Starting phenix.real_space_refine on Wed Aug 5 10:04:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jg3_61449/08_2026/9jg3_61449.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jg3_61449/08_2026/9jg3_61449.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9jg3_61449/08_2026/9jg3_61449.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jg3_61449/08_2026/9jg3_61449.map" model { file = "/net/cci-nas-00/data/ceres_data/9jg3_61449/08_2026/9jg3_61449.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jg3_61449/08_2026/9jg3_61449.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.026 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 174 5.49 5 S 17 5.16 5 C 5161 2.51 5 N 1649 2.21 5 O 2187 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9188 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 579, 4699 Classifications: {'peptide': 579} Link IDs: {'PTRANS': 22, 'TRANS': 556} Chain breaks: 1 Chain: "B" Number of atoms: 2938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 2938 Classifications: {'RNA': 138} Modifications used: {'rna2p_pur': 8, 'rna2p_pyr': 6, 'rna3p_pur': 64, 'rna3p_pyr': 60} Link IDs: {'rna2p': 14, 'rna3p': 123} Chain breaks: 3 Chain: "C" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 546 Classifications: {'DNA': 26} Link IDs: {'rna3p': 25} Chain: "D" Number of atoms: 203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 203 Classifications: {'DNA': 10} Link IDs: {'rna3p': 9} Chain: "E" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 802 Classifications: {'peptide': 105} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 99} Time building chain proxies: 2.22, per 1000 atoms: 0.24 Number of scatterers: 9188 At special positions: 0 Unit cell: (105.664, 105.664, 124.8, 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 17 16.00 P 174 15.00 O 2187 8.00 N 1649 7.00 C 5161 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 550 " - pdb=" SG CYS A 567 " distance=2.03 Simple disulfide: pdb=" SG CYS E 33 " - pdb=" SG CYS E 36 " distance=2.04 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: 0.88 Conformation dependent library (CDL) restraints added in 151.8 milliseconds 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1286 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 7 sheets defined 48.8% alpha, 14.3% beta 68 base pairs and 98 stacking pairs defined. Time for finding SS restraints: 1.29 Creating SS restraints... Processing helix chain 'A' and resid 11 through 65 removed outlier: 4.760A pdb=" N CYS A 41 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N VAL A 42 " --> pdb=" O HIS A 38 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N THR A 43 " --> pdb=" O ASN A 39 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ALA A 46 " --> pdb=" O VAL A 42 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU A 65 " --> pdb=" O LYS A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 79 removed outlier: 3.606A pdb=" N GLN A 71 " --> pdb=" O PRO A 67 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N LEU A 72 " --> pdb=" O GLU A 68 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N TYR A 77 " --> pdb=" O VAL A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 96 removed outlier: 3.578A pdb=" N LEU A 92 " --> pdb=" O LYS A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 101 Processing helix chain 'A' and resid 182 through 186 removed outlier: 3.855A pdb=" N PHE A 185 " --> pdb=" O GLY A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 197 Processing helix chain 'A' and resid 198 through 209 Processing helix chain 'A' and resid 217 through 237 removed outlier: 3.633A pdb=" N ILE A 221 " --> pdb=" O SER A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 295 removed outlier: 3.501A pdb=" N ASN A 295 " --> pdb=" O VAL A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 332 removed outlier: 3.521A pdb=" N LYS A 327 " --> pdb=" O LEU A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 342 Processing helix chain 'A' and resid 345 through 365 removed outlier: 3.521A pdb=" N GLU A 349 " --> pdb=" O SER A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 428 removed outlier: 4.056A pdb=" N ARG A 401 " --> pdb=" O LEU A 397 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLY A 428 " --> pdb=" O TRP A 424 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 472 Processing helix chain 'A' and resid 480 through 485 removed outlier: 4.052A pdb=" N ASN A 483 " --> pdb=" O THR A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 511 through 517 removed outlier: 3.723A pdb=" N GLN A 517 " --> pdb=" O TRP A 513 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 535 Processing helix chain 'A' and resid 581 through 593 Processing helix chain 'E' and resid 12 through 19 Processing helix chain 'E' and resid 33 through 50 removed outlier: 3.570A pdb=" N LYS E 37 " --> pdb=" O CYS E 33 " (cutoff:3.500A) Proline residue: E 41 - end of helix Processing helix chain 'E' and resid 66 through 71 removed outlier: 3.808A pdb=" N LYS E 70 " --> pdb=" O GLY E 66 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N TYR E 71 " --> pdb=" O THR E 67 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 66 through 71' Processing helix chain 'E' and resid 96 through 108 Processing sheet with id=AA1, first strand: chain 'A' and resid 257 through 260 removed outlier: 6.607A pdb=" N VAL A 318 " --> pdb=" O ARG A 302 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N TYR A 304 " --> pdb=" O ASN A 316 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N ASN A 316 " --> pdb=" O TYR A 304 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N LEU A 306 " --> pdb=" O TYR A 314 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N TYR A 314 " --> pdb=" O LEU A 306 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N GLN A 308 " --> pdb=" O GLY A 312 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N GLY A 312 " --> pdb=" O GLN A 308 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N TYR A 313 " --> pdb=" O ILE A 8 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N THR A 284 " --> pdb=" O LYS A 9 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 127 through 128 Processing sheet with id=AA3, first strand: chain 'A' and resid 130 through 131 Processing sheet with id=AA4, first strand: chain 'A' and resid 135 through 148 removed outlier: 7.781A pdb=" N ASN A 141 " --> pdb=" O VAL A 155 " (cutoff:3.500A) removed outlier: 9.586A pdb=" N VAL A 155 " --> pdb=" O ASN A 141 " (cutoff:3.500A) removed