Starting phenix.real_space_refine on Thu Jul 2 03:09:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gml_51450/07_2026/9gml_51450.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gml_51450/07_2026/9gml_51450.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9gml_51450/07_2026/9gml_51450.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gml_51450/07_2026/9gml_51450.map" model { file = "/net/cci-nas-00/data/ceres_data/9gml_51450/07_2026/9gml_51450.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gml_51450/07_2026/9gml_51450.cif" } resolution = 3.12 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= 0.037 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 Ni 2 6.56 5 S 30 5.16 5 C 3788 2.51 5 N 1046 2.21 5 O 1186 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6052 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 777 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 94} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CXM:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 952 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain: "C" Number of atoms: 4318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 570, 4318 Classifications: {'peptide': 570} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 25, 'TRANS': 541} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 3 Ad-hoc single atom residues: {' NI': 2} Unusual residues: {' OH': 1} Classifications: {'undetermined': 1, 'water': 2} Link IDs: {None: 2} Chain breaks: 2 Residues with excluded nonbonded symmetry interactions: 16 residue: pdb=" N GLN A 12 " occ=0.50 ... (7 atoms not shown) pdb=" NE2 GLN A 12 " occ=0.50 residue: pdb=" N ARG A 66 " occ=0.50 ... (9 atoms not shown) pdb=" NH2 ARG A 66 " occ=0.50 residue: pdb=" N ASP A 67 " occ=0.50 ... (6 atoms not shown) pdb=" OD2 ASP A 67 " occ=0.50 residue: pdb=" N ASP A 79 " occ=0.50 ... (6 atoms not shown) pdb=" OD2 ASP A 79 " occ=0.50 residue: pdb=" N SER B 33 " occ=0.70 ... (4 atoms not shown) pdb=" OG SER B 33 " occ=0.70 residue: pdb=" N GLU B 54 " occ=0.70 ... (7 atoms not shown) pdb=" OE2 GLU B 54 " occ=0.70 residue: pdb=" N GLU B 111 " occ=0.50 ... (7 atoms not shown) pdb=" OE2 GLU B 111 " occ=0.50 residue: pdb=" N ARG C 5 " occ=0.50 ... (9 atoms not shown) pdb=" NH2 ARG C 5 " occ=0.50 residue: pdb=" N ASP C 26 " occ=0.50 ... (6 atoms not shown) pdb=" OD2 ASP C 26 " occ=0.50 residue: pdb=" N LYS C 48 " occ=0.50 ... (7 atoms not shown) pdb=" NZ LYS C 48 " occ=0.50 residue: pdb=" N LYS C 185 " occ=0.50 ... (7 atoms not shown) pdb=" NZ LYS C 185 " occ=0.50 residue: pdb=" N MET C 360 " occ=0.50 ... (6 atoms not shown) pdb=" CE MET C 360 " occ=0.50 ... (remaining 4 not shown) Time building chain proxies: 1.31, per 1000 atoms: 0.22 Number of scatterers: 6052 At special positions: 0 Unit cell: (114.24, 81.6, 81.6, 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) Ni 2 28.00 S 30 16.00 O 1186 8.00 N 1046 7.00 C 3788 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: 0.54 Conformation dependent library (CDL) restraints added in 228.3 milliseconds 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1416 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 11 sheets defined 33.8% alpha, 18.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'A' and resid 4 through 27 removed outlier: 3.634A pdb=" N LYS A 8 " --> pdb=" O ASN A 4 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N GLN A 12 " --> pdb=" O LYS A 8 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ILE A 13 " --> pdb=" O GLU A 9 " (cutoff:3.500A) Processing helix chain 'A' and resid 31 through 50 Processing helix chain 'A' and resid 52 through 60 Processing helix chain 'A' and resid 61 through 63 No H-bonds generated for 'chain 'A' and resid 61 through 63' Processing helix chain 'A' and resid 72 through 76 Processing helix chain 'B' and resid 109 through 120 removed outlier: 3.647A pdb=" N ILE B 113 " --> pdb=" O ASN B 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 5 through 12 Processing helix chain 'C' and resid 144 through 151 removed outlier: 3.996A pdb=" N VAL C 148 " --> pdb=" O ASP C 144 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 171 Processing helix chain 'C' and resid 175 through 187 removed outlier: 4.158A pdb=" N ASN C 179 " --> pdb=" O PRO C 175 " (cutoff:3.500A) Processing helix chain 'C' and resid 188 through 190 No H-bonds generated for 'chain 'C' and resid 188 through 190' Processing helix chain 'C' and resid 204 through 213 removed outlier: 3.983A pdb=" N ILE C 208 " --> pdb=" O SER C 204 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLN C 211 " --> pdb=" O PRO C 207 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ILE C 212 " --> pdb=" O ILE C 208 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 226 Processing helix chain 'C' and resid 228 through 243 Processing helix chain 'C' and resid 258 through 267 removed outlier: 3.659A pdb=" N THR C 262 " --> pdb=" O PHE C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 285 through 293 removed outlier: 4.529A pdb=" N MET C 288 " --> pdb=" O PRO C 285 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA C 289 " --> pdb=" O ASP C 286 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N HIS C 293 " --> pdb=" O MET C 290 " (cutoff:3.500A) Processing helix chain 'C' and resid 310 through 323 removed outlier: 3.547A pdb=" N GLU C 314 " --> pdb=" O ASN C 310 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N HIS C 323 " --> pdb=" O LEU C 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 329 through 340 removed outlier: 3.864A pdb=" N VAL C 333 " --> pdb=" O ILE C 329 " (cutoff:3.500A) Processing helix chain 'C' and resid 341 through 354 removed outlier: 3.559A pdb=" N ILE C 345 " --> pdb=" O ARG C 341 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ILE C 350 " --> pdb=" O ALA C 346 " (cutoff:3.500A) Processing helix chain 'C' and resid 369 through 371 No H-bonds generated for 'chain 'C' and resid 369 through 371' Processing helix chain 'C' and resid 372 through 389 Processing helix chain 'C' and resid 399 through 408 Processing helix chain 'C' and resid 412 through 419 Processing helix chain 'C' and resid 439 through 443 removed outlier: 3.650A pdb=" N PHE C 443 " --> pdb=" O PRO C 440 " (cutoff:3.500A) Processing helix chain 'C' and resid 480 through 483 removed