Starting phenix.real_space_refine on Sat Jun 7 04:08:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wju_32548/06_2025/7wju_32548_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wju_32548/06_2025/7wju_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_32548/06_2025/7wju_32548.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wju_32548/06_2025/7wju_32548.map" model { file = "/net/cci-nas-00/data/ceres_data/7wju_32548/06_2025/7wju_32548_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wju_32548/06_2025/7wju_32548_neut.cif" } resolution = 2.69 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 5.50, per 1000 atoms: 0.66 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: 2.16 Conformation dependent library (CDL) restraints added in 589.7 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: 3.57 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: 3.19 Time building geometry restraints manager: 2.57 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: 0.880 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: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 25.190 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 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:13.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.610 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.017 0.003 TRP B 43 HIS 0.008 0.001 HIS A 303 PHE 0.015 0.003 PHE B 48 TYR 0.030 0.003 TYR A 233 ARG 0.004 0.000 ARG A 371 Details of bonding type rmsd hydrogen bonds : bond 0.13787 ( 419) hydrogen bonds : angle 5.37277 ( 1059) covalent geometry : bond 0.00749 ( 8814) covalent geometry : angle 0.98763 (12639) *********************** 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 : 0.803 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 92 average time/residue: 1.6369 time to fit residues: 157.9696 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 : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 62 optimal weight: 8.9990 chunk 56 optimal weight: 0.8980 chunk 31 optimal weight: 3.9990 chunk 19 optimal weight: 0.7980 chunk 37 optimal weight: 0.9990 chunk 29 optimal weight: 0.7980 chunk 58 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 35 optimal weight: 4.9990 chunk 43 optimal weight: 0.9980 chunk 67 optimal weight: 3.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 = 0.3936 r_free = 0.3936 target = 0.179231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.136888 restraints weight = 7705.302| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 1.01 r_work: 0.3241 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3119 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.1377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8814 Z= 0.146 Angle : 0.586 6.030 12639 Z= 0.323 Chirality : 0.041 0.208 1493 Planarity : 0.004 0.041 1027 Dihedral : 23.091 177.086 3018 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.17 % Favored : 95.66 % Rotamer: Outliers : 2.07 % Allowed : 11.28 % Favored : 86.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.32), residues: 599 helix: 0.27 (0.29), residues: 291 sheet: -0.34 (0.42), residues: 130 loop : -2.21 (0.40), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 43 HIS 0.002 0.001 HIS A 77 PHE 0.013 0.002 PHE B 48 TYR 0.021 0.001 TYR A 351 ARG 0.002 0.000 ARG A 179 Details of bonding type rmsd hydrogen bonds : bond 0.04785 ( 419) hydrogen bonds : angle 3.59505 ( 1059) covalent geometry : bond 0.00299 ( 8814) covalent geometry : angle 0.58638 (12639) *********************** 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: 11 poor density : 69 time to evaluate : 0.733 Fit side-chains REVERT: A 155 GLN cc_start: 0.7765 (OUTLIER) cc_final: 0.7002 (mt0) REVERT: A 218 LEU cc_start: 0.8462 (OUTLIER) cc_final: 0.7914 (mm) REVERT: B 30 GLU cc_start: 0.8324 (OUTLIER) cc_final: 0.8089 (mt-10) REVERT: B 85 ARG cc_start: 0.8228 (mtt90) cc_final: 0.8014 (mtt90) REVERT: B 137 MET cc_start: 0.5328 (mpp) cc_final: 0.4966 (mpp) outliers start: 11 outliers final: 3 residues processed: 75 average time/residue: 1.4154 time to fit residues: 112.5825 Evaluate side-chains 66 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 60 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 199 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 24 optimal weight: 4.9990 chunk 8 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 67 optimal weight: 5.9990 chunk 5 optimal weight: 0.0870 chunk 27 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 70 optimal weight: 10.0000 chunk 62 optimal weight: 8.9990 chunk 71 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 overall best weight: 2.4166 ------------------------------------------------------------------------------- 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 151 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.174816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.129008 restraints weight = 7674.411| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 1.11 r_work: 