Starting phenix.real_space_refine on Thu Jul 2 11:03:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wju_32548/07_2026/7wju_32548_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wju_32548/07_2026/7wju_32548.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.69 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7wju_32548/07_2026/7wju_32548_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wju_32548/07_2026/7wju_32548_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7wju_32548/07_2026/7wju_32548.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wju_32548/07_2026/7wju_32548.map" } resolution = 2.69 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= -0.001 sd= 0.243 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 158 5.49 5 S 21 5.16 5 C 4652 2.51 5 N 1510 2.21 5 O 1981 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.00s 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: 8322 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 407, 3308 Classifications: {'peptide': 407} Link IDs: {'PTRANS': 10, 'TRANS': 396} Chain breaks: 1 Chain: "B" Number of atoms: 1652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1652 Classifications: {'peptide': 200} Link IDs: {'PTRANS': 4, 'TRANS': 195} Chain breaks: 1 Chain: "C" Number of atoms: 2845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 2845 Classifications: {'RNA': 133} Modifications used: {'rna2p_pur': 14, 'rna2p_pyr': 5, 'rna3p_pur': 59, 'rna3p_pyr': 55} Link IDs: {'rna2p': 19, 'rna3p': 113} Chain breaks: 3 Chain: "D" Number of atoms: 392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 392 Classifications: {'DNA': 19} Link IDs: {'rna3p': 18} Chain: "E" Number of atoms: 125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 125 Classifications: {'DNA': 6} Link IDs: {'rna3p': 5} Time building chain proxies: 1.53, per 1000 atoms: 0.18 Number of scatterers: 8322 At special positions: 0 Unit cell: (81.8748, 99.1116, 117.426, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 21 16.00 P 158 15.00 O 1981 8.00 N 1510 7.00 C 4652 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: 0.75 Conformation dependent library (CDL) restraints added in 345.6 milliseconds 1198 Ramachandran restraints generated. 599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1142 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 6 sheets defined 46.8% alpha, 21.9% beta 64 base pairs and 101 stacking pairs defined. Time for finding SS restraints: 0.99 Creating SS restraints... Processing helix chain 'A' and resid 16 through 56 Processing helix chain 'A' and resid 61 through 66 Processing helix chain 'A' and resid 70 through 80 removed outlier: 3.683A pdb=" N TYR A 74 " --> pdb=" O ASN A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 105 removed outlier: 3.505A pdb=" N TYR A 105 " --> pdb=" O ARG A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 111 Processing helix chain 'A' and resid 128 through 130 No H-bonds generated for 'chain 'A' and resid 128 through 130' Processing helix chain 'A' and resid 150 through 158 Processing helix chain 'A' and resid 171 through 182 removed outlier: 3.732A pdb=" N THR A 175 " --> pdb=" O GLY A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 257 removed outlier: 3.609A pdb=" N ARG A 255 " --> pdb=" O GLU A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 316 removed outlier: 3.867A pdb=" N LEU A 290 " --> pdb=" O PRO A 286 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLU A 316 " --> pdb=" O MET A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 335 Processing helix chain 'A' and resid 341 through 357 Processing helix chain 'A' and resid 400 through 409 Processing helix chain 'A' and resid 412 through 418 Processing helix chain 'B' and resid 18 through 46 Processing helix chain 'B' and resid 50 through 55 removed outlier: 4.341A pdb=" N ASP B 54 " --> pdb=" O SER B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 80 removed outlier: 3.504A pdb=" N TYR B 74 " --> pdb=" O ASN B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 105 Processing helix chain 'B' and resid 105 through 112 Processing helix chain 'B' and resid 128 through 130 No H-bonds generated for 'chain 'B' and resid 128 through 130' Processing helix chain 'B' and resid 150 through 155 Processing helix chain 'B' and resid 171 through 183 removed outlier: 3.808A pdb=" N THR B 175 " --> pdb=" O GLY B 171 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ILE B 176 " --> pdb=" O ALA B 172 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASP B 178 " --> pdb=" O LYS B 174 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ARG B 179 " --> pdb=" O THR B 175 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE B 180 " --> pdb=" O ILE B 176 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 125 through 127 removed outlier: 5.046A pdb=" N TRP A 201 " --> pdb=" O ILE A 9 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N ILE A 166 " --> pdb=" O VAL A 10 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N