Starting phenix.real_space_refine on Fri Sep 11 07:29:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wju_32548/09_2026/7wju_32548_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wju_32548/09_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7wju_32548/09_2026/7wju_32548.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wju_32548/09_2026/7wju_32548.map" model { file = "/net/cci-nas-00/data/ceres_data/7wju_32548/09_2026/7wju_32548_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wju_32548/09_2026/7wju_32548_neut.cif" } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/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: 2.06, per 1000 atoms: 0.25 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: 0.91 Conformation dependent library (CDL) restraints added in 187.0 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: 0.97 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: 1.61 Time building geometry restraints manager: 1.16 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: 12353 3.03 - 6.06: 269 6.06 - 9.10: 14 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 1.60e+00 3.91e-01 8.98e+01 angle pdb=" O5' A C 91 " pdb=" C5' A C 91 " pdb=" C4' A C 91 " ideal model delta sigma weight residual 109.40 104.43 4.97 8.00e-01 1.56e+00 3.86e+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=" O5' A C 76 " pdb=" C5' A C 76 " pdb=" C4' A C 76 " ideal model delta sigma weight residual 109.40 113.69 -4.29 8.00e-01 1.56e+00 2.88e+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 ... (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: 1229 0.096 - 0.192: 236 0.192 - 0.289: 13 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: 0.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.900 Find NCS groups from input model: 0.020 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:6.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.530 ------------------------------------------------------------------------------- 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= 0.675 Angle : 1.079 15.161 12639 Z= 0.874 Chirality : 0.078 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 0.00766 / 0.67 ( 8814) covalent geometry : angle 1.07860 / 0.87 (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 : 0.165 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 92 average time/residue: 0.6861 time to fit residues: 66.2577 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 : 0.233 ------------------------------------------------------------------------------- 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: 20.0000 chunk 62 optimal weight: 20.0000 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 9.9990 chunk 61 optimal weight: 8.9990 chunk 45 optimal weight: 5.9990 chunk 27 optimal weight: 0.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- 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 = 0.3917 r_free = 0.3917 target = 0.177465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.135742 restraints weight = 7703.338| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 1.65 r_work: 0.3152 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.1091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8814 Z= 0.177 Angle : 0.646 7.076 12639 Z= 0.373 Chirality : 0.048 0.283 1493 Planarity : 0.005 0.048 1027 Dihedral : 23.325 175.887 3018 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.01 % Favored : 95.83 % Rotamer: Outliers : 2.07 % Allowed : 10.71 % 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: -1.06 (0.32), residues: 599 helix: 0.18 (0.29), residues: 285 sheet: -0.36 (0.42), residues: 123 loop : -2.20 (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 0.016 0.002 TRP B 43 HIS 0.003 0.001 HIS A 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.18 ( 8814) covalent geometry : angle 0.64620 / 0.37 (12639) hydrogen bonds : bond 0.06495 / 4.35 ( 419) hydrogen bonds : angle 3.84466 / 2.86 ( 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: 11 poor density : 66 time to evaluate : 0.256 Fit side-chains REVERT: A 155 GLN cc_start: 0.7635 (OUTLIER) cc_final: 0.6851 (mt0) REVERT: A 218 LEU cc_start: 0.8412 (OUTLIER) cc_final: 0.7819 (mm) REVERT: B 30 GLU cc_start: 0.8214 (OUTLIER) cc_final: 0.7947 (mt-10) REVERT: B 44 GLU cc_start: 0.8206 (OUTLIER) cc_final: 0.7869 (mt-10) REVERT: B 85 ARG cc_start: 0.8245 (mtt90) cc_final: 0.8045 (mtt90) outliers start: 11 outliers final: 3 residues processed: 72 average time/residue: 0.5980 time to fit residues: 45.7105 Evaluate side-chains 66 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 59 time to evaluate : 0.245 ------------------------------------------------------------------------------- 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 156 GLU 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: 0.9980 chunk 44 optimal weight: 0.6980 chunk 43 optimal weight: 0.9980 chunk 64 optimal weight: 10.0000 chunk 28 optimal weight: 2.9990 chunk 5 optimal weight: 0.4980 chunk 65 optimal weight: 20.0000 chunk 24 optimal weight: 5.9990 chunk 69 optimal weight: 9.9990 chunk 62 optimal weight: 20.0000 overall best weight: 1.2382 ------------------------------------------------------------------------------- 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 = 0.3922 r_free = 0.3922 target = 0.177950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.132654 restraints weight = 7631.957| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 1.06 r_work: 0.3236 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3110 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.1393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8814 Z= 0.151 Angle : 0.583 7.829 12639 Z= 0.337 Chirality : 0.044 0.263 1493 Planarity : 0.004 0.043 1027 Dihedral : 23.199 179.292 3018 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.84 % Favored : 95.99 % Rotamer: Outliers : 1.50 % Allowed : 13.16 % Favored : 85.34 % 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 (0.33), residues: 599 helix: 0.98 (0.31), residues: 286 sheet: -0.28 (0.41), residues: 131 loop : -1.97 (0.42), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 179 TYR 0.021 0.002 TYR A 351 PHE 0.013 0.002 PHE B 48 TRP 0.013 0.002 TRP B 43 HIS 0.003 0.001 HIS A 303 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.15 ( 8814) covalent geometry : angle 0.58269 / 0.34 (12639) hydrogen bonds : bond 0.05556 / 3.67 ( 419) hydrogen bonds : angle 3.58630 / 2.67 ( 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 73 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 65 time to evaluate : 0.239 Fit side-chains REVERT: A 155 GLN cc_start: 0.7620 (OUTLIER) cc_final: 0.6873 (mt0) REVERT: A 218 LEU cc_start: 0.8396 (OUTLIER) cc_final: 0.7842 (mm) REVERT: B 30 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.7941 (mt-10) REVERT: B 44 GLU cc_start: 0.8206 (OUTLIER) cc_final: 0.7882 (mt-10) REVERT: B 137 MET cc_start: 0.5212 (mpp) cc_final: 0.4954 (mpp) outliers start: 8 outliers final: 1 residues processed: 69 average time/residue: 0.6153 time to fit residues: 44.8630 Evaluate side-chains 65 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 60 time to evaluate : 0.258 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 29 optimal weight: 2.9990 chunk 39 optimal weight: 5.9990 chunk 38 optimal weight: 10.0000 chunk 16 optimal weight: 1.9990 chunk 26 optimal weight: 9.9990 chunk 14 optimal weight: 1.9990 chunk 51 optimal weight: 0.0770 chunk 25 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 54 optimal weight: 0.7980 chunk 35 optimal weight: 3.9990 overall best weight: 1.1742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 70 ASN A 93 GLN B 26 GLN B 40 GLN B 151 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.178626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.133109 restraints weight = 7745.173| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 1.07 r_work: 0.3243 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3119 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.1561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8814 Z= 0.146 Angle : 0.567 6.691 12639 Z= 0.326 Chirality : 0.043 0.244 1493 Planarity : 0.004 0.040 1027 Dihedral : 23.151 178.217 3018 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 1.88 % Allowed : 12.78 % Favored : 85.34 % 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: 0.10 (0.34), residues: 599 helix: 1.36 (0.31), residues: 286 sheet: -0.15 (0.41), residues: 131 loop : -1.84 (0.43), residues: 182 