Starting phenix.real_space_refine on Tue Mar 3 17:49:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6rd6_4807/03_2026/6rd6_4807.cif Found real_map, /net/cci-nas-00/data/ceres_data/6rd6_4807/03_2026/6rd6_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 { model { file = "/net/cci-nas-00/data/ceres_data/6rd6_4807/03_2026/6rd6_4807.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6rd6_4807/03_2026/6rd6_4807.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6rd6_4807/03_2026/6rd6_4807.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6rd6_4807/03_2026/6rd6_4807.map" } resolution = 2.75 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.005 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: 1.57, per 1000 atoms: 0.20 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: 0.72 Conformation dependent library (CDL) restraints added in 312.8 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: 0.25 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: 1.16 Time building geometry restraints manager: 0.93 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: 7.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.270 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.950 ------------------------------------------------------------------------------- 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= 0.268 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 : 4.55 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.003 0.001 ARG 2 322 TYR 0.026 0.002 TYR 4 210 PHE 0.014 0.002 PHE P 218 TRP 0.025 0.004 TRP 7 107 HIS 0.009 0.002 HIS 4 232 Details of bonding type rmsd covalent geometry : bond 0.00564 ( 7859) covalent geometry : angle 0.81947 (10652) hydrogen bonds : bond 0.14331 ( 551) hydrogen bonds : angle 5.95557 ( 1629) *********************** 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 : 0.361 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: 0.7195 (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: 0.5782 time to fit residues: 78.5959 Evaluate side-chains 81 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 49 optimal weight: 0.6980 chunk 97 optimal weight: 0.6980 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 0.0170 chunk 51 optimal weight: 0.8980 chunk 100 optimal weight: 0.8980 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 0.8980 overall best weight: 0.6418 ------------------------------------------------------------------------------- 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 64 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.126706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.093047 restraints weight = 9942.711| |-----------------------------------------------------------------------------| r_work (start): 0.3034 rms_B_bonded: 1.84 r_work: 0.2916 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2787 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.1377 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= 0.137 Angle : 0.511 6.626 10652 Z= 0.273 Chirality : 0.038 0.138 1253 Planarity : 0.005 0.049 1357 Dihedral : 4.303 19.183 1092 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.03 % Allowed : 8.88 % Favored : 89.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.25), residues: 1025 helix: 0.52 (0.18), residues: 706 sheet: -0.13 (0.70), residues: 61 loop : -1.21 (0.34), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG P 205 TYR 0.027 0.002 TYR 4 210 PHE 0.012 0.001 PHE 4 161 TRP 0.018 0.002 TRP 4 205 HIS 0.004 0.001 HIS 7 123 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 7859) covalent geometry : angle 0.51072 (10652) hydrogen bonds : bond 0.04190 ( 551) hydrogen bonds : angle 3.90146 ( 1629) *********************** 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: 16 poor density : 93 time to evaluate : 0.315 Fit side-chains REVERT: 2 136 LYS cc_start: 0.7455 (OUTLIER) cc_final: 0.7082 (pttp) REVERT: 2 204 THR cc_start: 0.8065 (OUTLIER) cc_final: 0.7832 (m) REVERT: 4 18 ASP cc_start: 0.7501 (t70) cc_final: 0.6966 (t70) REVERT: 4 47 GLU cc_start: 0.7865 (mp0) cc_final: 0.7637 (mm-30) REVERT: 7 56 LYS cc_start: 0.7636 (mttm) cc_final: 0.7040 (mmtp) REVERT: P 183 LYS cc_start: 0.7328 (mtmm) cc_final: 0.6935 (mttp) REVERT: P 186 MET cc_start: 0.8267 (mtm) cc_final: 0.7963 (mtp) outliers start: 16 outliers final: 5 residues processed: 101 average time/residue: 0.5757 time to fit residues: 61.5072 Evaluate side-chains 88 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 81 time to evaluate : 0.279 ------------------------------------------------------------------------------- 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 34 SER 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 4 optimal weight: 0.7980 chunk 19 optimal weight: 5.9990 chunk 27 optimal weight: 0.4980 chunk 39 optimal weight: 0.1980 chunk 9 optimal weight: 0.8980 chunk 85 optimal weight: 0.6980 chunk 24 optimal weight: 0.6980 chunk 2 optimal weight: 0.7980 chunk 73 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 48 optimal weight: 0.5980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 4 110 GLN ** 4 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 60 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.127133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.093238 restraints weight = 9845.997| |-----------------------------------------------------------------------------| r_work (start): 0.3041 rms_B_bonded: 1.83 r_work: 0.2925 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2794 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.1646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7859 Z= 0.121 Angle : 0.481 7.367 10652 Z= 0.253 Chirality : 0.038 0.131 1253 Planarity : 0.004 0.046 1357 Dihedral : 3.983 18.174 1092 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.41 % Allowed : 10.66 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.13 (0.26), residues: 1025 helix: 1.40 (0.19), residues: 717 sheet: 0.26 (0.71), residues: 57 loop : -0.92 (0.36), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG P 205 TYR 0.026 0.002 TYR 4 210 PHE 0.010 0.001 PHE 4 161 TRP 0.016 0.002 TRP 4 205 HIS 0.004 0.001 HIS 4 232 Details of bonding type rmsd covalent geometry : bond 0.00272 ( 7859) covalent geometry : angle 0.48132 (10652) hydrogen bonds : bond 0.03780 ( 551) hydrogen bonds : angle 3.56952 ( 1629) *********************** 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 112 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 93 time to evaluate : 0.289 Fit side-chains REVERT: 2 409 GLN cc_start: 0.8258 (mt0) cc_final: 0.8007 (mt0) REVERT: 4 47 GLU cc_start: 0.7842 (mp0) cc_final: 0.7636 (mm-30) REVERT: 7 56 LYS cc_start: 0.7644 (mttm) cc_final: 0.7027 (mmtp) REVERT: P 183 LYS cc_start: 0.7328 (mtmm) cc_final: 0.6902 (mttp) REVERT: P 186 MET cc_start: 0.8410 (mtm) cc_final: 0.8108 (mtp) REVERT: P 188 GLU cc_start: 0.8607 (OUTLIER) cc_final: 0.6946 (mm-30) outliers start: 19 outliers final: 7 residues processed: 103 average time/residue: 0.5924 time to fit residues: 64.4270 Evaluate side-chains 88 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 80 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 25 optimal weight: 0.9980 chunk 96 optimal weight: 1.9990 chunk 47 optimal weight: 6.9990 chunk 89 optimal weight: 0.5980 chunk 98 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 86 optimal weight: 0.7980 chunk 73 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 76 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 74 ASN 4 232 HIS 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 = 0.126258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.092283 restraints weight = 10085.652| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 1.84 r_work: 0.2888 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2758 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.1763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7859 Z= 0.152 Angle : 0.491 7.610 10652 Z= 0.259 Chirality : 0.039 0.135 1253 Planarity : 0.004 0.043 1357 Dihedral : 3.958 17.522 1092 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.03 % Allowed : 12.31 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.52 (0.26), residues: 1025 helix: 1.66 (0.19), residues: 717 sheet: 0.62 (0.70), residues: 57 loop : -0.76 (0.37), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG P 205 TYR 0.026 0.002 TYR 4 210 PHE 0.011 0.002 PHE 4 161 TRP 0.016 0.002 TRP 4 205 HIS 0.005 0.001 HIS 7 123 Details of bonding type rmsd covalent geometry : bond 0.00353 ( 7859) covalent geometry : angle 0.49081 (10652) hydrogen bonds : bond 0.03931 ( 551) hydrogen bonds : angle 3.55282 ( 1629) *********************** 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 102 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 86 time to evaluate : 0.226 Fit side-chains REVERT: 2 409 GLN cc_start: 0.8180 (mt0) cc_final: 0.7940 (mt0) REVERT: 4 47 GLU cc_start: 0.7980 (mp0) cc_final: 0.7762 (mm-30) REVERT: 7 56 LYS cc_start: 0.7655 (mttm) cc_final: 0.7031 (mmtp) REVERT: 7 60 GLN cc_start: 0.7469 (OUTLIER) cc_final: 0.7156 (tt0) REVERT: P 183 LYS cc_start: 0.7331 (mtmm) cc_final: 0.6937 (mttp) outliers start: 16 outliers final: 10 residues processed: 96 average time/residue: 0.6100 time to fit residues: 61.6213 Evaluate side-chains 104 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 93 time to evaluate : 0.214 ------------------------------------------------------------------------------- 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 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 144 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 94 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 chunk 62 optimal weight: 0.0270 chunk 96 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 64 optimal weight: 0.9980 chunk 81 optimal weight: 0.5980 chunk 13 optimal weight: 0.0270 chunk 57 optimal weight: 1.9990 chunk 92 optimal weight: 0.9990 chunk 58 optimal weight: 0.7980 overall best weight: 0.4896 ------------------------------------------------------------------------------- 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 = 0.3514 r_free = 0.3514 target = 0.127622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.093785 restraints weight = 9933.503| |-----------------------------------------------------------------------------| r_work (start): 0.3033 rms_B_bonded: 1.83 r_work: 0.2915 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2783 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.1875 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= 0.114 Angle : 0.465 7.500 10652 Z= 0.243 Chirality : 0.038 0.142 1253 Planarity : 0.004 0.043 1357 Dihedral : 3.865 18.260 1092 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.86 (0.26), residues: 1025 helix: 1.91 (0.19), residues: 718 sheet: 0.87 (0.71), residues: 58 loop : -0.65 (0.37), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG P 205 TYR 0.023 0.002 TYR 4 210 PHE 0.010 0.001 PHE P 218 TRP 0.015 0.002 TRP 4 205 HIS 0.004 0.001 HIS 4 232 Details of bonding type rmsd covalent geometry : bond 0.00257 ( 7859) covalent geometry : angle 0.46469 (10652) hydrogen bonds : bond 0.03629 ( 551) hydrogen bonds : angle 3.43125 ( 1629) *********************** 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 119 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 101 time to evaluate : 0.227 Fit side-chains REVERT: 2 409 GLN cc_start: 0.8179 (mt0) cc_final: 0.7946 (mt0) REVERT: 4 47 GLU cc_start: 0.7871 (mp0) cc_final: 0.7670 (mm-30) REVERT: 7 56 LYS cc_start: 0.7634 (mttm) cc_final: 0.7027 (mmtp) REVERT: P 183 LYS cc_start: 0.7392 (mtmm) cc_final: 0.6871 (mttp) outliers start: 18 outliers final: 9 residues processed: 112 average time/residue: 0.5528 time to fit residues: 65.4702 Evaluate side-chains 98 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 89 time to evaluate : 0.276 ------------------------------------------------------------------------------- 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 50 optimal weight: 0.8980 chunk 87 optimal weight: 0.3980 chunk 32 optimal weight: 0.7980 chunk 22 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 chunk 95 optimal weight: 0.8980 chunk 13 optimal weight: 0.7980 chunk 70 optimal weight: 0.5980 chunk 89 optimal weight: 0.6980 chunk 20 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3497 r_free = 0.3497 target = 0.126277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.092084 restraints weight = 9948.585| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 1.84 r_work: 0.2887 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2755 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.1931 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= 0.132 Angle : 0.471 7.863 10652 Z= 0.248 Chirality : 0.038 0.131 1253 Planarity : 0.004 0.043 1357 Dihedral : 3.867 15.543 1092 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.03 % Allowed : 13.83 % Favored : 84.