SER A 164 " --> pdb=" O PRO A 12 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N TYR A 142 " --> pdb=" O ILE A 167 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 125 through 127 Processing sheet with id=AA3, first strand: chain 'A' and resid 242 through 245 removed outlier: 6.487A pdb=" N LEU A 218 " --> pdb=" O CYS A 318 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N THR A 320 " --> pdb=" O LEU A 218 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N LYS A 220 " --> pdb=" O THR A 320 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N GLN A 322 " --> pdb=" O LYS A 220 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N MET A 222 " --> pdb=" O GLN A 322 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 388 through 390 Processing sheet with id=AA5, first strand: chain 'B' and resid 125 through 127 removed outlier: 3.594A pdb=" N GLN B 191 " --> pdb=" O ASN B 204 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N TRP B 201 " --> pdb=" O ILE B 9 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N LYS B 11 " --> pdb=" O ILE B 166 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N TYR B 142 " --> pdb=" O ILE B 167 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 125 through 127 removed outlier: 3.594A pdb=" N GLN B 191 " --> pdb=" O ASN B 204 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLN B 186 " --> pdb=" O ASP B 208 " (cutoff:3.500A) 275 hydrogen bonds defined for protein. 765 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 163 hydrogen bonds 294 hydrogen bond angles 0 basepair planarities 64 basepair parallelities 101 stacking parallelities Total time for adding SS restraints: 1.46 Time building geometry restraints manager: 1.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1209 1.32 - 1.45: 3199 1.45 - 1.57: 4059 1.57 - 1.69: 310 1.69 - 1.81: 37 Bond restraints: 8814 Sorted by residual: bond pdb=" C8 G C 174 " pdb=" N7 G C 174 " ideal model delta sigma weight residual 1.305 1.275 0.030 6.00e-03 2.78e+04 2.44e+01 bond pdb=" C8 A C 104 " pdb=" N7 A C 104 " ideal model delta sigma weight residual 1.311 1.281 0.030 7.00e-03 2.04e+04 1.81e+01 bond pdb=" C3' DC E 2 " pdb=" O3' DC E 2 " ideal model delta sigma weight residual 1.435 1.380 0.055 1.30e-02 5.92e+03 1.78e+01 bond pdb=" C3' DG D 13 " pdb=" O3' DG D 13 " ideal model delta sigma weight residual 1.435 1.381 0.054 1.30e-02 5.92e+03 1.74e+01 bond pdb=" C8 G C 175 " pdb=" N7 G C 175 " ideal model delta sigma weight residual 1.305 1.280 0.025 6.00e-03 2.78e+04 1.73e+01 ... (remaining 8809 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.03: 12404 3.03 - 6.06: 216 6.06 - 9.10: 16 9.10 - 12.13: 2 12.13 - 15.16: 1 Bond angle restraints: 12639 Sorted by residual: angle pdb=" O3' A C 89 " pdb=" C3' A C 89 " pdb=" C2' A C 89 " ideal model delta sigma weight residual 113.70 98.54 15.16 1.50e+00 4.44e-01 1.02e+02 angle pdb=" O3' A C 91 " pdb=" P C C 92 " pdb=" O5' C C 92 " ideal model delta sigma weight residual 104.00 95.40 8.60 1.50e+00 4.44e-01 3.29e+01 angle pdb=" N LEU A 337 " pdb=" CA LEU A 337 " pdb=" C LEU A 337 " ideal model delta sigma weight residual 110.80 98.91 11.89 2.13e+00 2.20e-01 3.12e+01 angle pdb=" O4' DA D 16 " pdb=" C4' DA D 16 " pdb=" C3' DA D 16 " ideal model delta sigma weight residual 106.00 102.85 3.15 6.00e-01 2.78e+00 2.76e+01 angle pdb=" N1 C C 107 " pdb=" C2 C C 107 " pdb=" O2 C C 107 " ideal model delta sigma weight residual 118.90 121.90 -3.00 6.00e-01 2.78e+00 2.50e+01 ... (remaining 12634 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.86: 4860 33.86 - 67.73: 504 67.73 - 101.59: 43 101.59 - 135.46: 0 135.46 - 169.32: 2 Dihedral angle restraints: 5409 sinusoidal: 3627 harmonic: 1782 Sorted by residual: dihedral pdb=" O4' U C 75 " pdb=" C1' U C 75 " pdb=" N1 U C 75 " pdb=" C2 U C 75 " ideal model delta sinusoidal sigma weight residual -160.00 9.32 -169.32 1 1.50e+01 4.44e-03 8.46e+01 dihedral pdb=" CA GLY B 47 " pdb=" C GLY B 47 " pdb=" N PHE B 48 " pdb=" CA PHE B 48 " ideal model delta harmonic sigma weight residual 180.00 155.33 24.67 0 5.00e+00 4.00e-02 2.43e+01 dihedral pdb=" CA GLN A 191 " pdb=" C GLN A 191 " pdb=" N ILE A 192 " pdb=" CA ILE A 192 " ideal model delta harmonic sigma weight residual 180.00 157.38 22.62 0 5.00e+00 4.00e-02 2.05e+01 ... (remaining 5406 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 1331 0.096 - 0.192: 135 0.192 - 0.289: 12 0.289 - 0.385: 3 0.385 - 0.481: 12 Chirality restraints: 1493 Sorted by residual: chirality pdb=" P A C 90 " pdb=" OP1 A C 90 " pdb=" OP2 A C 90 " pdb=" O5' A C 90 " both_signs ideal model delta sigma weight residual True 2.41 -2.89 -0.48 2.00e-01 2.50e+01 5.78e+00 chirality pdb=" P U C 75 " pdb=" OP1 U C 75 " pdb=" OP2 U C 75 " pdb=" O5' U C 75 " both_signs ideal model delta sigma weight residual True 2.41 -2.86 -0.45 2.00e-01 2.50e+01 4.97e+00 chirality pdb=" P DA D 14 " pdb=" OP1 DA D 14 " pdb=" OP2 DA D 14 " pdb=" O5' DA D 14 " both_signs ideal model delta sigma weight residual True 