Starting phenix.real_space_refine on Tue Mar 3 16:04:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7l0r_23101/03_2026/7l0r_23101.cif Found real_map, /net/cci-nas-00/data/ceres_data/7l0r_23101/03_2026/7l0r_23101.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7l0r_23101/03_2026/7l0r_23101.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7l0r_23101/03_2026/7l0r_23101.map" model { file = "/net/cci-nas-00/data/ceres_data/7l0r_23101/03_2026/7l0r_23101.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7l0r_23101/03_2026/7l0r_23101.cif" } resolution = 4.2 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= -0.000 sd= 0.002 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: 4 Type Number sf(0) Gaussians S 53 5.16 5 C 4450 2.51 5 N 1176 2.21 5 O 1289 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6968 Number of models: 1 Model: "" Number of chains: 5 Chain: "C" Number of atoms: 2424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2424 Classifications: {'peptide': 308} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 297} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 58 Classifications: {'peptide': 6} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 4} Chain: "A" Number of atoms: 1791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1791 Classifications: {'peptide': 223} Link IDs: {'PTRANS': 2, 'TRANS': 220} Chain breaks: 2 Chain: "B" Number of atoms: 2385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2385 Classifications: {'peptide': 311} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 305} Chain: "G" Number of atoms: 310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 310 Classifications: {'peptide': 39} Link IDs: {'PTRANS': 3, 'TRANS': 35} Time building chain proxies: 1.49, per 1000 atoms: 0.21 Number of scatterers: 6968 At special positions: 0 Unit cell: (75.075, 112.2, 121.275, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 53 16.00 O 1289 8.00 N 1176 7.00 C 4450 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS C 142 " - pdb=" SG CYS C 225 " distance=2.03 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: 0.77 Conformation dependent library (CDL) restraints added in 307.2 milliseconds 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1666 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 9 sheets defined 43.9% alpha, 17.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.16 Creating SS restraints... Processing helix chain 'C' and resid 60 through 91 Processing helix chain 'C' and resid 100 through 129 Proline residue: C 122 - end of helix Processing helix chain 'C' and resid 137 through 173 Processing helix chain 'C' and resid 173 through 181 Processing helix chain 'C' and resid 182 through 202 Processing helix chain 'C' and resid 202 through 207 removed outlier: 3.519A pdb=" N THR C 207 " --> pdb=" O PRO C 203 " (cutoff:3.500A) Processing helix chain 'C' and resid 230 through 270 Proline residue: C 249 - end of helix Processing helix chain 'C' and resid 300 through 334 Proline residue: C 323 - end of helix removed outlier: 3.533A pdb=" N ILE C 334 " --> pdb=" O MET C 330 " (cutoff:3.500A) Processing helix chain 'C' and resid 340 through 371 Proline residue: C 366 - end of helix Processing helix chain 'C' and resid 373 through 385 Processing helix chain 'A' and resid 7 through 32 removed outlier: 3.508A pdb=" N ALA A 11 " --> pdb=" O ALA A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 55 Processing helix chain 'A' and resid 202 through 204 No H-bonds generated for 'chain 'A' and resid 202 through 204' Processing helix chain 'A' and resid 207 through 216 removed outlier: 3.781A pdb=" N TRP A 211 " --> pdb=" O ARG A 208 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.683A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLU A 216 " --> pdb=" O HIS A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 231 removed outlier: 4.405A pdb=" N ASP A 231 " --> pdb=" O SER A 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 228 through 231' Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 270 through 281 Processing helix chain 'A' and resid 295 through 308 Processing helix chain 'A' and resid 331 through 351 Processing helix chain 'G' and resid 32 through 48 Processing sheet with id=AA1, first strand: chain 'C' and resid 208 through 212 Processing sheet with id=AA2, first strand: chain 'A' and resid 186 through 190 removed outlier: 6.527A pdb=" N VAL A 34 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N PHE A 199 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N LEU A 36 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 8.390A pdb=" N ALA A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 8.202A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.895A pdb=" N LEU B 336 " --> pdb=" O LEU B 51 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.837A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.974A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 148 through 151 Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.399A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.063A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.903A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) 364 hydrogen bonds defined for protein. 