outlier: 3.571A pdb=" N VAL C 483 " --> pdb=" O TYR C 480 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 480 through 483' Processing helix chain 'C' and resid 485 through 489 Processing helix chain 'C' and resid 497 through 502 Processing helix chain 'C' and resid 503 through 509 Processing sheet with id=AA1, first strand: chain 'A' and resid 79 through 86 Processing sheet with id=AA2, first strand: chain 'B' and resid 18 through 20 Processing sheet with id=AA3, first strand: chain 'B' and resid 55 through 56 Processing sheet with id=AA4, first strand: chain 'B' and resid 40 through 42 Processing sheet with id=AA5, first strand: chain 'B' and resid 95 through 96 Processing sheet with id=AA6, first strand: chain 'C' and resid 19 through 21 Processing sheet with id=AA7, first strand: chain 'C' and resid 33 through 34 removed outlier: 7.111A pdb=" N LYS C 33 " --> pdb=" O LYS C 84 " (cutoff:3.500A) removed outlier: 9.556A pdb=" N ASP C 86 " --> pdb=" O LYS C 33 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ILE C 87 " --> pdb=" O THR C 72 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N THR C 72 " --> pdb=" O ILE C 87 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N VAL C 89 " --> pdb=" O LEU C 70 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N LEU C 70 " --> pdb=" O VAL C 89 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N LEU C 70 " --> pdb=" O ILE C 122 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 93 through 98 removed outlier: 5.217A pdb=" N ILE C 94 " --> pdb=" O LYS C 90 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N LYS C 90 " --> pdb=" O ILE C 94 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ILE C 87 " --> pdb=" O THR C 72 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N THR C 72 " --> pdb=" O ILE C 87 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N VAL C 89 " --> pdb=" O LEU C 70 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N LEU C 70 " --> pdb=" O VAL C 89 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N VAL C 129 " --> pdb=" O ASN C 73 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N LEU C 75 " --> pdb=" O VAL C 129 " (cutoff:3.500A) removed outlier: 8.345A pdb=" N ALA C 131 " --> pdb=" O LEU C 75 " (cutoff:3.500A) removed outlier: 9.119A pdb=" N LEU C 77 " --> pdb=" O ALA C 131 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N LYS C 452 " --> pdb=" O ILE C 456 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N ILE C 456 " --> pdb=" O LYS C 452 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 133 through 139 removed outlier: 5.870A pdb=" N GLY C 133 " --> pdb=" O ILE C 154 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THR C 156 " --> pdb=" O GLY C 133 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N HIS C 137 " --> pdb=" O PHE C 158 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N GLY C 160 " --> pdb=" O HIS C 137 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N HIS C 139 " --> pdb=" O GLY C 160 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLY C 218 " --> pdb=" O ILE C 196 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N LEU C 219 " --> pdb=" O ALA C 247 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N VAL C 246 " --> pdb=" O HIS C 272 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 492 through 496 removed outlier: 6.403A pdb=" N THR C 493 " --> pdb=" O GLY C 515 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N VAL C 517 " --> pdb=" O THR C 493 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N MET C 495 " --> pdb=" O VAL C 517 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'C' and resid 538 through 539 216 hydrogen bonds defined for protein. 585 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: 0.92 Time building geometry restraints manager: 0.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2063 1.34 - 1.46: 1131 1.46 - 1.58: 2901 1.58 - 1.70: 0 1.70 - 1.82: 57 Bond restraints: 6152 Sorted by residual: bond pdb=" NZ KCX C 220 " pdb=" CX KCX C 220 " ideal model delta sigma weight residual 1.411 1.331 0.080 2.00e-02 2.50e+03 1.60e+01 bond pdb=" CE KCX C 220 " pdb=" NZ KCX C 220 " ideal model delta sigma weight residual 1.442 1.489 -0.047 2.00e-02 2.50e+03 5.48e+00 bond pdb=" SD CXM A 1 " pdb=" CE CXM A 1 " ideal model delta sigma weight residual 1.808 1.764 0.044 2.00e-02 2.50e+03 4.91e+00 bond pdb=" C CXM A 1 " pdb=" O CXM A 1 " ideal model delta sigma weight residual 1.231 1.268 -0.037 2.00e-02 2.50e+03 3.49e+00 bond pdb=" CA CXM A 1 " pdb=" C CXM A 1 " ideal model delta sigma weight residual 1.525 1.561 -0.036 2.10e-02 2.27e+03 3.01e+00 ... (remaining 6147 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.12: 8159 2.12 - 4.25: 133 4.25 - 6.37: 28 6.37 - 8.49: 6 8.49 - 10.61: 2 Bond angle restraints: 8328 Sorted by residual: angle pdb=" N VAL B 49 " pdb=" CA VAL B 49 " pdb=" C VAL B 49 " ideal model delta sigma weight residual 112.96 108.33 4.63 1.00e+00 1.00e+00 2.14e+01 angle pdb=" CB LYS C 2 " pdb=" CG LYS C 2 " pdb=" CD LYS C 2 " ideal model delta sigma weight residual 111.30 121.91 -10.61 2.30e+00 1.89e-01 2.13e+01 angle pdb=" C ALA C 23 " pdb=" CA ALA C 23 " pdb=" CB ALA C 23 " ideal model delta sigma weight residual 115.89 110.54 5.35 1.32e+00 5.74e-01 1.64e+01 angle pdb=" CA LYS B 118 " pdb=" CB LYS B 118 " pdb=" CG LYS B 118 " ideal model delta sigma weight residual 114.10 121.39 -7.29 2.00e+00 2.50e-01 1.33e+01 angle pdb=" N THR C 470 " pdb=" CA THR C 470 " pdb=" C THR C 470 " ideal model delta sigma weight residual 109.81 117.43 -7.62 2.21e+00 2.05e-01 1.19e+01 ... (remaining 8323 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.10: 3124 18.10 - 36.19: 456 36.19 - 54.29: 105 54.29 - 72.38: 13 72.38 - 90.48: 14 Dihedral angle restraints: 3712 sinusoidal: 1489 harmonic: 2223 Sorted by residual: dihedral pdb=" CA MET C 563 " pdb=" C MET C 563 " pdb=" N ALA C 564 " pdb=" CA ALA C 564 " ideal model delta harmonic sigma weight residual -180.00 -154.00 -26.00 0 5.00e+00 4.00e-02 2.70e+01 dihedral pdb=" CA TRP C 438 " pdb=" C TRP C 438 " pdb=" N GLU C 439 " pdb=" CA GLU C 439 " ideal model delta harmonic sigma weight residual 180.00 163.28 16.72 0 5.00e+00 4.00e-02 1.12e+01 dihedral pdb=" CB GLU A 83 " pdb=" CG GLU A 83 " pdb=" CD GLU A 83 " pdb=" OE1 GLU A 83 " ideal model delta