2.34 -2.78 -0.44 2.00e-01 2.50e+01 4.95e+00 ... (remaining 1490 not shown) Planarity restraints: 1027 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G C 117 " 0.050 2.00e-02 2.50e+03 1.98e-02 1.17e+01 pdb=" N9 G C 117 " -0.013 2.00e-02 2.50e+03 pdb=" C8 G C 117 " -0.016 2.00e-02 2.50e+03 pdb=" N7 G C 117 " -0.006 2.00e-02 2.50e+03 pdb=" C5 G C 117 " -0.007 2.00e-02 2.50e+03 pdb=" C6 G C 117 " 0.007 2.00e-02 2.50e+03 pdb=" O6 G C 117 " 0.020 2.00e-02 2.50e+03 pdb=" N1 G C 117 " 0.011 2.00e-02 2.50e+03 pdb=" C2 G C 117 " -0.001 2.00e-02 2.50e+03 pdb=" N2 G C 117 " 0.001 2.00e-02 2.50e+03 pdb=" N3 G C 117 " -0.023 2.00e-02 2.50e+03 pdb=" C4 G C 117 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U C 173 " -0.045 2.00e-02 2.50e+03 2.19e-02 1.08e+01 pdb=" N1 U C 173 " 0.040 2.00e-02 2.50e+03 pdb=" C2 U C 173 " 0.009 2.00e-02 2.50e+03 pdb=" O2 U C 173 " 0.005 2.00e-02 2.50e+03 pdb=" N3 U C 173 " -0.003 2.00e-02 2.50e+03 pdb=" C4 U C 173 " -0.010 2.00e-02 2.50e+03 pdb=" O4 U C 173 " -0.014 2.00e-02 2.50e+03 pdb=" C5 U C 173 " 0.002 2.00e-02 2.50e+03 pdb=" C6 U C 173 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G C 174 " -0.043 2.00e-02 2.50e+03 1.74e-02 9.09e+00 pdb=" N9 G C 174 " 0.024 2.00e-02 2.50e+03 pdb=" C8 G C 174 " 0.022 2.00e-02 2.50e+03 pdb=" N7 G C 174 " 0.001 2.00e-02 2.50e+03 pdb=" C5 G C 174 " 0.009 2.00e-02 2.50e+03 pdb=" C6 G C 174 " -0.009 2.00e-02 2.50e+03 pdb=" O6 G C 174 " -0.016 2.00e-02 2.50e+03 pdb=" N1 G C 174 " -0.011 2.00e-02 2.50e+03 pdb=" C2 G C 174 " 0.008 2.00e-02 2.50e+03 pdb=" N2 G C 174 " 0.009 2.00e-02 2.50e+03 pdb=" N3 G C 174 " 0.007 2.00e-02 2.50e+03 pdb=" C4 G C 174 " -0.001 2.00e-02 2.50e+03 ... (remaining 1024 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.84: 2436 2.84 - 3.36: 6488 3.36 - 3.87: 16453 3.87 - 4.39: 18912 4.39 - 4.90: 27169 Nonbonded interactions: 71458 Sorted by model distance: nonbonded pdb=" O ASN A 302 " pdb=" OG SER A 306 " model vdw 2.325 3.040 nonbonded pdb=" O3' A C 89 " pdb=" O2' A C 89 " model vdw 2.332 2.432 nonbonded pdb=" N ILE B 2 " pdb=" O TYR B 207 " model vdw 2.337 3.120 nonbonded pdb=" O TYR A 84 " pdb=" OG SER A 150 " model vdw 2.378 3.040 nonbonded pdb=" O2' A C 20 " pdb=" OP2 A C 22 " model vdw 2.384 3.040 ... (remaining 71453 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.170 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: 0.120 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.260 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 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:6.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 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 : 0.008 0.076 8814 Z= 0.656 Angle : 1.001 15.161 12639 Z= 0.793 Chirality : 0.070 0.481 1493 Planarity : 0.006 0.057 1027 Dihedral : 21.910 169.321 4267 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.34 % Favored : 94.49 % Rotamer: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % 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 (0.29), residues: 599 helix: -1.37 (0.26), residues: 280 sheet: -0.65 (0.42), residues: 124 loop : -2.46 (0.36), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 371 TYR 0.030 0.003 TYR A 233 PHE 0.015 0.003 PHE B 48 TRP 0.017 0.003 TRP B 43 HIS 0.008 0.001 HIS A 303 Details of bonding type rmsd/Z covalent geometry : bond 0.00762 / 0.66 ( 8814) covalent geometry : angle 1.00052 / 0.79 (12639) hydrogen bonds : bond 0.13787 / 9.18 ( 419) hydrogen bonds : angle 5.37277 / 4.02 ( 1059) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1198 Ramachandran restraints generated. 599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1198 Ramachandran restraints generated. 599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.236 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 92 average time/residue: 0.6560 time to fit residues: 63.3856 Evaluate side-chains 66 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 9.9990 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 10.0000 chunk 62 optimal weight: 20.0000 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 9.9990 chunk 61 optimal weight: 6.9990 chunk 45 optimal weight: 5.9990 chunk 27 optimal weight: 0.0980 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 70 ASN A 106 GLN A 252 ASN A 303 HIS A 322 GLN A 412 ASN B 26 GLN B 72 HIS B 87 ASN B 151 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.177913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.136284 restraints weight = 7707.521| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 1.61 r_work: 0.3165 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3035 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.1102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8814 Z= 0.166 Angle : 0.609 7.067 12639 Z= 0.361 Chirality : 0.047 0.272 1493 Planarity : 0.005 0.047 1027 Dihedral : 23.386 176.205 3018 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.01 % Favored : 95.83 % Rotamer: Outliers : 1.88 % Allowed : 10.90 % Favored : 87.22 % 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: -1.02 (0.32), residues: 599 helix: 0.22 (0.29), residues: 285 sheet: -0.36 (0.42), residues: 123 loop : -2.18 (0.39), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 254 TYR 0.024 0.002 TYR A 351 PHE 0.014 0.002 PHE B 48 TRP 0.015 0.002 TRP B 43 HIS 0.003 0.001 HIS A 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.17 ( 8814) covalent geometry : angle 0.60949 / 0.36 (12639) hydrogen bonds : bond 0.06174 / 4.16 ( 419) hydrogen bonds : angle 3.80657 / 2.83 ( 1059) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1198 Ramachandran restraints generated. 