outlier: 8.476A pdb=" N ASN A 143 " --> pdb=" O ILE A 153 " (cutoff:3.500A) removed outlier: 9.331A pdb=" N ILE A 153 " --> pdb=" O ASN A 143 " (cutoff:3.500A) removed outlier: 8.650A pdb=" N GLY A 151 " --> pdb=" O PRO A 145 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 392 through 393 removed outlier: 3.957A pdb=" N VAL A 385 " --> pdb=" O PHE A 393 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ILE A 475 " --> pdb=" O HIS A 539 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 564 through 565 Processing sheet with id=AA7, first strand: chain 'E' and resid 6 through 7 removed outlier: 6.626A pdb=" N ILE E 6 " --> pdb=" O LYS E 58 " (cutoff:3.500A) removed outlier: 8.131A pdb=" N ASN E 60 " --> pdb=" O ILE E 6 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N ALA E 23 " --> pdb=" O THR E 55 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N ALA E 57 " --> pdb=" O ALA E 23 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N LEU E 25 " --> pdb=" O ALA E 57 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N LEU E 59 " --> pdb=" O LEU E 25 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ASP E 27 " --> pdb=" O LEU E 59 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N THR E 78 " --> pdb=" O PHE E 28 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N LEU E 79 " --> pdb=" O THR E 90 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N THR E 90 " --> pdb=" O LEU E 79 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N LEU E 81 " --> pdb=" O ALA E 88 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLU E 86 " --> pdb=" O LYS E 83 " (cutoff:3.500A) 272 hydrogen bonds defined for protein. 765 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 170 hydrogen bonds 332 hydrogen bond angles 0 basepair planarities 68 basepair parallelities 98 stacking parallelities Total time for adding SS restraints: 1.30 Time building geometry restraints manager: 0.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2299 1.33 - 1.46: 2996 1.46 - 1.58: 4078 1.58 - 1.70: 342 1.70 - 1.82: 22 Bond restraints: 9737 Sorted by residual: bond pdb=" C1' DT D 10 " pdb=" N1 DT D 10 " ideal model delta sigma weight residual 1.468 1.521 -0.053 1.40e-02 5.10e+03 1.42e+01 bond pdb=" C3' DG C 25 " pdb=" O3' DG C 25 " ideal model delta sigma weight residual 1.435 1.388 0.047 1.30e-02 5.92e+03 1.31e+01 bond pdb=" C5 DG C 25 " pdb=" C6 DG C 25 " ideal model delta sigma weight residual 1.419 1.387 0.032 1.00e-02 1.00e+04 1.05e+01 bond pdb=" C8 DG C 25 " pdb=" N7 DG C 25 " ideal model delta sigma weight residual 1.305 1.287 0.018 6.00e-03 2.78e+04 8.78e+00 bond pdb=" C3' DA C 15 " pdb=" O3' DA C 15 " ideal model delta sigma weight residual 1.435 1.398 0.037 1.30e-02 5.92e+03 8.07e+00 ... (remaining 9732 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.04: 12374 1.04 - 2.09: 1181 2.09 - 3.13: 360 3.13 - 4.17: 53 4.17 - 5.22: 4 Bond angle restraints: 13972 Sorted by residual: angle pdb=" N3 DT D 8 " pdb=" C4 DT D 8 " pdb=" O4 DT D 8 " ideal model delta sigma weight residual 119.90 122.57 -2.67 6.00e-01 2.78e+00 1.98e+01 angle pdb=" N3 DT D 1 " pdb=" C4 DT D 1 " pdb=" O4 DT D 1 " ideal model delta sigma weight residual 119.90 122.50 -2.60 6.00e-01 2.78e+00 1.88e+01 angle pdb=" O4 DT D 1 " pdb=" C4 DT D 1 " pdb=" C5 DT D 1 " ideal model delta sigma weight residual 124.90 121.89 3.01 7.00e-01 2.04e+00 1.85e+01 angle pdb=" N3 DT C 24 " pdb=" C4 DT C 24 " pdb=" O4 DT C 24 " ideal model delta sigma weight residual 119.90 122.46 -2.56 6.00e-01 2.78e+00 1.83e+01 angle pdb=" O5' U B 174 " pdb=" C5' U B 174 " pdb=" C4' U B 174 " ideal model delta sigma weight residual 109.40 112.82 -3.42 8.00e-01 1.56e+00 1.82e+01 ... (remaining 13967 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.89: 5384 30.89 - 61.78: 452 61.78 - 92.67: 116 92.67 - 123.57: 1 123.57 - 154.46: 2 Dihedral angle restraints: 5955 sinusoidal: 3970 harmonic: 1985 Sorted by residual: dihedral pdb=" CA PHE E 28 " pdb=" C PHE E 28 " pdb=" N TRP E 29 " pdb=" CA TRP E 29 " ideal model delta harmonic sigma weight residual -180.00 -155.78 -24.22 0 5.00e+00 4.00e-02 2.35e+01 dihedral pdb=" CA LEU A 65 " pdb=" C LEU A 65 " pdb=" N LYS A 66 " pdb=" CA LYS A 66 " ideal model delta harmonic sigma weight residual -180.00 -160.31 -19.69 0 5.00e+00 4.00e-02 1.55e+01 dihedral pdb=" O4' U B 174 " pdb=" C1' U B 174 " pdb=" N1 U B 174 " pdb=" C2 U B 174 " ideal model delta sinusoidal sigma weight residual -128.00 -71.35 -56.65 1 1.70e+01 3.46e-03 1.50e+01 ... (remaining 5952 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1212 0.047 - 0.093: 273 0.093 - 0.140: 150 0.140 - 0.187: 30 0.187 - 0.234: 2 Chirality restraints: 1667 Sorted by residual: chirality pdb=" C3' DA C 15 " pdb=" C4' DA C 15 " pdb=" O3' DA C 15 " pdb=" C2' DA C 15 " both_signs ideal model delta sigma weight residual False -2.73 -2.50 -0.23 2.00e-01 2.50e+01 1.36e+00 chirality pdb=" C3' DG C 25 " pdb=" C4' DG C 25 " pdb=" O3' DG C 25 " pdb=" C2' DG C 25 " both_signs ideal model delta sigma weight residual False -2.73 -2.53 -0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" CG LEU A 449 " pdb=" CB LEU A 449 " pdb=" CD1 LEU A 449 " pdb=" CD2 LEU A 449 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 8.63e-01 ... (remaining 1664 not shown) Planarity restraints: 1142 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G B 175 " -0.031 2.00e-02 2.50e+03 1.38e-02 5.75e+00 pdb=" N9 G B 175 " 0.034 2.00e-02 2.50e+03 pdb=" C8 G B 175 " 0.004 2.00e-02 2.50e+03 pdb=" N7 G B 175 " -0.002 2.00e-02 2.50e+03 pdb=" C5 G B 175 " -0.003 2.00e-02 2.50e+03 pdb=" C6 G B 175 " -0.001 2.00e-02 2.50e+03 pdb=" O6 G B 175 " -0.009 2.00e-02 2.50e+03 pdb=" N1 G B 175 " 0.000 2.00e-02 2.50e+03 pdb=" C2 G B 175 " 0.000 2.00e-02 2.50e+03 pdb=" N2 G B 175 " 0.000 2.00e-02 2.50e+03 pdb=" N3 G B 175 " 0.005 2.00e-02 2.50e+03 pdb=" C4 G B 175 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A B 102 " -0.031 2.00e-02 2.50e+03 1.43e-02 5.59e+00 pdb=" N9 A B 102 " 0.034 2.00e-02 2.50e+03 pdb=" C8 A B 102 " 0.002 2.00e-02 2.50e+03 pdb=" N7 A B 102 " -0.002 2.00e-02 2.50e+03 pdb=" C5 A B 102 " -0.001 2.00e-02 2.50e+03 pdb=" C6 A B 102 " -0.003 2.00e-02 2.50e+03 pdb=" N6 A B 102 " -0.008 2.00e-02 2.50e+03 pdb=" N1 A B 102 " -0.001 2.00e-02 2.50e+03 pdb=" C2 A B 102 " 0.002 2.00e-02 2.50e+03 pdb=" N3 A B 102 " 0.004 2.00e-02 2.50e+03 pdb=" C4 A B 102 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU E 102 " 0.011 2.00e-02 2.50e+03 2.32e-02 5.39e+00 pdb=" CD GLU E 102 " -0.040 2.00e-02 2.50e+03 pdb=" OE1 GLU E 102 " 0.015 2.00e-02 2.50e+03 pdb=" OE2 GLU E 102 " 0.014 2.00e-02 2.50e+03 ... (remaining 1139 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 127 2.60 - 3.18: 7835 3.18 - 3.75: 15938 3.75 - 4.33: 21472 4.33 - 4.90: 31108 Nonbonded interactions: 76480 Sorted by model distance: nonbonded pdb=" OD2 ASP A 414 " pdb=" O2' U B 185 " model vdw 2.026 3.040 nonbonded pdb=" OD1 ASN A 198 " pdb=" N ASN A 200 " model vdw 2.102 3.120 nonbonded pdb=" OH TYR A 45 " pdb=" O VAL A 113 " model vdw 2.124 3.040 nonbonded pdb=" OG1 THR A 11 " pdb=" OD1 ASP A 13 " model vdw 2.159 3.040 nonbonded pdb=" OD1 ASP A 421 " pdb=" NH1 ARG A 433 " model vdw 2.192 3.120 ... (remaining 76475 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: 3.740 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: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.950 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 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 : 0.005 0.053 9739 Z= 0.432 Angle : 0.733 5.216 13976 Z= 0.595 Chirality : 0.053 0.234 1667 Planarity : 0.005 0.047 1142 Dihedral : 20.304 154.457 4663 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.07 (0.34), residues: 678 helix: 2.13 (0.31), residues: 300 sheet: 0.41 (0.63), residues: 70 loop : -0.65 (0.36), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 587 TYR 0.018 0.002 TYR A 472 PHE 0.020 0.002 PHE E 28 TRP 0.020 0.002 TRP A 290 HIS 0.010 0.002 HIS A 450 Details of bonding type rmsd/Z covalent geometry : bond 0.00529 / 0.43 ( 9737) covalent geometry : angle 0.73302 / 0.60 (13972) SS BOND : bond 0.00402 / 0.20 ( 2) SS BOND : angle 1.10143 / 0.57 ( 4) hydrogen bonds : bond 0.11649 / 7.67 ( 442) hydrogen bonds : angle 4.80976 / 3.63 ( 1097) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 204 time to evaluate : 0.264 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 CYS cc_start: 0.8169 (t) cc_final: 0.7934 (t) REVERT: A 101 ARG cc_start: 0.6721 (mtp180) cc_final: 0.6398 (ttm110) REVERT: A 175 HIS cc_start: 0.7681 (t70) cc_final: 0.7330 (t70) REVERT: A 215 GLN cc_start: 0.8452 (mt0) cc_final: 0.8191 (mt0) REVERT: A 243 SER cc_start: 0.8510 (m) cc_final: 0.8307 (p) REVERT: A 252 SER cc_start: 0.9020 (p) cc_final: 0.8739 (p) REVERT: A 269 ASP cc_start: 0.7104 (t70) cc_final: 0.6664 (t70) REVERT: A 323 LEU cc_start: 0.9053 (mp) cc_final: 0.8720 (mt) REVERT: A 326 GLU cc_start: 0.7657 (mp0) cc_final: 0.7372 (mp0) REVERT: A 333 LYS cc_start: 0.8677 (mttm) cc_final: 0.8243 (mttm) REVERT: A 347 GLU cc_start: 0.7416 (mp0) cc_final: 0.7197 (mm-30) REVERT: A 378 ASP cc_start: 0.8278 (t0) cc_final: 0.7954 (t0) REVERT: A 386 SER cc_start: 0.8781 (t) cc_final: 0.8270 (p) REVERT: A 387 THR cc_start: 0.9000 (m) cc_final: 0.8667 (p) REVERT: A 407 GLU cc_start: 0.7744 (mt-10) cc_final: 0.7530 (mt-10) REVERT: A 424 TRP cc_start: 0.8293 (t-100) cc_final: 0.7954 (t-100) REVERT: A 433 ARG cc_start: 0.7267 (ttp-170) cc_final: 0.6448 (ttp-170) REVERT: A 444 GLU cc_start: 0.7965 (mt-10) cc_final: 0.7645 (mt-10) REVERT: A 469 SER cc_start: 0.9076 (m) cc_final: 0.8023 (t) REVERT: A 537 ASN cc_start: 0.7790 (m110) cc_final: 0.7508 (m110) REVERT: A 590 LYS cc_start: 0.8647 (tttt) cc_final: 0.8274 (ttmt) REVERT: E 91 LYS cc_start: 0.8113 (tppt) cc_final: 0.7582 (tptp) REVERT: E 97 LYS cc_start: 0.7237 (tttt) cc_final: 0.6996 (tttt) outliers start: 0 outliers final: 0 residues processed: 204 average time/residue: 0.1026 time to fit residues: 27.7788 Evaluate side-chains 173 residues out of total 607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 173 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 0.0010 chunk 65 optimal weight: 7.9990 chunk 62 optimal weight: 7.9990 chunk 51 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 10.0000 chunk 45 optimal weight: 0.5980 chunk 74 optimal weight: 3.9990 overall best weight: 0.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 40 HIS ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 90 GLN A 219 HIS A 389 HIS A 420 ASN A 443 GLN ** A 589 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 84 ASN E 107 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.115746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.090973 restraints weight = 21639.001| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 2.83 r_work: 0.3210 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.1548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 9739 Z= 0.182 Angle : 0.601 7.864 13976 Z= 0.344 Chirality : 0.041 0.382 1667 Planarity : 0.005 0.050 1142 Dihedral : 22.067 160.604 3255 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.31 % Allowed : 11.86 % Favored : 85.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.30 (0.34), residues: 678 helix: 2.24 (0.31), residues: 301 sheet: 0.31 (0.62), residues: 70 loop : -0.40 (0.37), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 534 TYR 0.015 0.002 TYR A 472 PHE 0.020 0.002 PHE E 103 TRP 0.015 0.002 TRP A 167 HIS 0.007 0.001 HIS A 589 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.18 ( 9737) covalent geometry : angle 0.60053 / 0.34 (13972) SS BOND : bond 0.00354 / 0.17 ( 2) SS BOND : angle 1.14579 / 0.60 ( 4) hydrogen bonds : bond 0.05742 / 3.86 ( 442) hydrogen bonds : angle 3.86493 / 2.90 ( 1097) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 175 time to evaluate : 0.175 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 CYS cc_start: 0.8496 (t) cc_final: 0.8212 (t) REVERT: A 47 TRP cc_start: 0.8845 (t60) cc_final: 0.8334 (t60) REVERT: A 61 LYS cc_start: 0.8652 (mmmt) cc_final: 0.8136 (tttm) REVERT: A 78 ARG cc_start: 0.7313 (tpt90) cc_final: 0.7090 (tpt170) REVERT: A 101 ARG cc_start: 0.7373 (mtp180) cc_final: 0.6841 (ttm110) REVERT: A 170 ILE cc_start: 0.8605 (mm) cc_final: 0.8238 (mm) REVERT: A 175 HIS cc_start: 0.8108 (t70) cc_final: 0.7704 (t70) REVERT: A 215 GLN cc_start: 0.9049 (mt0) cc_final: 0.8808 (mt0) REVERT: A 243 SER cc_start: 0.8799 (m) cc_final: 0.8452 (p) REVERT: A 267 ARG cc_start: 0.8364 (ttm-80) cc_final: 0.7941 (mtp85) REVERT: A 269 ASP cc_start: 0.7570 (t70) cc_final: 0.7091 (t70) REVERT: A 314 TYR cc_start: 0.8731 (m-80) cc_final: 0.8527 (m-10) REVERT: A 333 LYS cc_start: 0.8818 (mttm) cc_final: 0.8370 (mttm) REVERT: A 360 GLN cc_start: 0.8771 (mm110) cc_final: 0.8222 (mp10) REVERT: A 407 GLU cc_start: 0.8248 (mt-10) cc_final: 0.7892 (mt-10) REVERT: A 433 ARG cc_start: 0.7675 (ttp-170) cc_final: 0.6815 (ttp-170) REVERT: A 444 GLU cc_start: 0.8543 (mt-10) cc_final: 