Starting phenix.real_space_refine on Mon Nov 17 19:19:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ukc_26576/11_2025/7ukc_26576.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ukc_26576/11_2025/7ukc_26576.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7ukc_26576/11_2025/7ukc_26576.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ukc_26576/11_2025/7ukc_26576.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ukc_26576/11_2025/7ukc_26576.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ukc_26576/11_2025/7ukc_26576.map" } resolution = 3.0 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= 0.005 sd= 0.060 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 K 4 8.98 5 S 56 5.16 5 C 5252 2.51 5 N 1332 2.21 5 O 1356 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8000 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 1999 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 1999 Classifications: {'peptide': 259} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 10, 'TRANS': 248} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1, 'GLU:plan': 2, 'ASP:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 22 Chain: "A" Number of atoms: 1999 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 1999 Classifications: {'peptide': 259} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 10, 'TRANS': 248} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1, 'GLU:plan': 2, 'ASP:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 22 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' K': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Restraints were copied for chains: C, D Time building chain proxies: 2.47, per 1000 atoms: 0.31 Number of scatterers: 8000 At special positions: 0 Unit cell: (108.206, 106.554, 83.426, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) K 4 19.00 S 56 16.00 O 1356 8.00 N 1332 7.00 C 5252 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.60 Conformation dependent library (CDL) restraints added in 371.4 milliseconds 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1952 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 0 sheets defined 82.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'B' and resid 166 through 177 Processing helix chain 'B' and resid 182 through 205 Processing helix chain 'B' and resid 220 through 225 Processing helix chain 'B' and resid 225 through 250 Processing helix chain 'B' and resid 253 through 260 Processing helix chain 'B' and resid 260 through 280 Proline residue: B 272 - end of helix Processing helix chain 'B' and resid 288 through 296 Processing helix chain 'B' and resid 297 through 306 removed outlier: 3.507A pdb=" N ARG B 305 " --> pdb=" O LYS B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 320 Processing helix chain 'B' and resid 321 through 347 Processing helix chain 'B' and resid 356 through 369 removed outlier: 3.939A pdb=" N TRP B 362 " --> pdb=" O PRO B 358 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N TYR B 363 " --> pdb=" O ALA B 359 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 400 removed outlier: 3.640A pdb=" N LEU B 396 " --> pdb=" O LEU B 392 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ALA B 399 " --> pdb=" O VAL B 395 " (cutoff:3.500A) Processing helix chain 'B' and resid 401 through 424 Processing helix chain 'C' and resid 167 through 177 Processing helix chain 'C' and resid 178 through 180 No H-bonds generated for 'chain 'C' and resid 178 through 180' Processing helix chain 'C' and resid 181 through 205 Processing helix chain 'C' and resid 220 through 225 removed outlier: 3.538A pdb=" N TYR C 225 " --> pdb=" O CYS C 221 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 250 Processing helix chain 'C' and resid 253 through 260 Processing helix chain 'C' and resid 260 through 278 Proline residue: C 272 - end of helix Processing helix chain 'C' and resid 287 through 295 Processing helix chain 'C' and resid 298 through 307 removed outlier: 3.802A pdb=" N LYS C 302 " --> pdb=" O PHE C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 311 through 347 removed outlier: 5.359A pdb=" N SER C 322 " --> pdb=" O LYS C 318 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N GLU C 323 " --> pdb=" O SER C 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 356 through 369 removed outlier: 3.844A pdb=" N TRP C 362 " --> pdb=" O PRO C 358 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N TYR C 363 " --> pdb=" O ALA C 359 