599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1198 Ramachandran restraints generated. 599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 67 time to evaluate : 0.170 Fit side-chains REVERT: A 155 GLN cc_start: 0.7699 (OUTLIER) cc_final: 0.6930 (mt0) REVERT: A 218 LEU cc_start: 0.8350 (OUTLIER) cc_final: 0.7746 (mm) REVERT: B 30 GLU cc_start: 0.8406 (OUTLIER) cc_final: 0.8162 (mt-10) REVERT: B 44 GLU cc_start: 0.8436 (OUTLIER) cc_final: 0.8128 (mt-10) REVERT: B 85 ARG cc_start: 0.8316 (mtt90) cc_final: 0.8111 (mtt90) outliers start: 10 outliers final: 2 residues processed: 72 average time/residue: 0.5220 time to fit residues: 39.8731 Evaluate side-chains 67 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 61 time to evaluate : 0.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ILE Chi-restraints excluded: chain A residue 155 GLN Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 233 TYR Chi-restraints excluded: chain B residue 30 GLU Chi-restraints excluded: chain B residue 44 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 30 optimal weight: 7.9990 chunk 20 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 64 optimal weight: 10.0000 chunk 28 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 65 optimal weight: 10.0000 chunk 24 optimal weight: 5.9990 chunk 69 optimal weight: 9.9990 chunk 62 optimal weight: 20.0000 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 70 ASN B 26 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.176557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.130887 restraints weight = 7611.126| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 1.09 r_work: 0.3219 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3091 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.1264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8814 Z= 0.191 Angle : 0.611 8.265 12639 Z= 0.359 Chirality : 0.047 0.264 1493 Planarity : 0.005 0.046 1027 Dihedral : 23.315 179.813 3018 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 1.69 % Allowed : 13.16 % Favored : 85.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -0.42 (0.33), residues: 599 helix: 0.90 (0.31), residues: 285 sheet: -0.27 (0.41), residues: 124 loop : -2.07 (0.40), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 179 TYR 0.020 0.002 TYR A 351 PHE 0.016 0.003 PHE B 48 TRP 0.014 0.002 TRP B 43 HIS 0.004 0.001 HIS A 303 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.19 ( 8814) covalent geometry : angle 0.61107 / 0.36 (12639) hydrogen bonds : bond 0.06069 / 4.04 ( 419) hydrogen bonds : angle 3.68070 / 2.74 ( 1059) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1198 Ramachandran restraints generated. 599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1198 Ramachandran restraints generated. 599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 63 time to evaluate : 0.168 Fit side-chains REVERT: A 155 GLN cc_start: 0.7567 (OUTLIER) cc_final: 0.6827 (mt0) REVERT: A 218 LEU cc_start: 0.8419 (OUTLIER) cc_final: 0.7834 (mm) REVERT: B 30 GLU cc_start: 0.8262 (OUTLIER) cc_final: 0.7960 (mt-10) REVERT: B 44 GLU cc_start: 0.8213 (OUTLIER) cc_final: 0.7888 (mt-10) outliers start: 9 outliers final: 2 residues processed: 69 average time/residue: 0.5746 time to fit residues: 41.8428 Evaluate side-chains 67 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 61 time to evaluate : 0.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ILE Chi-restraints excluded: chain A residue 155 GLN Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 233 TYR Chi-restraints excluded: chain B residue 30 GLU Chi-restraints excluded: chain B residue 44 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 29 optimal weight: 1.9990 chunk 39 optimal weight: 7.9990 chunk 38 optimal weight: 10.0000 chunk 16 optimal weight: 0.9980 chunk 26 optimal weight: 10.0000 chunk 14 optimal weight: 0.8980 chunk 51 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 54 optimal weight: 0.8980 chunk 35 optimal weight: 4.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 70 ASN B 26 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.178363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.133082 restraints weight = 7738.312| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 1.06 r_work: 0.3245 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3120 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.1468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 8814 Z= 0.138 Angle : 0.554 6.831 12639 Z= 0.328 Chirality : 0.043 0.251 1493 Planarity : 0.004 0.041 1027 Dihedral : 23.245 179.215 3018 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 1.88 % Allowed : 13.91 % Favored : 84.