0.8213 (mt-10) REVERT: A 478 GLU cc_start: 0.6629 (tp30) cc_final: 0.6234 (tp30) REVERT: A 537 ASN cc_start: 0.8353 (m110) cc_final: 0.8028 (m110) REVERT: A 590 LYS cc_start: 0.8735 (tttt) cc_final: 0.8460 (tttt) REVERT: E 45 GLU cc_start: 0.8649 (tp30) cc_final: 0.7962 (tp30) REVERT: E 71 TYR cc_start: 0.7830 (m-80) cc_final: 0.7579 (m-80) REVERT: E 91 LYS cc_start: 0.8270 (tppt) cc_final: 0.7522 (tptp) REVERT: E 97 LYS cc_start: 0.7575 (tttt) cc_final: 0.7249 (tttt) REVERT: E 102 GLU cc_start: 0.8267 (OUTLIER) cc_final: 0.7753 (mm-30) REVERT: E 105 ASP cc_start: 0.8236 (m-30) cc_final: 0.7788 (m-30) outliers start: 14 outliers final: 8 residues processed: 180 average time/residue: 0.0940 time to fit residues: 22.1570 Evaluate side-chains 165 residues out of total 607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 156 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 CYS Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 426 SER Chi-restraints excluded: chain A residue 515 MET Chi-restraints excluded: chain E residue 62 ASP Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain E residue 102 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 49 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 chunk 6 optimal weight: 0.7980 chunk 67 optimal weight: 10.0000 chunk 79 optimal weight: 0.0870 chunk 54 optimal weight: 0.4980 chunk 72 optimal weight: 7.9990 chunk 63 optimal weight: 7.9990 chunk 19 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 78 optimal weight: 2.9990 overall best weight: 0.6560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 389 HIS ** A 579 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 589 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.116039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.091522 restraints weight = 21658.449| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 2.81 r_work: 0.3214 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.2044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9739 Z= 0.146 Angle : 0.549 7.253 13976 Z= 0.317 Chirality : 0.039 0.376 1667 Planarity : 0.005 0.059 1142 Dihedral : 22.052 163.371 3255 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.31 % Allowed : 14.50 % Favored : 83.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.41 (0.34), residues: 678 helix: 2.17 (0.30), residues: 307 sheet: 0.40 (0.56), residues: 80 loop : -0.21 (0.39), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 178 TYR 0.015 0.002 TYR A 472 PHE 0.013 0.002 PHE E 103 TRP 0.015 0.001 TRP E 29 HIS 0.008 0.001 HIS A 589 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.15 ( 9737) covalent geometry : angle 0.54852 / 0.32 (13972) SS BOND : bond 0.00309 / 0.15 ( 2) SS BOND : angle 0.85972 / 0.42 ( 4) hydrogen bonds : bond 0.05051 / 3.41 ( 442) hydrogen bonds : angle 3.57653 / 2.67 ( 1097) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 165 time to evaluate : 0.167 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 CYS cc_start: 0.8455 (t) cc_final: 0.8208 (t) REVERT: A 61 LYS cc_start: 0.8708 (mmmt) cc_final: 0.8226 (tttm) REVERT: A 78 ARG cc_start: 0.7356 (tpt90) cc_final: 0.6981 (tpt90) REVERT: A 101 ARG cc_start: 0.7447 (mtp180) cc_final: 0.6834 (ttm110) REVERT: A 175 HIS cc_start: 0.8055 (t70) cc_final: 0.7727 (t70) REVERT: A 215 GLN cc_start: 0.9083 (mt0) cc_final: 0.8860 (mt0) REVERT: A 243 SER cc_start: 0.8762 (m) cc_final: 0.8402 (p) REVERT: A 267 ARG cc_start: 0.8383 (ttm-80) cc_final: 0.7881 (mtp-110) REVERT: A 269 ASP cc_start: 0.7587 (t70) cc_final: 0.7041 (t70) REVERT: A 327 LYS cc_start: 0.8714 (ttpp) cc_final: 0.8510 (ttpp) REVERT: A 333 LYS cc_start: 0.8850 (mttm) cc_final: 0.8391 (mttm) REVERT: A 360 GLN cc_start: 0.8757 (mm110) cc_final: 0.8207 (mp10) REVERT: A 387 THR cc_start: 0.8986 (OUTLIER) cc_final: 0.8451 (p) REVERT: A 407 GLU cc_start: 0.8311 (mt-10) cc_final: 0.7950 (mt-10) REVERT: A 444 GLU cc_start: 0.8523 (mt-10) cc_final: 0.8187 (mt-10) REVERT: A 451 GLU cc_start: 0.7939 (tt0) cc_final: 0.7555 (tp30) REVERT: A 478 GLU cc_start: 0.6430 (tp30) cc_final: 0.5900 (tp30) REVERT: A 515 MET cc_start: 0.7685 (OUTLIER) cc_final: 0.7480 (mmt) REVERT: A 534 ARG cc_start: 0.8613 (mtp180) cc_final: 0.8355 (ttm170) REVERT: A 537 ASN cc_start: 0.8269 (m110) cc_final: 0.7967 (m110) REVERT: A 590 LYS cc_start: 0.8733 (tttt) cc_final: 0.8492 (tttt) REVERT: E 45 GLU cc_start: 0.8779 (tp30) cc_final: 0.8346 (tp30) REVERT: E 71 TYR cc_start: 0.7796 (m-80) cc_final: 0.7503 (m-80) REVERT: E 91 LYS cc_start: 0.8287 (tppt) cc_final: 0.7640 (tptp) REVERT: E 97 LYS cc_start: 0.7627 (tttt) cc_final: 0.7272 (tttt) outliers start: 14 outliers final: 11 residues processed: 171 average time/residue: 0.1146 time to fit residues: 25.5717 Evaluate side-chains 169 residues out of total 607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 156 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 417 GLU Chi-restraints excluded: chain A residue 420 ASN Chi-restraints excluded: chain A residue 426 SER Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 515 MET Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 62 ASP Chi-restraints excluded: chain E residue 74 ARG Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain E residue 102 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 1 optimal weight: 0.6980 chunk 52 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 41 optimal weight: 0.0870 chunk 42 optimal weight: 0.6980 chunk 54 optimal weight: 5.9990 chunk 47 optimal weight: 0.9980 chunk 45 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 chunk 43 optimal weight: 0.5980 chunk 15 optimal weight: 6.9990 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 579 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 589 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.115523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.090771 restraints weight = 21908.892| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 2.85 r_work: 0.3211 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.2265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9739 Z= 0.140 Angle : 0.526 6.857 13976 Z= 0.306 Chirality : 0.037 0.383 1667 Planarity : 0.005 0.052 1142 Dihedral : 22.053 164.216 3255 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.31 % Allowed : 16.14 % Favored : 81.