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 400 Processing helix chain 'C' and resid 400 through 423 removed outlier: 4.419A pdb=" N VAL C 404 " --> pdb=" O LEU C 400 " (cutoff:3.500A) Processing helix chain 'D' and resid 167 through 177 Processing helix chain 'D' and resid 182 through 205 Processing helix chain 'D' and resid 220 through 225 Processing helix chain 'D' and resid 225 through 250 Processing helix chain 'D' and resid 253 through 260 Processing helix chain 'D' and resid 260 through 280 Proline residue: D 272 - end of helix Processing helix chain 'D' and resid 288 through 296 Processing helix chain 'D' and resid 297 through 306 removed outlier: 3.507A pdb=" N ARG D 305 " --> pdb=" O LYS D 302 " (cutoff:3.500A) Processing helix chain 'D' and resid 307 through 320 Processing helix chain 'D' and resid 321 through 347 Processing helix chain 'D' and resid 356 through 369 removed outlier: 3.939A pdb=" N TRP D 362 " --> pdb=" O PRO D 358 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N TYR D 363 " --> pdb=" O ALA D 359 " (cutoff:3.500A) Processing helix chain 'D' and resid 380 through 400 removed outlier: 3.640A pdb=" N LEU D 396 " --> pdb=" O LEU D 392 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ALA D 399 " --> pdb=" O VAL D 395 " (cutoff:3.500A) Processing helix chain 'D' and resid 401 through 424 Processing helix chain 'A' and resid 167 through 177 Processing helix chain 'A' and resid 178 through 180 No H-bonds generated for 'chain 'A' and resid 178 through 180' Processing helix chain 'A' and resid 181 through 205 Processing helix chain 'A' and resid 220 through 225 removed outlier: 3.538A pdb=" N TYR A 225 " --> pdb=" O CYS A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 250 Processing helix chain 'A' and resid 253 through 260 Processing helix chain 'A' and resid 260 through 278 Proline residue: A 272 - end of helix Processing helix chain 'A' and resid 287 through 295 Processing helix chain 'A' and resid 298 through 307 removed outlier: 3.803A pdb=" N LYS A 302 " --> pdb=" O PHE A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 347 removed outlier: 5.359A pdb=" N SER A 322 " --> pdb=" O LYS A 318 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N GLU A 323 " --> pdb=" O SER A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 369 removed outlier: 3.844A pdb=" N TRP A 362 " --> pdb=" O PRO A 358 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N TYR A 363 " --> pdb=" O ALA A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 400 Processing helix chain 'A' and resid 400 through 423 removed outlier: 4.420A pdb=" N VAL A 404 " --> pdb=" O LEU A 400 " (cutoff:3.500A) 617 hydrogen bonds defined for protein. 1815 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: 1.17 Time building geometry restraints manager: 0.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2436 1.34 - 1.46: 1525 1.46 - 1.57: 4139 1.57 - 1.69: 0 1.69 - 1.81: 88 Bond restraints: 8188 Sorted by residual: bond pdb=" CB GLU C 346 " pdb=" CG GLU C 346 " ideal model delta sigma weight residual 1.520 1.480 0.040 3.00e-02 1.11e+03 1.81e+00 bond pdb=" CB GLU A 346 " pdb=" CG GLU A 346 " ideal model delta sigma weight residual 1.520 1.480 0.040 3.00e-02 1.11e+03 1.79e+00 bond pdb=" CG GLU A 346 " pdb=" CD GLU A 346 " ideal model delta sigma weight residual 1.516 1.483 0.033 2.50e-02 1.60e+03 1.76e+00 bond pdb=" CG GLU C 346 " pdb=" CD GLU C 346 " ideal model delta sigma weight residual 1.516 1.483 0.033 2.50e-02 1.60e+03 1.76e+00 bond pdb=" CB LEU D 371 " pdb=" CG LEU D 371 " ideal model delta sigma weight residual 1.530 1.504 0.026 2.00e-02 2.50e+03 1.63e+00 ... (remaining 8183 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.68: 10814 1.68 - 3.37: 244 3.37 - 5.05: 52 5.05 - 6.74: 8 6.74 - 8.42: 6 Bond angle restraints: 11124 Sorted by residual: angle pdb=" C PHE A 175 " pdb=" N GLU A 176 " pdb=" CA GLU A 176 " ideal model delta sigma weight residual 122.38 114.93 7.45 1.81e+00 3.05e-01 1.70e+01 angle pdb=" C PHE C 175 " pdb=" N GLU C 176 " pdb=" CA GLU C 176 " ideal model delta sigma weight residual 122.38 114.93 7.45 1.81e+00 3.05e-01 1.69e+01 angle pdb=" C ILE B 270 " pdb=" CA ILE B 270 " pdb=" CB ILE B 270 " ideal model delta sigma weight residual 111.65 107.18 4.47 1.41e+00 5.03e-01 1.00e+01 angle pdb=" C ILE D 270 " pdb=" CA ILE D 270 " pdb=" CB ILE D 270 " ideal model delta sigma weight residual 111.65 107.20 4.45 1.41e+00 5.03e-01 9.98e+00 angle pdb=" N GLU A 176 " pdb=" CA GLU A 