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -0.05 (0.34), residues: 599 helix: 1.23 (0.31), residues: 286 sheet: -0.22 (0.41), residues: 131 loop : -1.88 (0.43), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 254 TYR 0.019 0.001 TYR A 351 PHE 0.011 0.002 PHE B 48 TRP 0.013 0.001 TRP B 43 HIS 0.001 0.000 HIS A 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.14 ( 8814) covalent geometry : angle 0.55437 / 0.33 (12639) hydrogen bonds : bond 0.05237 / 3.46 ( 419) hydrogen bonds : angle 3.55324 / 2.65 ( 1059) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1198 Ramachandran restraints generated. 599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1198 Ramachandran restraints generated. 599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 64 time to evaluate : 0.216 Fit side-chains REVERT: A 155 GLN cc_start: 0.7603 (OUTLIER) cc_final: 0.6868 (mt0) REVERT: A 218 LEU cc_start: 0.8376 (OUTLIER) cc_final: 0.7821 (mm) REVERT: B 30 GLU cc_start: 0.8307 (OUTLIER) cc_final: 0.8039 (mt-10) REVERT: B 44 GLU cc_start: 0.8206 (OUTLIER) cc_final: 0.7885 (mt-10) outliers start: 10 outliers final: 3 residues processed: 69 average time/residue: 0.5694 time to fit residues: 41.3808 Evaluate side-chains 65 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 58 time to evaluate : 0.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 GLN Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 233 TYR Chi-restraints excluded: chain B residue 30 GLU Chi-restraints excluded: chain B residue 44 GLU Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 199 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 24 optimal weight: 5.9990 chunk 54 optimal weight: 0.5980 chunk 67 optimal weight: 9.9990 chunk 39 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 26 optimal weight: 10.0000 chunk 58 optimal weight: 5.9990 chunk 52 optimal weight: 6.9990 chunk 4 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 70 ASN B 40 GLN B 151 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.176309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.134306 restraints weight = 7615.439| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 1.61 r_work: 0.3146 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.1429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 8814 Z= 0.226 Angle : 0.628 6.844 12639 Z= 0.364 Chirality : 0.048 0.257 1493 Planarity : 0.005 0.044 1027 Dihedral : 23.286 179.923 3018 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 2.82 % Allowed : 13.35 % Favored : 83.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -0.06 (0.34), residues: 599 helix: 1.24 (0.31), residues: 285 sheet: -0.14 (0.42), residues: 124 loop : -1.94 (0.41), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 97 TYR 0.016 0.002 TYR A 5 PHE 0.018 0.003 PHE B 48 TRP 0.014 0.003 TRP B 43 HIS 0.003 0.001 HIS A 194 Details of bonding type rmsd/Z covalent geometry : bond 0.00493 / 0.23 ( 8814) covalent geometry : angle 0.62754 / 0.36 (12639) hydrogen bonds : bond 0.06125 / 4.08 ( 419) hydrogen bonds : angle 3.64155 / 2.72 ( 1059) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1198 Ramachandran restraints generated. 599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1198 Ramachandran restraints generated. 599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 62 time to evaluate : 0.166 Fit side-chains REVERT: A 155 GLN cc_start: 0.7649 (OUTLIER) cc_final: 0.6918 (mt0) REVERT: A 218 LEU cc_start: 0.8395 (OUTLIER) cc_final: 0.7759 (mm) REVERT: A 254 ARG cc_start: 0.7305 (mtt-85) cc_final: 0.7093 (mtm-85) REVERT: B 30 GLU cc_start: 0.8407 (OUTLIER) cc_final: 0.8100 (mt-10) REVERT: B 44 GLU cc_start: 0.8362 (OUTLIER) cc_final: 0.8043 (mt-10) REVERT: B 208 ASP cc_start: 0.6627 (OUTLIER) cc_final: 0.6368 (m-30) outliers start: 15 outliers final: 5 residues processed: 68 average time/residue: 0.5751 time to fit residues: 41.1952 Evaluate side-chains 72 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 62 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ILE Chi-restraints excluded: chain A residue 155 GLN Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 233 TYR Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain B residue 30 GLU Chi-restraints excluded: chain B residue 44 GLU Chi-restraints excluded: chain B residue 46 MET Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 208 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 18 optimal weight: 0.6980 chunk 12 optimal weight: 0.8980 chunk 56 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 6 optimal weight: 2.9990 chunk 29 optimal weight: 0.6980 chunk 45 optimal weight: 5.9990 chunk 36 optimal weight: 5.9990 chunk 17 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 70 ASN B 26 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.179092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.137657 restraints weight = 7655.336| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 1.66 r_work: 0.3185 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.1627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8814 Z= 0.133 Angle : 0.538 6.638 12639 Z= 0.319 Chirality : 0.042 0.240 1493 Planarity : 0.004 0.040 1027 Dihedral : 23.179 178.610 3018 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 1.88 % Allowed : 13.72 % Favored : 84.