sinusoidal sigma weight residual 0.00 90.48 -90.48 1 3.00e+01 1.11e-03 1.08e+01 ... (remaining 3709 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 598 0.036 - 0.073: 212 0.073 - 0.109: 100 0.109 - 0.145: 26 0.145 - 0.181: 5 Chirality restraints: 941 Sorted by residual: chirality pdb=" CA ILE C 97 " pdb=" N ILE C 97 " pdb=" C ILE C 97 " pdb=" CB ILE C 97 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 8.23e-01 chirality pdb=" CA THR C 470 " pdb=" N THR C 470 " pdb=" C THR C 470 " pdb=" CB THR C 470 " both_signs ideal model delta sigma weight residual False 2.53 2.35 0.18 2.00e-01 2.50e+01 8.04e-01 chirality pdb=" CA ASN C 302 " pdb=" N ASN C 302 " pdb=" C ASN C 302 " pdb=" CB ASN C 302 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.23e-01 ... (remaining 938 not shown) Planarity restraints: 1100 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN C 302 " 0.038 5.00e-02 4.00e+02 5.74e-02 5.27e+00 pdb=" N PRO C 303 " -0.099 5.00e-02 4.00e+02 pdb=" CA PRO C 303 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO C 303 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP C 26 " 0.011 2.00e-02 2.50e+03 2.20e-02 4.85e+00 pdb=" C ASP C 26 " -0.038 2.00e-02 2.50e+03 pdb=" O ASP C 26 " 0.014 2.00e-02 2.50e+03 pdb=" N LEU C 27 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP C 26 " 0.010 2.00e-02 2.50e+03 2.02e-02 4.10e+00 pdb=" CG ASP C 26 " -0.035 2.00e-02 2.50e+03 pdb=" OD1 ASP C 26 " 0.013 2.00e-02 2.50e+03 pdb=" OD2 ASP C 26 " 0.012 2.00e-02 2.50e+03 ... (remaining 1097 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 69 2.54 - 3.13: 4787 3.13 - 3.72: 9497 3.72 - 4.31: 12744 4.31 - 4.90: 21826 Nonbonded interactions: 48923 Sorted by model distance: nonbonded pdb=" NE2 HIS C 137 " pdb="NI NI C 602 " model vdw 1.950 3.000 nonbonded pdb=" NE2 HIS C 275 " pdb="NI NI C 601 " model vdw 1.963 3.000 nonbonded pdb="NI NI C 602 " pdb=" O OH C 603 " model vdw 1.969 2.920 nonbonded pdb="NI NI C 601 " pdb=" O OH C 603 " model vdw 1.975 2.920 nonbonded pdb=" OQ1 KCX C 220 " pdb="NI NI C 601 " model vdw 1.976 2.920 ... (remaining 48918 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=0.50 max=1.00 mean=0.98 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: 1.120 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: 0.020 Extract box with map and model: 0.110 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 7.120 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: 0.000 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 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 : 0.004 0.080 6152 Z= 0.166 Angle : 0.693 10.614 8328 Z= 0.364 Chirality : 0.048 0.181 941 Planarity : 0.004 0.057 1100 Dihedral : 17.847 90.481 2296 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.58 % Favored : 96.29 % Rotamer: Outliers : 0.31 % Allowed : 34.58 % Favored : 65.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % 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 (0.30), residues: 782 helix: 0.72 (0.35), residues: 231 sheet: 1.11 (0.55), residues: 94 loop : -0.91 (0.30), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 341 TYR 0.010 0.001 TYR C 12 PHE 0.006 0.001 PHE C 443 TRP 0.016 0.001 TRP C 438 HIS 0.003 0.001 HIS C 422 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.17 ( 6152) covalent geometry : angle 0.69286 / 0.36 ( 8328) hydrogen bonds : bond 0.13343 / 9.20 ( 210) hydrogen bonds : angle 6.41445 / 4.80 ( 585) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 212 time to evaluate : 0.231 Fit side-chains REVERT: A 10 LYS cc_start: 0.9027 (mmmt) cc_final: 0.8440 (pttt) REVERT: A 34 GLU cc_start: 0.8260 (pm20) cc_final: 0.7963 (pm20) REVERT: C 43 ASN cc_start: 0.8581 (OUTLIER) cc_final: 0.8354 (p0) REVERT: C 223 GLU cc_start: 0.7864 (tm-30) cc_final: 0.7663 (pt0) outliers start: 2 outliers final: 0 residues processed: 212 average time/residue: 0.0724 time to fit residues: 20.3229 Evaluate side-chains 197 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 196 time to evaluate : 0.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 43 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 49 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 5.9990 chunk 38 optimal weight: 0.0970 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 74 optimal weight: 2.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 5 ASN ** C 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 400 ASN C 488 HIS ** C 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.107436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.095211 restraints weight = 14015.633| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 3.09 r_work: 0.3362 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3366 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3366 r_free = 0.3366 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3314 r_free = 0.3314 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 19 (25 function evaluations) r_final: 0.3314 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.1211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6152 Z= 0.120 Angle : 0.615 7.708 8328 Z= 0.313 Chirality : 0.047 0.188 941 Planarity : 0.004 0.056 1100 Dihedral : 4.946 58.752 855 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.71 % Favored : 96.16 % Rotamer: Outliers : 4.36 % Allowed : 30.06 % Favored : 65.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % 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: -0.19 (0.30), residues: 782 helix: 0.93 (0.35), residues: 233 sheet: 0.86 (0.58), residues: 87 loop : -0.90 (0.29), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 264 TYR 0.016 0.001 TYR A 32 PHE 0.013 0.001 PHE A 14 TRP 0.013 0.001 TRP C 438 HIS 0.004 0.001 HIS C 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 ( 6152) covalent geometry : angle 0.61465 / 0.31 ( 8328) hydrogen bonds : bond 0.03400 / 2.41 ( 210) hydrogen bonds : angle 4.89379 / 3.71 ( 585) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 199 time to evaluate : 0.228 Fit side-chains REVERT: A 8 LYS cc_start: 0.8970 (mtmm) cc_final: 0.8575 (mtmm) REVERT: A 10 LYS cc_start: 0.9276 (mmmt) cc_final: 0.8370 (pttt) REVERT: A 49 ASP cc_start: 0.8747 (m-30) cc_final: 0.8475 (t0) REVERT: C 43 ASN cc_start: 0.8654 (p0) cc_final: 0.8198 (p0) REVERT: C 166 GLU cc_start: 0.2341 (mp0) cc_final: 0.1935 (mp0) REVERT: C 446 LYS cc_start: 0.5613 (mtpt) cc_final: 0.5357 (mtmt) REVERT: C 511 LYS cc_start: 0.9070 (mttp) cc_final: 0.8830 (mtmm) outliers start: 28 outliers final: 19 residues processed: 210 average time/residue: 0.0748 time to fit residues: 20.9782 Evaluate side-chains 214 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 195 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain A residue 81 GLN Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 83 MET Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain C residue 91 ASP Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 158 PHE Chi-restraints excluded: chain C residue 266 ILE Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 384 MET Chi-restraints excluded: chain C residue 510 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 20 optimal weight: 9.9990 chunk 7 optimal weight: 5.9990 chunk 13 optimal weight: 4.9990 chunk 16 optimal weight: 5.9990 chunk 32 optimal weight: 0.0770 chunk 73 optimal weight: 9.9990 chunk 36 optimal weight: 2.9990 chunk 23 optimal weight: 6.9990 chunk 35 optimal weight: 7.9990 chunk 47 optimal weight: 0.0980 chunk 52 optimal weight: 8.9990 overall best weight: 2.8344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 81 GLN B 5 ASN ** C 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 283 HIS C 418 GLN ** C 491 ASN ** 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 = 0.3585 r_free = 0.3585 target = 0.102208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.089691 restraints weight = 13957.290| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 3.03 r_work: 0.3233 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3235 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3235 r_free = 0.3235 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3233 r_free = 0.3233 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 14 (20 function evaluations) r_final: 0.3233 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.1492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 6152 Z= 0.229 Angle : 0.644 8.101 8328 Z= 0.334 Chirality : 0.049 0.203 941 Planarity : 0.004 0.059 1100 Dihedral : 4.940 46.197 853 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.22 % Favored : 95.65 % Rotamer: Outliers : 6.23 % Allowed : 29.28 % Favored : 64.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % 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 (0.30), residues: 782 helix: 0.83 (0.34), residues: 233 sheet: 0.73 (0.57), residues: 90 loop : -1.03 (0.29), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 264 TYR 0.011 0.001 TYR A 32 PHE 0.013 0.001 PHE A 14 TRP 0.014 0.002 TRP C 438 HIS 0.003 0.001 HIS C 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00509 / 0.23 ( 6152) covalent geometry : angle 0.64405 / 0.33 ( 8328) hydrogen bonds : bond 0.04326 / 3.12 ( 210) hydrogen bonds : angle 4.83672 / 3.63 ( 585) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 198 time to evaluate : 0.151 Fit side-chains revert: symmetry clash REVERT: A 10 LYS cc_start: 0.9289 (mmmt) cc_final: 0.8354 (pttt) REVERT: A 34 GLU cc_start: 0.8440 (OUTLIER) cc_final: 0.8197 (pm20) REVERT: B 31 ARG cc_start: 0.8973 (tpp80) cc_final: 0.8647 (ttm-80) REVERT: B 52 ASN cc_start: 0.7116 (t0) cc_final: 0.6244 (t0) REVERT: C 43 ASN cc_start: 0.8571 (p0) cc_final: 0.8137 (p0) REVERT: C 166 GLU cc_start: 0.2320 (mp0) cc_final: 0.0879 (mp0) REVERT: C 181 GLU cc_start: 0.8716 (mm-30) cc_final: 0.8502 (mm-30) REVERT: C 185 LYS cc_start: 0.5022 (tmtt) cc_final: 0.4535 (tmtt) REVERT: C 341 ARG cc_start: 0.8337 (ptt-90) cc_final: 0.7717 (ptp-170) outliers start: 40 outliers final: 32 residues processed: 215 average time/residue: 0.0668 time to fit residues: 19.2858 Evaluate side-chains 228 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 195 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain A residue 34 GLU Chi-restraints excluded: chain A residue 41 SER Chi-restraints excluded: chain A residue 51 LYS Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 81 GLN Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 83 MET Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain C residue 40 ASP Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 91 ASP Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 158 PHE Chi-restraints excluded: chain C residue 223 GLU Chi-restraints excluded: chain C residue 266 ILE Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 394 GLU Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 510 LEU Chi-restraints excluded: chain C residue 543 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 0 optimal weight: 7.9990 chunk 23 optimal weight: 7.9990 chunk 45 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 20 optimal weight: 9.9990 chunk 10 optimal weight: 0.7980 chunk 68 optimal weight: 0.9980 chunk 41 optimal weight: 4.9990 chunk 61 optimal weight: 4.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 5 ASN B 68 ASN ** C 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 491 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 = 0.3595 r_free = 0.3595 target = 0.098836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.086604 restraints weight = 13855.268| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 3.06 r_work: 0.3259 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3265 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3265 r_free = 0.3265 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3265 r_free = 0.3265 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (11 function evaluations) r_final: 0.3265 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.1690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6152 Z= 0.134 Angle : 0.618 11.863 8328 Z= 0.313 Chirality : 0.048 0.198 941 Planarity : 0.004 0.057 1100 Dihedral : 4.797 44.986 853 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.96 % Favored : 95.91 % Rotamer: Outliers : 5.30 % Allowed : 31.31 % Favored : 63.