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.98 (0.26), residues: 1025 helix: 1.98 (0.19), residues: 718 sheet: 1.03 (0.71), residues: 58 loop : -0.56 (0.38), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG P 205 TYR 0.024 0.002 TYR 4 210 PHE 0.011 0.001 PHE P 218 TRP 0.015 0.002 TRP 4 205 HIS 0.004 0.001 HIS 4 232 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 7859) covalent geometry : angle 0.47103 (10652) hydrogen bonds : bond 0.03717 ( 551) hydrogen bonds : angle 3.43181 ( 1629) *********************** 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 111 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 95 time to evaluate : 0.307 Fit side-chains REVERT: 2 136 LYS cc_start: 0.7580 (OUTLIER) cc_final: 0.6900 (pttp) REVERT: 2 223 LYS cc_start: 0.8126 (OUTLIER) cc_final: 0.7542 (mppt) REVERT: 2 409 GLN cc_start: 0.8227 (mt0) cc_final: 0.7999 (mt0) REVERT: 4 18 ASP cc_start: 0.7348 (t70) cc_final: 0.7103 (t70) REVERT: 4 20 GLU cc_start: 0.7495 (pm20) cc_final: 0.7217 (pm20) REVERT: 4 47 GLU cc_start: 0.7987 (mp0) cc_final: 0.7766 (mm-30) REVERT: 7 56 LYS cc_start: 0.7623 (mttm) cc_final: 0.7009 (mmtp) REVERT: P 183 LYS cc_start: 0.7385 (mtmm) cc_final: 0.6865 (mttp) outliers start: 16 outliers final: 10 residues processed: 106 average time/residue: 0.5797 time to fit residues: 65.0270 Evaluate side-chains 106 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 94 time to evaluate : 0.283 ------------------------------------------------------------------------------- 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 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 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 54 optimal weight: 0.8980 chunk 39 optimal weight: 3.9990 chunk 38 optimal weight: 0.0470 chunk 79 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 86 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 67 optimal weight: 0.5980 chunk 61 optimal weight: 0.1980 overall best weight: 0.5480 ------------------------------------------------------------------------------- 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 = 0.3525 r_free = 0.3525 target = 0.128244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.094536 restraints weight = 9528.613| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 1.78 r_work: 0.2929 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2791 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 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 0.034 7859 Z= 0.122 Angle : 0.478 7.766 10652 Z= 0.248 Chirality : 0.038 0.129 1253 Planarity : 0.004 0.043 1357 Dihedral : 3.839 16.222 1092 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.03 % Allowed : 14.47 % Favored : 83.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.09 (0.26), residues: 1025 helix: 2.04 (0.19), residues: 718 sheet: 1.13 (0.71), residues: 58 loop : -0.48 (0.38), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG P 205 TYR 0.024 0.002 TYR 4 210 PHE 0.011 0.001 PHE P 218 TRP 0.015 0.002 TRP 4 205 HIS 0.004 0.001 HIS 4 232 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 7859) covalent geometry : angle 0.47765 (10652) hydrogen bonds : bond 0.03625 ( 551) hydrogen bonds : angle 3.39433 ( 1629) *********************** 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 116 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 100 time to evaluate : 0.343 Fit side-chains REVERT: 2 136 LYS cc_start: 0.7665 (OUTLIER) cc_final: 0.7023 (pttp) REVERT: 2 223 LYS cc_start: 0.8129 (OUTLIER) cc_final: 0.7561 (mppt) REVERT: 2 226 LYS cc_start: 0.7760 (tppt) cc_final: 0.7540 (tttp) REVERT: 2 409 GLN cc_start: 0.8200 (mt0) cc_final: 0.7971 (mt0) REVERT: 4 18 ASP cc_start: 0.7272 (t70) cc_final: 0.6942 (t70) REVERT: 4 20 GLU cc_start: 0.7490 (pm20) cc_final: 0.7210 (pm20) REVERT: 4 37 GLN cc_start: 0.8808 (mm110) cc_final: 0.8584 (mm110) REVERT: 7 56 LYS cc_start: 0.7667 (mttm) cc_final: 0.7084 (mmtp) REVERT: P 160 GLU cc_start: 0.8114 (mt-10) cc_final: 0.7635 (pt0) REVERT: P 183 LYS cc_start: 0.7412 (mtmm) cc_final: 0.6936 (mttp) outliers start: 16 outliers final: 11 residues processed: 110 average time/residue: 0.6002 time to fit residues: 69.6459 Evaluate side-chains 105 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 92 time to evaluate : 0.243 ------------------------------------------------------------------------------- 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 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 84 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 chunk 77 optimal weight: 5.9990 chunk 34 optimal weight: 0.9990 chunk 69 optimal weight: 0.0970 chunk 38 optimal weight: 0.0030 chunk 41 optimal weight: 0.4980 chunk 5 optimal weight: 3.9990 chunk 67 optimal weight: 0.6980 overall best weight: 0.4588 ------------------------------------------------------------------------------- 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 = 0.3534 r_free = 0.3534 target = 0.129197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.096294 restraints weight = 9597.147| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 1.92 r_work: 0.2932 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2800 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.2073 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= 0.115 Angle : 0.475 7.705 10652 Z= 0.250 Chirality : 0.038 0.128 1253 Planarity : 0.004 0.043 1357 Dihedral : 3.783 15.256 1092 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.90 % Allowed : 14.85 % Favored : 83.