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: 0.29 (0.34), residues: 599 helix: 1.53 (0.31), residues: 286 sheet: -0.10 (0.41), residues: 131 loop : -1.75 (0.44), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 85 TYR 0.019 0.001 TYR A 351 PHE 0.011 0.002 PHE B 48 TRP 0.012 0.002 TRP B 43 HIS 0.001 0.000 HIS A 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.13 ( 8814) covalent geometry : angle 0.53751 / 0.32 (12639) hydrogen bonds : bond 0.05005 / 3.31 ( 419) hydrogen bonds : angle 3.47289 / 2.60 ( 1059) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1198 Ramachandran restraints generated. 599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1198 Ramachandran restraints generated. 599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 63 time to evaluate : 0.137 Fit side-chains REVERT: A 155 GLN cc_start: 0.7548 (OUTLIER) cc_final: 0.6824 (mt0) REVERT: A 218 LEU cc_start: 0.8334 (OUTLIER) cc_final: 0.7784 (mm) REVERT: B 30 GLU cc_start: 0.8220 (OUTLIER) cc_final: 0.7863 (mt-10) REVERT: B 44 GLU cc_start: 0.8095 (OUTLIER) cc_final: 0.7759 (mt-10) outliers start: 10 outliers final: 4 residues processed: 69 average time/residue: 0.5621 time to fit residues: 40.9243 Evaluate side-chains 67 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 59 time to evaluate : 0.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 GLN Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 233 TYR Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain B residue 30 GLU Chi-restraints excluded: chain B residue 44 GLU Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 199 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 73 optimal weight: 10.0000 chunk 35 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 30 optimal weight: 0.0770 chunk 21 optimal weight: 0.0670 chunk 56 optimal weight: 9.9990 chunk 36 optimal weight: 5.9990 chunk 67 optimal weight: 10.0000 chunk 41 optimal weight: 0.6980 chunk 65 optimal weight: 10.0000 chunk 46 optimal weight: 1.9990 overall best weight: 0.9680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 70 ASN A 93 GLN A 194 HIS B 151 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.179816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.138200 restraints weight = 7692.400| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 1.59 r_work: 0.3193 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3065 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.1742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8814 Z= 0.137 Angle : 0.528 6.429 12639 Z= 0.313 Chirality : 0.042 0.221 1493 Planarity : 0.004 0.040 1027 Dihedral : 23.095 178.190 3018 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 2.26 % Allowed : 14.10 % Favored : 83.65 % 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: 0.48 (0.34), residues: 599 helix: 1.68 (0.31), residues: 287 sheet: -0.04 (0.41), residues: 131 loop : -1.62 (0.44), residues: 181 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 254 TYR 0.018 0.001 TYR A 351 PHE 0.013 0.002 PHE B 48 TRP 0.012 0.002 TRP B 43 HIS 0.002 0.001 HIS A 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.14 ( 8814) covalent geometry : angle 0.52815 / 0.31 (12639) hydrogen bonds : bond 0.05008 / 3.33 ( 419) hydrogen bonds : angle 3.40730 / 2.55 ( 1059) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1198 Ramachandran restraints generated. 599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1198 Ramachandran restraints generated. 599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 66 time to evaluate : 0.139 Fit side-chains REVERT: A 155 GLN cc_start: 0.7639 (OUTLIER) cc_final: 0.6888 (mt0) REVERT: A 218 LEU cc_start: 0.8344 (OUTLIER) cc_final: 0.7786 (mm) REVERT: A 224 ILE cc_start: 0.8857 (mp) cc_final: 0.8632 (mt) REVERT: B 30 GLU cc_start: 0.8445 (OUTLIER) cc_final: 0.8175 (mt-10) outliers start: 12 outliers final: 4 residues processed: 75 average time/residue: 0.6042 time to fit residues: 47.7069 Evaluate side-chains 68 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 61 time to evaluate : 0.