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.44 (0.34), residues: 678 helix: 2.21 (0.30), residues: 308 sheet: 0.43 (0.56), residues: 80 loop : -0.24 (0.38), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 178 TYR 0.030 0.002 TYR A 472 PHE 0.012 0.002 PHE A 595 TRP 0.013 0.002 TRP E 29 HIS 0.008 0.001 HIS A 589 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.14 ( 9737) covalent geometry : angle 0.52623 / 0.31 (13972) SS BOND : bond 0.00319 / 0.16 ( 2) SS BOND : angle 0.77558 / 0.38 ( 4) hydrogen bonds : bond 0.04835 / 3.26 ( 442) hydrogen bonds : angle 3.50569 / 2.62 ( 1097) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 158 time to evaluate : 0.282 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 CYS cc_start: 0.8445 (t) cc_final: 0.8202 (t) REVERT: A 61 LYS cc_start: 0.8751 (mmmt) cc_final: 0.8301 (tttm) REVERT: A 78 ARG cc_start: 0.7313 (tpt90) cc_final: 0.6835 (tpt90) REVERT: A 101 ARG cc_start: 0.7504 (mtp180) cc_final: 0.6928 (ttm110) REVERT: A 175 HIS cc_start: 0.8061 (t70) cc_final: 0.7719 (t70) REVERT: A 215 GLN cc_start: 0.9087 (mt0) cc_final: 0.8772 (mt0) REVERT: A 243 SER cc_start: 0.8753 (m) cc_final: 0.8410 (p) REVERT: A 267 ARG cc_start: 0.8429 (ttm-80) cc_final: 0.8004 (mtp-110) REVERT: A 269 ASP cc_start: 0.7630 (t70) cc_final: 0.7054 (t70) REVERT: A 327 LYS cc_start: 0.8761 (ttpp) cc_final: 0.8506 (ttpp) REVERT: A 333 LYS cc_start: 0.8860 (mttm) cc_final: 0.8405 (mttm) REVERT: A 407 GLU cc_start: 0.8299 (mt-10) cc_final: 0.7934 (mt-10) REVERT: A 444 GLU cc_start: 0.8520 (mt-10) cc_final: 0.8185 (mt-10) REVERT: A 478 GLU cc_start: 0.6154 (tp30) cc_final: 0.5680 (tp30) REVERT: A 515 MET cc_start: 0.7700 (OUTLIER) cc_final: 0.7495 (mmt) REVERT: A 534 ARG cc_start: 0.8605 (mtp180) cc_final: 0.8222 (ttm170) REVERT: A 537 ASN cc_start: 0.8264 (m110) cc_final: 0.7951 (m110) REVERT: E 45 GLU cc_start: 0.8794 (tp30) cc_final: 0.8356 (tp30) REVERT: E 71 TYR cc_start: 0.7743 (m-80) cc_final: 0.7449 (m-80) REVERT: E 91 LYS cc_start: 0.8284 (tppt) cc_final: 0.7708 (tptp) REVERT: E 97 LYS cc_start: 0.7659 (tttt) cc_final: 0.7311 (tttt) outliers start: 14 outliers final: 11 residues processed: 164 average time/residue: 0.1131 time to fit residues: 24.3473 Evaluate side-chains 164 residues out of total 607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 152 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 426 SER Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 515 MET Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 62 ASP Chi-restraints excluded: chain E residue 74 ARG Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain E residue 102 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 18 optimal weight: 1.9990 chunk 67 optimal weight: 9.9990 chunk 30 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 chunk 79 optimal weight: 4.9990 chunk 82 optimal weight: 3.9990 chunk 23 optimal weight: 0.0060 chunk 44 optimal weight: 0.5980 chunk 76 optimal weight: 0.2980 chunk 24 optimal weight: 0.3980 chunk 4 optimal weight: 0.9980 overall best weight: 0.4596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 563 HIS A 589 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.116392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.091645 restraints weight = 21674.884| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 2.83 r_work: 0.3235 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.2554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 9739 Z= 0.126 Angle : 0.507 6.781 13976 Z= 0.297 Chirality : 0.037 0.382 1667 Planarity : 0.004 0.049 1142 Dihedral : 22.054 164.877 3255 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 3.29 % Allowed : 16.14 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.47 (0.33), residues: 678 helix: 2.31 (0.30), residues: 308 sheet: 0.55 (0.58), residues: 78 loop : -0.35 (0.38), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 433 TYR 0.048 0.002 TYR A 472 PHE 0.011 0.001 PHE A 595 TRP 0.029 0.002 TRP A 424 HIS 0.005 0.001 HIS A 389 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.13 ( 9737) covalent geometry : angle 0.50680 / 0.30 (13972) SS BOND : bond 0.00124 / 0.06 ( 2) SS BOND : angle 0.51797 / 0.30 ( 4) hydrogen bonds : bond 0.04551 / 3.07 ( 442) hydrogen bonds : angle 3.40899 / 2.55 ( 1097) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 149 time to evaluate : 0.288 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 CYS cc_start: 0.8409 (t) cc_final: 0.8179 (t) REVERT: A 37 LEU cc_start: 0.9336 (mm) cc_final: 0.9095 (mt) REVERT: A 47 TRP cc_start: 0.8837 (t60) cc_final: 0.8354 (t60) REVERT: A 61 LYS cc_start: 0.8759 (mmmt) cc_final: 0.8357 (tttm) REVERT: A 78 ARG cc_start: 0.7282 (tpt90) cc_final: 0.6905 (tpt170) REVERT: A 101 ARG cc_start: 0.7424 (mtp180) cc_final: 0.6914 (ttm110) REVERT: A 116 ARG cc_start: 0.8645 (ttm110) cc_final: 0.8191 (ttm110) REVERT: A 175 HIS cc_start: 0.7990 (t70) cc_final: 0.7668 (t70) REVERT: A 215 GLN cc_start: 0.9092 (mt0) cc_final: 0.8802 (mt0) REVERT: A 243 SER cc_start: 0.8766 (m) cc_final: 0.8459 (p) REVERT: A 267 ARG cc_start: 0.8422 (ttm-80) cc_final: 0.8029 (mtp-110) REVERT: A 269 ASP cc_start: 0.7690 (t70) cc_final: 0.7010 (t70) REVERT: A 333 LYS cc_start: 0.8844 (mttm) cc_final: 0.8430 (mttm) REVERT: A 360 GLN cc_start: 0.8768 (mm110) cc_final: 0.8280 (tm-30) REVERT: A 387 THR cc_start: 0.8951 (OUTLIER) cc_final: 0.8343 (p) REVERT: A 407 GLU cc_start: 0.8265 (mt-10) cc_final: 0.7896 (mt-10) REVERT: A 515 MET cc_start: 0.7752 (OUTLIER) cc_final: 0.7540 (mmt) REVERT: A 534 ARG cc_start: 0.8580 (mtp180) cc_final: 0.8265 (ttm170) REVERT: A 537 ASN cc_start: 0.8244 (m110) cc_final: 0.7915 (m110) REVERT: E 45 GLU cc_start: 0.8769 (tp30) cc_final: 0.8198 (tp30) REVERT: E 71 TYR cc_start: 0.7678 (m-80) cc_final: 0.7384 (m-80) REVERT: E 91 LYS cc_start: 0.8286 (tppt) cc_final: 0.7776 (tptp) REVERT: E 97 LYS cc_start: 0.7701 (tttt) cc_final: 0.7332 (tttt) outliers start: 20 outliers final: 13 residues processed: 159 average time/residue: 0.1021 time to fit residues: 21.1676 Evaluate side-chains 161 residues out of total 607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 146 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 250 LYS Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 515 MET Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 62 ASP Chi-restraints excluded: chain E residue 74 ARG Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain E residue 102 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 70 optimal weight: 7.9990 chunk 74 optimal weight: 4.9990 chunk 0 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 72 optimal weight: 7.9990 chunk 79 optimal weight: 0.0070 chunk 60 optimal weight: 6.9990 chunk 77 optimal weight: 0.6980 chunk 62 optimal weight: 6.9990 chunk 19 optimal weight: 0.5980 chunk 49 optimal weight: 0.8980 overall best weight: 0.8400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 7 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.115355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.090617 restraints weight = 21841.756| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 2.83 r_work: 0.3210 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.2704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9739 Z= 0.158 Angle : 0.534 6.294 13976 Z= 0.307 Chirality : 0.038 0.393 1667 Planarity : 0.004 0.047 1142 Dihedral : 22.062 167.154 3255 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 3.46 % Allowed : 15.49 % Favored : 81.