Starting phenix.real_space_refine on Wed Mar 12 10:22:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6rd6_4807/03_2025/6rd6_4807.cif Found real_map, /net/cci-nas-00/data/ceres_data/6rd6_4807/03_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_4807/03_2025/6rd6_4807.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6rd6_4807/03_2025/6rd6_4807.map" model { file = "/net/cci-nas-00/data/ceres_data/6rd6_4807/03_2025/6rd6_4807.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6rd6_4807/03_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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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: 14.91, per 1000 atoms: 1.92 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: 2.17 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 0.70 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: 2.20 Time building geometry restraints manager: 2.59 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 158.530 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: 0.450 Check model and map are aligned: 0.060 Set scattering table: 0.100 Process input model: 38.390 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.160 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: 0.010 Load rotamer database and sin/cos tables:26.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 224.340 ------------------------------------------------------------------------------- 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 : 0.730 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: 1.6456 time to fit residues: 225.7718 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 : 1.921 ------------------------------------------------------------------------------- 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 = 0.128097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.094723 restraints weight = 9831.358| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 1.82 r_work: 0.2942 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2813 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.1412 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= 0.172 Angle : 0.493 6.335 10652 Z= 0.264 Chirality : 0.038 0.134 1253 Planarity : 0.005 0.049 1357 Dihedral : 4.272 19.288 1092 Min Nonbonded Distance : 2.574 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: -0.00 (0.25), residues: 1025 helix: 0.53 (0.18), residues: 706 sheet: -0.16 (0.70), residues: 61 loop : -1.20 (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 0.011 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 : 0.896 Fit side-chains REVERT: 2 136 LYS cc_start: 0.7411 (OUTLIER) cc_final: 0.7054 (pttp) REVERT: 2 204 THR cc_start: 0.8048 (OUTLIER) cc_final: 0.7820 (m) REVERT: 2 409 GLN cc_start: 0.8183 (mt0) cc_final: 0.7869 (mt0) REVERT: 4 18 ASP cc_start: 0.7451 (t70) cc_final: 0.6938 (t70) REVERT: 7 56 LYS cc_start: 0.7675 (mttm) cc_final: 0.7085 (mmtp) REVERT: P 183 LYS cc_start: 0.7299 (mtmm) cc_final: 0.6914 (mttp) REVERT: P 186 MET cc_start: 0.8260 (mtm) cc_final: 0.8040 (mtm) outliers start: 15 outliers final: 4 residues processed: 101 average time/residue: 1.2706 time to fit residues: 136.5649 Evaluate side-chains 85 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 79 time to evaluate : 1.471 ------------------------------------------------------------------------------- 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: 0.9990 chunk 18 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 27 optimal weight: 0.3980 chunk 77 optimal weight: 9.9990 chunk 22 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 67 optimal weight: 0.8980 chunk 41 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- 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 = 0.3479 r_free = 0.3479 target = 0.124998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.090746 restraints weight = 10033.331| |-----------------------------------------------------------------------------| r_work (start): 0.2968 rms_B_bonded: 1.86 r_work: 0.2845 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2712 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.1640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 7859 Z= 0.279 Angle : 0.530 7.467 10652 Z= 0.280 Chirality : 0.040 0.139 1253 Planarity : 0.005 0.044 1357 Dihedral : 4.125 18.202 1092 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.66 % Allowed : 10.41 % Favored : 86.93 % 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: 