Starting phenix.real_space_refine on Tue Mar 3 19:58:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wju_32548/03_2026/7wju_32548_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wju_32548/03_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_32548/03_2026/7wju_32548_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wju_32548/03_2026/7wju_32548_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7wju_32548/03_2026/7wju_32548.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wju_32548/03_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-5986/lib/python3.9/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: 2.07, 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: 0.68 Conformation dependent library (CDL) restraints added in 180.9 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: 1.13 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: 1.57 Time building geometry restraints manager: 0.91 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=" N ARG A 283 " pdb=" CA ARG A 283 " ideal model delta sigma weight residual 1.456 1.495 -0.038 1.23e-02 6.61e+03 9.80e+00 bond pdb=" N LEU A 337 " pdb=" CA LEU A 337 " ideal model delta sigma weight residual 1.457 1.497 -0.040 1.29e-02 6.01e+03 9.59e+00 bond pdb=" O5' A C 90 " pdb=" C5' A C 90 " ideal model delta sigma weight residual 1.420 1.462 -0.042 1.50e-02 4.44e+03 7.67e+00 bond pdb=" O5' G C 117 " pdb=" C5' G C 117 " ideal model delta sigma weight residual 1.420 1.461 -0.041 1.50e-02 4.44e+03 7.58e+00 bond pdb=" O5' C C 118 " pdb=" C5' C C 118 " ideal model delta sigma weight residual 1.420 1.456 -0.036 1.50e-02 4.44e+03 5.71e+00 ... (remaining 8809 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.03: 12409 3.03 - 6.06: 211 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=" O5' A C 91 " pdb=" C5' A C 91 " pdb=" C4' A C 91 " ideal model delta sigma weight residual 111.70 104.43 7.27 1.50e+00 4.44e-01 2.35e+01 angle pdb=" C ILE A 329 " pdb=" N ARG A 330 " pdb=" CA ARG A 330 " ideal model delta sigma weight residual 121.54 130.77 -9.23 1.91e+00 2.74e-01 2.34e+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: 1333 0.096 - 0.192: 133 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 2.35 -2.78 -0.43 2.00e-01 2.50e+01 4.72e+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: 0.840 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: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 9.530 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 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 : 0.007 0.076 8814 Z= 0.374 Angle : 0.988 15.161 12639 Z= 0.549 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 covalent geometry : bond 0.00749 ( 8814) covalent geometry : angle 0.98763 (12639) hydrogen bonds : bond 0.13787 ( 419) hydrogen bonds : angle 5.37277 ( 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 : 0.205 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 92 average time/residue: 0.7228 time to fit residues: 69.5447 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 : 0.174 ------------------------------------------------------------------------------- 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: 7.9990 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 9.9990 chunk 61 optimal weight: 3.9990 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3924 r_free = 0.3924 target = 0.178059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.132246 restraints weight = 7739.422| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 1.08 r_work: 0.3227 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3103 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.1274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8814 Z= 0.177 Angle : 0.617 5.995 12639 Z= 0.339 Chirality : 0.043 0.213 1493 Planarity : 0.005 0.043 1027 Dihedral : 23.138 177.105 3018 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.01 % Favored : 95.83 % Rotamer: Outliers : 2.26 % Allowed : 11.28 % Favored : 86.47 % 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: -0.96 (0.32), residues: 599 helix: 0.26 (0.30), residues: 291 sheet: -0.36 (0.42), residues: 130 loop : -2.24 (0.40), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 179 TYR 0.023 0.002 TYR A 351 PHE 0.015 0.002 PHE B 48 TRP 0.014 0.002 TRP B 43 HIS 0.003 0.001 HIS A 303 Details of bonding type rmsd covalent geometry : bond 0.00379 ( 8814) covalent geometry : angle 0.61665 (12639) hydrogen bonds : bond 0.05169 ( 419) hydrogen bonds : angle 3.65544 ( 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 80 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 68 time to evaluate : 0.192 Fit side-chains REVERT: A 155 GLN cc_start: 0.7611 (OUTLIER) cc_final: 0.6857 (mt0) REVERT: A 218 LEU cc_start: 0.8416 (OUTLIER) cc_final: 0.7833 (mm) REVERT: B 30 GLU cc_start: 0.8250 (OUTLIER) cc_final: 0.7940 (mt-10) REVERT: B 137 MET cc_start: 0.5361 (mpp) cc_final: 0.5033 (mpp) outliers start: 12 outliers final: 3 residues processed: 74 average time/residue: 0.5969 time to