176 " pdb=" CB GLU A 176 " ideal model delta sigma weight residual 110.44 114.14 -3.70 1.53e+00 4.27e-01 5.84e+00 ... (remaining 11119 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.23: 4334 16.23 - 32.46: 376 32.46 - 48.69: 72 48.69 - 64.93: 6 64.93 - 81.16: 4 Dihedral angle restraints: 4792 sinusoidal: 1760 harmonic: 3032 Sorted by residual: dihedral pdb=" CA ARG C 293 " pdb=" C ARG C 293 " pdb=" N VAL C 294 " pdb=" CA VAL C 294 " ideal model delta harmonic sigma weight residual 180.00 159.06 20.94 0 5.00e+00 4.00e-02 1.75e+01 dihedral pdb=" CA ARG A 293 " pdb=" C ARG A 293 " pdb=" N VAL A 294 " pdb=" CA VAL A 294 " ideal model delta harmonic sigma weight residual 180.00 159.13 20.87 0 5.00e+00 4.00e-02 1.74e+01 dihedral pdb=" CA THR A 370 " pdb=" C THR A 370 " pdb=" N LEU A 371 " pdb=" CA LEU A 371 " ideal model delta harmonic sigma weight residual 180.00 163.69 16.31 0 5.00e+00 4.00e-02 1.06e+01 ... (remaining 4789 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 793 0.035 - 0.070: 388 0.070 - 0.106: 92 0.106 - 0.141: 43 0.141 - 0.176: 4 Chirality restraints: 1320 Sorted by residual: chirality pdb=" CA GLU B 176 " pdb=" N GLU B 176 " pdb=" C GLU B 176 " pdb=" CB GLU B 176 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.76e-01 chirality pdb=" CA GLU D 176 " pdb=" N GLU D 176 " pdb=" C GLU D 176 " pdb=" CB GLU D 176 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.55e-01 chirality pdb=" CA PHE C 194 " pdb=" N PHE C 194 " pdb=" C PHE C 194 " pdb=" CB PHE C 194 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.21e-01 ... (remaining 1317 not shown) Planarity restraints: 1360 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 172 " 0.020 2.00e-02 2.50e+03 1.61e-02 6.51e+00 pdb=" CG TRP B 172 " -0.042 2.00e-02 2.50e+03 pdb=" CD1 TRP B 172 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 TRP B 172 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP B 172 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP B 172 " -0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP B 172 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 172 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 172 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP B 172 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 172 " -0.020 2.00e-02 2.50e+03 1.61e-02 6.47e+00 pdb=" CG TRP D 172 " 0.041 2.00e-02 2.50e+03 pdb=" CD1 TRP D 172 " -0.020 2.00e-02 2.50e+03 pdb=" CD2 TRP D 172 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP D 172 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP D 172 " 0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP D 172 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 172 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 172 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP D 172 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU D 346 " -0.008 2.00e-02 2.50e+03 1.62e-02 2.63e+00 pdb=" CD GLU D 346 " 0.028 2.00e-02 2.50e+03 pdb=" OE1 GLU D 346 " -0.010 2.00e-02 2.50e+03 pdb=" OE2 GLU D 346 " -0.010 2.00e-02 2.50e+03 ... (remaining 1357 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.73: 661 2.73 - 3.33: 10452 3.33 - 3.93: 15425 3.93 - 4.54: 21774 4.54 - 5.14: 32004 Nonbonded interactions: 80316 Sorted by model distance: nonbonded pdb=" OH TYR C 188 " pdb=" O HIS C 306 " model vdw 2.127 3.040 nonbonded pdb=" OH TYR A 188 " pdb=" O HIS A 306 " model vdw 2.128 3.040 nonbonded pdb=" OE2 GLU D 205 " pdb=" NH2 ARG D 293 " model vdw 2.282 3.120 nonbonded pdb=" OE2 GLU B 205 " pdb=" NH2 ARG B 293 " model vdw 2.283 3.120 nonbonded pdb=" OG1 THR D 367 " pdb=" OH TYR A 373 " model vdw 2.307 3.040 ... (remaining 80311 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 Found NCS groups: ncs_group { reference = (chain 'A' and resid 166 through 424) selection = (chain 'B' and resid 166 through 424) selection = chain 'C' selection = chain 'D' } 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: 3.480 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: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.420 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 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 : 0.006 0.047 8188 Z= 0.234 Angle : 0.670 8.420 11124 Z= 0.385 Chirality : 0.045 0.176 1320 Planarity : 0.004 0.037 1360 Dihedral : 12.536 81.157 2840 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 0.24 % Allowed : 0.00 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.26), residues: 1028 helix: 0.61 (0.18), residues: 812 sheet: None (None), residues: 0 loop : -0.42 (0.47), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 296 TYR 0.015 0.002 TYR B 188 PHE 0.017 0.002 PHE C 175 TRP 0.042 0.004 TRP B 172 HIS 0.006 0.001 HIS A 306 Details of bonding type rmsd covalent geometry : bond 0.00563 ( 8188) covalent geometry : angle 0.67040 (11124) hydrogen bonds : bond 0.11899 ( 617) hydrogen bonds : angle 5.28877 ( 1815) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 143 time to evaluate : 0.262 Fit side-chains REVERT: D 187 PHE cc_start: 0.7783 (t80) cc_final: 0.7431 (t80) REVERT: D 418 ARG cc_start: 0.7889 (mtp85) cc_final: 0.7585 (ptm160) outliers start: 2 outliers final: 1 residues processed: 143 average time/residue: 0.5557 time to fit residues: 84.2414 Evaluate side-chains 117 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 116 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 0.6980 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 0.6980 chunk 61 optimal weight: 5.9990 chunk 45 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 177 ASN C 408 ASN D 177 ASN A 408 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.177718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.115273 restraints weight = 9399.723| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 2.38 r_work: 0.3140 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.1152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8188 Z= 0.154 Angle : 0.560 7.394 11124 Z= 0.300 Chirality : 0.042 0.142 1320 Planarity : 0.005 0.042 1360 Dihedral : 4.203 23.826 1150 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.90 % Allowed : 11.49 % Favored : 86.61 % 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: 1.21 (0.27), residues: 1028 helix: 1.12 (0.18), residues: 808 sheet: None (None), residues: 0 loop : -0.13 (0.48), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 247 TYR 0.015 0.001 TYR D 188 PHE 0.015 0.001 PHE A 257 TRP 0.016 0.002 TRP D 172 HIS 0.002 0.001 HIS B 306 Details of bonding type rmsd covalent geometry : bond 0.00361 ( 8188) covalent geometry : angle 0.56010 (11124) hydrogen bonds : bond 0.04287 ( 617) hydrogen bonds : angle 4.22552 ( 1815) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 127 time to evaluate : 0.349 Fit side-chains REVERT: B 207 VAL cc_start: 0.8433 (t) cc_final: 0.8056 (m) REVERT: B 241 THR cc_start: 0.7630 (m) cc_final: 0.7351 (p) REVERT: D 241 THR cc_start: 0.7617 (m) cc_final: 0.7356 (p) REVERT: D 308 GLN cc_start: 0.7292 (tm-30) cc_final: 0.7091 (tm-30) REVERT: D 418 ARG cc_start: 0.7919 (mtp85) cc_final: 0.7546 (ptm160) outliers start: 16 outliers final: 5 residues processed: 133 average time/residue: 0.5380 time to fit residues: 75.8051 Evaluate side-chains 128 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 123 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 404 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 1 optimal weight: 2.9990 chunk 92 optimal weight: 0.5980 chunk 51 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 chunk 2 optimal weight: 0.9980 chunk 5 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 95 optimal weight: 0.0980 chunk 57 optimal weight: 3.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 177 ASN C 408 ASN D 177 ASN A 408 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.178200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 98)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.130936 restraints weight = 9417.383| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 1.52 r_work: 0.3218 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3099 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.1367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8188 Z= 0.163 Angle : 0.538 6.996 11124 Z= 0.287 Chirality : 0.041 0.175 1320 Planarity : 0.005 0.045 1360 Dihedral : 4.036 24.011 1150 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.25 % Allowed : 13.15 % Favored : 84.60 % 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: 1.42 (0.26), residues: 1028 helix: 1.25 (0.18), residues: 816 sheet: None (None), residues: 0 loop : 0.04 (0.48), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 247 TYR 0.015 0.001 TYR D 188 PHE 0.017 0.001 PHE C 257 TRP 0.009 0.002 TRP B 172 HIS 0.002 0.001 HIS B 306 Details of bonding type rmsd covalent geometry : bond 0.00393 ( 8188) covalent geometry : angle 0.53797 (11124) hydrogen bonds : bond 0.04210 ( 617) hydrogen bonds : angle 4.06713 ( 