1062 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.90 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: 1875 1.33 - 1.45: 1457 1.45 - 1.57: 3699 1.57 - 1.69: 0 1.69 - 1.81: 77 Bond restraints: 7108 Sorted by residual: bond pdb=" C HIS C 133 " pdb=" N PRO C 134 " ideal model delta sigma weight residual 1.331 1.385 -0.053 1.28e-02 6.10e+03 1.72e+01 bond pdb=" N LEU B 95 " pdb=" CA LEU B 95 " ideal model delta sigma weight residual 1.454 1.488 -0.034 1.17e-02 7.31e+03 8.30e+00 bond pdb=" N ASP A 309 " pdb=" CA ASP A 309 " ideal model delta sigma weight residual 1.456 1.489 -0.034 1.33e-02 5.65e+03 6.36e+00 bond pdb=" N LEU C 256 " pdb=" CA LEU C 256 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.17e-02 7.31e+03 6.14e+00 bond pdb=" N ASP B 323 " pdb=" CA ASP B 323 " ideal model delta sigma weight residual 1.456 1.488 -0.032 1.31e-02 5.83e+03 5.83e+00 ... (remaining 7103 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.06: 8677 2.06 - 4.13: 764 4.13 - 6.19: 132 6.19 - 8.26: 38 8.26 - 10.32: 20 Bond angle restraints: 9631 Sorted by residual: angle pdb=" N PHE C 376 " pdb=" CA PHE C 376 " pdb=" C PHE C 376 " ideal model delta sigma weight residual 112.54 105.52 7.02 1.22e+00 6.72e-01 3.31e+01 angle pdb=" N VAL C 131 " pdb=" CA VAL C 131 " pdb=" C VAL C 131 " ideal model delta sigma weight residual 107.51 99.00 8.51 1.49e+00 4.50e-01 3.26e+01 angle pdb=" N LYS A 46 " pdb=" CA LYS A 46 " pdb=" C LYS A 46 " ideal model delta sigma weight residual 111.28 105.13 6.15 1.09e+00 8.42e-01 3.18e+01 angle pdb=" C SER B 227 " pdb=" N ASP B 228 " pdb=" CA ASP B 228 " ideal model delta sigma weight residual 120.82 127.90 -7.08 1.47e+00 4.63e-01 2.32e+01 angle pdb=" C CYS A 3 " pdb=" N THR A 4 " pdb=" CA THR A 4 " ideal model delta sigma weight residual 121.54 130.72 -9.18 1.91e+00 2.74e-01 2.31e+01 ... (remaining 9626 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.98: 3770 15.98 - 31.96: 329 31.96 - 47.93: 77 47.93 - 63.91: 24 63.91 - 79.89: 4 Dihedral angle restraints: 4204 sinusoidal: 1628 harmonic: 2576 Sorted by residual: dihedral pdb=" CB CYS C 142 " pdb=" SG CYS C 142 " pdb=" SG CYS C 225 " pdb=" CB CYS C 225 " ideal model delta sinusoidal sigma weight residual -86.00 -165.89 79.89 1 1.00e+01 1.00e-02 7.91e+01 dihedral pdb=" CA PHE G 64 " pdb=" C PHE G 64 " pdb=" N LYS G 65 " pdb=" CA LYS G 65 " ideal model delta harmonic sigma weight residual 180.00 153.89 26.11 0 5.00e+00 4.00e-02 2.73e+01 dihedral pdb=" CA ASP B 290 " pdb=" C ASP B 290 " pdb=" N ASP B 291 " pdb=" CA ASP B 291 " ideal model delta harmonic sigma weight residual 180.00 156.29 23.71 0 5.00e+00 4.00e-02 2.25e+01 ... (remaining 4201 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 836 0.082 - 0.164: 221 0.164 - 0.246: 41 0.246 - 0.328: 13 0.328 - 0.410: 1 Chirality restraints: 1112 Sorted by residual: chirality pdb=" CA HIS C 133 " pdb=" N HIS C 133 " pdb=" C HIS C 133 " pdb=" CB HIS C 133 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.20e+00 chirality pdb=" CB ILE B 157 " pdb=" CA ILE B 157 " pdb=" CG1 ILE B 157 " pdb=" CG2 ILE B 157 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.32 2.00e-01 2.50e+01 2.57e+00 chirality pdb=" CB VAL C 266 " pdb=" CA VAL C 266 " pdb=" CG1 VAL C 266 " pdb=" CG2 VAL C 266 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.30 2.00e-01 2.50e+01 2.20e+00 ... (remaining 1109 not shown) Planarity restraints: 1209 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA C 374 " 0.027 2.00e-02 2.50e+03 5.30e-02 2.81e+01 pdb=" C ALA C 374 " -0.092 2.00e-02 2.50e+03 pdb=" O ALA C 374 " 0.034 2.00e-02 2.50e+03 pdb=" N ASN C 375 " 0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG B 49 " -0.017 2.00e-02 2.50e+03 3.35e-02 1.12e+01 pdb=" C ARG B 49 " 0.058 2.00e-02 2.50e+03 pdb=" O ARG B 49 " -0.022 2.00e-02 2.50e+03 pdb=" N THR B 50 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL C 300 " -0.016 2.00e-02 2.50e+03 3.19e-02 1.01e+01 pdb=" C VAL C 300 " 0.055 2.00e-02 2.50e+03 pdb=" O VAL C 300 " -0.021 2.00e-02 2.50e+03 pdb=" N GLN C 301 " -0.018 2.00e-02 2.50e+03 ... (remaining 1206 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.66: 201 2.66 - 3.22: 6562 3.22 - 3.78: 11590 3.78 - 4.34: 14908 4.34 - 4.90: 24418 Nonbonded interactions: 57679 Sorted by model distance: nonbonded pdb=" OH TYR C 146 " pdb=" OXT LEU D 13 " model vdw 2.106 3.040 nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.232 3.040 nonbonded pdb=" OG SER B 74 " pdb=" OD1 ASP B 76 " model vdw 2.279 3.040 nonbonded pdb=" N GLU A 43 " pdb=" OE1 GLU A 43 " model vdw 2.286 3.120 nonbonded pdb=" OH TYR B 264 " pdb=" O ALA B 299 " model vdw 2.304 3.040 ... (remaining 57674 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.850 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6894 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 0.081 7109 Z= 0.376 Angle : 1.372 10.325 9633 Z= 0.787 Chirality : 0.079 0.410 1112 Planarity : 0.008 0.058 1209 Dihedral : 13.578 70.468 2535 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 1.05 % Allowed : 11.26 % Favored : 87.70 % Cbeta Deviations : 0.24 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.44 (0.24), residues: 869 helix: -1.98 (0.20), residues: 376 sheet: -2.25 (0.36), residues: 173 loop : -2.41 (0.30), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 314 TYR 0.029 0.004 TYR C 349 PHE 0.038 0.004 PHE C 376 TRP 0.050 0.004 TRP B 297 HIS 0.008 0.003 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00745 ( 7108) covalent geometry : angle 1.37215 ( 9631) SS BOND : bond 0.00362 ( 1) SS BOND : angle 1.86174 ( 2) hydrogen bonds : bond 0.12914 ( 364) hydrogen bonds : angle 7.58938 ( 1062) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 301 time to evaluate : 0.276 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 169 LEU cc_start: 0.8671 (tp) cc_final: 0.8436 (tp) REVERT: C 305 ARG cc_start: 0.8692 (mtt90) cc_final: 0.8325 (mtt-85) REVERT: A 21 ARG cc_start: 0.8062 (tpt170) cc_final: 0.7589 (tpp80) REVERT: A 22 ASN cc_start: 0.8967 (m-40) cc_final: 0.8759 (m110) REVERT: A 28 GLU cc_start: 0.8303 (tt0) cc_final: 0.7857 (tm-30) REVERT: A 321 THR cc_start: 0.7498 (p) cc_final: 0.7253 (p) REVERT: A 334 PHE cc_start: 0.7965 (t80) cc_final: 0.7749 (t80) REVERT: B 51 LEU cc_start: 0.8445 (mp) cc_final: 0.8083 (mp) REVERT: B 79 LEU cc_start: 0.9142 (pt) cc_final: 0.8912 (pp) REVERT: B 82 TRP cc_start: 0.8585 (m100) cc_final: 0.8378 (m100) REVERT: B 93 ILE cc_start: 0.9144 (mt) cc_final: 0.8895 (mt) REVERT: B 99 TRP cc_start: 0.8466 (m100) cc_final: 0.8051 (m100) REVERT: B 126 LEU cc_start: 0.8266 (mp) cc_final: 0.8017 (mp) REVERT: B 149 CYS cc_start: 0.8130 (p) cc_final: 0.7716 (m) REVERT: B 188 MET cc_start: 0.8407 (mmm) cc_final: 0.8063 (mmm) REVERT: B 212 ASP cc_start: 0.4851 (t0) cc_final: 0.3827 (t0) REVERT: B 308 LEU cc_start: 0.8750 (tp) cc_final: 0.7649 (tp) REVERT: B 312 ASP cc_start: 0.7384 (p0) cc_final: 0.6928 (t0) REVERT: B 329 THR cc_start: 0.9075 (t) cc_final: 0.8807 (t) outliers start: 8 outliers final: 3 residues processed: 306 average time/residue: 0.1131 time to fit residues: 43.5655 Evaluate side-chains 207 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 204 time to evaluate : 0.