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.17 (0.26), residues: 1025 helix: 2.08 (0.19), residues: 719 sheet: 1.01 (0.69), residues: 64 loop : -0.35 (0.39), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG P 205 TYR 0.023 0.001 TYR 4 210 PHE 0.011 0.001 PHE P 218 TRP 0.015 0.002 TRP 4 205 HIS 0.004 0.001 HIS 4 232 Details of bonding type rmsd covalent geometry : bond 0.00258 ( 7859) covalent geometry : angle 0.47494 (10652) hydrogen bonds : bond 0.03522 ( 551) hydrogen bonds : angle 3.32072 ( 1629) *********************** 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 100 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 85 time to evaluate : 0.311 Fit side-chains REVERT: 2 136 LYS cc_start: 0.7748 (OUTLIER) cc_final: 0.7548 (ptpp) REVERT: 2 223 LYS cc_start: 0.8208 (OUTLIER) cc_final: 0.7682 (mppt) REVERT: 2 226 LYS cc_start: 0.7653 (tppt) cc_final: 0.7447 (tttm) REVERT: 2 409 GLN cc_start: 0.8188 (mt0) cc_final: 0.7979 (mt0) REVERT: 4 18 ASP cc_start: 0.7265 (t70) cc_final: 0.6885 (t70) REVERT: 4 20 GLU cc_start: 0.7473 (pm20) cc_final: 0.7198 (pm20) REVERT: 4 37 GLN cc_start: 0.8799 (mm110) cc_final: 0.8572 (mm110) REVERT: 4 47 GLU cc_start: 0.7826 (mm-30) cc_final: 0.7609 (mp0) REVERT: 7 56 LYS cc_start: 0.7647 (mttm) cc_final: 0.7078 (mmtp) REVERT: P 183 LYS cc_start: 0.7407 (mtmm) cc_final: 0.6897 (mttp) REVERT: T 50 LYS cc_start: 0.9062 (ptpt) cc_final: 0.7997 (ptmt) outliers start: 15 outliers final: 7 residues processed: 95 average time/residue: 0.6484 time to fit residues: 64.7153 Evaluate side-chains 91 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 82 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 92 optimal weight: 2.9990 chunk 88 optimal weight: 0.0870 chunk 71 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 76 optimal weight: 0.9990 chunk 8 optimal weight: 0.9990 chunk 16 optimal weight: 0.4980 chunk 55 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 overall best weight: 0.6760 ------------------------------------------------------------------------------- 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 = 0.3522 r_free = 0.3522 target = 0.128182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.095829 restraints weight = 9541.482| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 1.93 r_work: 0.2914 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2780 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.2057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7859 Z= 0.134 Angle : 0.483 7.873 10652 Z= 0.254 Chirality : 0.038 0.129 1253 Planarity : 0.004 0.043 1357 Dihedral : 3.816 15.756 1092 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.52 % Allowed : 15.36 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.18 (0.26), residues: 1025 helix: 2.07 (0.19), residues: 719 sheet: 1.11 (0.69), residues: 64 loop : -0.32 (0.39), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG P 205 TYR 0.024 0.002 TYR 4 210 PHE 0.011 0.001 PHE P 218 TRP 0.015 0.002 TRP 4 205 HIS 0.004 0.001 HIS 7 123 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 7859) covalent geometry : angle 0.48266 (10652) hydrogen bonds : bond 0.03682 ( 551) hydrogen bonds : angle 3.36337 ( 1629) *********************** 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 98 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 86 time to evaluate : 0.186 Fit side-chains REVERT: 2 136 LYS cc_start: 0.7788 (OUTLIER) cc_final: 0.7194 (pttp) REVERT: 2 226 LYS cc_start: 0.7687 (tppt) cc_final: 0.7482 (tttp) REVERT: 2 409 GLN cc_start: 0.8193 (mt0) cc_final: 0.7977 (mt0) REVERT: 4 20 GLU cc_start: 0.7462 (pm20) cc_final: 0.7202 (pm20) REVERT: 4 37 GLN cc_start: 0.8810 (mm110) cc_final: 0.8585 (mm110) REVERT: 4 47 GLU cc_start: 0.7880 (mm-30) cc_final: 0.7644 (mp0) REVERT: 7 56 LYS cc_start: 0.7668 (mttm) cc_final: 0.7105 (tptm) REVERT: P 183 LYS cc_start: 0.7433 (mtmm) cc_final: 0.6975 (mttp) REVERT: T 50 LYS cc_start: 0.9061 (ptpt) cc_final: 0.7984 (ptmt) outliers start: 12 outliers final: 8 residues processed: 94 average time/residue: 0.6597 time to fit residues: 65.0215 Evaluate side-chains 87 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 78 