1815) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 134 time to evaluate : 0.296 Fit side-chains REVERT: B 241 THR cc_start: 0.8434 (m) cc_final: 0.8230 (p) outliers start: 19 outliers final: 8 residues processed: 144 average time/residue: 0.5670 time to fit residues: 86.4781 Evaluate side-chains 125 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 117 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 263 SER Chi-restraints excluded: chain C residue 333 MET Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain D residue 415 GLN Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 404 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 58 optimal weight: 6.9990 chunk 81 optimal weight: 2.9990 chunk 25 optimal weight: 9.9990 chunk 31 optimal weight: 2.9990 chunk 88 optimal weight: 0.7980 chunk 52 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 20 optimal weight: 0.6980 chunk 32 optimal weight: 0.8980 chunk 14 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 177 ASN C 408 ASN D 177 ASN A 408 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.178017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.128990 restraints weight = 9560.273| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 1.60 r_work: 0.3210 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3097 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.1628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 8188 Z= 0.160 Angle : 0.547 6.689 11124 Z= 0.293 Chirality : 0.041 0.146 1320 Planarity : 0.005 0.044 1360 Dihedral : 3.943 24.989 1150 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.01 % Allowed : 15.40 % Favored : 82.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.52 (0.26), residues: 1028 helix: 1.34 (0.18), residues: 818 sheet: None (None), residues: 0 loop : -0.06 (0.47), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 247 TYR 0.015 0.001 TYR D 188 PHE 0.020 0.001 PHE A 257 TRP 0.011 0.002 TRP A 172 HIS 0.002 0.001 HIS C 179 Details of bonding type rmsd covalent geometry : bond 0.00386 ( 8188) covalent geometry : angle 0.54729 (11124) hydrogen bonds : bond 0.04093 ( 617) hydrogen bonds : angle 3.98118 ( 1815) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 121 time to evaluate : 0.303 Fit side-chains REVERT: B 308 GLN cc_start: 0.7584 (tm-30) cc_final: 0.7316 (tm-30) REVERT: C 275 ILE cc_start: 0.8628 (mp) cc_final: 0.8412 (mt) outliers start: 17 outliers final: 7 residues processed: 129 average time/residue: 0.5900 time to fit residues: 80.5402 Evaluate side-chains 119 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 112 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain D residue 323 GLU Chi-restraints excluded: chain D residue 415 GLN Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 404 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 87 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 16 optimal weight: 0.9980 chunk 40 optimal weight: 0.8980 chunk 75 optimal weight: 9.9990 chunk 37 optimal weight: 3.9990 chunk 65 optimal weight: 0.9980 chunk 88 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 177 ASN C 408 ASN D 177 ASN A 408 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.176380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.131155 restraints weight = 9545.166| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 1.68 r_work: 0.3179 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.1676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 8188 Z= 0.182 Angle : 0.559 6.505 11124 Z= 0.297 Chirality : 0.042 0.196 1320 Planarity : 0.005 0.045 1360 Dihedral : 3.868 17.590 1148 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.37 % Allowed : 16.94 % Favored : 80.69 % 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: 1.55 (0.26), residues: 1028 helix: 1.34 (0.18), residues: 818 sheet: None (None), residues: 0 loop : 0.09 (0.47), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 293 TYR 0.014 0.001 TYR D 188 PHE 0.024 0.001 PHE A 257 TRP 0.011 0.002 TRP C 172 HIS 0.002 0.001 HIS D 306 Details of bonding type rmsd covalent geometry : bond 0.00445 ( 8188) covalent geometry : angle 0.55890 (11124) hydrogen bonds : bond 0.04181 ( 617) hydrogen bonds : angle 3.97414 ( 1815) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 113 time to evaluate : 0.242 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 308 GLN cc_start: 0.7626 (tm-30) cc_final: 0.7357 (tm-30) outliers start: 20 outliers final: 12 residues processed: 126 average time/residue: 