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.42 (0.33), residues: 678 helix: 2.33 (0.30), residues: 308 sheet: 0.38 (0.63), residues: 66 loop : -0.38 (0.37), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 433 TYR 0.042 0.002 TYR A 472 PHE 0.010 0.002 PHE A 595 TRP 0.041 0.002 TRP A 424 HIS 0.004 0.001 HIS A 450 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.16 ( 9737) covalent geometry : angle 0.53349 / 0.31 (13972) SS BOND : bond 0.00338 / 0.16 ( 2) SS BOND : angle 1.06534 / 0.51 ( 4) hydrogen bonds : bond 0.04659 / 3.16 ( 442) hydrogen bonds : angle 3.46290 / 2.57 ( 1097) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 149 time to evaluate : 0.213 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 CYS cc_start: 0.8431 (t) cc_final: 0.8199 (t) REVERT: A 37 LEU cc_start: 0.9331 (mm) cc_final: 0.9086 (mt) REVERT: A 61 LYS cc_start: 0.8859 (mmmt) cc_final: 0.8503 (tttm) REVERT: A 78 ARG cc_start: 0.7140 (tpt90) cc_final: 0.6705 (tpt170) REVERT: A 101 ARG cc_start: 0.7434 (mtp180) cc_final: 0.6931 (ttm110) REVERT: A 175 HIS cc_start: 0.8005 (t70) cc_final: 0.7674 (t70) REVERT: A 215 GLN cc_start: 0.9096 (mt0) cc_final: 0.8803 (mt0) REVERT: A 230 GLU cc_start: 0.8163 (tp30) cc_final: 0.7938 (mm-30) REVERT: A 243 SER cc_start: 0.8788 (m) cc_final: 0.8482 (p) REVERT: A 267 ARG cc_start: 0.8439 (ttm-80) cc_final: 0.8053 (mtp-110) REVERT: A 269 ASP cc_start: 0.7700 (t70) cc_final: 0.7037 (t70) REVERT: A 333 LYS cc_start: 0.8869 (mttm) cc_final: 0.8460 (mttm) REVERT: A 360 GLN cc_start: 0.8767 (mm110) cc_final: 0.8337 (tm-30) REVERT: A 382 GLN cc_start: 0.8520 (mm-40) cc_final: 0.8183 (mp10) REVERT: A 387 THR cc_start: 0.8986 (OUTLIER) cc_final: 0.8423 (p) REVERT: A 407 GLU cc_start: 0.8272 (mt-10) cc_final: 0.7876 (mt-10) REVERT: A 451 GLU cc_start: 0.7971 (tt0) cc_final: 0.7520 (tp30) REVERT: A 537 ASN cc_start: 0.8273 (m110) cc_final: 0.7933 (m110) REVERT: E 45 GLU cc_start: 0.8765 (tp30) cc_final: 0.8205 (tp30) REVERT: E 71 TYR cc_start: 0.7694 (m-80) cc_final: 0.7414 (m-80) REVERT: E 97 LYS cc_start: 0.7800 (tttt) cc_final: 0.7438 (tttt) outliers start: 21 outliers final: 17 residues processed: 158 average time/residue: 0.0994 time to fit residues: 20.4459 Evaluate side-chains 162 residues out of total 607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 144 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 CYS Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 250 LYS Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 336 LYS Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 426 SER Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 62 ASP Chi-restraints excluded: chain E residue 74 ARG Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain E residue 102 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 74 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 chunk 40 optimal weight: 0.8980 chunk 11 optimal weight: 0.2980 chunk 68 optimal weight: 8.9990 chunk 55 optimal weight: 0.0870 chunk 47 optimal weight: 0.7980 chunk 4 optimal weight: 0.5980 chunk 50 optimal weight: 0.7980 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 579 GLN A 589 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.116223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.091773 restraints weight = 21802.933| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 2.82 r_work: 0.3229 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.2910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9739 Z= 0.128 Angle : 0.519 6.672 13976 Z= 0.300 Chirality : 0.037 0.387 1667 Planarity : 0.004 0.047 1142 Dihedral : 22.091 166.768 3255 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.97 % Allowed : 17.63 % Favored : 79.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.35 (0.33), residues: 678 helix: 2.29 (0.30), residues: 310 sheet: 0.29 (0.64), residues: 66 loop : -0.44 (0.36), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 433 TYR 0.020 0.001 TYR A 472 PHE 0.018 0.001 PHE E 103 TRP 0.057 0.002 TRP A 424 HIS 0.003 0.001 HIS E 7 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.13 ( 9737) covalent geometry : angle 0.51848 / 0.30 (13972) SS BOND : bond 0.00185 / 0.09 ( 2) SS BOND : angle 0.82026 / 0.43 ( 4) hydrogen bonds : bond 0.04518 / 3.06 ( 442) hydrogen bonds : angle 3.43592 / 2.55 ( 1097) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 148 time to evaluate : 0.259 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 CYS cc_start: 0.8379 (t) cc_final: 0.8164 (t) REVERT: A 37 LEU cc_start: 0.9335 (mm) cc_final: 0.9088 (mt) REVERT: A 47 TRP cc_start: 0.8869 (t60) cc_final: 0.8355 (t60) REVERT: A 61 LYS cc_start: 0.8874 (mmmt) cc_final: 0.8590 (tttm) REVERT: A 78 ARG cc_start: 0.7138 (tpt90) cc_final: 0.6715 (tpt170) REVERT: A 101 ARG cc_start: 0.7439 (mtp180) cc_final: 0.6922 (ttm110) REVERT: A 116 ARG cc_start: 0.8608 (ttm110) cc_final: 0.8137 (ttm110) REVERT: A 175 HIS cc_start: 0.7960 (t70) cc_final: 0.7594 (t70) REVERT: A 230 GLU cc_start: 0.8144 (tp30) cc_final: 0.7935 (mm-30) REVERT: A 243 SER cc_start: 0.8774 (m) cc_final: 0.8449 (p) REVERT: A 267 ARG cc_start: 0.8452 (ttm-80) cc_final: 0.8066 (mtp-110) REVERT: A 269 ASP cc_start: 0.7654 (t70) cc_final: 0.7087 (t70) REVERT: A 333 LYS cc_start: 0.8862 (mttm) cc_final: 0.8452 (mttm) REVERT: A 360 GLN cc_start: 0.8776 (mm110) cc_final: 0.8338 (tm-30) REVERT: A 382 GLN cc_start: 0.8505 (mm-40) cc_final: 0.8144 (mp10) REVERT: A 387 THR cc_start: 0.8947 (OUTLIER) cc_final: 0.8359 (p) REVERT: A 407 GLU cc_start: 0.8268 (mt-10) cc_final: 0.7882 (mt-10) REVERT: A 537 ASN cc_start: 0.8254 (m110) cc_final: 0.7913 (m110) REVERT: E 45 GLU cc_start: 0.8748 (tp30) cc_final: 0.8243 (tp30) REVERT: E 71 TYR