0.3199 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3076 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.1362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 8814 Z= 0.268 Angle : 0.697 7.950 12639 Z= 0.376 Chirality : 0.047 0.220 1493 Planarity : 0.005 0.045 1027 Dihedral : 23.188 177.853 3018 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 2.26 % Allowed : 12.03 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.33), residues: 599 helix: 0.91 (0.31), residues: 284 sheet: -0.14 (0.42), residues: 124 loop : -2.16 (0.39), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 43 HIS 0.003 0.001 HIS A 278 PHE 0.018 0.003 PHE B 48 TYR 0.018 0.002 TYR A 351 ARG 0.004 0.001 ARG A 179 Details of bonding type rmsd hydrogen bonds : bond 0.06150 ( 419) hydrogen bonds : angle 3.70475 ( 1059) covalent geometry : bond 0.00595 ( 8814) covalent geometry : angle 0.69654 (12639) *********************** 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 80 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 68 time to evaluate : 0.757 Fit side-chains REVERT: A 155 GLN cc_start: 0.7609 (OUTLIER) cc_final: 0.6871 (mt0) REVERT: A 218 LEU cc_start: 0.8573 (OUTLIER) cc_final: 0.7916 (mm) REVERT: A 222 MET cc_start: 0.8866 (ttp) cc_final: 0.8654 (ttp) REVERT: A 254 ARG cc_start: 0.7189 (mtt-85) cc_final: 0.6976 (mtm-85) REVERT: B 30 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.7994 (mt-10) REVERT: B 44 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.7887 (mt-10) outliers start: 12 outliers final: 3 residues processed: 74 average time/residue: 1.4634 time to fit residues: 114.4984 Evaluate side-chains 73 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 66 time to evaluate : 0.705 ------------------------------------------------------------------------------- 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 69 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 25 optimal weight: 0.9980 chunk 52 optimal weight: 6.9990 chunk 14 optimal weight: 0.1980 chunk 56 optimal weight: 4.9990 chunk 58 optimal weight: 4.9990 chunk 62 optimal weight: 10.0000 chunk 11 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 chunk 5 optimal weight: 0.7980 chunk 53 optimal weight: 5.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 = 0.3942 r_free = 0.3942 target = 0.179861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.138398 restraints weight = 7649.422| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 1.57 r_work: 0.3193 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3065 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.1691 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= 0.144 Angle : 0.572 6.719 12639 Z= 0.311 Chirality : 0.040 0.202 1493 Planarity : 0.004 0.041 1027 Dihedral : 23.025 176.960 3018 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 1.50 % Allowed : 13.72 % Favored : 84.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.34), residues: 599 helix: 1.31 (0.31), residues: 287 sheet: -0.09 (0.41), residues: 131 loop : -1.80 (0.44), residues: 181 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 43 HIS 0.003 0.001 HIS A 303 PHE 0.012 0.002 PHE B 48 TYR 0.018 0.001 TYR A 351 ARG 0.002 0.000 ARG A 179 Details of bonding type rmsd hydrogen bonds : bond 0.04567 ( 419) hydrogen bonds : angle 3.43399 ( 1059) covalent geometry : bond 0.00304 ( 8814) covalent geometry : angle 0.57223 (12639) *********************** 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 77 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 69 time to evaluate : 1.315 Fit side-chains REVERT: A 218 LEU cc_start: 0.8381 (OUTLIER) cc_final: 0.7807 (mm) REVERT: B 30 GLU cc_start: 0.8381 (OUTLIER) cc_final: 0.8158 (mt-10) outliers start: 8 outliers final: 3 residues processed: 74 average time/residue: 1.8121 time to fit residues: 141.9704 Evaluate side-chains 66 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 61 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ILE 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 10 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 19 optimal weight: 0.0980 chunk 63 optimal weight: 10.0000 chunk 27 optimal weight: 0.0070 chunk 21 optimal weight: 5.9990 chunk 12 optimal weight: 0.9980 chunk 43 optimal weight: 0.6980 chunk 51 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 overall best weight: 0.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 ASN A 93 GLN A 194 HIS B 40 GLN B 131 ASN B 151 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.183289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.142472 restraints weight = 7618.969| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 1.59 r_work: 0.3240 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3112 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.2031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 8814 Z= 0.117 Angle : 0.534 6.836 12639 Z= 0.288 Chirality : 0.038 0.193 1493 Planarity : 0.003 0.036 1027 Dihedral : 22.940 177.861 3018 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 1.32 % Allowed : 14.66 % Favored : 84.