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % 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: -0.30 (0.30), residues: 782 helix: 0.94 (0.34), residues: 233 sheet: 0.88 (0.58), residues: 87 loop : -1.05 (0.29), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 264 TYR 0.022 0.001 TYR A 32 PHE 0.016 0.001 PHE A 14 TRP 0.016 0.001 TRP C 438 HIS 0.002 0.001 HIS C 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.13 ( 6152) covalent geometry : angle 0.61825 / 0.31 ( 8328) hydrogen bonds : bond 0.03577 / 2.54 ( 210) hydrogen bonds : angle 4.65683 / 3.51 ( 585) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 200 time to evaluate : 0.259 Fit side-chains revert: symmetry clash REVERT: A 10 LYS cc_start: 0.9294 (mmmt) cc_final: 0.8311 (pttt) REVERT: A 34 GLU cc_start: 0.8361 (OUTLIER) cc_final: 0.8120 (pm20) REVERT: B 31 ARG cc_start: 0.8804 (tpp80) cc_final: 0.8518 (ttm-80) REVERT: B 52 ASN cc_start: 0.7058 (t0) cc_final: 0.6179 (t0) REVERT: C 43 ASN cc_start: 0.8572 (p0) cc_final: 0.8128 (p0) REVERT: C 158 PHE cc_start: 0.8909 (OUTLIER) cc_final: 0.8633 (m-80) REVERT: C 166 GLU cc_start: 0.2004 (mp0) cc_final: 0.0183 (mp0) REVERT: C 181 GLU cc_start: 0.8668 (mm-30) cc_final: 0.8417 (mm-30) REVERT: C 185 LYS cc_start: 0.4242 (tmtt) cc_final: 0.3817 (tmtt) outliers start: 34 outliers final: 25 residues processed: 212 average time/residue: 0.0689 time to fit residues: 19.5749 Evaluate side-chains 221 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 194 time to evaluate : 0.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain A residue 34 GLU Chi-restraints excluded: chain A residue 41 SER Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 70 MET Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 91 ASP Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 158 PHE Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 223 GLU Chi-restraints excluded: chain C residue 266 ILE Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 510 LEU Chi-restraints excluded: chain C residue 543 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 15 optimal weight: 5.9990 chunk 6 optimal weight: 4.9990 chunk 1 optimal weight: 0.9980 chunk 9 optimal weight: 0.9980 chunk 25 optimal weight: 0.0980 chunk 16 optimal weight: 5.9990 chunk 73 optimal weight: 10.0000 chunk 64 optimal weight: 2.9990 chunk 42 optimal weight: 0.0050 chunk 35 optimal weight: 6.9990 chunk 57 optimal weight: 0.9980 overall best weight: 0.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 418 GLN ** C 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.100044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.087784 restraints weight = 14086.585| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 3.17 r_work: 0.3281 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3290 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3290 r_free = 0.3290 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3290 r_free = 0.3290 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 7 (14 function evaluations) r_final: 0.3290 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.1867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6152 Z= 0.108 Angle : 0.607 12.224 8328 Z= 0.304 Chirality : 0.047 0.202 941 Planarity : 0.004 0.056 1100 Dihedral : 4.572 42.204 853 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.71 % Favored : 96.16 % Rotamer: Outliers : 6.07 % Allowed : 31.78 % Favored : 62.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % 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: -0.21 (0.30), residues: 782 helix: 0.98 (0.35), residues: 233 sheet: 0.67 (0.57), residues: 91 loop : -0.93 (0.29), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 264 TYR 0.017 0.001 TYR A 32 PHE 0.014 0.001 PHE B 97 TRP 0.016 0.001 TRP C 438 HIS 0.003 0.001 HIS C 293 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 ( 6152) covalent geometry : angle 0.60686 / 0.30 ( 8328) hydrogen bonds : bond 0.03091 / 2.18 ( 210) hydrogen bonds : angle 4.53743 / 3.42 ( 585) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 199 time to evaluate : 0.242 Fit side-chains revert: symmetry clash REVERT: A 10 LYS cc_start: 0.9276 (mmmt) cc_final: 0.8229 (tttt) REVERT: B 27 LYS cc_start: 0.9012 (mtpp) cc_final: 0.8687 (mtpp) REVERT: B 31 ARG cc_start: 0.8749 (tpp80) cc_final: 0.8443 (ttm-80) REVERT: B 52 ASN cc_start: 0.7048 (t0) cc_final: 0.6152 (t0) REVERT: C 43 ASN cc_start: 0.8551 (p0) cc_final: 0.8104 (p0) REVERT: C 158 PHE cc_start: 0.8834 (OUTLIER) cc_final: 0.8586 (m-80) REVERT: C 166 GLU cc_start: 0.1919 (mp0) cc_final: 0.1062 (mp0) REVERT: C 185 LYS cc_start: 0.4525 (tmtt) cc_final: 0.4078 (tmtt) REVERT: C 470 THR cc_start: 0.8798 (OUTLIER) cc_final: 0.8595 (t) REVERT: C 511 LYS cc_start: 0.9061 (mttp) cc_final: 0.8819 (mtmm) outliers start: 39 outliers final: 26 residues processed: 218 average time/residue: 0.0702 time to fit residues: 20.5460 Evaluate side-chains 223 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 195 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain A residue 41 SER Chi-restraints excluded: chain A residue 51 LYS Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 158 PHE Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 223 GLU Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 424 VAL Chi-restraints excluded: chain C residue 465 SER Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 510 LEU Chi-restraints excluded: chain C residue 543 THR Chi-restraints excluded: chain C residue 552 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 35 optimal weight: 8.9990 chunk 40 optimal weight: 0.8980 chunk 2 optimal weight: 4.9990 chunk 41 optimal weight: 6.9990 chunk 53 optimal weight: 8.9990 chunk 78 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 73 optimal weight: 4.9990 chunk 56 optimal weight: 8.9990 chunk 16 optimal weight: 10.0000 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.096464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.084049 restraints weight = 13940.298| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 3.12 r_work: 0.3207 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3212 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3212 r_free = 0.3212 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3212 r_free = 0.3212 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.3212 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.1987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 6152 Z= 0.241 Angle : 0.697 14.008 8328 Z= 0.353 Chirality : 0.050 0.195 941 Planarity : 0.005 0.059 1100 Dihedral : 4.896 36.012 853 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.86 % Favored : 95.01 % Rotamer: Outliers : 7.01 % Allowed : 31.78 % Favored : 61.