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 0.013 0.002 PHE B 48 TRP 0.014 0.002 TRP B 43 HIS 0.002 0.001 HIS A 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.15 ( 8814) covalent geometry : angle 0.56681 / 0.33 (12639) hydrogen bonds : bond 0.05300 / 3.50 ( 419) hydrogen bonds : angle 3.53024 / 2.63 ( 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 73 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 63 time to evaluate : 0.290 Fit side-chains REVERT: A 155 GLN cc_start: 0.7612 (OUTLIER) cc_final: 0.6884 (mt0) REVERT: A 218 LEU cc_start: 0.8323 (OUTLIER) cc_final: 0.7778 (mm) REVERT: B 30 GLU cc_start: 0.8300 (OUTLIER) cc_final: 0.8024 (mt-10) REVERT: B 44 GLU cc_start: 0.8215 (OUTLIER) cc_final: 0.7893 (mt-10) REVERT: B 137 MET cc_start: 0.5198 (mpp) cc_final: 0.4939 (mpp) outliers start: 10 outliers final: 3 residues processed: 67 average time/residue: 0.6335 time to fit residues: 44.9139 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 : 0.219 ------------------------------------------------------------------------------- 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 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: 0.0980 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: 9.9990 chunk 58 optimal weight: 1.9990 chunk 52 optimal weight: 5.9990 chunk 4 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 overall best weight: 1.8188 ------------------------------------------------------------------------------- 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 = 0.177639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.132029 restraints weight = 7643.502| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 1.05 r_work: 0.3221 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3093 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.1550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8814 Z= 0.186 Angle : 0.605 6.454 12639 Z= 0.343 Chirality : 0.046 0.252 1493 Planarity : 0.005 0.042 1027 Dihedral : 23.145 179.124 3018 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 2.07 % Allowed : 13.53 % 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: 0.13 (0.34), residues: 599 helix: 1.43 (0.31), residues: 285 sheet: -0.07 (0.42), residues: 124 loop : -1.91 (0.42), residues: 190 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 0.016 0.002 PHE B 48 TRP 0.013 0.002 TRP B 43 HIS 0.002 0.001 HIS A 278 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.19 ( 8814) covalent geometry : angle 0.60523 / 0.34 (12639) hydrogen bonds : bond 0.05754 / 3.82 ( 419) hydrogen bonds : angle 3.58402 / 2.67 ( 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 74 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 63 time to evaluate : 0.221 Fit side-chains REVERT: A 155 GLN cc_start: 0.7594 (OUTLIER) cc_final: 0.6868 (mt0) REVERT: A 218 LEU cc_start: 0.8304 (OUTLIER) cc_final: 0.7749 (mm) REVERT: B 30 GLU cc_start: 0.8264 (OUTLIER) cc_final: 0.7967 (mt-10) REVERT: B 44 GLU cc_start: 0.8212 (OUTLIER) cc_final: 0.7882 (mt-10) outliers start: 11 outliers final: 5 residues processed: 69 average time/residue: 0.6311 time to fit residues: 46.1305 Evaluate side-chains 68 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 59 time to evaluate : 0.279 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 18 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 56 optimal weight: 8.9990 chunk 9 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 45 optimal weight: 6.9990 chunk 36 optimal weight: 5.9990 chunk 17 optimal weight: 0.7980 chunk 0 optimal weight: 2.9990 chunk 57 optimal weight: 0.9980 overall best weight: 1.5184 ------------------------------------------------------------------------------- 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 = 0.178174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.136852 restraints weight = 7621.657| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 1.55 r_work: 0.3175 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3049 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.1631 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= 0.165 Angle : 0.581 6.519 12639 Z= 0.332 Chirality : 0.044 0.244 1493 Planarity : 0.004 0.041 1027 Dihedral : 23.110 178.222 3018 