fit residues: 46.6658 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 : 0.131 ------------------------------------------------------------------------------- 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 69 THR 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: 0.6980 chunk 44 optimal weight: 0.5980 chunk 43 optimal weight: 1.9990 chunk 64 optimal weight: 7.9990 chunk 28 optimal weight: 2.9990 chunk 5 optimal weight: 0.0870 chunk 65 optimal weight: 10.0000 chunk 24 optimal weight: 5.9990 chunk 69 optimal weight: 5.9990 chunk 62 optimal weight: 7.9990 overall best weight: 1.2762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 ASN B 26 GLN B 40 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 = 0.3932 r_free = 0.3932 target = 0.178895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.137458 restraints weight = 7621.982| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 1.62 r_work: 0.3172 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3043 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.1552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8814 Z= 0.169 Angle : 0.595 6.681 12639 Z= 0.323 Chirality : 0.041 0.205 1493 Planarity : 0.004 0.039 1027 Dihedral : 23.060 176.552 3018 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 2.26 % Allowed : 11.65 % Favored : 86.09 % 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: -0.16 (0.34), residues: 599 helix: 1.09 (0.31), residues: 286 sheet: -0.17 (0.41), residues: 131 loop : -1.96 (0.42), residues: 182 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 0.014 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 covalent geometry : bond 0.00363 ( 8814) covalent geometry : angle 0.59500 (12639) hydrogen bonds : bond 0.04961 ( 419) hydrogen bonds : angle 3.49657 ( 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 76 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 64 time to evaluate : 0.227 Fit side-chains REVERT: A 155 GLN cc_start: 0.7637 (OUTLIER) cc_final: 0.6912 (mt0) REVERT: A 218 LEU cc_start: 0.8378 (OUTLIER) cc_final: 0.7803 (mm) REVERT: B 30 GLU cc_start: 0.8414 (OUTLIER) cc_final: 0.8163 (mt-10) REVERT: B 44 GLU cc_start: 0.8370 (OUTLIER) cc_final: 0.8082 (mt-10) REVERT: B 137 MET cc_start: 0.5232 (mpp) cc_final: 0.5027 (mpp) outliers start: 12 outliers final: 4 residues processed: 69 average time/residue: 0.6145 time to fit residues: 44.7385 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 : 0.224 ------------------------------------------------------------------------------- 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 199 ASN 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: 3.9990 chunk 38 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 26 optimal weight: 9.9990 chunk 14 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 9 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 35 optimal weight: 4.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3913 r_free = 0.3913 target = 0.177215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.135577 restraints weight = 7738.031| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 1.63 r_work: 0.3161 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.1599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8814 Z= 0.188 Angle : 0.609 6.803 12639 Z= 0.329 Chirality : 0.042 0.207 1493 Planarity : 0.004 0.041 1027 Dihedral : 23.043 176.985 3018 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 2.82 % Allowed : 11.09 % Favored : 86.09 % 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: 0.11 (0.34), residues: 599 helix: 1.33 (0.31), residues: 286 sheet: -0.06 (0.41), residues: 131 loop : -1.85 (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 0.014 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 covalent geometry : bond 0.00410 ( 8814) covalent geometry : angle 0.60893 (12639) hydrogen bonds : bond 0.05148 ( 419) hydrogen bonds : angle 3.49717 ( 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 79 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 64 time to evaluate : 0.202 Fit side-chains REVERT: A 155 GLN cc_start: 0.7640 (OUTLIER) cc_final: 0.6902 (mt0) REVERT: A 218 LEU cc_start: 0.8403 (OUTLIER) cc_final: 0.7763 (mm) REVERT: B 30 GLU cc_start: 0.8417 (OUTLIER) cc_final: 0.8110 (mt-10) REVERT: B 44 GLU cc_start: 0.8363 (OUTLIER) cc_final: 0.8061 (mt-10) outliers start: 15 outliers final: 5 residues processed: 72 average time/residue: 0.6784 time to fit residues: 51.3345 Evaluate side-chains 69 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 60 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 46 MET 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: 0.8980 chunk 67 optimal weight: 5.9990 chunk 39 optimal weight: 1.9990 chunk 55 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 26 optimal weight: 20.0000 chunk 58 optimal weight: 4.9990 chunk 52 optimal weight: 6.9990 chunk 4 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3901 r_free = 0.3901 target = 