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % 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: -0.37 (0.30), residues: 782 helix: 0.86 (0.35), residues: 233 sheet: 0.78 (0.59), residues: 90 loop : -1.08 (0.29), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 21 TYR 0.014 0.001 TYR A 32 PHE 0.019 0.002 PHE A 14 TRP 0.014 0.002 TRP C 438 HIS 0.006 0.001 HIS C 272 Details of bonding type rmsd/Z covalent geometry : bond 0.00541 / 0.24 ( 6152) covalent geometry : angle 0.69659 / 0.35 ( 8328) hydrogen bonds : bond 0.04370 / 3.13 ( 210) hydrogen bonds : angle 4.77761 / 3.56 ( 585) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 195 time to evaluate : 0.236 Fit side-chains REVERT: A 10 LYS cc_start: 0.9300 (mmmt) cc_final: 0.8339 (tttt) REVERT: B 27 LYS cc_start: 0.8955 (mtpp) cc_final: 0.8730 (mtpp) REVERT: B 31 ARG cc_start: 0.8825 (tpp80) cc_final: 0.8505 (ttm-80) REVERT: B 52 ASN cc_start: 0.7113 (t0) cc_final: 0.6277 (t0) REVERT: C 32 GLU cc_start: 0.8636 (OUTLIER) cc_final: 0.8096 (mt-10) REVERT: C 43 ASN cc_start: 0.8566 (p0) cc_final: 0.8134 (p0) REVERT: C 158 PHE cc_start: 0.9012 (OUTLIER) cc_final: 0.8733 (m-80) REVERT: C 166 GLU cc_start: 0.2430 (mp0) cc_final: 0.0640 (mp0) REVERT: C 185 LYS cc_start: 0.4398 (tmtt) cc_final: 0.3865 (tmtt) REVERT: C 275 HIS cc_start: 0.9195 (OUTLIER) cc_final: 0.8698 (p90) REVERT: C 545 GLU cc_start: 0.8776 (OUTLIER) cc_final: 0.8543 (tt0) outliers start: 45 outliers final: 36 residues processed: 216 average time/residue: 0.0688 time to fit residues: 19.9046 Evaluate side-chains 233 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 193 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LYS Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain A residue 18 GLU Chi-restraints excluded: chain A residue 41 SER Chi-restraints excluded: chain A residue 51 LYS Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain C residue 32 GLU Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 91 ASP Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 158 PHE Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 209 MET Chi-restraints excluded: chain C residue 223 GLU Chi-restraints excluded: chain C residue 266 ILE Chi-restraints excluded: chain C residue 275 HIS Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 394 GLU Chi-restraints excluded: chain C residue 424 VAL Chi-restraints excluded: chain C residue 465 SER Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 478 ARG Chi-restraints excluded: chain C residue 543 THR Chi-restraints excluded: chain C residue 545 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 16 optimal weight: 7.9990 chunk 8 optimal weight: 1.9990 chunk 51 optimal weight: 0.0040 chunk 1 optimal weight: 0.9990 chunk 12 optimal weight: 10.0000 chunk 47 optimal weight: 0.7980 chunk 72 optimal weight: 0.0670 chunk 56 optimal weight: 4.9990 chunk 22 optimal weight: 5.9990 chunk 73 optimal weight: 2.9990 chunk 26 optimal weight: 7.9990 overall best weight: 0.7734 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 418 GLN ** C 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.099225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.086930 restraints weight = 14004.949| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 3.17 r_work: 0.3268 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3272 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3272 r_free = 0.3272 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3272 r_free = 0.3272 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.3272 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.2053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6152 Z= 0.117 Angle : 0.648 13.642 8328 Z= 0.323 Chirality : 0.048 0.202 941 Planarity : 0.004 0.057 1100 Dihedral : 4.651 37.975 853 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.84 % Favored : 96.04 % Rotamer: Outliers : 6.07 % Allowed : 33.80 % Favored : 60.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % 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: -0.24 (0.30), residues: 782 helix: 1.03 (0.35), residues: 232 sheet: 0.93 (0.60), residues: 86 loop : -1.04 (0.29), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 264 TYR 0.024 0.001 TYR A 32 PHE 0.007 0.001 PHE A 14 TRP 0.018 0.001 TRP C 438 HIS 0.005 0.001 HIS C 272 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 ( 6152) covalent geometry : angle 0.64787 / 0.32 ( 8328) hydrogen bonds : bond 0.03202 / 2.26 ( 210) hydrogen bonds : angle 4.48816 / 3.37 ( 585) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 197 time to evaluate : 0.248 Fit side-chains REVERT: A 8 LYS cc_start: 0.8843 (OUTLIER) cc_final: 0.8451 (ptpp) REVERT: A 10 LYS cc_start: 0.9251 (mmmt) cc_final: 0.8268 (tttt) REVERT: A 34 GLU cc_start: 0.8383 (pm20) cc_final: 0.7868 (pm20) REVERT: A 76 MET cc_start: 0.8583 (mmt) cc_final: 0.8168 (mmp) REVERT: B 27 LYS cc_start: 0.8962 (mtpp) cc_final: 0.8718 (mtpp) REVERT: B 31 ARG cc_start: 0.8749 (tpp80) cc_final: 0.8492 (ttm-80) REVERT: B 52 ASN cc_start: 0.7095 (t0) cc_final: 0.6234 (t0) REVERT: C 43 ASN cc_start: 0.8593 (p0) cc_final: 0.8133 (p0) REVERT: C 158 PHE cc_start: 0.8888 (OUTLIER) cc_final: 0.8634 (m-80) REVERT: C 166 GLU cc_start: 0.2341 (mp0) cc_final: 0.0451 (mp0) REVERT: C 185 LYS cc_start: 0.4302 (tmtt) cc_final: 0.3736 (tmtt) REVERT: C 423 GLU cc_start: 0.7993 (mp0) cc_final: 0.7736 (mp0) REVERT: C 545 GLU cc_start: 0.8783 (OUTLIER) cc_final: 0.8195 (tm-30) outliers start: 39 outliers final: 27 residues processed: 219 average time/residue: 0.0678 time to fit residues: 19.8969 Evaluate side-chains 226 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 196 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LYS Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain A residue 18 GLU Chi-restraints excluded: chain A residue 51 LYS Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 81 GLN Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 147 ASP Chi-restraints excluded: chain C residue 158 PHE Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 223 GLU Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 424 VAL Chi-restraints excluded: chain C residue 465 SER Chi-restraints excluded: chain