Starting phenix.real_space_refine on Fri Jul 3 12:13:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9o95_70242/07_2026/9o95_70242.cif Found real_map, /net/cci-nas-00/data/ceres_data/9o95_70242/07_2026/9o95_70242.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9o95_70242/07_2026/9o95_70242.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9o95_70242/07_2026/9o95_70242.map" model { file = "/net/cci-nas-00/data/ceres_data/9o95_70242/07_2026/9o95_70242.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9o95_70242/07_2026/9o95_70242.cif" } resolution = 3.2 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= 0.002 sd= 0.223 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: 6 Type Number sf(0) Gaussians S 40 5.16 5 Cl 4 4.86 5 C 4380 2.51 5 N 1120 2.21 5 O 1126 1.98 5 H 6970 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13640 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 444, 6818 Classifications: {'peptide': 444} Link IDs: {'PTRANS': 19, 'TRANS': 424} Chain: "B" Number of atoms: 6818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 444, 6818 Classifications: {'peptide': 444} Link IDs: {'PTRANS': 19, 'TRANS': 424} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' CL': 2} Chain breaks: 2 Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' CL': 2} Chain breaks: 2 Time building chain proxies: 2.30, per 1000 atoms: 0.17 Number of scatterers: 13640 At special positions: 0 Unit cell: (76.26, 113.98, 74.62, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 4 17.00 S 40 16.00 O 1126 8.00 N 1120 7.00 C 4380 6.00 H 6970 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.22 Conformation dependent library (CDL) restraints added in 325.0 milliseconds 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1548 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 0 sheets defined 84.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'A' and resid 17 through 26 Processing helix chain 'A' and resid 32 through 67 Processing helix chain 'A' and resid 74 through 101 removed outlier: 3.634A pdb=" N SER A 86 " --> pdb=" O ALA A 82 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLY A 93 " --> pdb=" O LEU A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 105 Processing helix chain 'A' and resid 108 through 117 Processing helix chain 'A' and resid 123 through 141 Proline residue: A 129 - end of helix Processing helix chain 'A' and resid 147 through 167 Processing helix chain 'A' and resid 170 through 191 removed outlier: 3.550A pdb=" N ARG A 174 " --> pdb=" O GLY A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 204 removed outlier: 3.583A pdb=" N ILE A 200 " --> pdb=" O GLY A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 233 removed outlier: 3.742A pdb=" N PHE A 232 " --> pdb=" O MET A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 250 No H-bonds generated for 'chain 'A' and resid 248 through 250' Processing helix chain 'A' and resid 251 through 285 removed outlier: 3.966A pdb=" N TYR A 255 " --> pdb=" O THR A 251 " (cutoff:3.500A) Proline residue: A 267 - end of helix removed outlier: 3.611A pdb=" N HIS A 281 " --> pdb=" O GLN A 277 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ARG A 282 " --> pdb=" O ASP A 278 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N VAL A 283 " --> pdb=" O LEU A 279 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N HIS A 284 " --> pdb=" O LEU A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 309 Processing helix chain 'A' and resid 310 through 313 Processing helix chain 'A' and resid 318 through 325 removed outlier: 4.336A pdb=" N ILE A 322 " --> pdb=" O ASN A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 349 Processing helix chain 'A' and resid 356 through 379 removed outlier: 3.529A pdb=" N VAL A 374 " --> pdb=" O ALA A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 383 removed outlier: 3.601A pdb=" N HIS A 383 " --> pdb=" O PRO A 380 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 380 through 383' Processing helix chain 'A' and resid 385 through 395 removed outlier: 4.180A pdb=" N PHE A 389 " --> pdb=" O GLU A 385 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA A 390 " --> pdb=" O ALA A 386 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N GLY A 395 " --> pdb=" O ILE A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 402 removed outlier: 3.560A pdb=" N ALA A 399 " --> pdb=" O GLY A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 417 Processing helix chain 'A' and resid 418 through 420 No H-bonds generated for 'chain 'A' and resid 418 