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 49 optimal weight: 9.9990 chunk 53 optimal weight: 7.9990 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 10.0000 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 45 optimal weight: 4.9990 chunk 74 optimal weight: 5.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 82 ASN C 132 HIS C 159 ASN C 219 HIS C 239 GLN C 292 ASN B 230 ASN B 295 ASN B 311 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.108158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.087382 restraints weight = 21901.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.089866 restraints weight = 13328.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.091566 restraints weight = 9402.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.092742 restraints weight = 7331.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.093564 restraints weight = 6133.221| |-----------------------------------------------------------------------------| r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.3401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 7109 Z= 0.194 Angle : 0.736 8.546 9633 Z= 0.394 Chirality : 0.046 0.187 1112 Planarity : 0.005 0.046 1209 Dihedral : 5.902 59.333 955 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 14.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 0.26 % Allowed : 5.63 % Favored : 94.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.04 (0.26), residues: 869 helix: -0.34 (0.24), residues: 380 sheet: -1.71 (0.34), residues: 191 loop : -2.26 (0.32), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 205 TYR 0.017 0.002 TYR C 369 PHE 0.042 0.002 PHE C 246 TRP 0.029 0.002 TRP B 339 HIS 0.011 0.002 HIS C 325 Details of bonding type rmsd covalent geometry : bond 0.00401 ( 7108) covalent geometry : angle 0.73624 ( 9631) SS BOND : bond 0.00309 ( 1) SS BOND : angle 0.99375 ( 2) hydrogen bonds : bond 0.05185 ( 364) hydrogen bonds : angle 5.91372 ( 1062) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 257 time to evaluate : 0.275 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 167 ARG cc_start: 0.8482 (mtt-85) cc_final: 0.8249 (mtp85) REVERT: C 169 LEU cc_start: 0.9025 (tp) cc_final: 0.8799 (tp) REVERT: C 345 ASP cc_start: 0.8377 (m-30) cc_final: 0.7294 (p0) REVERT: C 346 PHE cc_start: 0.8833 (t80) cc_final: 0.8357 (t80) REVERT: C 357 LEU cc_start: 0.9387 (mt) cc_final: 0.9088 (mt) REVERT: A 18 MET cc_start: 0.8310 (tpp) cc_final: 0.7761 (tpp) REVERT: A 196 PHE cc_start: 0.8233 (m-80) cc_final: 0.7887 (m-80) REVERT: A 243 MET cc_start: 0.8509 (tpp) cc_final: 0.8107 (tpp) REVERT: A 343 ILE cc_start: 0.9279 (tp) cc_final: 0.9033 (tp) REVERT: B 61 MET cc_start: 0.7870 (ppp) cc_final: 0.7634 (ppp) REVERT: B 118 ASP cc_start: 0.8227 (p0) cc_final: 0.7907 (p0) REVERT: B 149 CYS cc_start: 0.8257 (p) cc_final: 0.7886 (m) REVERT: B 243 THR cc_start: 0.8648 (m) cc_final: 0.8401 (p) REVERT: B 289 TYR cc_start: 0.8089 (m-80) cc_final: 0.7782 (m-80) REVERT: B 312 ASP cc_start: 0.7572 (p0) cc_final: 0.6714 (t70) outliers start: 2 outliers final: 0 residues processed: 259 average time/residue: 0.0914 time to fit residues: 31.3095 Evaluate side-chains 184 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 184 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 83 optimal weight: 1.9990 chunk 11 optimal weight: 7.9990 chunk 36 optimal weight: 5.9990 chunk 32 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 13 optimal weight: 10.0000 chunk 54 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 33 optimal weight: 7.9990 chunk 34 optimal weight: 0.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 159 ASN C 239 GLN C 270 GLN C 355 ASN ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 306 GLN B 142 HIS B 266 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.107562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.086240 restraints weight = 21535.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.088963 restraints weight = 12600.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.090791 restraints weight = 8644.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.092027 restraints weight = 6627.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.092771 restraints weight = 5513.233| |-----------------------------------------------------------------------------| r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.4238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7109 Z= 0.202 Angle : 0.719 8.120 9633 Z= 0.383 Chirality : 0.046 0.194 1112 Planarity : 0.005 0.051 1209 Dihedral : 5.649 59.345 955 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 16.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 0.13 % Allowed : 4.32 % Favored : 95.