain 7 residue 103 LEU Chi-restraints excluded: chain 7 residue 144 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 57 optimal weight: 0.2980 chunk 48 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 46 optimal weight: 0.8980 chunk 87 optimal weight: 0.9980 chunk 101 optimal weight: 0.9980 chunk 51 optimal weight: 0.5980 chunk 34 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 92 optimal weight: 0.0170 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 74 ASN 7 60 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.128647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.095663 restraints weight = 9490.470| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 1.88 r_work: 0.2924 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2789 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.2129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7859 Z= 0.184 Angle : 0.483 7.814 10652 Z= 0.251 Chirality : 0.038 0.129 1253 Planarity : 0.004 0.042 1357 Dihedral : 3.794 15.298 1092 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.78 % Allowed : 15.86 % Favored : 82.36 % 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: 2.32 (0.26), residues: 1025 helix: 2.17 (0.19), residues: 717 sheet: 1.18 (0.69), residues: 64 loop : -0.24 (0.40), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP 4 205 HIS 0.004 0.001 HIS 4 232 PHE 0.011 0.001 PHE P 218 TYR 0.024 0.002 TYR 4 210 ARG 0.004 0.000 ARG P 205 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6275.59 seconds wall clock time: 111 minutes 53.24 seconds (6713.24 seconds total)