through 420' Processing helix chain 'A' and resid 421 through 439 Processing helix chain 'A' and resid 443 through 459 removed outlier: 3.680A pdb=" N GLU A 459 " --> pdb=" O LYS A 455 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 26 Processing helix chain 'B' and resid 32 through 67 Processing helix chain 'B' and resid 74 through 101 removed outlier: 3.634A pdb=" N SER B 86 " --> pdb=" O ALA B 82 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLY B 93 " --> pdb=" O LEU B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 105 Processing helix chain 'B' and resid 108 through 117 Processing helix chain 'B' and resid 123 through 141 Proline residue: B 129 - end of helix Processing helix chain 'B' and resid 147 through 167 Processing helix chain 'B' and resid 170 through 191 removed outlier: 3.551A pdb=" N ARG B 174 " --> pdb=" O GLY B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 192 through 204 removed outlier: 3.579A pdb=" N ILE B 200 " --> pdb=" O GLY B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 233 removed outlier: 3.742A pdb=" N PHE B 232 " --> pdb=" O MET B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 250 No H-bonds generated for 'chain 'B' and resid 248 through 250' Processing helix chain 'B' and resid 251 through 285 removed outlier: 3.954A pdb=" N TYR B 255 " --> pdb=" O THR B 251 " (cutoff:3.500A) Proline residue: B 267 - end of helix removed outlier: 3.611A pdb=" N HIS B 281 " --> pdb=" O GLN B 277 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ARG B 282 " --> pdb=" O ASP B 278 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N VAL B 283 " --> pdb=" O LEU B 279 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N HIS B 284 " --> pdb=" O LEU B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 309 Processing helix chain 'B' and resid 310 through 313 Processing helix chain 'B' and resid 318 through 325 removed outlier: 4.336A pdb=" N ILE B 322 " --> pdb=" O ASN B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 349 Processing helix chain 'B' and resid 356 through 379 removed outlier: 3.529A pdb=" N VAL B 374 " --> pdb=" O ALA B 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 383 removed outlier: 3.600A pdb=" N HIS B 383 " --> pdb=" O PRO B 380 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 380 through 383' Processing helix chain 'B' and resid 385 through 395 removed outlier: 4.179A pdb=" N PHE B 389 " --> pdb=" O GLU B 385 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA B 390 " --> pdb=" O ALA B 386 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N GLY B 395 " --> pdb=" O ILE B 391 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 402 removed outlier: 3.559A pdb=" N ALA B 399 " --> pdb=" O GLY B 395 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 417 Processing helix chain 'B' and resid 418 through 420 No H-bonds generated for 'chain 'B' and resid 418 through 420' Processing helix chain 'B' and resid 421 through 439 Processing helix chain 'B' and resid 443 through 459 removed outlier: 3.683A pdb=" N GLU B 459 " --> pdb=" O LYS B 455 " (cutoff:3.500A) 523 hydrogen bonds defined for protein. 1557 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: 2.89 Time building geometry restraints manager: 1.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 6964 1.03 - 1.23: 7 1.23 - 1.42: 2735 1.42 - 1.61: 4000 1.61 - 1.81: 74 Bond restraints: 13780 Sorted by residual: bond pdb=" N ARG A 17 " pdb=" CA ARG A 17 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.00e+00 bond pdb=" N ARG B 17 " pdb=" CA ARG B 17 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.76e+00 bond pdb=" C ARG B 205 " pdb=" N PRO B 206 " ideal model delta sigma weight residual 1.330 1.349 -0.019 1.19e-02 7.06e+03 2.54e+00 bond pdb=" C ARG A 205 " pdb=" N PRO A 206 " ideal model delta sigma weight residual 1.330 1.349 -0.019 1.19e-02 7.06e+03 2.46e+00 bond pdb=" N ARG A 17 " pdb=" H ARG A 17 " ideal model delta sigma weight residual 0.860 0.891 -0.031 2.00e-02 2.50e+03 2.35e+00 ... (remaining 13775 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.98: 25022 6.98 - 13.96: 0 13.96 - 20.94: 0 20.94 - 27.92: 0 27.92 - 34.90: 6 Bond angle restraints: 25028 Sorted by residual: angle pdb=" C LEU B 304 " pdb=" CA LEU B 304 " pdb=" HA LEU B 304 " ideal model delta sigma weight residual 109.00 74.10 34.90 3.00e+00 1.11e-01 1.35e+02 angle pdb=" C LEU A 304 " pdb=" CA LEU A 304 " pdb=" HA LEU A 304 " ideal model delta sigma weight residual 109.00 74.20 34.80 3.00e+00 1.11e-01 1.35e+02 angle pdb=" CB LEU A 304 " pdb=" CA