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 3.01 % Allowed : 12.78 % 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: 0.26 (0.34), residues: 599 helix: 1.51 (0.31), residues: 286 sheet: -0.07 (0.41), residues: 131 loop : -1.79 (0.44), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 179 TYR 0.017 0.002 TYR A 351 PHE 0.013 0.002 PHE B 48 TRP 0.013 0.002 TRP B 43 HIS 0.002 0.001 HIS A 278 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.16 ( 8814) covalent geometry : angle 0.58084 / 0.33 (12639) hydrogen bonds : bond 0.05467 / 3.62 ( 419) hydrogen bonds : angle 3.51437 / 2.62 ( 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 77 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 61 time to evaluate : 0.239 Fit side-chains REVERT: A 155 GLN cc_start: 0.7692 (OUTLIER) cc_final: 0.6966 (mt0) REVERT: A 218 LEU cc_start: 0.8303 (OUTLIER) cc_final: 0.7749 (mm) REVERT: B 30 GLU cc_start: 0.8417 (OUTLIER) cc_final: 0.8141 (mt-10) REVERT: B 44 GLU cc_start: 0.8362 (OUTLIER) cc_final: 0.8052 (mt-10) outliers start: 16 outliers final: 7 residues processed: 69 average time/residue: 0.6918 time to fit residues: 50.3124 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 : 0.239 ------------------------------------------------------------------------------- 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 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 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: 9.9990 chunk 35 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 30 optimal weight: 0.8980 chunk 21 optimal weight: 0.0020 chunk 56 optimal weight: 8.9990 chunk 36 optimal weight: 4.9990 chunk 67 optimal weight: 10.0000 chunk 41 optimal weight: 0.7980 chunk 65 optimal weight: 20.0000 chunk 46 optimal weight: 5.9990 overall best weight: 1.5392 ------------------------------------------------------------------------------- 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 = 0.3923 r_free = 0.3923 target = 0.178091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.136362 restraints weight = 7681.910| |-----------------------------------------------------------------------------| r_work (start): 0.3480 rms_B_bonded: 1.58 r_work: 0.3163 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.1694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8814 Z= 0.168 Angle : 0.582 6.472 12639 Z= 0.332 Chirality : 0.044 0.245 1493 Planarity : 0.004 0.041 1027 Dihedral : 23.108 178.197 3018 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 3.01 % Allowed : 12.78 % Favored : 84.21 % 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: 0.32 (0.34), residues: 599 helix: 1.54 (0.31), residues: 286 sheet: -0.01 (0.41), residues: 131 loop : -1.75 (0.43), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 179 TYR 0.016 0.002 TYR A 351 PHE 0.014 0.002 PHE B 48 TRP 0.013 0.002 TRP B 43 HIS 0.002 0.001 HIS A 278 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.17 ( 8814) covalent geometry : angle 0.58190 / 0.33 (12639) hydrogen bonds : bond 0.05504 / 3.65 ( 419) hydrogen bonds : angle 3.49825 / 2.61 ( 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 76 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 60 time to evaluate : 0.253 Fit side-chains REVERT: A 155 GLN cc_start: 0.7566 (OUTLIER) cc_final: 0.6828 (mt0) REVERT: A 218 LEU cc_start: 0.8378 (OUTLIER) cc_final: 0.7759 (mm) REVERT: B 30 GLU cc_start: 0.8186 (OUTLIER) cc_final: 0.7893 (mt-10) REVERT: B 44 GLU cc_start: 0.8120 (OUTLIER) cc_final: 0.7778 (mt-10) outliers start: 16 outliers final: 6 residues processed: 68 average time/residue: 0.6578 time to fit residues: 47.3190 Evaluate side-chains 69 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 59 time to evaluate : 0.400 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 71 optimal weight: 10.0000 chunk 64 optimal weight: 10.0000 chunk 37 optimal weight: 3.9990 chunk 31 optimal weight: 7.9990 chunk 45 optimal weight: 0.9990 chunk 69 optimal weight: 10.0000 chunk 8 optimal weight: 3.9990 chunk 30 optimal weight: 0.4980 chunk 49 optimal weight: 0.7980 chunk 7 optimal weight: 0.8980 chunk 62 optimal weight: 20.0000 overall best weight: 1.4384 ------------------------------------------------------------------------------- 