0.96 (0.26), residues: 1025 helix: 1.24 (0.19), residues: 715 sheet: 0.19 (0.72), residues: 57 loop : -0.87 (0.36), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP 4 205 HIS 0.006 0.001 HIS 7 123 PHE 0.014 0.002 PHE 4 161 TYR 0.029 0.002 TYR 4 210 ARG 0.003 0.001 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 111 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 90 time to evaluate : 0.873 Fit side-chains REVERT: 2 409 GLN cc_start: 0.8201 (mt0) cc_final: 0.7931 (mt0) REVERT: 4 47 GLU cc_start: 0.7843 (mm-30) cc_final: 0.7585 (mp0) REVERT: 7 56 LYS cc_start: 0.7653 (mttm) cc_final: 0.7033 (mmtp) REVERT: P 183 LYS cc_start: 0.7361 (mtmm) cc_final: 0.6945 (mttp) REVERT: P 186 MET cc_start: 0.8456 (mtm) cc_final: 0.8204 (mtm) REVERT: P 188 GLU cc_start: 0.8589 (OUTLIER) cc_final: 0.8251 (mm-30) outliers start: 21 outliers final: 7 residues processed: 100 average time/residue: 1.2322 time to fit residues: 130.7878 Evaluate side-chains 85 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 77 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 130 SER 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 Chi-restraints excluded: chain P residue 188 GLU 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: 5.9990 chunk 63 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 71 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 86 optimal weight: 0.7980 chunk 2 optimal weight: 0.5980 chunk 35 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3483 r_free = 0.3483 target = 0.125400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.091368 restraints weight = 9862.757| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 1.82 r_work: 0.2891 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2760 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.1773 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= 0.218 Angle : 0.491 7.664 10652 Z= 0.260 Chirality : 0.039 0.132 1253 Planarity : 0.004 0.042 1357 Dihedral : 4.028 18.367 1092 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.28 % Allowed : 12.06 % 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: 1.44 (0.26), residues: 1025 helix: 1.60 (0.19), residues: 717 sheet: 0.50 (0.71), 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 4 232 PHE 0.011 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 105 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 87 time to evaluate : 0.814 Fit side-chains REVERT: 2 409 GLN cc_start: 0.8143 (mt0) cc_final: 0.7891 (mt0) REVERT: 4 47 GLU cc_start: 0.7845 (mm-30) cc_final: 0.7607 (mp0) REVERT: 7 56 LYS cc_start: 0.7638 (mttm) cc_final: 0.7025 (mmtp) REVERT: P 183 LYS cc_start: 0.7368 (mtmm) cc_final: 0.7001 (mttp) REVERT: P 186 MET cc_start: 0.8440 (mtm) cc_final: 0.8210 (mtm) outliers start: 18 outliers final: 10 residues processed: 97 average time/residue: 1.2739 time to fit residues: 130.7605 Evaluate side-chains 98 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 88 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 13 LYS 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: 0.9990 chunk 20 optimal weight: 0.9980 chunk 75 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 chunk 49 optimal weight: 0.8980 chunk 63 optimal weight: 2.9990 chunk 50 optimal weight: 0.0870 chunk 11 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 chunk 65 optimal weight: 0.6980 overall best weight: 0.6958 ------------------------------------------------------------------------------- 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 = 0.3496 r_free = 0.3496 target = 0.126336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.092324 restraints weight = 9875.856| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 1.84 r_work: 0.2872 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2741 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.1846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7859 Z= 0.204 Angle : 0.485 7.852 10652 Z= 0.254 Chirality : 0.038 0.132 1253 Planarity : 0.004 0.042 1357 Dihedral : 3.954 18.703 1092 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.28 % Allowed : 12.82 % 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: 1.73 (0.26), residues: 1025 helix: 1.80 (0.19), residues: 717 sheet: 0.84 (0.73), 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 0.024 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 108 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 90 time to evaluate : 1.185 