LEU A 304 " pdb=" HA LEU A 304 " ideal model delta sigma weight residual 109.00 74.54 34.46 3.00e+00 1.11e-01 1.32e+02 angle pdb=" CB LEU B 304 " pdb=" CA LEU B 304 " pdb=" HA LEU B 304 " ideal model delta sigma weight residual 109.00 74.60 34.40 3.00e+00 1.11e-01 1.32e+02 angle pdb=" N LEU A 304 " pdb=" CA LEU A 304 " pdb=" HA LEU A 304 " ideal model delta sigma weight residual 110.00 76.04 33.96 3.00e+00 1.11e-01 1.28e+02 ... (remaining 25023 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.87: 5623 16.87 - 33.75: 424 33.75 - 50.62: 192 50.62 - 67.49: 137 67.49 - 84.37: 24 Dihedral angle restraints: 6400 sinusoidal: 3498 harmonic: 2902 Sorted by residual: dihedral pdb=" C LEU B 304 " pdb=" N LEU B 304 " pdb=" CA LEU B 304 " pdb=" CB LEU B 304 " ideal model delta harmonic sigma weight residual -122.60 -132.02 9.42 0 2.50e+00 1.60e-01 1.42e+01 dihedral pdb=" C LEU A 304 " pdb=" N LEU A 304 " pdb=" CA LEU A 304 " pdb=" CB LEU A 304 " ideal model delta harmonic sigma weight residual -122.60 -131.99 9.39 0 2.50e+00 1.60e-01 1.41e+01 dihedral pdb=" CA GLU A 203 " pdb=" C GLU A 203 " pdb=" N MET A 204 " pdb=" CA MET A 204 " ideal model delta harmonic sigma weight residual 180.00 -162.94 -17.06 0 5.00e+00 4.00e-02 1.16e+01 ... (remaining 6397 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 1020 0.073 - 0.146: 64 0.146 - 0.220: 0 0.220 - 0.293: 0 0.293 - 0.366: 2 Chirality restraints: 1086 Sorted by residual: chirality pdb=" CA LEU B 304 " pdb=" N LEU B 304 " pdb=" C LEU B 304 " pdb=" CB LEU B 304 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.35e+00 chirality pdb=" CA LEU A 304 " pdb=" N LEU A 304 " pdb=" C LEU A 304 " pdb=" CB LEU A 304 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.29e+00 chirality pdb=" CA ILE A 213 " pdb=" N ILE A 213 " pdb=" C ILE A 213 " pdb=" CB ILE A 213 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.77e-01 ... (remaining 1083 not shown) Planarity restraints: 2008 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 423 " 0.023 5.00e-02 4.00e+02 3.42e-02 1.87e+00 pdb=" N PRO A 424 " -0.059 5.00e-02 4.00e+02 pdb=" CA PRO A 424 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 424 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 423 " -0.023 5.00e-02 4.00e+02 3.41e-02 1.86e+00 pdb=" N PRO B 424 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO B 424 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 424 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 149 " -0.022 5.00e-02 4.00e+02 3.26e-02 1.70e+00 pdb=" N PRO A 150 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO A 150 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 150 " -0.018 5.00e-02 4.00e+02 ... (remaining 2005 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.20: 679 2.20 - 2.80: 27377 2.80 - 3.40: 38360 3.40 - 4.00: 49358 4.00 - 4.60: 78422 Nonbonded interactions: 194196 Sorted by model distance: nonbonded pdb=" HH TYR A 419 " pdb=" OE1 GLU B 414 " model vdw 1.601 2.450 nonbonded pdb=" OE1 GLU A 414 " pdb=" HH TYR B 419 " model vdw 1.601 2.450 nonbonded pdb=" O GLN B 153 " pdb="HD21 ASN B 157 " model vdw 1.641 2.450 nonbonded pdb=" O GLN A 153 " pdb="HD21 ASN A 157 " model vdw 1.641 2.450 nonbonded pdb=" HA LEU B 304 " pdb=" HB3 LEU B 304 " model vdw 1.645 1.952 ... (remaining 194191 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.090 Extract box with map and model: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 13.310 Find NCS groups from input model: 0.070 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:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 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 : 0.003 0.034 6810 Z= 0.142 Angle : 0.512 4.275 9242 Z= 0.299 Chirality : 0.039 0.366 1086 Planarity : 0.004 0.034 1160 Dihedral : 13.894 80.367 2404 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 2.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 0.30 % Allowed : 6.87 % Favored : 92.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.67 (0.29), residues: 884 helix: 2.64 (0.21), residues: 664 sheet: None (None), residues: 0 loop : -1.10 (0.39), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 17 TYR 0.011 0.001 TYR B 75 PHE 0.011 0.001 PHE A 307 TRP 0.007 0.001 TRP A 253 HIS 0.002 0.001 HIS B 70 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.14 ( 6810) covalent geometry : angle 0.51170 / 0.30 ( 9242) hydrogen bonds : bond 0.14653 / 10.45 ( 523) hydrogen bonds : angle 5.14860 / 3.84 ( 1557) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 74 time to evaluate : 0.350 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 391 ILE cc_start: 0.8505 (mt) cc_final: 0.8247 (mm) REVERT: B 391 ILE cc_start: 0.8509 (mt) cc_final: 0.8253 (mm) outliers start: 2 outliers final: 1 residues processed: 74 average time/residue: 0.2412 time to fit residues: 22.9716 Evaluate side-chains 71 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 70 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 455 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 49 optimal weight: 5.