C residue 478 ARG Chi-restraints excluded: chain C residue 545 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 19 optimal weight: 10.0000 chunk 38 optimal weight: 2.9990 chunk 30 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 61 optimal weight: 10.0000 chunk 74 optimal weight: 4.9990 chunk 42 optimal weight: 0.0670 chunk 69 optimal weight: 0.0030 overall best weight: 0.5328 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.101054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.088886 restraints weight = 13955.428| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 3.06 r_work: 0.3298 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3304 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3304 r_free = 0.3304 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3304 r_free = 0.3304 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.3304 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.2281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6152 Z= 0.117 Angle : 0.653 11.697 8328 Z= 0.326 Chirality : 0.048 0.197 941 Planarity : 0.004 0.056 1100 Dihedral : 4.466 35.479 853 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.60 % Favored : 95.27 % Rotamer: Outliers : 5.14 % Allowed : 33.80 % Favored : 61.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % 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: -0.15 (0.30), residues: 782 helix: 1.07 (0.35), residues: 235 sheet: 0.90 (0.60), residues: 86 loop : -0.95 (0.29), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 264 TYR 0.022 0.001 TYR A 32 PHE 0.024 0.001 PHE A 14 TRP 0.017 0.001 TRP C 438 HIS 0.005 0.001 HIS C 272 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 ( 6152) covalent geometry : angle 0.65278 / 0.33 ( 8328) hydrogen bonds : bond 0.02925 / 2.04 ( 210) hydrogen bonds : angle 4.45231 / 3.38 ( 585) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 191 time to evaluate : 0.231 Fit side-chains REVERT: A 8 LYS cc_start: 0.8758 (OUTLIER) cc_final: 0.8412 (ptpp) REVERT: A 10 LYS cc_start: 0.9222 (mmmt) cc_final: 0.8261 (tttt) REVERT: B 27 LYS cc_start: 0.8955 (mtpp) cc_final: 0.8700 (mtpp) REVERT: B 31 ARG cc_start: 0.8738 (tpp80) cc_final: 0.8455 (ttm-80) REVERT: C 43 ASN cc_start: 0.8543 (p0) cc_final: 0.8099 (p0) REVERT: C 166 GLU cc_start: 0.2170 (mp0) cc_final: 0.0154 (mp0) REVERT: C 185 LYS cc_start: 0.4355 (tmtt) cc_final: 0.3787 (tmtt) REVERT: C 196 ILE cc_start: 0.8149 (mm) cc_final: 0.7876 (mm) REVERT: C 439 GLU cc_start: 0.8683 (mp0) cc_final: 0.8298 (mp0) REVERT: C 545 GLU cc_start: 0.8771 (OUTLIER) cc_final: 0.7984 (tm-30) outliers start: 33 outliers final: 25 residues processed: 209 average time/residue: 0.0679 time to fit residues: 19.0114 Evaluate side-chains 218 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 191 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LYS Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain A residue 18 GLU Chi-restraints excluded: chain A residue 51 LYS Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain C residue 113 MET Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 158 PHE Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 223 GLU Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 424 VAL Chi-restraints excluded: chain C residue 465 SER Chi-restraints excluded: chain C residue 478 ARG Chi-restraints excluded: chain C residue 545 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 58 optimal weight: 7.9990 chunk 38 optimal weight: 2.9990 chunk 46 optimal weight: 10.0000 chunk 63 optimal weight: 0.5980 chunk 27 optimal weight: 6.9990 chunk 3 optimal weight: 0.8980 chunk 6 optimal weight: 0.8980 chunk 75 optimal weight: 4.9990 chunk 49 optimal weight: 6.9990 chunk 28 optimal weight: 3.9990 chunk 2 optimal weight: 0.8980 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 315 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 379 GLN C 418 GLN ** C 491 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 = 0.3608 r_free = 0.3608 target = 0.099410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.087092 restraints weight = 13948.605| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 3.18 r_work: 0.3273 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3277 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3277 r_free = 0.3277 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3277 r_free = 0.3277 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3277 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.2256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6152 Z= 0.138 Angle : 0.672 10.921 8328 Z= 0.334 Chirality : 0.048 0.200 941 Planarity : 0.004 0.056 1100 Dihedral : 4.493 33.805 853 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.96 % Favored : 95.91 % Rotamer: Outliers : 5.30 % Allowed : 32.87 % Favored : 61.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % 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: -0.09 (0.30), residues: 782 helix: 1.21 (0.35), residues: 234 sheet: 0.82 (0.61), residues: 86 loop : -0.94 (0.28), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 264 TYR 0.020 0.001 TYR A 32 PHE 0.006 0.001 PHE C 494 TRP 0.015 0.001 TRP C 438 HIS 0.005 0.001 HIS C 272 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 ( 6152) covalent geometry : angle 0.67183 / 0.33 ( 8328) hydrogen bonds : bond 0.03242 / 2.30 ( 210) hydrogen bonds : angle 4.44714 / 3.37 ( 585) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 191 time to evaluate : 0.235 Fit side-chains revert: symmetry clash REVERT: A 8 LYS cc_start: 0.8765 (OUTLIER) cc_final: 0.8453 (ptpp) REVERT: A 10 LYS cc_start: 0.9233 (mmmt) cc_final: 0.8276 (tttt) REVERT: A 76 MET cc_start: 0.8352 (mmp) cc_final: 0.8089 (mmp) REVERT: B 31 ARG cc_start: 0.8752 (tpp80) cc_final: 0.8469 (ttm-80) REVERT: B 52 ASN cc_start: 0.7121 (t0) cc_final: 0.6229 (t0) REVERT: C 43 ASN cc_start: 0.8508 (p0) cc_final: 0.8043 (p0) REVERT: C 158 PHE cc_start: 0.8948 (OUTLIER) cc_final: 0.8634 (m-80) REVERT: C 166 GLU cc_start: 0.2130 (mp0) cc_final: 0.0905 (mp0) REVERT: C 185 LYS cc_start: 0.4147 (tmtt) cc_final: 0.3665 (tmtt) REVERT: C 196 ILE cc_start: 0.8181 (mm) cc_final: 0.7923 (mm) REVERT: C 470 THR cc_start: 0.8826 (p) cc_final: 0.8621 (t) REVERT: C 495 MET cc_start: 0.9259 (mtp) cc_final: 0.9049 (mtp) REVERT: C 545 GLU cc_start: 0.8795 (OUTLIER) cc_final: 0.8245 (tm-30) outliers start: 34 outliers final: 28 residues processed: 209 average time/residue: 0.0729 time to fit residues: 20.4594 Evaluate side-chains 220 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 189 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LYS Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain A residue 18 GLU Chi-restraints excluded: chain A residue 41 SER Chi-restraints excluded: chain A residue 51 LYS Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 113 MET Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 147 ASP Chi-restraints excluded: chain C residue 158 PHE Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 223 GLU Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 424 VAL Chi-restraints excluded: chain C residue 510 LEU Chi-restraints excluded: chain C residue 545 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 21 optimal weight: 0.0980 chunk 25 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 61 optimal weight: 0.2980 chunk 75 optimal weight: 5.9990 chunk 27 optimal weight: 7.9990 chunk 30 optimal weight: 0.9980 chunk 69 optimal weight: 0.6980 chunk 6 optimal weight: 0.9980 chunk 70 optimal weight: 5.9990 chunk 18 optimal weight: 5.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 315 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.101668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.089517 restraints weight = 13797.227| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 3.05 r_work: 0.3311 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3317 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3317 r_free = 0.3317 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3317 r_free = 0.3317 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3317 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.2445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6152 Z= 0.118 Angle : 0.669 11.565 8328 Z= 0.332 Chirality : 0.048 0.200 941 Planarity : 0.004 0.055 1100 Dihedral : 4.359 32.854 853 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.84 % Favored : 96.04 % Rotamer: Outliers : 4.21 % Allowed : 34.42 % Favored : 61.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % 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: -0.07 (0.30), residues: 782 helix: 1.19 (0.35), residues: 235 sheet: 0.83 (0.61), residues: 86 loop : -0.90 (0.29), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 264 TYR 0.019 0.001 TYR A 32 PHE 0.027 0.001 PHE A 14 TRP 0.017 0.001 TRP C 438 HIS 0.008 0.001 HIS C 272 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 ( 6152) covalent geometry : angle 0.66881 / 0.33 ( 8328) hydrogen bonds : bond 0.02881 / 2.03 ( 210) hydrogen bonds : angle 4.42876 / 3.38 ( 585) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 189 time to evaluate : 0.178 Fit side-chains revert: symmetry clash REVERT: A 8 LYS cc_start: 0.8690 (OUTLIER) cc_final: 0.8398 (ptpp) REVERT: A 10 LYS cc_start: 0.9176 (mmmt) cc_final: 0.8263 (tttt) REVERT: B 31 ARG cc_start: 0.8730 (tpp80) cc_final: 0.8489 (ttm-80) REVERT: B 78 GLU cc_start: 0.8555 (mm-30) cc_final: 0.8219 (pm20) REVERT: C 158 PHE cc_start: 0.8905 (OUTLIER) cc_final: 0.8626 (m-80) REVERT: C 166 GLU cc_start: 0.2349 (mp0) cc_final: 0.1136 (mp0) REVERT: C 185 LYS cc_start: 0.4255 (tmtt) cc_final: 0.3689 (tmtt) REVERT: C 196 ILE cc_start: 0.8179 (mm) cc_final: 0.7939 (mm) REVERT: C 439 GLU cc_start: 0.8673 (mp0) cc_final: 0.8287 (mp0) outliers start: 27 outliers final: 24 residues processed: 204 average time/residue: 0.0687 time to fit residues: 19.0148 Evaluate side-chains 210 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 184 time to evaluate : 0.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LYS Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain A residue 18 GLU Chi-restraints excluded: chain A residue 51 LYS Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain C residue 113 MET Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 158 PHE Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain C residue 223 GLU Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 424 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 42 optimal weight: 0.1980 chunk 77 optimal weight: 7.9990 chunk 54 optimal weight: 5.9990 chunk 75 optimal weight: 0.9990 chunk 32 optimal weight: 7.9990 chunk 56 optimal weight: 4.9990 chunk 2 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 11 optimal weight: 6.9990 chunk 48 optimal weight: 7.9990 overall best weight: 1.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 315 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 379 GLN C 418 GLN ** C 491 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 = 0.3597 r_free = 0.3597 target = 0.098748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.086402 restraints weight = 13920.271| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 3.15 r_work: 0.3256 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3263 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3263 r_free = 0.3263 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3263 r_free = 0.3263 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3263 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.2334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 6152 Z= 0.173 Angle : 0.696 11.403 8328 Z= 0.349 Chirality : 0.049 0.242 941 Planarity : 0.005 0.057 1100 Dihedral : 4.612 33.593 853 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.73 % Favored : 95.14 % Rotamer: Outliers : 5.14 % Allowed : 33.80 % Favored : 61.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % 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: -0.12 (0.30), residues: 782 helix: 1.16 (0.35), residues: 234 sheet: 0.81 (0.60), residues: 86 loop : -0.93 (0.29), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 21 TYR 0.018 0.001 TYR A 32 PHE 0.011 0.001 PHE C 494 TRP 0.015 0.001 TRP C 438 HIS 0.007 0.001 HIS C 272 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.17 ( 6152) covalent geometry : angle 0.69613 / 0.35 ( 8328) hydrogen bonds : bond 0.03598 / 2.58 ( 210) hydrogen bonds : angle 4.48987 / 3.40 ( 585) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1491.77 seconds wall clock time: 26 minutes 19.97 seconds (1579.97 seconds total)