Fit side-chains REVERT: 2 136 LYS cc_start: 0.7532 (OUTLIER) cc_final: 0.6967 (pttp) REVERT: 2 409 GLN cc_start: 0.8137 (mt0) cc_final: 0.7935 (mt0) REVERT: 4 47 GLU cc_start: 0.7840 (mm-30) cc_final: 0.7584 (mp0) REVERT: 7 56 LYS cc_start: 0.7620 (mttm) cc_final: 0.7000 (mmtp) REVERT: P 183 LYS cc_start: 0.7347 (mtmm) cc_final: 0.6967 (mttp) REVERT: P 186 MET cc_start: 0.8468 (mtm) cc_final: 0.8195 (mtm) outliers start: 18 outliers final: 10 residues processed: 100 average time/residue: 1.6069 time to fit residues: 170.1854 Evaluate side-chains 94 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 83 time to evaluate : 0.884 ------------------------------------------------------------------------------- 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: 0.9990 chunk 2 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 77 optimal weight: 8.9990 chunk 95 optimal weight: 0.8980 chunk 90 optimal weight: 0.0970 chunk 50 optimal weight: 0.9990 chunk 15 optimal weight: 0.7980 chunk 61 optimal weight: 0.9990 chunk 55 optimal weight: 3.9990 chunk 99 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3494 r_free = 0.3494 target = 0.126167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.092122 restraints weight = 9840.870| |-----------------------------------------------------------------------------| r_work (start): 0.3019 rms_B_bonded: 1.83 r_work: 0.2903 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2771 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.1891 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= 0.211 Angle : 0.482 7.940 10652 Z= 0.254 Chirality : 0.038 0.132 1253 Planarity : 0.004 0.041 1357 Dihedral : 3.927 16.266 1092 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.79 % Allowed : 13.20 % Favored : 84.01 % 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: 1.89 (0.26), residues: 1025 helix: 1.89 (0.19), residues: 718 sheet: 1.10 (0.72), residues: 58 loop : -0.56 (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 0.003 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 109 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 87 time to evaluate : 0.880 Fit side-chains REVERT: 2 101 VAL cc_start: 0.8467 (OUTLIER) cc_final: 0.8234 (p) REVERT: 2 136 LYS cc_start: 0.7526 (OUTLIER) cc_final: 0.6880 (pttp) REVERT: 2 223 LYS cc_start: 0.8152 (OUTLIER) cc_final: 0.7556 (mppt) REVERT: 2 409 GLN cc_start: 0.8113 (mt0) cc_final: 0.7903 (mt0) REVERT: 7 56 LYS cc_start: 0.7622 (mttm) cc_final: 0.7003 (mmtp) REVERT: P 183 LYS cc_start: 0.7355 (mtmm) cc_final: 0.6973 (mttp) REVERT: P 186 MET cc_start: 0.8493 (mtm) cc_final: 0.8246 (mtm) outliers start: 22 outliers final: 12 residues processed: 99 average time/residue: 1.2741 time to fit residues: 133.5412 Evaluate side-chains 107 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 92 time to evaluate : 0.871 ------------------------------------------------------------------------------- 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 130 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 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: 0.9980 chunk 35 optimal weight: 0.7980 chunk 4 optimal weight: 0.9980 chunk 12 optimal weight: 0.8980 chunk 72 optimal weight: 3.9990 chunk 92 optimal weight: 0.9990 chunk 56 optimal weight: 3.9990 chunk 6 optimal weight: 0.9990 chunk 74 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 59 optimal weight: 0.1980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3486 r_free = 0.3486 target = 0.125605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.091591 restraints weight = 9852.722| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 1.82 r_work: 0.2901 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2769 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.1921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7859 Z= 0.220 Angle : 0.492 7.974 10652 Z= 0.257 Chirality : 0.039 0.132 1253 Planarity : 0.004 0.041 1357 Dihedral : 3.918 16.949 1092 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.41 % Allowed : 14.47 % Favored : 83.12 % 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: 1.96 (0.26), residues: 1025 helix: 1.93 (0.19), residues: 717 sheet: 1.17 (0.72), residues: 58 loop : -0.50 (0.38), residues: 250 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 0.011 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 114 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 95 time to evaluate : 0.923 Fit side-chains