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.101997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2798 r_free = 0.2798 target = 0.084692 restraints weight = 23811.121| |-----------------------------------------------------------------------------| r_work (start): 0.2787 rms_B_bonded: 1.77 r_work: 0.2690 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2568 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.2568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8727 moved from start: 0.0662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 6810 Z= 0.219 Angle : 0.534 4.420 9242 Z= 0.295 Chirality : 0.043 0.335 1086 Planarity : 0.005 0.043 1160 Dihedral : 4.347 47.953 950 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 1.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 0.45 % Allowed : 7.31 % Favored : 92.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.11 (0.28), residues: 884 helix: 2.21 (0.20), residues: 678 sheet: None (None), residues: 0 loop : -1.48 (0.39), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 17 TYR 0.012 0.002 TYR B 419 PHE 0.015 0.001 PHE A 307 TRP 0.006 0.001 TRP B 253 HIS 0.002 0.001 HIS A 70 Details of bonding type rmsd/Z covalent geometry : bond 0.00543 / 0.22 ( 6810) covalent geometry : angle 0.53399 / 0.29 ( 9242) hydrogen bonds : bond 0.07014 / 4.88 ( 523) hydrogen bonds : angle 4.52674 / 3.40 ( 1557) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 74 time to evaluate : 0.396 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 417 ASP cc_start: 0.8308 (t0) cc_final: 0.7909 (t0) REVERT: B 417 ASP cc_start: 0.8319 (t0) cc_final: 0.7907 (t0) outliers start: 3 outliers final: 2 residues processed: 76 average time/residue: 0.2795 time to fit residues: 26.6424 Evaluate side-chains 74 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 72 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 GLN Chi-restraints excluded: chain A residue 455 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 69 optimal weight: 0.7980 chunk 38 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 23 optimal weight: 0.0970 chunk 2 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 84 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.107017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.089946 restraints weight = 23424.190| |-----------------------------------------------------------------------------| r_work (start): 0.2846 rms_B_bonded: 1.71 r_work: 0.2750 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2627 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.2627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8715 moved from start: 0.0877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6810 Z= 0.122 Angle : 0.455 4.334 9242 Z= 0.248 Chirality : 0.040 0.334 1086 Planarity : 0.005 0.044 1160 Dihedral : 3.778 17.014 946 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 1.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 0.75 % Allowed : 8.51 % Favored : 90.75 % 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: 2.47 (0.28), residues: 884 helix: 2.51 (0.20), residues: 678 sheet: None (None), residues: 0 loop : -1.52 (0.38), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 17 TYR 0.006 0.001 TYR B 419 PHE 0.011 0.001 PHE B 37 TRP 0.005 0.001 TRP B 253 HIS 0.002 0.001 HIS B 70 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 ( 6810) covalent geometry : angle 0.45517 / 0.25 ( 9242) hydrogen bonds : bond 0.05444 / 3.80 ( 523) hydrogen bonds : angle 4.19831 / 3.15 ( 1557) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 67 time to evaluate : 0.304 Fit side-chains REVERT: A 417 ASP cc_start: 0.8301 (t0) cc_final: 0.7889 (t0) REVERT: B 417 ASP cc_start: 0.8308 (t0) cc_final: 0.7890 (t0) outliers start: 5 outliers final: 3 residues processed: 71 average time/residue: 0.2596 time to fit residues: 23.3918 Evaluate side-chains 67 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 64 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 PHE Chi-restraints excluded: chain A residue 455 LYS Chi-restraints