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.48 (0.27), residues: 869 helix: 0.22 (0.25), residues: 378 sheet: -1.52 (0.35), residues: 187 loop : -2.04 (0.33), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 52 TYR 0.018 0.002 TYR C 349 PHE 0.021 0.002 PHE C 344 TRP 0.022 0.002 TRP B 82 HIS 0.006 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00427 ( 7108) covalent geometry : angle 0.71821 ( 9631) SS BOND : bond 0.00499 ( 1) SS BOND : angle 2.41438 ( 2) hydrogen bonds : bond 0.04835 ( 364) hydrogen bonds : angle 5.72225 ( 1062) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 242 time to evaluate : 0.311 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 167 ARG cc_start: 0.8506 (mtt-85) cc_final: 0.8296 (mtp85) REVERT: C 234 LEU cc_start: 0.9220 (tt) cc_final: 0.8864 (mt) REVERT: C 250 MET cc_start: 0.7879 (ptm) cc_final: 0.7600 (ptm) REVERT: C 305 ARG cc_start: 0.8834 (mtt90) cc_final: 0.8290 (mtt-85) REVERT: C 345 ASP cc_start: 0.8433 (m-30) cc_final: 0.7869 (m-30) REVERT: C 346 PHE cc_start: 0.8887 (t80) cc_final: 0.8565 (t80) REVERT: A 333 GLN cc_start: 0.8155 (pm20) cc_final: 0.7792 (pm20) REVERT: A 343 ILE cc_start: 0.9340 (tp) cc_final: 0.8930 (tp) REVERT: A 347 ASN cc_start: 0.8536 (m110) cc_final: 0.8169 (m110) REVERT: B 61 MET cc_start: 0.7875 (ppp) cc_final: 0.7651 (ppp) REVERT: B 82 TRP cc_start: 0.7959 (m-10) cc_final: 0.7470 (m-10) REVERT: B 118 ASP cc_start: 0.8320 (p0) cc_final: 0.8020 (p0) REVERT: B 146 LEU cc_start: 0.9259 (mp) cc_final: 0.8468 (mp) REVERT: B 251 ARG cc_start: 0.7642 (mpt-90) cc_final: 0.7183 (mmt90) REVERT: B 289 TYR cc_start: 0.8266 (m-80) cc_final: 0.7849 (m-80) outliers start: 1 outliers final: 1 residues processed: 242 average time/residue: 0.1015 time to fit residues: 31.6020 Evaluate side-chains 189 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 188 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 25 optimal weight: 4.9990 chunk 2 optimal weight: 10.0000 chunk 64 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 35 optimal weight: 9.9990 chunk 13 optimal weight: 9.9990 chunk 38 optimal weight: 0.8980 chunk 50 optimal weight: 2.9990 chunk 0 optimal weight: 30.0000 chunk 66 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS ** B 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 ASN ** B 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.108921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.088058 restraints weight = 21325.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.090747 restraints weight = 12565.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.092552 restraints weight = 8619.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.093897 restraints weight = 6571.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 17)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.094569 restraints weight = 5360.895| |-----------------------------------------------------------------------------| r_work (final): 0.3545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.4758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 7109 Z= 0.162 Angle : 0.685 8.059 9633 Z= 0.360 Chirality : 0.046 0.294 1112 Planarity : 0.005 0.052 1209 Dihedral : 5.569 60.485 955 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 15.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 0.26 % Allowed : 3.66 % Favored : 96.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.07 (0.28), residues: 869 helix: 0.56 (0.26), residues: 379 sheet: -1.08 (0.37), residues: 175 loop : -2.01 (0.33), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 208 TYR 0.016 0.002 TYR B 145 PHE 0.028 0.002 PHE C 246 TRP 0.012 0.002 TRP B 339 HIS 0.011 0.001 HIS C 325 Details of bonding type rmsd covalent geometry : bond 0.00345 ( 7108) covalent geometry : angle 0.68513 ( 9631) SS BOND : bond 0.00207 ( 1) SS BOND : angle 1.08025 ( 2) hydrogen bonds : bond 0.04720 ( 364) hydrogen bonds : angle 5.59475 ( 1062) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 248 time to evaluate : 0.274 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: symmetry clash revert: symmetry clash REVERT: C 180 LEU cc_start: 0.8169 (tt) cc_final: 0.7746 (pp) REVERT: C 234 LEU cc_start: 0.9217 (tt) cc_final: 0.8845 (mt) REVERT: C 250 MET cc_start: 0.7939 (ptm) cc_final: 0.7483 (ptm) REVERT: C 305 ARG cc_start: 0.8816 (mtt90) cc_final: 0.8301 (mtt-85) REVERT: C 345 ASP cc_start: 0.8462 (m-30) cc_final: 0.7419 (p0) REVERT: C 346 PHE cc_start: 0.8883 (t80) cc_final: 0.8436 (t80) REVERT: C 357 LEU cc_start: 0.9402 (mt) cc_final: 0.9132 (mt) REVERT: D 9 ARG cc_start: 0.7952 (tpt-90) cc_final: 0.7616 (tpt-90) REVERT: A 22 ASN cc_start: 0.9028 (m110) cc_final: 0.8665 (m110) REVERT: A 197 LYS cc_start: 0.7557 (mmtt) cc_final: 0.7288 (mmtt) REVERT: A 333 GLN cc_start: 0.8085 (pm20) cc_final: 0.7866 (pm20) REVERT: A 343 ILE cc_start: 0.9341 (tp) cc_final: 0.8901 (tp) REVERT: A 347 ASN cc_start: 0.8539 (m110) cc_final: 0.8131 (m110) REVERT: B 61 MET cc_start: 0.7988 (ppp) cc_final: 0.7673 (ppp) REVERT: B 118 ASP cc_start: 0.8271 (p0) cc_final: 0.8027 (p0) REVERT: B 220 GLN cc_start: 0.7035 (mp10) cc_final: 0.6723 (mp10) REVERT: B 289 TYR cc_start: 0.8118 (m-80) cc_final: 0.7872 (m-80) REVERT: B 325 MET cc_start: 0.8390 (mmm) cc_final: 0.8048 (mmm) REVERT: B 331 SER cc_start: 0.9153 (p) cc_final: 0.8649 (t) REVERT: G 41 ARG cc_start: 0.8282 (tmm160) cc_final: 0.7904 (ttp80) outliers start: 2 outliers final: 0 residues processed: 249 average time/residue: 0.1005 time to fit residues: 32.3089 Evaluate side-chains 192 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 192 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 75 optimal weight: 0.0980 chunk 21 optimal weight: 0.2980 chunk 12 optimal weight: 8.9990 chunk 84 optimal weight: 6.9990 chunk 1 optimal weight: 4.9990 chunk 29 optimal weight: 10.0000 chunk 35 optimal weight: 8.9990 chunk 82 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 chunk 34 optimal weight: 3.9990 chunk 53 optimal weight: 9.