0.176051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.130063 restraints weight = 7632.288| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 1.10 r_work: 0.3203 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3078 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.1600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 8814 Z= 0.245 Angle : 0.662 6.747 12639 Z= 0.357 Chirality : 0.045 0.216 1493 Planarity : 0.005 0.044 1027 Dihedral : 23.115 177.687 3018 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % 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 : 0.17 % 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: 0.09 (0.34), residues: 599 helix: 1.26 (0.31), residues: 287 sheet: 0.06 (0.43), residues: 124 loop : -1.81 (0.42), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 179 TYR 0.015 0.002 TYR A 351 PHE 0.015 0.003 PHE B 48 TRP 0.014 0.002 TRP B 43 HIS 0.002 0.001 HIS A 278 Details of bonding type rmsd covalent geometry : bond 0.00544 ( 8814) covalent geometry : angle 0.66227 (12639) hydrogen bonds : bond 0.05767 ( 419) hydrogen bonds : angle 3.58522 ( 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 79 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 66 time to evaluate : 0.179 Fit side-chains REVERT: A 155 GLN cc_start: 0.7572 (OUTLIER) cc_final: 0.6837 (mt0) REVERT: B 30 GLU cc_start: 0.8284 (OUTLIER) cc_final: 0.7931 (mt-10) REVERT: B 44 GLU cc_start: 0.8239 (OUTLIER) cc_final: 0.7873 (mt-10) outliers start: 13 outliers final: 7 residues processed: 71 average time/residue: 0.6786 time to fit residues: 50.5984 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 : 0.240 ------------------------------------------------------------------------------- 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 18 optimal weight: 0.6980 chunk 12 optimal weight: 0.9980 chunk 56 optimal weight: 4.9990 chunk 9 optimal weight: 0.7980 chunk 6 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 45 optimal weight: 5.9990 chunk 36 optimal weight: 0.0370 chunk 17 optimal weight: 0.8980 chunk 0 optimal weight: 1.9990 chunk 57 optimal weight: 6.9990 overall best weight: 0.6858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 ASN A 194 HIS B 151 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.181653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.140481 restraints weight = 7686.418| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 1.72 r_work: 0.3208 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.2004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8814 Z= 0.127 Angle : 0.544 6.761 12639 Z= 0.294 Chirality : 0.038 0.197 1493 Planarity : 0.004 0.040 1027 Dihedral : 22.979 178.202 3018 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 1.69 % Allowed : 15.04 % 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: 0.54 (0.35), residues: 599 helix: 1.66 (0.31), residues: 287 sheet: 0.16 (0.42), residues: 131 loop : -1.62 (0.45), residues: 181 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 254 TYR 0.016 0.001 TYR A 351 PHE 0.011 0.002 PHE A 102 TRP 0.011 0.001 TRP B 43 HIS 0.002 0.001 HIS A 303 Details of bonding type rmsd covalent geometry : bond 0.00261 ( 8814) covalent geometry : angle 0.54418 (12639) hydrogen bonds : bond 0.04261 ( 419) hydrogen bonds : angle 3.31802 ( 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 72 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 63 time to evaluate : 0.167 Fit side-chains REVERT: A 218 LEU cc_start: 0.8324 (OUTLIER) cc_final: 0.7789 (mm) REVERT: B 30 GLU cc_start: 0.8097 (OUTLIER) cc_final: 0.7855 (mt-10) outliers start: 9 outliers final: 3 residues processed: 67 average time/residue: 0.5357 time to fit residues: 38.1049 Evaluate side-chains 64 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 59 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 69 THR 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: 4.9990 chunk 35 optimal weight: 4.9990 chunk 2 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 56 optimal weight: 8.9990 chunk 36 optimal weight: 4.9990 chunk 67 optimal weight: 5.9990 chunk 41 optimal weight: 0.0270 chunk 65 optimal weight: 10.0000 chunk 46 optimal weight: 0.9990 overall best weight: 1.3644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3924 r_free = 0.3924 target = 0.178528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.136976 restraints weight = 7753.067| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 1.66 r_work: 0.3171 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3041 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.1896 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= 0.174 Angle : 0.584 6.503 12639 Z= 0.314 Chirality : 0.041 0.204 1493 Planarity : 0.004 0.040 1027 Dihedral : 23.024 177.393 3018 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 2.82 % Allowed : 14.10 % Favored : 83.08 % 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: 0.55 (0.35), residues: 599 helix: 1.67 (0.31), residues: 287 sheet: 0.18 (0.42), residues: 131 loop : -1.65 (0.44), residues: 