excluded: chain B residue 219 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 80 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 1 optimal weight: 0.6980 chunk 40 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.104050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.086891 restraints weight = 23794.429| |-----------------------------------------------------------------------------| r_work (start): 0.2791 rms_B_bonded: 1.74 r_work: 0.2694 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2574 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.2574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8730 moved from start: 0.1031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 6810 Z= 0.170 Angle : 0.483 4.340 9242 Z= 0.264 Chirality : 0.041 0.332 1086 Planarity : 0.005 0.045 1160 Dihedral : 3.786 17.009 946 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 1.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 0.45 % Allowed : 9.25 % Favored : 90.30 % 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: 2.35 (0.28), residues: 884 helix: 2.43 (0.20), residues: 678 sheet: None (None), residues: 0 loop : -1.61 (0.38), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 17 TYR 0.009 0.001 TYR B 419 PHE 0.012 0.001 PHE A 219 TRP 0.005 0.001 TRP B 253 HIS 0.002 0.001 HIS A 70 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.17 ( 6810) covalent geometry : angle 0.48327 / 0.26 ( 9242) hydrogen bonds : bond 0.06077 / 4.23 ( 523) hydrogen bonds : angle 4.23557 / 3.18 ( 1557) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 68 time to evaluate : 0.352 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 417 ASP cc_start: 0.8274 (t0) cc_final: 0.7981 (t0) REVERT: B 417 ASP cc_start: 0.8303 (t0) cc_final: 0.8016 (t0) outliers start: 3 outliers final: 3 residues processed: 70 average time/residue: 0.2461 time to fit residues: 22.1370 Evaluate side-chains 71 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 68 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 PHE Chi-restraints excluded: chain A residue 455 LYS Chi-restraints excluded: chain B residue 219 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 45 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 46 optimal weight: 0.8980 chunk 43 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 55 optimal weight: 0.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.104993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.087647 restraints weight = 23630.142| |-----------------------------------------------------------------------------| r_work (start): 0.2818 rms_B_bonded: 1.76 r_work: 0.2720 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2598 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.2598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8682 moved from start: 0.1095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6810 Z= 0.128 Angle : 0.450 4.243 9242 Z= 0.244 Chirality : 0.040 0.332 1086 Planarity : 0.005 0.045 1160 Dihedral : 3.691 16.617 946 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 1.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 0.75 % Allowed : 8.81 % Favored : 90.45 % 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: 2.56 (0.28), residues: 884 helix: 2.59 (0.20), residues: 680 sheet: None (None), residues: 0 loop : -1.61 (0.39), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 17 TYR 0.006 0.001 TYR B 419 PHE 0.009 0.001 PHE A 219 TRP 0.004 0.001 TRP A 253 HIS 0.002 0.001 HIS A 70 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 ( 6810) covalent geometry : angle 0.45029 / 0.24 ( 9242) hydrogen bonds : bond 0.05280 / 3.68 ( 523) hydrogen bonds : angle 4.07649 / 3.06 ( 1557) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 67 time to evaluate : 0.402 Fit side-chains REVERT: A 136 LEU cc_start: 0.8556 (OUTLIER) cc_final: 0.7906 (mp) REVERT: A 417 ASP cc_start: 0.8234 (t0) cc_final: 0.7794 (t0) REVERT: B 136 LEU cc_start: 0.8561 (OUTLIER) cc_final: 0.7913 (mp) REVERT: B 417 ASP cc_start: 0.8272 (t0) cc_final: 0.7829 (t0) outliers start: 5 outliers final: 3 residues processed: 71 average time/residue: 0.2217 time to fit residues: 20.4976 Evaluate side-chains 70 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 65 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 219 PHE Chi-restraints excluded: chain A residue 455 LYS Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 219 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 56 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 48 optimal weight: 