0.6046 time to fit residues: 80.3812 Evaluate side-chains 122 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 110 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 415 GLN Chi-restraints excluded: chain C residue 176 GLU Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 275 ILE Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 323 GLU Chi-restraints excluded: chain D residue 415 GLN Chi-restraints excluded: chain A residue 176 GLU Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 404 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 36 optimal weight: 0.0670 chunk 84 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 69 optimal weight: 0.8980 chunk 27 optimal weight: 0.5980 chunk 74 optimal weight: 0.9990 chunk 39 optimal weight: 4.9990 chunk 61 optimal weight: 5.9990 chunk 28 optimal weight: 0.9990 overall best weight: 0.7122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 177 ASN C 408 ASN D 177 ASN A 408 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.178805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.134095 restraints weight = 9465.335| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 1.65 r_work: 0.3195 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.1860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8188 Z= 0.141 Angle : 0.532 6.747 11124 Z= 0.281 Chirality : 0.040 0.146 1320 Planarity : 0.005 0.044 1360 Dihedral : 3.774 17.613 1148 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.13 % Allowed : 17.77 % Favored : 80.09 % 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: 1.78 (0.26), residues: 1028 helix: 1.49 (0.18), residues: 818 sheet: None (None), residues: 0 loop : 0.19 (0.47), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 247 TYR 0.014 0.001 TYR D 188 PHE 0.027 0.001 PHE A 257 TRP 0.012 0.002 TRP C 172 HIS 0.001 0.000 HIS D 306 Details of bonding type rmsd covalent geometry : bond 0.00332 ( 8188) covalent geometry : angle 0.53184 (11124) hydrogen bonds : bond 0.03898 ( 617) hydrogen bonds : angle 3.89194 ( 1815) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 121 time to evaluate : 0.192 Fit side-chains revert: symmetry clash REVERT: B 308 GLN cc_start: 0.7677 (tm-30) cc_final: 0.7392 (tm-30) REVERT: D 308 GLN cc_start: 0.7653 (tm-30) cc_final: 0.7444 (tm-30) outliers start: 18 outliers final: 9 residues processed: 131 average time/residue: 0.5959 time to fit residues: 82.4140 Evaluate side-chains 121 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 112 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 415 GLN Chi-restraints excluded: chain C residue 176 GLU Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 275 ILE Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain D residue 323 GLU Chi-restraints excluded: chain D residue 415 GLN Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 404 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 58 optimal weight: 0.0470 chunk 21 optimal weight: 0.5980 chunk 54 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 12 optimal weight: 0.1980 chunk 71 optimal weight: 0.8980 chunk 68 optimal weight: 0.7980 chunk 99 optimal weight: 0.6980 chunk 70 optimal weight: 0.9980 chunk 44 optimal weight: 0.9980 chunk 59 optimal weight: 0.7980 overall best weight: 0.4678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 177 ASN C 408 ASN D 177 ASN A 408 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.180535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.132277 restraints weight = 9503.896| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 1.64 r_work: 0.3267 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3153 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.2033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8188 Z= 0.124 Angle : 0.537 8.617 11124 Z= 0.280 Chirality : 0.039 0.159 1320 Planarity : 0.005 0.045 1360 Dihedral : 3.695 17.711 1148 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.01 % Allowed : 19.43 % Favored : 78.55 % 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: 1.85 (0.26), residues: 1028 helix: 1.57 (0.18), residues: 818 sheet: None (None), residues: 0 loop : 0.06 (0.45), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 247 TYR 0.013 0.001 TYR D 188 PHE 0.031 0.001 PHE A 257 TRP 0.013 0.002 TRP C 172 HIS 0.001 0.000 HIS B 306 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 8188) covalent geometry : angle 0.53699 (11124) hydrogen bonds : bond 0.03655 ( 617) hydrogen bonds : angle 3.82309 ( 