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 159 ASN B 88 ASN B 142 HIS B 230 ASN ** B 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.109019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.088574 restraints weight = 21718.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.091058 restraints weight = 13320.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.092793 restraints weight = 9370.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.093885 restraints weight = 7242.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.094782 restraints weight = 6059.283| |-----------------------------------------------------------------------------| r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7496 moved from start: 0.5099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7109 Z= 0.162 Angle : 0.685 7.281 9633 Z= 0.359 Chirality : 0.045 0.226 1112 Planarity : 0.005 0.052 1209 Dihedral : 5.309 50.919 955 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 14.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 0.13 % Allowed : 3.27 % Favored : 96.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.85 (0.28), residues: 869 helix: 0.76 (0.26), residues: 380 sheet: -1.04 (0.37), residues: 176 loop : -1.87 (0.35), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 208 TYR 0.026 0.002 TYR C 146 PHE 0.020 0.002 PHE C 344 TRP 0.011 0.002 TRP B 339 HIS 0.008 0.001 HIS B 311 Details of bonding type rmsd covalent geometry : bond 0.00344 ( 7108) covalent geometry : angle 0.68376 ( 9631) SS BOND : bond 0.00995 ( 1) SS BOND : angle 2.97282 ( 2) hydrogen bonds : bond 0.04639 ( 364) hydrogen bonds : angle 5.44200 ( 1062) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 238 time to evaluate : 0.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 186 THR cc_start: 0.8052 (m) cc_final: 0.7852 (t) REVERT: C 234 LEU cc_start: 0.9176 (tt) cc_final: 0.8797 (mt) REVERT: C 250 MET cc_start: 0.7831 (ptm) cc_final: 0.7509 (ptm) REVERT: C 305 ARG cc_start: 0.8839 (mtt90) cc_final: 0.8328 (mtt-85) REVERT: C 327 ARG cc_start: 0.8295 (ttp80) cc_final: 0.8080 (ttp80) REVERT: C 336 ASP cc_start: 0.7465 (m-30) cc_final: 0.6083 (m-30) REVERT: C 345 ASP cc_start: 0.8399 (m-30) cc_final: 0.7408 (p0) REVERT: C 346 PHE cc_start: 0.8758 (t80) cc_final: 0.8319 (t80) REVERT: C 357 LEU cc_start: 0.9360 (mt) cc_final: 0.9137 (mt) REVERT: D 9 ARG cc_start: 0.7810 (tpt-90) cc_final: 0.7406 (tpt170) REVERT: A 19 ILE cc_start: 0.9247 (tt) cc_final: 0.9045 (tt) REVERT: A 22 ASN cc_start: 0.8960 (m110) cc_final: 0.8533 (m110) REVERT: A 197 LYS cc_start: 0.7683 (mmtt) cc_final: 0.7468 (mmtt) REVERT: A 208 ARG cc_start: 0.7969 (mtm110) cc_final: 0.7684 (ptp-110) REVERT: A 209 LYS cc_start: 0.8523 (mtmt) cc_final: 0.8081 (ttpp) REVERT: A 333 GLN cc_start: 0.7906 (pm20) cc_final: 0.7627 (pm20) REVERT: A 343 ILE cc_start: 0.9336 (tp) cc_final: 0.8942 (tp) REVERT: A 347 ASN cc_start: 0.8486 (m110) cc_final: 0.8126 (m110) REVERT: B 45 MET cc_start: 0.7715 (mmm) cc_final: 0.7386 (mmm) REVERT: B 61 MET cc_start: 0.8002 (ppp) cc_final: 0.7701 (ppp) REVERT: B 74 SER cc_start: 0.9144 (p) cc_final: 0.8702 (t) REVERT: B 325 MET cc_start: 0.8325 (mmm) cc_final: 0.8027 (tpp) REVERT: B 331 SER cc_start: 0.9072 (p) cc_final: 0.8726 (t) REVERT: G 37 CYS cc_start: 0.8472 (m) cc_final: 0.8239 (m) outliers start: 1 outliers final: 0 residues processed: 238 average time/residue: 0.0986 time to fit residues: 30.6228 Evaluate side-chains 176 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 176 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 54 optimal weight: 3.9990 chunk 28 optimal weight: 6.9990 chunk 62 optimal weight: 10.0000 chunk 75 optimal weight: 6.9990 chunk 49 optimal weight: 0.0370 chunk 5 optimal weight: 0.9990 chunk 39 optimal weight: 6.9990 chunk 6 optimal weight: 9.9990 chunk 27 optimal weight: 5.9990 chunk 59 optimal weight: 5.9990 chunk 4 optimal weight: 10.0000 overall best weight: 3.4066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 127 ASN C 239 GLN C 241 ASN B 142 HIS B 230 ASN B 311 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.105095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.084744 restraints weight = 22373.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.087262 restraints weight = 13050.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.089005 restraints weight = 8892.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.090222 restraints weight = 6747.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.090914 restraints weight = 5556.387| |-----------------------------------------------------------------------------| r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.5483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 7109 Z= 0.237 Angle : 0.758 7.221 9633 Z= 0.402 Chirality : 0.047 0.203 1112 Planarity : 0.005 0.054 1209 Dihedral : 5.499 42.186 955 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 19.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 0.39 % Allowed : 3.40 % Favored : 96.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.69 (0.29), residues: 869 helix: 0.91 (0.26), residues: 378 sheet: -1.06 (0.37), residues: 178 loop : -1.73 (0.36), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 205 TYR 0.020 0.002 TYR C 62 PHE 0.025 0.002 PHE C 344 TRP 0.016 0.002 TRP C 321 HIS 0.012 0.002 HIS B 311 Details of bonding type rmsd covalent geometry : bond 0.00501 ( 7108) covalent geometry : angle 0.75807 ( 9631) SS BOND : bond 0.00485 ( 1) SS BOND : angle 1.26897 ( 2) hydrogen bonds : bond 0.04716 ( 364) hydrogen bonds : angle 5.57623 ( 1062) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 220 time to evaluate : 0.