0.5980 chunk 18 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 29 optimal weight: 0.3980 chunk 23 optimal weight: 0.5980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.106406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.089322 restraints weight = 23466.819| |-----------------------------------------------------------------------------| r_work (start): 0.2842 rms_B_bonded: 1.73 r_work: 0.2746 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2624 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.2624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8689 moved from start: 0.1242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6810 Z= 0.122 Angle : 0.440 4.231 9242 Z= 0.239 Chirality : 0.039 0.329 1086 Planarity : 0.005 0.045 1160 Dihedral : 3.604 16.144 946 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 1.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 0.75 % Allowed : 9.10 % Favored : 90.15 % 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: 2.69 (0.29), residues: 884 helix: 2.69 (0.20), residues: 680 sheet: None (None), residues: 0 loop : -1.58 (0.39), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 209 TYR 0.006 0.001 TYR A 419 PHE 0.012 0.001 PHE A 307 TRP 0.005 0.001 TRP B 253 HIS 0.002 0.001 HIS A 70 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 ( 6810) covalent geometry : angle 0.43955 / 0.24 ( 9242) hydrogen bonds : bond 0.05061 / 3.53 ( 523) hydrogen bonds : angle 4.00101 / 3.00 ( 1557) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 69 time to evaluate : 0.344 Fit side-chains REVERT: A 65 MET cc_start: 0.6944 (mtp) cc_final: 0.6670 (mtt) REVERT: A 136 LEU cc_start: 0.8601 (OUTLIER) cc_final: 0.7957 (mp) REVERT: B 65 MET cc_start: 0.6931 (mtp) cc_final: 0.6680 (mtt) REVERT: B 136 LEU cc_start: 0.8607 (OUTLIER) cc_final: 0.7964 (mp) outliers start: 5 outliers final: 2 residues processed: 73 average time/residue: 0.2072 time to fit residues: 19.8698 Evaluate side-chains 71 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 67 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 219 PHE Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 219 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 37 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 36 optimal weight: 0.5980 chunk 71 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.104193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.087203 restraints weight = 23411.465| |-----------------------------------------------------------------------------| r_work (start): 0.2826 rms_B_bonded: 1.72 r_work: 0.2731 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2610 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.2610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8729 moved from start: 0.1265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 6810 Z= 0.165 Angle : 0.472 4.229 9242 Z= 0.257 Chirality : 0.040 0.330 1086 Planarity : 0.005 0.046 1160 Dihedral : 3.692 16.266 946 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 1.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 0.45 % Allowed : 10.15 % Favored : 89.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.48 (0.28), residues: 884 helix: 2.54 (0.19), residues: 680 sheet: None (None), residues: 0 loop : -1.63 (0.39), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 230 TYR 0.008 0.001 TYR B 419 PHE 0.013 0.001 PHE A 307 TRP 0.005 0.001 TRP A 253 HIS 0.002 0.001 HIS A 234 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.17 ( 6810) covalent geometry : angle 0.47238 / 0.26 ( 9242) hydrogen bonds : bond 0.05796 / 4.04 ( 523) hydrogen bonds : angle 4.10918 / 3.08 ( 1557) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 66 time to evaluate : 0.326 Fit side-chains REVERT: A 65 MET cc_start: 0.6966 (mtp) cc_final: 0.6690 (mtt) REVERT: A 373 MET cc_start: 0.8099 (mtt) cc_final: 0.7887 (mtt) REVERT: A 417 ASP cc_start: 0.8169 (t0) cc_final: 0.7802 (t0) REVERT: B 65 MET cc_start: 0.7008 (mtp) cc_final: 0.6736 (mtt) REVERT: B 373 MET cc_start: 0.8103 (mtt) cc_final: 0.7889 (mtt) REVERT: B 417 ASP cc_start: 0.8202 (t0) cc_final: 0.7847 (t0) outliers start: 3 outliers final: 3 residues processed: 68 average time/residue: 0.2056 time to fit residues: 18.5319 Evaluate side-chains 69 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 66 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 PHE Chi-restraints excluded: chain A residue 455 LYS Chi-restraints excluded: chain B residue 219 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 13 