1815) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 127 time to evaluate : 0.256 Fit side-chains REVERT: B 308 GLN cc_start: 0.7626 (tm-30) cc_final: 0.7309 (tm-30) REVERT: D 308 GLN cc_start: 0.7624 (tm-30) cc_final: 0.7408 (tm-30) outliers start: 17 outliers final: 9 residues processed: 138 average time/residue: 0.5813 time to fit residues: 84.7895 Evaluate side-chains 123 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 114 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 415 GLN Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 275 ILE Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain D residue 415 GLN Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 404 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 68 optimal weight: 1.9990 chunk 75 optimal weight: 10.0000 chunk 66 optimal weight: 0.6980 chunk 5 optimal weight: 0.0980 chunk 99 optimal weight: 0.6980 chunk 40 optimal weight: 3.9990 chunk 38 optimal weight: 0.6980 chunk 4 optimal weight: 0.8980 chunk 46 optimal weight: 0.5980 chunk 67 optimal weight: 0.3980 chunk 56 optimal weight: 2.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 177 ASN C 408 ASN D 177 ASN A 408 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.180595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.134251 restraints weight = 9596.637| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 1.66 r_work: 0.3265 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3162 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.2133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8188 Z= 0.128 Angle : 0.543 9.170 11124 Z= 0.283 Chirality : 0.040 0.144 1320 Planarity : 0.005 0.043 1360 Dihedral : 3.628 17.043 1148 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.54 % Allowed : 21.56 % Favored : 76.90 % 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: 1.90 (0.26), residues: 1028 helix: 1.63 (0.18), residues: 818 sheet: None (None), residues: 0 loop : 0.00 (0.45), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 411 TYR 0.012 0.001 TYR D 188 PHE 0.032 0.001 PHE C 257 TRP 0.012 0.002 TRP C 172 HIS 0.002 0.000 HIS D 306 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 8188) covalent geometry : angle 0.54323 (11124) hydrogen bonds : bond 0.03656 ( 617) hydrogen bonds : angle 3.80316 ( 1815) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 123 time to evaluate : 0.331 Fit side-chains REVERT: B 308 GLN cc_start: 0.7684 (tm-30) cc_final: 0.7372 (tm-30) REVERT: D 308 GLN cc_start: 0.7705 (tm-30) cc_final: 0.7486 (tm-30) outliers start: 13 outliers final: 6 residues processed: 130 average time/residue: 0.6000 time to fit residues: 82.4434 Evaluate side-chains 122 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 116 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 415 GLN Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain D residue 415 GLN Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 404 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 33 optimal weight: 2.9990 chunk 36 optimal weight: 0.0670 chunk 20 optimal weight: 0.0980 chunk 39 optimal weight: 0.4980 chunk 19 optimal weight: 0.7980 chunk 24 optimal weight: 0.8980 chunk 32 optimal weight: 0.8980 chunk 48 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 26 optimal weight: 0.9990 chunk 75 optimal weight: 9.9990 overall best weight: 0.4518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 177 ASN C 408 ASN D 177 ASN A 408 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.181392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.137480 restraints weight = 9402.295| |-----------------------------------------------------------------------------| r_work (start): 0.3589 rms_B_bonded: 1.65 r_work: 0.3246 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.2251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8188 Z= 0.127 Angle : 0.561 10.316 11124 Z= 0.288 Chirality : 0.039 0.140 1320 Planarity : 0.004 0.043 1360 Dihedral : 3.606 16.535 1148 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.66 % Allowed : 21.80 % Favored : 76.54 % 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: 1.97 (0.26), residues: 1028 helix: 1.66 (0.18), residues: 820 sheet: None (None), residues: 0 loop : 0.06 (0.44), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 247 TYR 0.012 0.001 TYR D 188 PHE 0.038 0.001 PHE C 257 TRP 0.011 0.002 TRP B 172 HIS 0.002 0.000 HIS D 306 Details of bonding type rmsd covalent geometry : bond 0.00293 ( 8188) covalent