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ILE Chi-restraints excluded: chain A residue 61 LYS Chi-restraints excluded: chain A residue 155 GLN Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 233 TYR Chi-restraints excluded: chain B residue 30 GLU Chi-restraints excluded: chain B residue 50 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 71 optimal weight: 7.9990 chunk 64 optimal weight: 10.0000 chunk 37 optimal weight: 6.9990 chunk 31 optimal weight: 0.8980 chunk 45 optimal weight: 2.9990 chunk 69 optimal weight: 10.0000 chunk 8 optimal weight: 3.9990 chunk 30 optimal weight: 6.9990 chunk 49 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 62 optimal weight: 20.0000 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 70 ASN B 40 GLN B 131 ASN B 151 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.176420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.134725 restraints weight = 7600.952| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 1.57 r_work: 0.3154 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.1650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 8814 Z= 0.210 Angle : 0.602 6.968 12639 Z= 0.350 Chirality : 0.046 0.230 1493 Planarity : 0.005 0.041 1027 Dihedral : 23.147 179.729 3018 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 2.26 % Allowed : 14.29 % Favored : 83.46 % 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: 0.33 (0.34), residues: 599 helix: 1.53 (0.31), residues: 287 sheet: 0.06 (0.42), residues: 124 loop : -1.74 (0.42), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 179 TYR 0.016 0.002 TYR A 351 PHE 0.017 0.003 PHE B 48 TRP 0.014 0.002 TRP B 43 HIS 0.003 0.001 HIS A 194 Details of bonding type rmsd/Z covalent geometry : bond 0.00458 / 0.21 ( 8814) covalent geometry : angle 0.60194 / 0.35 (12639) hydrogen bonds : bond 0.05885 / 3.92 ( 419) hydrogen bonds : angle 3.53308 / 2.64 ( 1059) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1198 Ramachandran restraints generated. 599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1198 Ramachandran restraints generated. 599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 66 time to evaluate : 0.145 Fit side-chains REVERT: A 155 GLN cc_start: 0.7679 (OUTLIER) cc_final: 0.6955 (mt0) REVERT: A 218 LEU cc_start: 0.8380 (OUTLIER) cc_final: 0.7771 (mm) REVERT: A 323 MET cc_start: 0.8606 (ptt) cc_final: 0.8313 (ptt) REVERT: B 30 GLU cc_start: 0.8444 (OUTLIER) cc_final: 0.8134 (mt-10) REVERT: B 44 GLU cc_start: 0.8371 (OUTLIER) cc_final: 0.8059 (mt-10) outliers start: 12 outliers final: 5 residues processed: 73 average time/residue: 0.6041 time to fit residues: 46.6247 Evaluate side-chains 73 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 64 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ILE Chi-restraints excluded: chain A residue 155 GLN Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 233 TYR Chi-restraints excluded: chain B residue 30 GLU Chi-restraints excluded: chain B residue 44 GLU Chi-restraints excluded: chain B residue 46 MET Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 164 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 32 optimal weight: 3.9990 chunk 60 optimal weight: 6.9990 chunk 57 optimal weight: 7.9990 chunk 21 optimal weight: 0.0060 chunk 71 optimal weight: 7.9990 chunk 28 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 42 optimal weight: 5.9990 chunk 27 optimal weight: 0.9980 overall best weight: 1.2002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 70 ASN B 26 GLN B 151 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.178295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.136685 restraints weight = 7634.815| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 1.60 r_work: 0.3178 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.1746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8814 Z= 0.149 Angle : 0.547 6.612 12639 Z= 0.322 Chirality : 0.043 0.215 1493 Planarity : 0.004 0.039 1027 Dihedral : 23.119 178.842 3018 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 2.26 % Allowed : 14.47 % Favored : 83.27 % 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: 0.46 (0.34), residues: 599 helix: 1.63 (0.31), residues: 287 sheet: 0.01 (0.41), residues: 131 loop : -1.63 (0.44), residues: 181 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 25 TYR 0.019 0.002 TYR A 351 PHE 0.012 0.002 PHE B 48 TRP 0.013 0.002 TRP B 43 HIS 0.001 0.000 HIS A 278 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.15 ( 8814) covalent geometry : angle 0.54663 / 0.32 (12639) hydrogen bonds : bond 0.05171 / 3.43 ( 419) hydrogen bonds : angle 3.45486 / 2.59 ( 1059) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1198 Ramachandran restraints generated. 599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1198 Ramachandran restraints generated. 599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 63 time to evaluate : 0.183 Fit side-chains REVERT: A 155 GLN cc_start: 0.7649 (OUTLIER) cc_final: 0.6910 (mt0) REVERT: A 218 LEU cc_start: 0.8357 (OUTLIER) cc_final: 0.7802 (mm) REVERT: A 323 MET cc_start: 0.8621 (ptt) cc_final: 0.8342 (ptt) REVERT: B 30 GLU cc_start: 0.8436 (OUTLIER) cc_final: 0.8138 (mt-10) REVERT: B 44 GLU cc_start: 0.8356 (OUTLIER) cc_final: 0.8055 (mt-10) outliers start: 12 outliers final: 7 residues processed: 67 average time/residue: 0.6366 time to fit residues: 44.8795 Evaluate side-chains 71 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 60 time to evaluate : 0.