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 166 GLU cc_start: 0.8209 (tm-30) cc_final: 0.7915 (tm-30) REVERT: C 186 THR cc_start: 0.8123 (m) cc_final: 0.7910 (t) REVERT: C 234 LEU cc_start: 0.9176 (tt) cc_final: 0.8889 (mt) REVERT: C 238 ILE cc_start: 0.7539 (tt) cc_final: 0.7318 (tt) REVERT: C 250 MET cc_start: 0.7866 (ptm) cc_final: 0.7528 (ptm) REVERT: C 346 PHE cc_start: 0.8812 (t80) cc_final: 0.8480 (t80) REVERT: D 13 LEU cc_start: 0.6531 (tp) cc_final: 0.6223 (tp) REVERT: A 19 ILE cc_start: 0.9326 (tt) cc_final: 0.9063 (tt) REVERT: A 22 ASN cc_start: 0.9029 (m110) cc_final: 0.8619 (m110) REVERT: A 197 LYS cc_start: 0.7618 (mmtt) cc_final: 0.7396 (mmtt) REVERT: A 209 LYS cc_start: 0.8548 (mtmt) cc_final: 0.7997 (ttpp) REVERT: A 333 GLN cc_start: 0.8054 (pm20) cc_final: 0.7844 (pm20) REVERT: A 343 ILE cc_start: 0.9376 (tp) cc_final: 0.8971 (tp) REVERT: A 347 ASN cc_start: 0.8595 (m110) cc_final: 0.8209 (m110) REVERT: B 61 MET cc_start: 0.8053 (ppp) cc_final: 0.7829 (ppp) REVERT: B 325 MET cc_start: 0.8564 (mmm) cc_final: 0.8151 (tpp) REVERT: B 331 SER cc_start: 0.8861 (p) cc_final: 0.8635 (t) REVERT: G 35 LYS cc_start: 0.9130 (pptt) cc_final: 0.8885 (pptt) REVERT: G 38 GLU cc_start: 0.8808 (mp0) cc_final: 0.8347 (mp0) outliers start: 3 outliers final: 0 residues processed: 222 average time/residue: 0.0819 time to fit residues: 24.1107 Evaluate side-chains 176 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 176 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 49 optimal weight: 0.0870 chunk 23 optimal weight: 1.9990 chunk 15 optimal weight: 20.0000 chunk 42 optimal weight: 0.7980 chunk 72 optimal weight: 7.9990 chunk 7 optimal weight: 1.9990 chunk 68 optimal weight: 8.9990 chunk 38 optimal weight: 3.9990 chunk 74 optimal weight: 0.9980 chunk 57 optimal weight: 0.8980 chunk 43 optimal weight: 0.9990 overall best weight: 0.7560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 325 HIS A 195 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.111786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.090836 restraints weight = 21356.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.093477 restraints weight = 12801.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.095278 restraints weight = 8882.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.096335 restraints weight = 6807.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.097267 restraints weight = 5689.106| |-----------------------------------------------------------------------------| r_work (final): 0.3576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 moved from start: 0.5691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7109 Z= 0.145 Angle : 0.713 8.455 9633 Z= 0.372 Chirality : 0.045 0.173 1112 Planarity : 0.005 0.066 1209 Dihedral : 5.101 31.050 955 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 14.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.49 (0.29), residues: 869 helix: 1.00 (0.26), residues: 382 sheet: -0.83 (0.38), residues: 184 loop : -1.65 (0.36), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 208 TYR 0.020 0.002 TYR B 59 PHE 0.020 0.002 PHE C 344 TRP 0.017 0.002 TRP B 297 HIS 0.006 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 7108) covalent geometry : angle 0.71292 ( 9631) SS BOND : bond 0.00000 ( 1) SS BOND : angle 0.62502 ( 2) hydrogen bonds : bond 0.04641 ( 364) hydrogen bonds : angle 5.41097 ( 1062) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 243 time to evaluate : 0.260 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 186 THR cc_start: 0.8133 (m) cc_final: 0.7901 (t) REVERT: C 234 LEU cc_start: 0.9112 (tt) cc_final: 0.8837 (mt) REVERT: C 250 MET cc_start: 0.7769 (ptm) cc_final: 0.7403 (ptm) REVERT: C 344 PHE cc_start: 0.7786 (t80) cc_final: 0.6545 (t80) REVERT: C 346 PHE cc_start: 0.8729 (t80) cc_final: 0.8423 (t80) REVERT: C 348 HIS cc_start: 0.8343 (m-70) cc_final: 0.7772 (m170) REVERT: C 357 LEU cc_start: 0.9365 (mt) cc_final: 0.9148 (mt) REVERT: D 13 LEU cc_start: 0.6050 (tp) cc_final: 0.5831 (tp) REVERT: A 22 ASN cc_start: 0.8940 (m110) cc_final: 0.8567 (m110) REVERT: A 204 GLN cc_start: 0.8061 (pp30) cc_final: 0.7799 (pp30) REVERT: A 206 SER cc_start: 0.8180 (m) cc_final: 0.7517 (m) REVERT: A 208 ARG cc_start: 0.7968 (mtm110) cc_final: 0.7684 (ptp-110) REVERT: A 209 LYS cc_start: 0.8396 (mtmt) cc_final: 0.7954 (ttpp) REVERT: B 45 MET cc_start: 0.7657 (mmm) cc_final: 0.7006 (mmm) REVERT: B 61 MET cc_start: 0.8137 (ppp) cc_final: 0.7894 (ppp) REVERT: B 118 ASP cc_start: 0.8161 (p0) cc_final: 0.7879 (p0) REVERT: G 38 GLU cc_start: 0.8759 (mp0) cc_final: 0.8347 (mp0) REVERT: G 41 ARG cc_start: 0.8867 (ptt90) cc_final: 0.8492 (ptm-80) REVERT: G 42 ASP cc_start: 0.8715 (p0) cc_final: 0.8486 (p0) outliers start: 0 outliers final: 0 residues processed: 243 average time/residue: 0.0786 time to fit residues: 25.5562 Evaluate side-chains 186 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 186 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 83 optimal weight: 0.5980 chunk 7 optimal weight: 7.9990 chunk 37 optimal weight: 0.9980 chunk 73 optimal weight: 9.9990 chunk 48 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 chunk 20 optimal weight: 4.9990 chunk 40 optimal weight: 9.9990 chunk 53 optimal weight: 9.9990 chunk 80 optimal weight: 6.9990 chunk 76 optimal weight: 1.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 159 ASN C 325 HIS B 230 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.108271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.087521 restraints weight = 21903.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.090030 restraints weight = 13428.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.091673 restraints weight = 9435.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.092758 restraints weight = 7362.