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.35), residues: 599 helix: 1.68 (0.31), residues: 287 sheet: 0.07 (0.41), residues: 131 loop : -1.61 (0.45), residues: 181 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 43 HIS 0.002 0.001 HIS A 303 PHE 0.011 0.001 PHE B 48 TYR 0.016 0.001 TYR A 351 ARG 0.003 0.000 ARG B 85 Details of bonding type rmsd hydrogen bonds : bond 0.04140 ( 419) hydrogen bonds : angle 3.24209 ( 1059) covalent geometry : bond 0.00240 ( 8814) covalent geometry : angle 0.53431 (12639) *********************** 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: 7 poor density : 67 time to evaluate : 0.704 Fit side-chains REVERT: A 218 LEU cc_start: 0.8299 (OUTLIER) cc_final: 0.7768 (mm) REVERT: B 30 GLU cc_start: 0.8426 (OUTLIER) cc_final: 0.8192 (mt-10) outliers start: 7 outliers final: 1 residues processed: 73 average time/residue: 1.4902 time to fit residues: 114.6669 Evaluate side-chains 69 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 66 time to evaluate : 0.657 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 49 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 61 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 59 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 64 optimal weight: 7.9990 chunk 41 optimal weight: 0.8980 chunk 30 optimal weight: 8.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- 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 151 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.176719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.134832 restraints weight = 7656.613| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 1.61 r_work: 0.3149 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3020 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.1743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 8814 Z= 0.224 Angle : 0.631 6.481 12639 Z= 0.339 Chirality : 0.043 0.210 1493 Planarity : 0.004 0.040 1027 Dihedral : 23.052 177.301 3018 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 2.44 % Allowed : 14.47 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.34), residues: 599 helix: 1.62 (0.31), residues: 286 sheet: 0.22 (0.42), residues: 124 loop : -1.75 (0.42), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 43 HIS 0.002 0.001 HIS A 194 PHE 0.012 0.002 PHE A 102 TYR 0.017 0.002 TYR A 351 ARG 0.003 0.000 ARG A 179 Details of bonding type rmsd hydrogen bonds : bond 0.05445 ( 419) hydrogen bonds : angle 3.47932 ( 1059) covalent geometry : bond 0.00493 ( 8814) covalent geometry : angle 0.63115 (12639) *********************** 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 84 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 71 time to evaluate : 0.737 Fit side-chains REVERT: A 218 LEU cc_start: 0.8434 (OUTLIER) cc_final: 0.7803 (mm) REVERT: B 25 ARG cc_start: 0.8034 (OUTLIER) cc_final: 0.7002 (mpp-170) REVERT: B 30 GLU cc_start: 0.8459 (OUTLIER) cc_final: 0.8158 (mt-10) REVERT: B 44 GLU cc_start: 0.8375 (OUTLIER) cc_final: 0.8077 (mt-10) outliers start: 13 outliers final: 6 residues processed: 77 average time/residue: 1.5920 time to fit residues: 129.0964 Evaluate side-chains 75 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 65 time to evaluate : 0.767 ------------------------------------------------------------------------------- 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 384 ILE Chi-restraints excluded: chain B residue 25 ARG 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 4 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 20 optimal weight: 0.5980 chunk 48 optimal weight: 3.9990 chunk 27 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 68 optimal weight: 6.9990 chunk 71 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 ASN B 131 ASN B 151 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.177173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.131222 restraints weight = 7627.789| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 1.08 r_work: 0.3224 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3097 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.1780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8814 Z= 0.186 Angle : 0.607 6.451 12639 Z= 0.327 Chirality : 0.042 0.208 1493 Planarity : 0.004 0.040 1027 Dihedral : 23.048 177.325 3018 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 3.01 % Allowed : 14.85 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.34), residues: 599 helix: 1.64 (0.31), residues: 286 sheet: 0.13 (0.42), residues: 131 loop : -1.67 (0.44), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 43 HIS 0.002 0.001 HIS A 278 PHE 0.011 0.002 PHE A 102 TYR 0.017 0.002 TYR A 351 ARG 0.004 0.000 ARG B 6 Details of bonding type rmsd hydrogen bonds : bond 0.05164 ( 419) hydrogen bonds : angle 3.45779 ( 1059) covalent geometry : bond 0.00404 ( 8814) covalent geometry : angle 0.60661 (12639) *********************** 