cc_start: 0.7659 (m-80) cc_final: 0.7365 (m-80) REVERT: E 97 LYS cc_start: 0.7758 (tttt) cc_final: 0.7380 (tttt) outliers start: 18 outliers final: 12 residues processed: 157 average time/residue: 0.0996 time to fit residues: 20.3789 Evaluate side-chains 157 residues out of total 607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 144 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 250 LYS Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 336 LYS Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 62 ASP Chi-restraints excluded: chain E residue 74 ARG Chi-restraints excluded: chain E residue 102 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 50 optimal weight: 0.9980 chunk 75 optimal weight: 0.8980 chunk 62 optimal weight: 7.9990 chunk 69 optimal weight: 4.9990 chunk 43 optimal weight: 0.5980 chunk 42 optimal weight: 1.9990 chunk 45 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 chunk 71 optimal weight: 4.9990 chunk 46 optimal weight: 0.7980 chunk 36 optimal weight: 0.0170 overall best weight: 0.5818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 589 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.115750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.091159 restraints weight = 21799.852| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 2.81 r_work: 0.3214 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.3101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 9739 Z= 0.135 Angle : 0.532 6.999 13976 Z= 0.303 Chirality : 0.037 0.388 1667 Planarity : 0.004 0.046 1142 Dihedral : 22.098 167.933 3255 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.31 % Allowed : 18.45 % Favored : 79.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.21 (0.33), residues: 678 helix: 2.17 (0.30), residues: 310 sheet: 0.12 (0.67), residues: 66 loop : -0.48 (0.36), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 178 TYR 0.039 0.002 TYR A 472 PHE 0.011 0.001 PHE E 103 TRP 0.061 0.002 TRP A 424 HIS 0.003 0.001 HIS A 589 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.14 ( 9737) covalent geometry : angle 0.53186 / 0.30 (13972) SS BOND : bond 0.00204 / 0.10 ( 2) SS BOND : angle 0.81478 / 0.42 ( 4) hydrogen bonds : bond 0.04460 / 3.02 ( 442) hydrogen bonds : angle 3.48161 / 2.58 ( 1097) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 148 time to evaluate : 0.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 CYS cc_start: 0.8394 (t) cc_final: 0.8190 (t) REVERT: A 37 LEU cc_start: 0.9309 (mm) cc_final: 0.9033 (mt) REVERT: A 47 TRP cc_start: 0.8779 (t60) cc_final: 0.8348 (t60) REVERT: A 61 LYS cc_start: 0.8888 (mmmt) cc_final: 0.8678 (tttm) REVERT: A 78 ARG cc_start: 0.7083 (tpt90) cc_final: 0.6875 (tpt170) REVERT: A 101 ARG cc_start: 0.7467 (mtp180) cc_final: 0.7024 (ttm110) REVERT: A 175 HIS cc_start: 0.7858 (t70) cc_final: 0.7462 (t70) REVERT: A 243 SER cc_start: 0.8731 (m) cc_final: 0.8452 (p) REVERT: A 267 ARG cc_start: 0.8467 (ttm-80) cc_final: 0.8098 (mtp-110) REVERT: A 269 ASP cc_start: 0.7706 (t70) cc_final: 0.7119 (t70) REVERT: A 333 LYS cc_start: 0.8871 (mttm) cc_final: 0.8477 (mttm) REVERT: A 356 LYS cc_start: 0.8896 (pptt) cc_final: 0.8351 (mmtm) REVERT: A 360 GLN cc_start: 0.8747 (mm110) cc_final: 0.8345 (mt0) REVERT: A 382 GLN cc_start: 0.8528 (mm-40) cc_final: 0.8165 (mp10) REVERT: A 387 THR cc_start: 0.8970 (OUTLIER) cc_final: 0.8401 (p) REVERT: A 407 GLU cc_start: 0.8261 (mt-10) cc_final: 0.7885 (mt-10) REVERT: A 537 ASN cc_start: 0.8246 (m110) cc_final: 0.7910 (m110) REVERT: E 45 GLU cc_start: 0.8734 (tp30) cc_final: 0.8415 (tp30) REVERT: E 71 TYR cc_start: 0.7602 (m-80) cc_final: 0.7345 (m-80) REVERT: E 91 LYS cc_start: 0.7809 (tptp) cc_final: 0.7515 (tmtt) REVERT: E 97 LYS cc_start: 0.7729 (tttt) cc_final: 0.7364 (tttt) outliers start: 14 outliers final: 11 residues processed: 151 average time/residue: 0.1040 time to fit residues: 20.4518 Evaluate side-chains 155 residues out of total 607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 143 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 250 LYS Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 62 ASP Chi-restraints excluded: chain E residue 74 ARG Chi-restraints excluded: chain E residue 102 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 61 optimal weight: 10.0000 chunk 39 optimal weight: 0.3980 chunk 66 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 58 optimal weight: 5.9990 chunk 11 optimal weight: 1.9990 chunk 79 optimal weight: 0.2980 chunk 43 optimal weight: 0.5980 chunk 8 optimal weight: 0.2980 chunk 22 optimal weight: 0.9980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 389 HIS A 589 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.116788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.092342 restraints weight = 21863.459| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 2.80 r_work: 0.3239 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.3256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9739 Z= 0.129 Angle : 0.540 7.160 13976 Z= 0.306 Chirality : 0.037 0.388 1667 Planarity : 0.004 0.046 1142 Dihedral : 22.126 168.057 3255 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.81 % Allowed : 19.93 % Favored : 78.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.36 (0.33), residues: 678 helix: 2.32 (0.30), residues: 304 sheet: 0.28 (0.59), residues: 79 loop : -0.43 (0.37), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 534 TYR 0.042 0.002 TYR A 472 PHE 0.010 0.001 PHE E 13 TRP 0.049 0.002 TRP A 424 HIS 0.004 0.001 HIS A 389 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.13 ( 9737) covalent geometry : angle 0.54017 / 0.31 (13972) SS BOND : bond 0.00293 / 0.15 ( 2) SS BOND : angle 0.58367 / 0.31 ( 4) hydrogen bonds : bond 0.04379 / 2.96 ( 442) hydrogen bonds : angle 3.45101 / 2.57 ( 1097) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 146 time to evaluate : 0.178 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 CYS cc_start: 0.8379 (t) cc_final: 0.8176 (t) REVERT: A 37 LEU cc_start: 0.9302 (mm) cc_final: 0.9026 (mt) REVERT: A 47 TRP cc_start: 0.8749 (t60) cc_final: 0.8348 (t60) REVERT: A 61 LYS cc_start: 0.8900 (mmmt) cc_final: 0.8686 (tttm) REVERT: A 78 ARG cc_start: 0.7078 (tpt90) cc_final: 0.6620 (tpt170) REVERT: A 101 ARG cc_start: 0.7471 (mtp180) cc_final: 0.7032 (ttm110) REVERT: A 116 ARG cc_start: 0.8615 (ttm110) cc_final: 0.8188 (mtm110) REVERT: A 175 HIS cc_start: 0.7825 (t70) cc_final: 0.7442 (t70) REVERT: A 243 SER cc_start: 0.8712 (m) cc_final: 0.8443 (p) REVERT: A 267 ARG cc_start: 0.8467 (ttm-80) cc_final: 0.8098 (mtp-110) REVERT: A 269 ASP cc_start: 0.7674 (t70) cc_final: 0.7126 (t70) REVERT: A 333 LYS cc_start: 0.8829 (mttm) cc_final: 0.8435 (mttm) REVERT: A 356 LYS cc_start: 0.8913 (pptt) cc_final: 0.8392 (mmtm) REVERT: A 360 GLN cc_start: 0.8751 (mm110) cc_final: 0.8351 (mt0) REVERT: A 382 GLN cc_start: 0.8525 (mm-40) cc_final: 0.8164 (mp10) REVERT: A 387 THR cc_start: 0.8946 (OUTLIER) cc_final: 0.8361 (p) REVERT: A 407 GLU cc_start: 0.8271 (mt-10) cc_final: 0.7900 (mt-10) REVERT: A 478 GLU cc_start: 0.5678 (tp30) cc_final: 0.5219 (tp30) REVERT: A 537 ASN cc_start: 0.8235 (m110) cc_final: 0.7905 (m110) REVERT: E 45 GLU cc_start: 0.8704 (tp30) cc_final: 0.8181 (tp30) REVERT: E 71 TYR cc_start: 0.7564 (m-80) cc_final: 0.7305 (m-80) REVERT: E 97 LYS cc_start: 0.7747 (tttt) cc_final: 0.7371 (tttt) outliers start: 11 outliers final: 10 residues processed: 147 average time/residue: 0.1083 time to fit residues: 20.6184 Evaluate side-chains 155 residues out of total 607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 144 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 250 LYS Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 62 ASP Chi-restraints excluded: chain E residue 74 ARG Chi-restraints excluded: chain E residue 102 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 45 optimal weight: 0.5980 chunk 31 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 60 optimal weight: 6.9990 chunk 71 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 19 optimal weight: 0.3980 chunk 41 optimal weight: 0.7980 chunk 32 optimal weight: 0.5980 chunk 42 optimal weight: 2.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 589 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.116430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.091874 restraints weight = 22057.098| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 2.83 r_work: 0.3233 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.3366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9739 Z= 0.137 Angle : 0.540 7.445 13976 Z= 0.306 Chirality : 0.037 0.389 1667 Planarity : 0.004 0.044 1142 Dihedral : 22.141 168.895 3255 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.98 % Allowed : 20.26 % Favored : 77.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.39 (0.33), residues: 678 helix: 2.36 (0.30), residues: 304 sheet: 0.24 (0.60), residues: 79 loop : -0.41 (0.37), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 534 TYR 0.015 0.002 TYR A 348 PHE 0.010 0.001 PHE A 595 TRP 0.036 0.002 TRP A 424 HIS 0.004 0.001 HIS A 389 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.14 ( 9737) covalent geometry : angle 0.54014 / 0.31 (13972) SS BOND : bond 0.00185 / 0.10 ( 2) SS BOND : angle 0.78914 / 0.42 ( 4) hydrogen bonds : bond 0.04381 / 2.97 ( 442) hydrogen bonds : angle 3.47885 / 2.58 ( 1097) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 150 time to evaluate : 0.225 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 CYS cc_start: 0.8424 (t) cc_final: 0.8215 (t) REVERT: A 37 LEU cc_start: 0.9302 (mm) cc_final: 0.9026 (mt) REVERT: A 47 TRP cc_start: 0.8770 (t60) cc_final: 0.8373 (t60) REVERT: A 78 ARG cc_start: 0.7000 (tpt90) cc_final: 0.6784 (tpt170) REVERT: A 101 ARG cc_start: 0.7471 (mtp180) cc_final: 0.6983 (ttm110) REVERT: A 175 HIS cc_start: 0.7844 (t70) cc_final: 0.7473 (t70) REVERT: A 243 SER cc_start: 0.8714 (m) cc_final: 0.8450 (p) REVERT: A 267 ARG cc_start: 0.8477 (ttm-80) cc_final: 0.8114 (mtp-110) REVERT: A 269 ASP cc_start: 0.7674 (t70) cc_final: 0.7130 (t70) REVERT: A 333 LYS cc_start: 0.8843 (mttm) cc_final: 0.8420 (mttm) REVERT: A 360 GLN cc_start: 0.8751 (mm110) cc_final: 0.8355 (tm-30) REVERT: A 382 GLN cc_start: 0.8528 (mm-40) cc_final: 0.8158 (mp10) REVERT: A 387 THR cc_start: 0.8973 (OUTLIER) cc_final: 0.8398 (p) REVERT: A 407 GLU cc_start: 0.8272 (mt-10) cc_final: 0.7908 (mt-10) REVERT: A 478 GLU cc_start: 0.5617 (tp30) cc_final: 0.4967 (tp30) REVERT: A 537 ASN cc_start: 0.8242 (m110) cc_final: 0.7929 (m110) REVERT: E 45 GLU cc_start: 0.8715 (tp30) cc_final: 0.8438 (tp30) REVERT: E 71 TYR cc_start: 0.7599 (m-80) cc_final: 0.7363 (m-80) REVERT: E 91 LYS cc_start: 0.8083 (tptp) cc_final: 0.7828 (tptp) REVERT: E 97 LYS cc_start: 0.7724 (tttt) cc_final: 0.7351 (tttt) outliers start: 12 outliers final: 11 residues processed: 151 average time/residue: 0.1184 time to fit residues: 23.2869 Evaluate side-chains 156 residues out of total 607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 144 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 250 LYS Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain E residue 6 ILE Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 62 ASP Chi-restraints excluded: chain E residue 74 ARG Chi-restraints excluded: chain E residue 102 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 50 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 72 optimal weight: 7.9990 chunk 13 optimal weight: 9.9990 chunk 32 optimal weight: 0.6980 chunk 76 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 2 optimal weight: 0.7980 chunk 57 optimal weight: 4.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 589 HIS E 7 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.114878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.090488 restraints weight = 21654.868| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 2.79 r_work: 0.3220 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.3475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9739 Z= 0.156 Angle : 0.566 8.305 13976 Z= 0.318 Chirality : 0.038 0.396 1667 Planarity : 0.005 0.049 1142 Dihedral : 22.164 169.816 3255 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.98 % Allowed : 20.92 % Favored : 77.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.27 (0.33), residues: 678 helix: 2.31 (0.30), residues: 304 sheet: 0.15 (0.68), residues: 67 loop : -0.50 (0.36), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 178 TYR 0.023 0.002 TYR A 472 PHE 0.017 0.002 PHE A 96 TRP 0.037 0.002 TRP A 424 HIS 0.005 0.001 HIS E 7 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.16 ( 9737) covalent geometry : angle 0.56623 / 0.32 (13972) SS BOND : bond 0.00324 / 0.16 ( 2) SS BOND : angle 0.55066 / 0.30 ( 4) hydrogen bonds : bond 0.04532 / 3.07 ( 442) hydrogen bonds : angle 3.53505 / 2.63 ( 1097) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2016.48 seconds wall clock time: 35 minutes 18.55 seconds (2118.55 seconds total)