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.093639 restraints weight = 6204.763| |-----------------------------------------------------------------------------| r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.5909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 7109 Z= 0.191 Angle : 0.741 8.313 9633 Z= 0.388 Chirality : 0.047 0.247 1112 Planarity : 0.005 0.065 1209 Dihedral : 5.185 20.964 955 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 17.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 0.13 % Allowed : 2.09 % Favored : 97.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.29), residues: 869 helix: 1.06 (0.26), residues: 379 sheet: -0.80 (0.38), residues: 184 loop : -1.66 (0.35), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 208 TYR 0.019 0.002 TYR B 59 PHE 0.021 0.002 PHE C 344 TRP 0.020 0.002 TRP B 297 HIS 0.007 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00411 ( 7108) covalent geometry : angle 0.73897 ( 9631) SS BOND : bond 0.00715 ( 1) SS BOND : angle 3.72911 ( 2) hydrogen bonds : bond 0.04686 ( 364) hydrogen bonds : angle 5.53230 ( 1062) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 217 time to evaluate : 0.271 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 234 LEU cc_start: 0.9125 (tt) cc_final: 0.8797 (mt) REVERT: C 250 MET cc_start: 0.7833 (ptm) cc_final: 0.7454 (ptm) REVERT: C 301 GLN cc_start: 0.8194 (pm20) cc_final: 0.7940 (pm20) REVERT: C 345 ASP cc_start: 0.8523 (m-30) cc_final: 0.8013 (m-30) REVERT: C 346 PHE cc_start: 0.8753 (t80) cc_final: 0.8458 (t80) REVERT: C 357 LEU cc_start: 0.9363 (mt) cc_final: 0.9119 (mt) REVERT: D 9 ARG cc_start: 0.7781 (tpt-90) cc_final: 0.7567 (tpt-90) REVERT: A 22 ASN cc_start: 0.8894 (m110) cc_final: 0.8536 (m110) REVERT: A 208 ARG cc_start: 0.7883 (mtm110) cc_final: 0.7597 (ptp-110) REVERT: A 209 LYS cc_start: 0.8402 (mtmt) cc_final: 0.7989 (ttpp) REVERT: A 343 ILE cc_start: 0.9371 (tp) cc_final: 0.9011 (tp) REVERT: A 347 ASN cc_start: 0.8527 (m110) cc_final: 0.8173 (m110) REVERT: B 45 MET cc_start: 0.7668 (mmm) cc_final: 0.7020 (mmm) REVERT: B 118 ASP cc_start: 0.8278 (p0) cc_final: 0.7939 (p0) REVERT: B 190 LEU cc_start: 0.9239 (tt) cc_final: 0.9009 (tp) REVERT: G 35 LYS cc_start: 0.8431 (pptt) cc_final: 0.7992 (pptt) REVERT: G 37 CYS cc_start: 0.8498 (m) cc_final: 0.8247 (m) REVERT: G 38 GLU cc_start: 0.8754 (mp0) cc_final: 0.8285 (mp0) outliers start: 1 outliers final: 0 residues processed: 217 average time/residue: 0.0769 time to fit residues: 22.7190 Evaluate side-chains 171 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 171 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 54 optimal weight: 0.9980 chunk 53 optimal weight: 10.0000 chunk 77 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 56 optimal weight: 2.9990 chunk 47 optimal weight: 8.9990 chunk 16 optimal weight: 10.0000 chunk 81 optimal weight: 0.9980 chunk 3 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 127 ASN C 325 HIS C 348 HIS A 52 GLN B 230 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.110633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.090207 restraints weight = 21657.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.092679 restraints weight = 13488.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.094203 restraints weight = 9518.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.095616 restraints weight = 7461.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.096353 restraints weight = 6119.893| |-----------------------------------------------------------------------------| r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.6082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7109 Z= 0.153 Angle : 0.732 8.781 9633 Z= 0.378 Chirality : 0.046 0.235 1112 Planarity : 0.004 0.055 1209 Dihedral : 5.013 20.040 955 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 14.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 0.13 % Allowed : 0.79 % Favored : 99.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.29), residues: 869 helix: 1.15 (0.26), residues: 380 sheet: -0.81 (0.38), residues: 184 loop : -1.57 (0.36), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 208 TYR 0.018 0.002 TYR C 349 PHE 0.024 0.002 PHE C 344 TRP 0.017 0.002 TRP B 339 HIS 0.006 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00328 ( 7108) covalent geometry : angle 0.73016 ( 9631) SS BOND : bond 0.00119 ( 1) SS BOND : angle 3.29123 ( 2) hydrogen bonds : bond 0.04622 ( 364) hydrogen bonds : angle 5.46783 ( 1062) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 225 time to evaluate : 0.272 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 166 GLU cc_start: 0.8168 (tm-30) cc_final: 0.7845 (tm-30) REVERT: C 234 LEU cc_start: 0.9105 (tt) cc_final: 0.8804 (mt) REVERT: C 250 MET cc_start: 0.7790 (ptm) cc_final: 0.7407 (ptm) REVERT: C 301 GLN cc_start: 0.8201 (pm20) cc_final: 0.7949 (pm20) REVERT: C 344 PHE cc_start: 0.7943 (t80) cc_final: 0.7005 (t80) REVERT: C 345 ASP cc_start: 0.8513 (m-30) cc_final: 0.7545 (p0) REVERT: C 346 PHE cc_start: 0.8751 (t80) cc_final: 0.8358 (t80) REVERT: C 357 LEU cc_start: 0.9360 (mt) cc_final: 0.9122 (mt) REVERT: D 9 ARG cc_start: 0.7779 (tpt-90) cc_final: 0.7503 (tpt-90) REVERT: A 22 ASN cc_start: 0.8910 (m110) cc_final: 0.8607 (m110) REVERT: A 197 LYS cc_start: 0.7802 (mmtt) cc_final: 0.7393 (mmtt) REVERT: A 206 SER cc_start: 0.8227 (m) cc_final: 0.7400 (m) REVERT: A 209 LYS cc_start: 0.8323 (mtmt) cc_final: 0.7856 (ttpp) REVERT: A 265 ILE cc_start: 0.9114 (mt) cc_final: 0.8863 (mm) REVERT: A 343 ILE cc_start: 0.9358 (tp) cc_final: 0.8991 (tp) REVERT: A 347 ASN cc_start: 0.8470 (m110) cc_final: 0.8112 (m110) REVERT: B 45 MET cc_start: 0.7618 (mmm) cc_final: 0.7066 (mmm) REVERT: B 61 MET cc_start: 0.7958 (ppp) cc_final: 0.7703 (ppp) REVERT: B 123 ILE cc_start: 0.9131 (mm) cc_final: 0.8661 (pt) REVERT: B 260 GLU cc_start: 0.7293 (tp30) cc_final: 0.6292 (mp0) REVERT: B 318 LEU cc_start: 0.8483 (pt) cc_final: 0.8178 (pp) REVERT: G 38 GLU cc_start: 0.8609 (mp0) cc_final: 0.8046 (mp0) outliers start: 1 outliers final: 0 residues processed: 225 average time/residue: 0.0833 time to fit residues: 25.1363 Evaluate side-chains 180 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 180 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 67 optimal weight: 6.9990 chunk 0 optimal weight: 30.0000 chunk 36 optimal weight: 0.8980 chunk 14 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 chunk 17 optimal weight: 7.9990 chunk 73 optimal weight: 10.0000 chunk 30 optimal weight: 7.9990 chunk 60 optimal weight: 3.