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 = 0.3922 r_free = 0.3922 target = 0.178143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.136457 restraints weight = 7635.433| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 1.59 r_work: 0.3171 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.1744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 8814 Z= 0.161 Angle : 0.571 7.087 12639 Z= 0.326 Chirality : 0.043 0.242 1493 Planarity : 0.004 0.040 1027 Dihedral : 23.108 177.747 3018 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 2.44 % Allowed : 12.97 % Favored : 84.59 % 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: 0.40 (0.34), residues: 599 helix: 1.58 (0.31), residues: 287 sheet: 0.03 (0.41), residues: 131 loop : -1.70 (0.44), residues: 181 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 254 TYR 0.016 0.002 TYR A 351 PHE 0.013 0.002 PHE B 48 TRP 0.013 0.002 TRP B 43 HIS 0.002 0.001 HIS A 278 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.16 ( 8814) covalent geometry : angle 0.57130 / 0.33 (12639) hydrogen bonds : bond 0.05375 / 3.56 ( 419) hydrogen bonds : angle 3.47716 / 2.60 ( 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 76 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 63 time to evaluate : 0.288 Fit side-chains REVERT: A 155 GLN cc_start: 0.7564 (OUTLIER) cc_final: 0.6821 (mt0) REVERT: A 218 LEU cc_start: 0.8357 (OUTLIER) cc_final: 0.7797 (mm) REVERT: A 323 MET cc_start: 0.8515 (ptt) cc_final: 0.8232 (ptt) REVERT: B 30 GLU cc_start: 0.8177 (OUTLIER) cc_final: 0.7882 (mt-10) REVERT: B 44 GLU cc_start: 0.8120 (OUTLIER) cc_final: 0.7779 (mt-10) outliers start: 13 outliers final: 7 residues processed: 69 average time/residue: 0.6893 time to fit residues: 50.1494 Evaluate side-chains 69 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 58 time to evaluate : 0.185 ------------------------------------------------------------------------------- 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 32 optimal weight: 4.9990 chunk 60 optimal weight: 7.9990 chunk 57 optimal weight: 8.9990 chunk 21 optimal weight: 0.0060 chunk 71 optimal weight: 8.9990 chunk 28 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 11 optimal weight: 0.8980 chunk 42 optimal weight: 6.9990 chunk 27 optimal weight: 0.7980 overall best weight: 1.7400 ------------------------------------------------------------------------------- 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 = 0.3912 r_free = 0.3912 target = 0.177197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.135476 restraints weight = 7635.206| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 1.62 r_work: 0.3160 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.1750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8814 Z= 0.180 Angle : 0.594 6.623 12639 Z= 0.336 Chirality : 0.045 0.247 1493 Planarity : 0.004 0.041 1027 Dihedral : 23.122 178.271 3018 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 2.26 % Allowed : 13.53 % Favored : 84.21 % 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: 0.38 (0.34), residues: 599 helix: 1.56 (0.31), residues: 287 sheet: 0.03 (0.42), residues: 131 loop : -1.71 (0.44), residues: 181 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 335 TYR 0.018 0.002 TYR A 351 PHE 0.014 0.002 PHE B 48 TRP 0.013 0.002 TRP B 43 HIS 0.002 0.001 HIS A 278 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.18 ( 8814) covalent geometry : angle 0.59361 / 0.34 (12639) hydrogen bonds : bond 0.05628 / 3.75 ( 419) hydrogen bonds : angle 3.51176 / 2.62 ( 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 78 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 66 time to evaluate : 0.230 Fit side-chains REVERT: A 155 GLN cc_start: 0.7570 (OUTLIER) cc_final: 0.6830 (mt0) REVERT: A 218 LEU cc_start: 0.8449 (OUTLIER) cc_final: 0.7800 (mm) REVERT: B 30 GLU cc_start: 0.8176 (OUTLIER) cc_final: 0.7873 (mt-10) REVERT: B 44 GLU cc_start: 0.8116 (OUTLIER) cc_final: 0.7774 (mt-10) outliers start: 12 outliers final: 5 residues processed: 71 average time/residue: 0.6564 time to fit residues: 49.1479 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 : 0.243 ------------------------------------------------------------------------------- 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 69 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 57 optimal weight: 7.9990 chunk 1 optimal weight: 0.8980 chunk 0 optimal weight: 1.9990 chunk 67 optimal weight: 9.9990 chunk 53 optimal weight: 7.9990 chunk 45 optimal weight: 0.8980 chunk 16 optimal weight: 0.9990 chunk 47 optimal weight: 0.7980 chunk 4 optimal weight: 2.9990 chunk 22 optimal weight: 6.9990 chunk 60 optimal weight: 6.