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 82 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 66 time to evaluate : 0.673 Fit side-chains REVERT: A 218 LEU cc_start: 0.8432 (OUTLIER) cc_final: 0.7852 (mm) REVERT: B 25 ARG cc_start: 0.7941 (OUTLIER) cc_final: 0.6896 (mpp-170) REVERT: B 30 GLU cc_start: 0.8308 (OUTLIER) cc_final: 0.7985 (mt-10) REVERT: B 44 GLU cc_start: 0.8223 (OUTLIER) cc_final: 0.7905 (mt-10) outliers start: 16 outliers final: 9 residues processed: 73 average time/residue: 1.4601 time to fit residues: 112.8427 Evaluate side-chains 78 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 65 time to evaluate : 1.107 ------------------------------------------------------------------------------- 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 218 LEU Chi-restraints excluded: chain A residue 233 TYR Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain B residue 25 ARG 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 199 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 52 optimal weight: 7.9990 chunk 58 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 70 optimal weight: 9.9990 chunk 27 optimal weight: 0.0980 chunk 1 optimal weight: 0.1980 chunk 33 optimal weight: 2.9990 chunk 67 optimal weight: 5.9990 chunk 40 optimal weight: 5.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- 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 = 0.3924 r_free = 0.3924 target = 0.178192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.136339 restraints weight = 7682.915| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 1.53 r_work: 0.3174 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3046 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.1827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8814 Z= 0.182 Angle : 0.601 6.505 12639 Z= 0.324 Chirality : 0.041 0.207 1493 Planarity : 0.004 0.040 1027 Dihedral : 23.027 177.346 3018 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 2.44 % Allowed : 15.98 % Favored : 81.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.34), residues: 599 helix: 1.70 (0.31), residues: 286 sheet: 0.16 (0.42), residues: 131 loop : -1.68 (0.44), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 43 HIS 0.002 0.001 HIS B 194 PHE 0.011 0.002 PHE A 102 TYR 0.017 0.002 TYR A 351 ARG 0.002 0.000 ARG A 179 Details of bonding type rmsd hydrogen bonds : bond 0.05010 ( 419) hydrogen bonds : angle 3.42693 ( 1059) covalent geometry : bond 0.00396 ( 8814) covalent geometry : angle 0.60119 (12639) *********************** 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 79 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 66 time to evaluate : 1.822 Fit side-chains REVERT: A 218 LEU cc_start: 0.8413 (OUTLIER) cc_final: 0.7831 (mm) REVERT: B 25 ARG cc_start: 0.8048 (OUTLIER) cc_final: 0.6996 (mpp-170) REVERT: B 30 GLU cc_start: 0.8431 (OUTLIER) cc_final: 0.8131 (mt-10) REVERT: B 44 GLU cc_start: 0.8348 (OUTLIER) cc_final: 0.8054 (mt-10) outliers start: 13 outliers final: 8 residues processed: 72 average time/residue: 1.6014 time to fit residues: 122.2472 Evaluate side-chains 74 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 62 time to evaluate : 0.688 ------------------------------------------------------------------------------- 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 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 25 ARG Chi-restraints excluded: chain B residue 30 GLU Chi-restraints excluded: chain B residue 44 GLU Chi-restraints excluded: chain B residue 50 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 43 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 46 optimal weight: 6.9990 chunk 13 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 40 optimal weight: 6.9990 chunk 59 optimal weight: 1.9990 chunk 5 optimal weight: 0.0060 overall best weight: 1.8004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 ASN B 131 ASN B 151 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.177258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.135762 restraints weight = 7725.833| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 1.71 r_work: 0.3142 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.1809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 8814 Z= 0.212 Angle : 0.627 6.437 12639 Z= 0.337 Chirality : 0.043 0.211 1493 Planarity : 0.004 0.041 1027 Dihedral : 23.056 177.467 3018 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 2.63 % Allowed : 15.60 % Favored : 81.