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 325 HIS A 52 GLN A 331 ASN B 230 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.107751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.086790 restraints weight = 21857.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.089347 restraints weight = 12935.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.091174 restraints weight = 8941.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.092461 restraints weight = 6835.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.093163 restraints weight = 5609.260| |-----------------------------------------------------------------------------| r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.6237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 7109 Z= 0.206 Angle : 0.765 8.628 9633 Z= 0.399 Chirality : 0.047 0.186 1112 Planarity : 0.005 0.063 1209 Dihedral : 5.171 20.870 955 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 18.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.34 (0.29), residues: 869 helix: 1.09 (0.26), residues: 382 sheet: -0.74 (0.39), residues: 182 loop : -1.54 (0.35), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 208 TYR 0.019 0.002 TYR C 349 PHE 0.026 0.003 PHE C 128 TRP 0.020 0.002 TRP B 82 HIS 0.008 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00444 ( 7108) covalent geometry : angle 0.76426 ( 9631) SS BOND : bond 0.00028 ( 1) SS BOND : angle 2.68734 ( 2) hydrogen bonds : bond 0.04717 ( 364) hydrogen bonds : angle 5.54877 ( 1062) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 215 time to evaluate : 0.288 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 166 GLU cc_start: 0.8263 (tm-30) cc_final: 0.7950 (tm-30) REVERT: C 234 LEU cc_start: 0.9171 (tt) cc_final: 0.8930 (mt) REVERT: C 250 MET cc_start: 0.7785 (ptm) cc_final: 0.7400 (ptm) REVERT: C 293 MET cc_start: 0.6351 (pmm) cc_final: 0.5821 (pmm) REVERT: C 301 GLN cc_start: 0.8167 (pm20) cc_final: 0.7910 (pm20) REVERT: C 345 ASP cc_start: 0.8564 (m-30) cc_final: 0.8098 (m-30) REVERT: C 346 PHE cc_start: 0.8829 (t80) cc_final: 0.8554 (t80) REVERT: C 357 LEU cc_start: 0.9384 (mt) cc_final: 0.9119 (mt) REVERT: D 9 ARG cc_start: 0.7840 (tpt-90) cc_final: 0.7534 (tpt-90) REVERT: A 18 MET cc_start: 0.8511 (tpp) cc_final: 0.8291 (tpp) REVERT: A 22 ASN cc_start: 0.8974 (m110) cc_final: 0.8612 (m110) REVERT: A 197 LYS cc_start: 0.7657 (mmtt) cc_final: 0.7302 (mmtt) REVERT: A 204 GLN cc_start: 0.8146 (pp30) cc_final: 0.7660 (pp30) REVERT: A 206 SER cc_start: 0.8320 (m) cc_final: 0.7428 (m) REVERT: A 209 LYS cc_start: 0.8372 (mtmt) cc_final: 0.7853 (ttpp) REVERT: A 343 ILE cc_start: 0.9401 (tp) cc_final: 0.9011 (tp) REVERT: A 347 ASN cc_start: 0.8572 (m110) cc_final: 0.8194 (m110) REVERT: B 123 ILE cc_start: 0.9192 (mm) cc_final: 0.8698 (pt) REVERT: B 129 ARG cc_start: 0.8495 (ppt170) cc_final: 0.8197 (ttp80) REVERT: B 260 GLU cc_start: 0.7545 (tp30) cc_final: 0.6661 (mp0) REVERT: G 38 GLU cc_start: 0.8722 (mp0) cc_final: 0.8235 (mp0) outliers start: 0 outliers final: 0 residues processed: 215 average time/residue: 0.0888 time to fit residues: 25.4634 Evaluate side-chains 171 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 171 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 36 optimal weight: 0.8980 chunk 48 optimal weight: 0.2980 chunk 55 optimal weight: 6.9990 chunk 4 optimal weight: 10.0000 chunk 66 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 35 optimal weight: 0.2980 chunk 28 optimal weight: 5.9990 chunk 53 optimal weight: 3.9990 chunk 18 optimal weight: 8.9990 chunk 14 optimal weight: 8.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 325 HIS C 348 HIS ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.109943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.089854 restraints weight = 21635.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.092224 restraints weight = 13397.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.093961 restraints weight = 9431.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 18)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.094908 restraints weight = 7306.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.095776 restraints weight = 6158.925| |-----------------------------------------------------------------------------| r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.6411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 7109 Z= 0.163 Angle : 0.748 8.888 9633 Z= 0.385 Chirality : 0.047 0.244 1112 Planarity : 0.005 0.067 1209 Dihedral : 5.065 20.427 955 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 16.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.29), residues: 869 helix: 1.20 (0.27), residues: 379 sheet: -0.72 (0.39), residues: 182 loop : -1.45 (0.35), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 208 TYR 0.018 0.002 TYR C 349 PHE 0.027 0.002 PHE C 344 TRP 0.016 0.002 TRP B 297 HIS 0.006 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00355 ( 7108) covalent geometry : angle 0.74722 ( 9631) SS BOND : bond 0.00043 ( 1) SS BOND : angle 2.33718 ( 2) hydrogen bonds : bond 0.04586 ( 364) hydrogen bonds : angle 5.45052 ( 1062) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1358.63 seconds wall clock time: 24 minutes 16.19 seconds (1456.19 seconds total)