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 13 LYS Chi-restraints excluded: chain 2 residue 136 LYS Chi-restraints excluded: chain 2 residue 293 THR 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 16 optimal weight: 2.9990 chunk 12 optimal weight: 0.6980 chunk 44 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 51 optimal weight: 0.6980 chunk 9 optimal weight: 0.8980 chunk 37 optimal weight: 3.9990 chunk 96 optimal weight: 0.8980 chunk 98 optimal weight: 0.6980 chunk 6 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3520 r_free = 0.3520 target = 0.128061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.094790 restraints weight = 9546.156| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 1.86 r_work: 0.2909 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2773 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.2076 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= 0.135 Angle : 0.488 7.878 10652 Z= 0.256 Chirality : 0.039 0.130 1253 Planarity : 0.004 0.043 1357 Dihedral : 3.822 15.658 1092 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.40 % Allowed : 15.86 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.21 (0.26), residues: 1025 helix: 2.09 (0.19), residues: 718 sheet: 1.17 (0.70), residues: 64 loop : -0.33 (0.39), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG P 205 TYR 0.024 0.002 TYR 4 210 PHE 0.011 0.001 PHE P 218 TRP 0.015 0.002 TRP 4 205 HIS 0.004 0.001 HIS 4 232 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 7859) covalent geometry : angle 0.48762 (10652) hydrogen bonds : bond 0.03682 ( 551) hydrogen bonds : angle 3.37404 ( 1629) ********************** 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 90 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 79 time to evaluate : 0.304 Fit side-chains REVERT: 2 136 LYS cc_start: 0.7828 (OUTLIER) cc_final: 0.7188 (pttp) REVERT: 2 226 LYS cc_start: 0.7687 (tppt) cc_final: 0.7480 (tttp) REVERT: 2 409 GLN cc_start: 0.8190 (mt0) cc_final: 0.7974 (mt0) REVERT: 4 20 GLU cc_start: 0.7469 (pm20) cc_final: 0.7215 (pm20) REVERT: 4 37 GLN cc_start: 0.8811 (mm110) cc_final: 0.8584 (mm110) REVERT: 4 47 GLU cc_start: 0.7892 (mm-30) cc_final: 0.7646 (mp0) REVERT: 7 56 LYS cc_start: 0.7644 (mttm) cc_final: 0.7078 (tptm) REVERT: P 183 LYS cc_start: 0.7498 (mtmm) cc_final: 0.7048 (mttp) REVERT: T 50 LYS cc_start: 0.9062 (ptpt) cc_final: 0.7986 (ptmt) outliers start: 11 outliers final: 8 residues processed: 89 average time/residue: 0.6603 time to fit residues: 61.8249 Evaluate side-chains 92 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 83 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 13 LYS Chi-restraints excluded: chain 2 residue 136 LYS Chi-restraints excluded: chain 2 residue 293 THR 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 53 optimal weight: 0.9980 chunk 31 optimal weight: 0.6980 chunk 48 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 89 optimal weight: 0.6980 chunk 82 optimal weight: 0.7980 chunk 40 optimal weight: 0.7980 chunk 70 optimal weight: 0.9980 chunk 26 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 62 optimal weight: 0.0970 overall best weight: 0.6178 ------------------------------------------------------------------------------- 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 = 0.3523 r_free = 0.3523 target = 0.128295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.095058 restraints weight = 9553.436| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 1.86 r_work: 0.2916 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2781 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.2094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7859 Z= 0.128 Angle : 0.479 7.832 10652 Z= 0.252 Chirality : 0.038 0.130 1253 Planarity : 0.004 0.043 1357 Dihedral : 3.812 15.672 1092 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.40 % Allowed : 15.61 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.23 (0.26), residues: 1025 helix: 2.11 (0.19), residues: 718 sheet: 1.14 (0.70), residues: 64 loop : -0.31 (0.40), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG P 205 TYR 0.024 0.002 TYR 4 210 PHE 0.011 0.001 PHE P 218 TRP 0.015 0.002 TRP 4 205 HIS 0.004 0.001 HIS 4 232 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 7859) covalent geometry : angle 0.47878 (10652) hydrogen bonds : bond 0.03649 ( 551) hydrogen bonds : angle 3.36256 ( 1629) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2921.26 seconds wall clock time: 50 minutes 30.19 seconds (3030.19 seconds total)