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ILE Chi-restraints excluded: chain A residue 61 LYS Chi-restraints excluded: chain A residue 155 GLN Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 233 TYR Chi-restraints excluded: chain B residue 30 GLU Chi-restraints excluded: chain B residue 44 GLU Chi-restraints excluded: chain B residue 46 MET Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 199 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 57 optimal weight: 8.9990 chunk 1 optimal weight: 1.9990 chunk 0 optimal weight: 0.9990 chunk 67 optimal weight: 10.0000 chunk 53 optimal weight: 0.8980 chunk 45 optimal weight: 0.5980 chunk 16 optimal weight: 3.9990 chunk 47 optimal weight: 5.9990 chunk 4 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 60 optimal weight: 6.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 70 ASN B 26 GLN B 151 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.178946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.137745 restraints weight = 7661.168| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 1.65 r_work: 0.3179 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.1808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8814 Z= 0.142 Angle : 0.533 6.695 12639 Z= 0.315 Chirality : 0.042 0.201 1493 Planarity : 0.004 0.040 1027 Dihedral : 23.092 178.219 3018 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 1.88 % Allowed : 15.23 % Favored : 82.89 % 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: 0.56 (0.35), residues: 599 helix: 1.72 (0.31), residues: 287 sheet: 0.03 (0.41), residues: 131 loop : -1.57 (0.45), residues: 181 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 25 TYR 0.018 0.002 TYR A 351 PHE 0.013 0.002 PHE A 236 TRP 0.012 0.002 TRP B 43 HIS 0.002 0.001 HIS A 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.14 ( 8814) covalent geometry : angle 0.53334 / 0.32 (12639) hydrogen bonds : bond 0.05061 / 3.37 ( 419) hydrogen bonds : angle 3.43081 / 2.57 ( 1059) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1198 Ramachandran restraints generated. 599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1198 Ramachandran restraints generated. 599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 61 time to evaluate : 0.154 Fit side-chains REVERT: A 155 GLN cc_start: 0.7545 (OUTLIER) cc_final: 0.6793 (mt0) REVERT: A 218 LEU cc_start: 0.8388 (OUTLIER) cc_final: 0.7844 (mm) REVERT: B 30 GLU cc_start: 0.8211 (OUTLIER) cc_final: 0.7891 (mt-10) REVERT: B 44 GLU cc_start: 0.8110 (OUTLIER) cc_final: 0.7778 (mt-10) outliers start: 10 outliers final: 4 residues processed: 67 average time/residue: 0.5280 time to fit residues: 37.4546 Evaluate side-chains 66 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 58 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ILE Chi-restraints excluded: chain A residue 155 GLN Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 233 TYR Chi-restraints excluded: chain B residue 30 GLU Chi-restraints excluded: chain B residue 44 GLU Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 199 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 46 optimal weight: 6.9990 chunk 19 optimal weight: 0.8980 chunk 17 optimal weight: 0.7980 chunk 71 optimal weight: 8.9990 chunk 64 optimal weight: 10.0000 chunk 26 optimal weight: 1.9990 chunk 57 optimal weight: 6.9990 chunk 6 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 51 optimal weight: 3.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 70 ASN B 26 GLN B 131 ASN B 151 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.177817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.136181 restraints weight = 7640.920| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 1.63 r_work: 0.3167 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3040 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.1780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8814 Z= 0.171 Angle : 0.561 6.583 12639 Z= 0.328 Chirality : 0.043 0.206 1493 Planarity : 0.004 0.041 1027 Dihedral : 23.104 178.897 3018 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 2.26 % Allowed : 15.04 % Favored : 82.71 % 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: 0.50 (0.34), residues: 599 helix: 1.66 (0.31), residues: 287 sheet: 0.01 (0.41), residues: 131 loop : -1.59 (0.44), residues: 181 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 179 TYR 0.018 0.002 TYR A 351 PHE 0.015 0.002 PHE B 48 TRP 0.013 0.002 TRP B 43 HIS 0.002 0.001 HIS B 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.17 ( 8814) covalent geometry : angle 0.56066 / 0.33 (12639) hydrogen bonds : bond 0.05391 / 3.60 ( 419) hydrogen bonds : angle 3.46997 / 2.60 ( 1059) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2385.19 seconds wall clock time: 41 minutes 22.54 seconds (2482.54 seconds total)