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 70 ASN A 412 ASN B 26 GLN B 151 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.178697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.137098 restraints weight = 7656.076| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 1.63 r_work: 0.3179 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.1814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8814 Z= 0.145 Angle : 0.555 6.616 12639 Z= 0.318 Chirality : 0.042 0.239 1493 Planarity : 0.004 0.040 1027 Dihedral : 23.106 177.180 3018 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 1.88 % Allowed : 14.29 % Favored : 83.83 % 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: 0.49 (0.34), residues: 599 helix: 1.64 (0.31), residues: 287 sheet: 0.07 (0.42), residues: 131 loop : -1.65 (0.44), residues: 181 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 335 TYR 0.019 0.002 TYR A 351 PHE 0.011 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 0.00299 / 0.14 ( 8814) covalent geometry : angle 0.55473 / 0.32 (12639) hydrogen bonds : bond 0.05187 / 3.44 ( 419) hydrogen bonds : angle 3.45447 / 2.59 ( 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 69 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 59 time to evaluate : 0.230 Fit side-chains REVERT: A 155 GLN cc_start: 0.7640 (OUTLIER) cc_final: 0.6899 (mt0) REVERT: A 218 LEU cc_start: 0.8306 (OUTLIER) cc_final: 0.7742 (mm) REVERT: A 323 MET cc_start: 0.8594 (ptt) cc_final: 0.8347 (ptt) REVERT: B 30 GLU cc_start: 0.8389 (OUTLIER) cc_final: 0.8126 (mt-10) REVERT: B 44 GLU cc_start: 0.8340 (OUTLIER) cc_final: 0.8029 (mt-10) outliers start: 10 outliers final: 6 residues processed: 64 average time/residue: 0.6751 time to fit residues: 45.5894 Evaluate side-chains 69 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 59 time to evaluate : 0.150 ------------------------------------------------------------------------------- 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 50 SER Chi-restraints excluded: chain B residue 69 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 46 optimal weight: 5.9990 chunk 19 optimal weight: 0.6980 chunk 17 optimal weight: 0.5980 chunk 71 optimal weight: 9.9990 chunk 64 optimal weight: 10.0000 chunk 26 optimal weight: 9.9990 chunk 57 optimal weight: 8.9990 chunk 6 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 35 optimal weight: 5.9990 chunk 51 optimal weight: 3.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- 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 = 0.3916 r_free = 0.3916 target = 0.177584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.135885 restraints weight = 7647.054| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 1.62 r_work: 0.3165 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3036 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.1792 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= 0.173 Angle : 0.580 6.561 12639 Z= 0.330 Chirality : 0.044 0.244 1493 Planarity : 0.004 0.041 1027 Dihedral : 23.117 177.966 3018 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 2.07 % Allowed : 14.29 % 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: 0.45 (0.34), residues: 599 helix: 1.61 (0.31), residues: 287 sheet: 0.06 (0.42), residues: 131 loop : -1.66 (0.44), residues: 181 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 335 TYR 0.017 0.002 TYR A 351 PHE 0.014 0.002 PHE B 48 TRP 0.013 0.002 TRP B 43 HIS 0.002 0.001 HIS A 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.17 ( 8814) covalent geometry : angle 0.58033 / 0.33 (12639) hydrogen bonds : bond 0.05503 / 3.67 ( 419) hydrogen bonds : angle 3.49206 / 2.61 ( 1059) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2569.79 seconds wall clock time: 44 minutes 37.19 seconds (2677.19 seconds total)