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 50 optimal weight: 0.4980 chunk 45 optimal weight: 1.9990 chunk 36 optimal weight: 0.0370 chunk 11 optimal weight: 0.5980 chunk 70 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 77 optimal weight: 0.0670 chunk 25 optimal weight: 0.9990 overall best weight: 0.4398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.108685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.091778 restraints weight = 23080.907| |-----------------------------------------------------------------------------| r_work (start): 0.2913 rms_B_bonded: 1.68 r_work: 0.2818 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2695 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.2695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8691 moved from start: 0.1392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 6810 Z= 0.098 Angle : 0.422 4.204 9242 Z= 0.228 Chirality : 0.039 0.329 1086 Planarity : 0.005 0.044 1160 Dihedral : 3.530 15.707 946 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 2.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 0.60 % Allowed : 10.45 % Favored : 88.96 % 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: 2.98 (0.29), residues: 884 helix: 2.92 (0.20), residues: 680 sheet: None (None), residues: 0 loop : -1.56 (0.39), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 17 TYR 0.005 0.001 TYR B 75 PHE 0.011 0.001 PHE B 307 TRP 0.004 0.001 TRP B 253 HIS 0.002 0.000 HIS A 70 Details of bonding type rmsd/Z covalent geometry : bond 0.00194 / 0.10 ( 6810) covalent geometry : angle 0.42195 / 0.23 ( 9242) hydrogen bonds : bond 0.04401 / 3.07 ( 523) hydrogen bonds : angle 3.87180 / 2.90 ( 1557) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 64 time to evaluate : 0.351 Fit side-chains REVERT: A 65 MET cc_start: 0.6947 (mtp) cc_final: 0.6680 (mtt) REVERT: A 136 LEU cc_start: 0.8633 (OUTLIER) cc_final: 0.7978 (mp) REVERT: A 373 MET cc_start: 0.8081 (mtt) cc_final: 0.7869 (mtt) REVERT: B 65 MET cc_start: 0.6934 (mtp) cc_final: 0.6679 (mtt) REVERT: B 136 LEU cc_start: 0.8629 (OUTLIER) cc_final: 0.7977 (mp) REVERT: B 373 MET cc_start: 0.8078 (mtt) cc_final: 0.7864 (mtt) outliers start: 4 outliers final: 0 residues processed: 68 average time/residue: 0.1675 time to fit residues: 15.9339 Evaluate side-chains 64 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 62 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain B residue 136 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 71 optimal weight: 1.9990 chunk 6 optimal weight: 0.3980 chunk 20 optimal weight: 0.6980 chunk 22 optimal weight: 2.9990 chunk 67 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 74 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.113060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.096536 restraints weight = 22876.482| |-----------------------------------------------------------------------------| r_work (start): 0.2855 rms_B_bonded: 1.66 r_work: 0.2762 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2642 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.2642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8722 moved from start: 0.1367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6810 Z= 0.124 Angle : 0.437 4.210 9242 Z= 0.235 Chirality : 0.039 0.331 1086 Planarity : 0.005 0.045 1160 Dihedral : 3.526 15.607 946 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 2.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 0.75 % Allowed : 10.30 % Favored : 88.96 % 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: 2.92 (0.29), residues: 884 helix: 2.88 (0.20), residues: 680 sheet: None (None), residues: 0 loop : -1.60 (0.39), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 17 TYR 0.006 0.001 TYR B 419 PHE 0.011 0.001 PHE A 307 TRP 0.004 0.000 TRP A 253 HIS 0.002 0.001 HIS A 70 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.12 ( 6810) covalent geometry : angle 0.43665 / 0.24 ( 9242) hydrogen bonds : bond 0.04936 / 3.44 ( 523) hydrogen bonds : angle 3.93224 / 2.95 ( 1557) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 68 time to evaluate : 0.289 Fit side-chains REVERT: A 65 MET cc_start: 0.6961 (mtp) cc_final: 0.6687 (mtt) REVERT: A 136 LEU cc_start: 0.8670 (OUTLIER) cc_final: 0.8022 (mp) REVERT: A 373 MET cc_start: 0.8150 (mtt) cc_final: 0.7942 (mtt) REVERT: A 417 ASP cc_start: 0.8167 (t0) cc_final: 0.7800 (t0) REVERT: B 65 MET cc_start: 0.6951 (mtp) cc_final: 0.6682 (mtt) REVERT: B 136 LEU cc_start: 0.8657 (OUTLIER) cc_final: 0.8012 (mp) REVERT: B 373 MET cc_start: 0.8152 (mtt) cc_final: 