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.34), residues: 599 helix: 1.62 (0.31), residues: 286 sheet: 0.19 (0.42), residues: 131 loop : -1.72 (0.44), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 43 HIS 0.002 0.001 HIS A 72 PHE 0.012 0.002 PHE A 102 TYR 0.016 0.002 TYR A 351 ARG 0.003 0.000 ARG A 179 Details of bonding type rmsd hydrogen bonds : bond 0.05347 ( 419) hydrogen bonds : angle 3.48008 ( 1059) covalent geometry : bond 0.00466 ( 8814) covalent geometry : angle 0.62698 (12639) *********************** 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 79 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 65 time to evaluate : 0.654 Fit side-chains REVERT: A 323 MET cc_start: 0.8530 (ptt) cc_final: 0.8256 (ptt) REVERT: B 25 ARG cc_start: 0.7967 (OUTLIER) cc_final: 0.6903 (mpp-170) REVERT: B 30 GLU cc_start: 0.8225 (OUTLIER) cc_final: 0.7892 (mt-10) REVERT: B 44 GLU cc_start: 0.8140 (OUTLIER) cc_final: 0.7820 (mt-10) outliers start: 14 outliers final: 8 residues processed: 70 average time/residue: 1.3642 time to fit residues: 101.0016 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 : 0.632 ------------------------------------------------------------------------------- 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 25 ARG 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 22 optimal weight: 2.9990 chunk 70 optimal weight: 10.0000 chunk 5 optimal weight: 5.9990 chunk 64 optimal weight: 7.9990 chunk 47 optimal weight: 4.9990 chunk 19 optimal weight: 0.9980 chunk 41 optimal weight: 0.0870 chunk 57 optimal weight: 6.9990 chunk 65 optimal weight: 9.9990 chunk 34 optimal weight: 2.9990 chunk 1 optimal weight: 0.7980 overall best weight: 1.5762 ------------------------------------------------------------------------------- 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 = 0.3916 r_free = 0.3916 target = 0.177493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.135612 restraints weight = 7644.590| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 1.57 r_work: 0.3156 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.1823 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= 0.193 Angle : 0.616 6.467 12639 Z= 0.331 Chirality : 0.042 0.210 1493 Planarity : 0.004 0.041 1027 Dihedral : 23.053 177.564 3018 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 2.26 % Allowed : 15.98 % Favored : 81.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.34), residues: 599 helix: 1.65 (0.31), residues: 286 sheet: 0.22 (0.42), residues: 131 loop : -1.68 (0.44), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 43 HIS 0.002 0.001 HIS A 278 PHE 0.011 0.002 PHE A 102 TYR 0.017 0.002 TYR A 351 ARG 0.003 0.000 ARG A 179 Details of bonding type rmsd hydrogen bonds : bond 0.05162 ( 419) hydrogen bonds : angle 3.47363 ( 1059) covalent geometry : bond 0.00421 ( 8814) covalent geometry : angle 0.61571 (12639) ********************** 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 76 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 64 time to evaluate : 0.717 Fit side-chains REVERT: A 218 LEU cc_start: 0.8344 (tt) cc_final: 0.7789 (mm) REVERT: A 323 MET cc_start: 0.8529 (ptt) cc_final: 0.8234 (ptt) REVERT: A 384 ILE cc_start: 0.5303 (OUTLIER) cc_final: 0.4562 (mm) REVERT: B 25 ARG cc_start: 0.7965 (OUTLIER) cc_final: 0.6916 (mpp-170) REVERT: B 30 GLU cc_start: 0.8219 (OUTLIER) cc_final: 0.7887 (mt-10) REVERT: B 44 GLU cc_start: 0.8133 (OUTLIER) cc_final: 0.7809 (mt-10) outliers start: 12 outliers final: 7 residues processed: 69 average time/residue: 1.5732 time to fit residues: 114.9430 Evaluate side-chains 75 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 64 time to evaluate : 0.622 ------------------------------------------------------------------------------- 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 25 ARG 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 17 optimal weight: 0.8980 chunk 45 optimal weight: 0.6980 chunk 38 optimal weight: 8.9990 chunk 32 optimal weight: 3.9990 chunk 15 optimal weight: 0.9990 chunk 53 optimal weight: 8.9990 chunk 2 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 40 optimal weight: 5.9990 chunk 0 optimal weight: 1.9990 chunk 64 optimal weight: 7.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- 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 = 0.3908 r_free = 0.3908 target = 0.176760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.135137 restraints weight = 7748.287| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 1.62 r_work: 0.3149 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.1830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8814 Z= 0.205 Angle : 0.621 6.441 12639 Z= 0.334 Chirality : 0.042 0.211 1493 Planarity : 0.004 0.041 1027 Dihedral : 23.053 177.636 3018 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 2.44 % Allowed : 15.79 % Favored : 81.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.34), residues: 599 helix: 1.64 (0.31), residues: 286 sheet: 0.25 (0.43), residues: 131 loop : -1.70 (0.44), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 43 HIS 0.002 0.001 HIS A 77 PHE 0.012 0.002 PHE A 102 TYR 0.016 0.002 TYR A 351 ARG 0.003 0.000 ARG A 179 Details of bonding type rmsd hydrogen bonds : bond 0.05221 ( 419) hydrogen bonds : angle 3.47521 ( 1059) covalent geometry : bond 0.00449 ( 8814) covalent geometry : angle 0.62139 (12639) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6894.00 seconds wall clock time: 123 minutes 37.40 seconds (7417.40 seconds total)