181 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 179 TYR 0.018 0.002 TYR A 351 PHE 0.011 0.002 PHE A 102 TRP 0.013 0.002 TRP B 43 HIS 0.002 0.001 HIS A 303 Details of bonding type rmsd covalent geometry : bond 0.00378 ( 8814) covalent geometry : angle 0.58428 (12639) hydrogen bonds : bond 0.04874 ( 419) hydrogen bonds : angle 3.40426 ( 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 73 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 58 time to evaluate : 0.240 Fit side-chains REVERT: A 218 LEU cc_start: 0.8361 (OUTLIER) cc_final: 0.7788 (mm) REVERT: A 354 GLU cc_start: 0.7780 (mt-10) cc_final: 0.7511 (pt0) REVERT: A 384 ILE cc_start: 0.5391 (OUTLIER) cc_final: 0.4565 (mm) REVERT: B 30 GLU cc_start: 0.8377 (OUTLIER) cc_final: 0.8112 (mt-10) REVERT: B 44 GLU cc_start: 0.8351 (OUTLIER) cc_final: 0.8044 (mt-10) outliers start: 15 outliers final: 8 residues processed: 67 average time/residue: 0.5570 time to fit residues: 39.6138 Evaluate side-chains 70 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 58 time to evaluate : 0.232 ------------------------------------------------------------------------------- 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 218 LEU Chi-restraints excluded: chain A residue 233 TYR Chi-restraints excluded: chain A residue 351 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 Chi-restraints excluded: chain B residue 199 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 71 optimal weight: 4.9990 chunk 64 optimal weight: 7.9990 chunk 37 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 69 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 62 optimal weight: 10.0000 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 ASN B 151 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.175470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.133364 restraints weight = 7628.916| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 1.60 r_work: 0.3147 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.1758 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= 0.248 Angle : 0.663 6.793 12639 Z= 0.355 Chirality : 0.045 0.216 1493 Planarity : 0.005 0.042 1027 Dihedral : 23.123 177.724 3018 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 3.57 % Allowed : 13.53 % Favored : 82.89 % 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: 0.32 (0.34), residues: 599 helix: 1.51 (0.31), residues: 286 sheet: 0.05 (0.42), residues: 131 loop : -1.76 (0.43), residues: 182 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 0.012 0.002 PHE A 102 TRP 0.013 0.002 TRP B 43 HIS 0.002 0.001 HIS A 278 Details of bonding type rmsd covalent geometry : bond 0.00550 ( 8814) covalent geometry : angle 0.66333 (12639) hydrogen bonds : bond 0.05764 ( 419) hydrogen bonds : angle 3.57321 ( 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 83 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 64 time to evaluate : 0.155 Fit side-chains REVERT: A 354 GLU cc_start: 0.7770 (mt-10) cc_final: 0.7496 (pt0) REVERT: A 384 ILE cc_start: 0.5389 (OUTLIER) cc_final: 0.4598 (mm) REVERT: B 30 GLU cc_start: 0.8374 (OUTLIER) cc_final: 0.8026 (mt-10) REVERT: B 44 GLU cc_start: 0.8340 (OUTLIER) cc_final: 0.8013 (mt-10) outliers start: 19 outliers final: 9 residues processed: 71 average time/residue: 0.5554 time to fit residues: 41.8541 Evaluate side-chains 73 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 61 time to evaluate : 0.202 ------------------------------------------------------------------------------- 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 114 MET Chi-restraints excluded: chain A residue 156 GLU 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 69 THR Chi-restraints excluded: chain B residue 164 SER 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: 3.9990 chunk 60 optimal weight: 3.9990 chunk 57 optimal weight: 9.9990 chunk 21 optimal weight: 0.0980 chunk 71 optimal weight: 3.9990 chunk 28 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 42 optimal weight: 5.9990 chunk 27 optimal weight: 0.8980 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3917 r_free = 0.3917 target = 0.177748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.134442 restraints weight = 7677.510| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 1.01 r_work: 0.3227 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3101 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.1860 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= 0.179 Angle : 0.599 6.602 12639 Z= 0.322 Chirality : 0.041 0.209 1493 Planarity : 0.004 0.041 1027 Dihedral : 23.048 177.679 3018 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 2.63 % Allowed : 15.23 % Favored : 82.