REVERT: 2 101 VAL cc_start: 0.8503 (OUTLIER) cc_final: 0.8277 (p) REVERT: 2 136 LYS cc_start: 0.7612 (OUTLIER) cc_final: 0.6964 (pttp) REVERT: 2 223 LYS cc_start: 0.8163 (OUTLIER) cc_final: 0.7552 (mppt) REVERT: 4 47 GLU cc_start: 0.7826 (mm-30) cc_final: 0.7572 (mp0) REVERT: 7 56 LYS cc_start: 0.7624 (mttm) cc_final: 0.7006 (mmtp) REVERT: P 160 GLU cc_start: 0.8150 (mt-10) cc_final: 0.7670 (pt0) REVERT: P 183 LYS cc_start: 0.7468 (mtmm) cc_final: 0.6981 (mttp) REVERT: P 186 MET cc_start: 0.8475 (mtm) cc_final: 0.8262 (mtm) outliers start: 19 outliers final: 13 residues processed: 106 average time/residue: 1.2827 time to fit residues: 144.3826 Evaluate side-chains 103 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 87 time to evaluate : 0.853 ------------------------------------------------------------------------------- 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 130 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 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: 3.9990 chunk 12 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 chunk 6 optimal weight: 0.7980 chunk 23 optimal weight: 3.9990 chunk 48 optimal weight: 0.9990 chunk 76 optimal weight: 0.7980 chunk 35 optimal weight: 0.1980 chunk 7 optimal weight: 2.9990 chunk 92 optimal weight: 0.9990 chunk 1 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 = 0.3491 r_free = 0.3491 target = 0.126097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.091949 restraints weight = 9932.683| |-----------------------------------------------------------------------------| r_work (start): 0.2984 rms_B_bonded: 1.83 r_work: 0.2861 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2729 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.1958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7859 Z= 0.216 Angle : 0.489 7.953 10652 Z= 0.257 Chirality : 0.039 0.131 1253 Planarity : 0.004 0.041 1357 Dihedral : 3.910 15.736 1092 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % 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: 2.02 (0.26), residues: 1025 helix: 1.96 (0.19), residues: 717 sheet: 1.02 (0.69), residues: 64 loop : -0.39 (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 7 123 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 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 109 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 90 time to evaluate : 0.816 Fit side-chains REVERT: 2 136 LYS cc_start: 0.7750 (OUTLIER) cc_final: 0.7532 (ptpp) REVERT: 2 223 LYS cc_start: 0.8248 (OUTLIER) cc_final: 0.7683 (mppt) REVERT: 4 47 GLU cc_start: 0.7847 (mm-30) cc_final: 0.7563 (mp0) REVERT: 7 56 LYS cc_start: 0.7628 (mttm) cc_final: 0.7011 (tptm) REVERT: P 160 GLU cc_start: 0.8164 (mt-10) cc_final: 0.7666 (pt0) REVERT: P 183 LYS cc_start: 0.7515 (mtmm) cc_final: 0.7089 (mttp) REVERT: P 186 MET cc_start: 0.8486 (mtm) cc_final: 0.8267 (mtm) REVERT: T 74 GLU cc_start: 0.8065 (tm-30) cc_final: 0.7848 (tp30) outliers start: 19 outliers final: 13 residues processed: 101 average time/residue: 1.3554 time to fit residues: 145.1817 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 : 1.025 ------------------------------------------------------------------------------- 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 130 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 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: 0.8980 chunk 66 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 chunk 20 optimal weight: 0.8980 chunk 31 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 74 optimal weight: 0.3980 chunk 95 optimal weight: 0.7980 chunk 101 optimal weight: 0.2980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3499 r_free = 0.3499 target = 0.126773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.092620 restraints weight = 9978.295| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 1.84 r_work: 0.2909 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2777 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.2017 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= 0.194 Angle : 0.482 7.825 10652 Z= 0.254 Chirality : 0.038 0.130 1253 Planarity : 0.004 0.041 1357 Dihedral : 3.894 15.455 1092 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.90 % Allowed : 15.10 % Favored : 82.99 % 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: 2.14 (0.26), residues: 1025 helix: 2.03 (0.19), residues: 717 sheet: 1.09 (0.70), residues: 64 loop : -0.31 (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 0.023 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 107 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 92 time to evaluate : 1.252 Fit side-chains REVERT: 2 136 LYS cc_start: 0.7781 (OUTLIER) cc_final: 0.7213 (pttp) REVERT: 4 47 GLU cc_start: 0.7854 (mm-30) cc_final: 0.7553 (mp0) REVERT: 7 56 LYS cc_start: 0.7620 (mttm) cc_final: 0.7004 (tptm) REVERT: P 183 LYS cc_start: 0.7513 (mtmm) cc_final: 0.7032 (mttp) REVERT: P 188 GLU cc_start: 0.8302 (mm-30) cc_final: 0.8091 (mm-30) REVERT: T 74 GLU cc_start: 0.8086 (tm-30) cc_final: 0.7866 (tp30) outliers start: 15 outliers final: 10 residues processed: 101 average time/residue: 1.2823 time to fit residues: 137.3748 Evaluate side-chains 88 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 77 time to evaluate : 0.898 ------------------------------------------------------------------------------- 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 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: 0.4980 chunk 55 optimal weight: 0.3980 chunk 2 optimal weight: 0.7980 chunk 62 optimal weight: 0.8980 chunk 27 optimal weight: 0.7980 chunk 59 optimal weight: 0.8980 chunk 75 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 12 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.3504 r_free = 0.3504 target = 0.127060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.092934 restraints weight = 9901.959| |-----------------------------------------------------------------------------| r_work (start): 0.3000 rms_B_bonded: 1.83 r_work: 0.2877 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2744 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.2071 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 : 0.476 7.817 10652 Z= 0.251 Chirality : 0.038 0.130 1253 Planarity : 0.004 0.042 1357 Dihedral : 3.871 15.375 1092 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.52 % Allowed : 15.99 % Favored : 82.49 % 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: 2.21 (0.26), residues: 1025 helix: 2.09 (0.19), residues: 717 sheet: 1.17 (0.70), residues: 64 loop : -0.28 (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 0.023 0.002 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 89 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 77 time to evaluate : 1.499 Fit side-chains REVERT: 2 136 LYS cc_start: 0.7737 (OUTLIER) cc_final: 0.7173 (pttp) REVERT: 4 47 GLU cc_start: 0.7871 (mm-30) cc_final: 0.7548 (mp0) REVERT: 7 56 LYS cc_start: 0.7609 (mttm) cc_final: 0.6992 (tptm) REVERT: P 183 LYS cc_start: 0.7371 (mtmm) cc_final: 0.6875 (mttp) REVERT: T 74 GLU cc_start: 0.8079 (tm-30) cc_final: 0.7867 (tp30) outliers start: 12 outliers final: 10 residues processed: 86 average time/residue: 1.9422 time to fit residues: 175.7700 Evaluate side-chains 93 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 82 time to evaluate : 1.939 ------------------------------------------------------------------------------- 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 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: 0.5980 chunk 48 optimal weight: 0.0470 chunk 44 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 87 optimal weight: 0.7980 chunk 101 optimal weight: 0.9980 chunk 51 optimal weight: 0.0370 chunk 34 optimal weight: 0.6980 chunk 33 optimal weight: 0.9990 chunk 92 optimal weight: 1.9990 overall best weight: 0.4356 ------------------------------------------------------------------------------- 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 = 0.128100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.094028 restraints weight = 9800.431| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 1.82 r_work: 0.2916 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2785 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 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 : 0.002 0.026 7859 Z= 0.160 Angle : 0.464 7.703 10652 Z= 0.244 Chirality : 0.038 0.130 1253 Planarity : 0.004 0.043 1357 Dihedral : 3.817 15.452 1092 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.52 % Allowed : 16.12 % 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: 2.34 (0.26), residues: 1025 helix: 2.18 (0.19), residues: 717 sheet: 1.32 (0.70), residues: 64 loop : -0.25 (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 0.023 0.001 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: 6957.45 seconds wall clock time: 122 minutes 59.63 seconds (7379.63 seconds total)