0.7940 (mtt) REVERT: B 417 ASP cc_start: 0.8200 (t0) cc_final: 0.7841 (t0) outliers start: 5 outliers final: 2 residues processed: 72 average time/residue: 0.1800 time to fit residues: 17.4046 Evaluate side-chains 72 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 68 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 219 PHE Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 219 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 1 optimal weight: 0.9980 chunk 82 optimal weight: 0.8980 chunk 78 optimal weight: 0.9980 chunk 87 optimal weight: 0.7980 chunk 26 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 52 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 75 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.107820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.090868 restraints weight = 23282.248| |-----------------------------------------------------------------------------| r_work (start): 0.2877 rms_B_bonded: 1.69 r_work: 0.2782 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2662 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.2662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8716 moved from start: 0.1447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6810 Z= 0.113 Angle : 0.433 4.615 9242 Z= 0.233 Chirality : 0.039 0.332 1086 Planarity : 0.005 0.044 1160 Dihedral : 3.500 15.532 946 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.60 % Allowed : 10.45 % Favored : 88.96 % 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: 2.99 (0.29), residues: 884 helix: 2.93 (0.19), residues: 680 sheet: None (None), residues: 0 loop : -1.58 (0.39), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 17 TYR 0.005 0.001 TYR B 419 PHE 0.008 0.001 PHE B 219 TRP 0.005 0.001 TRP A 253 HIS 0.001 0.001 HIS B 175 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 ( 6810) covalent geometry : angle 0.43342 / 0.23 ( 9242) hydrogen bonds : bond 0.04758 / 3.32 ( 523) hydrogen bonds : angle 3.90300 / 2.93 ( 1557) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 70 time to evaluate : 0.341 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 65 MET cc_start: 0.6960 (mtp) cc_final: 0.6693 (mtt) REVERT: A 136 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8006 (mp) REVERT: A 373 MET cc_start: 0.8131 (mtt) cc_final: 0.7921 (mtt) REVERT: A 455 LYS cc_start: 0.8046 (tttt) cc_final: 0.7596 (ttmt) REVERT: B 65 MET cc_start: 0.6973 (mtp) cc_final: 0.6710 (mtt) REVERT: B 136 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8002 (mp) REVERT: B 373 MET cc_start: 0.8141 (mtt) cc_final: 0.7929 (mtt) outliers start: 4 outliers final: 2 residues processed: 74 average time/residue: 0.1535 time to fit residues: 16.1681 Evaluate side-chains 72 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 68 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 219 PHE Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 219 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 67 optimal weight: 0.8980 chunk 54 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 80 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 234 HIS B 234 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.104375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.087574 restraints weight = 23754.426| |-----------------------------------------------------------------------------| r_work (start): 0.2831 rms_B_bonded: 1.70 r_work: 0.2735 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2614 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.2614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8741 moved from start: 0.1453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 6810 Z= 0.170 Angle : 0.476 4.208 9242 Z= 0.259 Chirality : 0.041 0.337 1086 Planarity : 0.005 0.045 1160 Dihedral : 3.623 15.899 946 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.04 % Allowed : 10.30 % Favored : 88.66 % 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: 2.67 (0.28), residues: 884 helix: 2.69 (0.19), residues: 680 sheet: None (None), residues: 0 loop : -1.67 (0.39), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 230 TYR 0.008 0.001 TYR B 419 PHE 0.015 0.001 PHE A 307 TRP 0.004 0.001 TRP B 253 HIS 0.010 0.002 HIS A 234 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.17 ( 6810) covalent geometry : angle 0.47590 / 0.26 ( 9242) hydrogen bonds : bond 0.05736 / 4.00 ( 523) hydrogen bonds : angle 4.04825 / 3.04 ( 1557) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2918.11 seconds wall clock time: 50 minutes 14.35 seconds (3014.35 seconds total)