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.35), residues: 599 helix: 1.61 (0.31), residues: 287 sheet: 0.10 (0.42), residues: 131 loop : -1.66 (0.44), residues: 181 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 254 TYR 0.017 0.002 TYR A 351 PHE 0.013 0.002 PHE A 102 TRP 0.012 0.002 TRP B 43 HIS 0.002 0.001 HIS B 77 Details of bonding type rmsd covalent geometry : bond 0.00391 ( 8814) covalent geometry : angle 0.59860 (12639) hydrogen bonds : bond 0.04892 ( 419) hydrogen bonds : angle 3.45118 ( 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 76 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 62 time to evaluate : 0.313 Fit side-chains REVERT: A 218 LEU cc_start: 0.8393 (OUTLIER) cc_final: 0.7824 (mm) REVERT: A 323 MET cc_start: 0.8592 (ptt) cc_final: 0.8281 (ptt) REVERT: A 354 GLU cc_start: 0.7615 (mt-10) cc_final: 0.7408 (pt0) REVERT: A 384 ILE cc_start: 0.5342 (OUTLIER) cc_final: 0.4535 (mm) REVERT: B 30 GLU cc_start: 0.8281 (OUTLIER) cc_final: 0.7994 (mt-10) REVERT: B 44 GLU cc_start: 0.8234 (OUTLIER) cc_final: 0.7905 (mt-10) outliers start: 14 outliers final: 10 residues processed: 66 average time/residue: 0.5524 time to fit residues: 38.7707 Evaluate side-chains 74 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 60 time to evaluate : 0.193 ------------------------------------------------------------------------------- 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 156 GLU 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 Chi-restraints excluded: chain B residue 132 ILE 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: 10.0000 chunk 1 optimal weight: 0.3980 chunk 0 optimal weight: 0.9990 chunk 67 optimal weight: 5.9990 chunk 53 optimal weight: 0.5980 chunk 45 optimal weight: 5.9990 chunk 16 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.178160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.136587 restraints weight = 7684.645| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 1.63 r_work: 0.3175 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3045 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.1884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8814 Z= 0.150 Angle : 0.585 6.639 12639 Z= 0.316 Chirality : 0.040 0.206 1493 Planarity : 0.004 0.041 1027 Dihedral : 23.051 177.804 3018 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 2.26 % Allowed : 15.60 % Favored : 82.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.35), residues: 599 helix: 1.69 (0.31), residues: 287 sheet: 0.07 (0.42), residues: 131 loop : -1.64 (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 A 236 TRP 0.012 0.002 TRP B 43 HIS 0.002 0.001 HIS A 72 Details of bonding type rmsd covalent geometry : bond 0.00318 ( 8814) covalent geometry : angle 0.58522 (12639) hydrogen bonds : bond 0.04739 ( 419) hydrogen bonds : angle 3.44501 ( 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 73 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 61 time to evaluate : 0.203 Fit side-chains REVERT: A 218 LEU cc_start: 0.8341 (OUTLIER) cc_final: 0.7769 (mm) REVERT: A 323 MET cc_start: 0.8632 (ptt) cc_final: 0.8310 (ptt) REVERT: A 354 GLU cc_start: 0.7770 (mt-10) cc_final: 0.7504 (pt0) REVERT: A 384 ILE cc_start: 0.5333 (OUTLIER) cc_final: 0.4494 (mm) REVERT: B 30 GLU cc_start: 0.8397 (OUTLIER) cc_final: 0.8125 (mt-10) REVERT: B 44 GLU cc_start: 0.8361 (OUTLIER) cc_final: 0.8054 (mt-10) outliers start: 12 outliers final: 7 residues processed: 64 average time/residue: 0.5543 time to fit residues: 37.6624 Evaluate side-chains 72 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 61 time to evaluate : 0.235 ------------------------------------------------------------------------------- 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 46 MET Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 132 ILE 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: 0.7980 chunk 17 optimal weight: 0.7980 chunk 71 optimal weight: 4.9990 chunk 64 optimal weight: 6.9990 chunk 26 optimal weight: 0.4980 chunk 57 optimal weight: 8.9990 chunk 6 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 35 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.178347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.136902 restraints weight = 7690.838| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 1.66 r_work: 0.3174 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.1897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8814 Z= 0.154 Angle : 0.583 6.621 12639 Z= 0.315 Chirality : 0.040 0.206 1493 Planarity : 0.004 0.041 1027 Dihedral : 23.050 177.715 3018 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 2.44 % Allowed : 15.60 % Favored : 81.95 % 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: 0.58 (0.35), residues: 599 helix: 1.74 (0.31), residues: 287 sheet: 0.08 (0.42), residues: 131 loop : -1.61 (0.45), residues: 181 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 254 TYR 0.019 0.001 TYR A 351 PHE 0.011 0.002 PHE A 102 TRP 0.013 0.002 TRP B 43 HIS 0.001 0.000 HIS A 77 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 8814) covalent geometry : angle 0.58295 (12639) hydrogen bonds : bond 0.04717 ( 419) hydrogen bonds : angle 3.43068 ( 1059) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2636.31 seconds wall clock time: 45 minutes 37.30 seconds (2737.30 seconds total)