geometry : angle 0.56082 (11124) hydrogen bonds : bond 0.03584 ( 617) hydrogen bonds : angle 3.77922 ( 1815) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 123 time to evaluate : 0.314 Fit side-chains REVERT: B 308 GLN cc_start: 0.7681 (tm-30) cc_final: 0.7378 (tm-30) REVERT: D 308 GLN cc_start: 0.7716 (tm-30) cc_final: 0.7502 (tm-30) outliers start: 14 outliers final: 7 residues processed: 133 average time/residue: 0.5790 time to fit residues: 81.2462 Evaluate side-chains 127 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 120 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 415 GLN Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain D residue 323 GLU Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 404 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 24 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 34 optimal weight: 7.9990 chunk 61 optimal weight: 0.0170 chunk 29 optimal weight: 0.0010 chunk 81 optimal weight: 0.6980 chunk 40 optimal weight: 0.9980 chunk 86 optimal weight: 0.8980 chunk 82 optimal weight: 0.7980 chunk 14 optimal weight: 5.9990 overall best weight: 0.4824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 177 ASN C 408 ASN D 177 ASN A 408 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.181168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.131086 restraints weight = 9449.419| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 1.67 r_work: 0.3221 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.2319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8188 Z= 0.128 Angle : 0.564 10.487 11124 Z= 0.292 Chirality : 0.039 0.136 1320 Planarity : 0.004 0.041 1360 Dihedral : 3.599 16.132 1148 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.07 % Allowed : 22.75 % Favored : 76.18 % 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: 2.05 (0.26), residues: 1028 helix: 1.73 (0.18), residues: 812 sheet: None (None), residues: 0 loop : 0.09 (0.43), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 170 TYR 0.012 0.001 TYR B 188 PHE 0.042 0.001 PHE C 257 TRP 0.014 0.002 TRP B 172 HIS 0.002 0.000 HIS D 306 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 8188) covalent geometry : angle 0.56360 (11124) hydrogen bonds : bond 0.03614 ( 617) hydrogen bonds : angle 3.76859 ( 1815) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 123 time to evaluate : 0.307 Fit side-chains REVERT: B 308 GLN cc_start: 0.7708 (tm-30) cc_final: 0.7385 (tm-30) REVERT: D 308 GLN cc_start: 0.7704 (tm-30) cc_final: 0.7477 (tm-30) outliers start: 9 outliers final: 7 residues processed: 129 average time/residue: 0.6045 time to fit residues: 82.3211 Evaluate side-chains 124 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 117 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 415 GLN Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain D residue 323 GLU Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 404 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 77 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 81 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 21 optimal weight: 0.9990 chunk 72 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 177 ASN C 408 ASN D 177 ASN A 408 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.176844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.129527 restraints weight = 9402.329| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 1.78 r_work: 0.3182 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3056 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.2109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 8188 Z= 0.214 Angle : 0.631 10.214 11124 Z= 0.327 Chirality : 0.043 0.145 1320 Planarity : 0.005 0.052 1360 Dihedral : 3.786 15.646 1148 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.30 % Allowed : 23.22 % Favored : 75.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.78 (0.26), residues: 1028 helix: 1.56 (0.18), residues: 810 sheet: None (None), residues: 0 loop : -0.08 (0.43), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 296 TYR 0.012 0.001 TYR D 188 PHE 0.048 0.002 PHE C 257 TRP 0.015 0.002 TRP B 172 HIS 0.002 0.001 HIS D 306 Details of bonding type rmsd covalent geometry : bond 0.00535 ( 8188) covalent geometry : angle 0.63063 (11124) hydrogen bonds : bond 0.04186 ( 617) hydrogen bonds : angle 3.89741 ( 1815) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3115.12 seconds wall clock time: 53 minutes 54.04 seconds (3234.04 seconds total)